diff --git a/.docs/.swagger/api.yaml b/.docs/.swagger/api.yaml
index a3f7eea7f2d4a34a3108ed41e5be9c0500615565..1857e4bb3fb434ddda387992a397488035816487 100644
--- a/.docs/.swagger/api.yaml
+++ b/.docs/.swagger/api.yaml
@@ -24,7 +24,7 @@ servers:
url: 'http://localhost'
externalDocs:
description: Project Website
- url: 'https://www.ifs.tuwien.ac.at/infrastructures/dbrepo/'
+ url: 'https://www.ifs.tuwien.ac.at/infrastructures/dbrepo/1.4.7/'
paths:
/api/analyse/datatypes:
get:
@@ -1102,6 +1102,64 @@ paths:
security:
- basicAuth: []
- bearerAuth: []
+ '/api/database/{databaseId}/view/{viewId}/export':
+ get:
+ tags:
+ - view-endpoint
+ summary: Get view data
+ description: >-
+ Gets data from view with id as downloadable file. For tables in private
+ databases, the user needs to have at least *READ* access to the
+ associated database.
+ operationId: exportDataset
+ parameters:
+ - name: databaseId
+ in: path
+ required: true
+ schema:
+ type: integer
+ format: int64
+ - name: viewId
+ in: path
+ required: true
+ schema:
+ type: integer
+ format: int64
+ responses:
+ '200':
+ description: Exported view data
+ content:
+ application/json:
+ schema:
+ type: string
+ format: binary
+ '400':
+ description: Request pagination or view data select query is malformed
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/ApiErrorDto'
+ '403':
+ description: Export view data not allowed
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/ApiErrorDto'
+ '404':
+ description: Failed to find view in metadata database or export dataset
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/ApiErrorDto'
+ '503':
+ description: Failed to establish connection with the metadata service
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/ApiErrorDto'
+ security:
+ - basicAuth: []
+ - bearerAuth: []
'/api/database/{databaseId}/table/{tableId}/statistic':
get:
tags:
@@ -1223,7 +1281,7 @@ paths:
Gets data from table with id as downloadable file. For tables in private
databases, the user needs to have at least *READ* access to the
associated database.
- operationId: exportDataset
+ operationId: exportDataset_1
parameters:
- name: databaseId
in: path
@@ -2313,12 +2371,6 @@ paths:
application/json:
schema:
$ref: '#/components/schemas/ApiErrorDto'
- '422':
- description: Failed to retrieve from database sidecar
- content:
- application/json:
- schema:
- $ref: '#/components/schemas/ApiErrorDto'
'502':
description: Connection to data service failed
content:
@@ -2560,7 +2612,9 @@ paths:
tags:
- table-endpoint
summary: Find table
- description: Finds a table with id.
+ description: >-
+ Finds a table with id. When the `system` role is present, the endpoint
+ responds with additional connection metadata in the header.
operationId: findById_2
parameters:
- name: databaseId
@@ -2578,6 +2632,31 @@ paths:
responses:
'200':
description: Find table successfully
+ headers:
+ X-Username:
+ description: The authentication username
+ style: simple
+ X-Table:
+ description: The table internal name
+ style: simple
+ Access-Control-Expose-Headers:
+ description: Expose custom headers
+ style: simple
+ X-Type:
+ description: The JDBC connection type
+ style: simple
+ X-Database:
+ description: The database internal name
+ style: simple
+ X-Password:
+ description: The authentication password
+ style: simple
+ X-Host:
+ description: The database hostname
+ style: simple
+ X-Port:
+ description: The database port number
+ style: simple
content:
application/json:
schema:
@@ -3824,6 +3903,16 @@ paths:
responses:
'200':
description: Database found successfully
+ headers:
+ X-Username:
+ description: The authentication username
+ style: simple
+ Access-Control-Expose-Headers:
+ description: Expose custom headers
+ style: simple
+ X-Password:
+ description: The authentication password
+ style: simple
content:
application/json:
schema:
@@ -3872,6 +3961,31 @@ paths:
responses:
'200':
description: Find view successfully
+ headers:
+ X-Username:
+ description: The authentication username
+ style: simple
+ Access-Control-Expose-Headers:
+ description: Expose custom headers
+ style: simple
+ X-Type:
+ description: The JDBC connection type
+ style: simple
+ X-View:
+ description: The view internal name
+ style: simple
+ X-Database:
+ description: The database internal name
+ style: simple
+ X-Password:
+ description: The authentication password
+ style: simple
+ X-Host:
+ description: The database hostname
+ style: simple
+ X-Port:
+ description: The database port number
+ style: simple
content:
application/json:
schema:
@@ -4172,58 +4286,7 @@ paths:
summary: Performs a fuzzy search
tags:
- search-endpoint
- '/api/search/{index}':
- get:
- consumes:
- - application/json
- description: Gets the index
- operationId: get_index
- parameters:
- - description: The search type.
- in: path
- name: type
- required: true
- schema:
- enum:
- - database
- - table
- - view
- - column
- - user
- - identifier
- - concept
- - unit
- type: string
- - in: body
- name: body
- required: true
- schema:
- properties:
- field_value_pairs:
- type: object
- search_term:
- example: air quality
- type: string
- t1:
- example: 0
- type: integer
- t2:
- example: 100
- type: integer
- type: object
- produces:
- - application/json
- responses:
- '200':
- content:
- application/json:
- schema:
- $ref: '#/components/schemas/IndexDto'
- description: 'OK, contains the elements formatted as an array of JSON arrays'
- summary: Gets the index
- tags:
- - search-endpoint
- '/api/search/{type}':
+ '/api/search/{field_type}':
post:
consumes:
- application/json
@@ -4287,7 +4350,7 @@ paths:
summary: Performs a general search
tags:
- search-endpoint
- '/api/search/{type}/fields':
+ '/api/search/{field_type}/fields':
get:
operationId: get_fields
parameters:
@@ -4318,56 +4381,57 @@ paths:
summary: Get searchable fields
tags:
- search-endpoint
- '/sidecar/export/{filename}':
- post:
+ '/api/search/{index}':
+ get:
consumes:
- application/json
- description: |
- Exports a specific .csv file to the Storage Service via S3
+ description: Gets the index
+ operationId: get_index
parameters:
- - description: Name of the object file to export to the Storage Service
+ - description: The search type.
in: path
- name: filename
+ name: type
required: true
- produces:
- - application/json
- responses:
- '202':
- content: {}
- description: Exported the .csv
- '400':
- description: The Storage Service could not be contacted or .csv was not found.
- security:
- - bearerAuth: []
- - basicAuth: []
- summary: Exports a .csv to the Storage Service
- tags:
- - sidecar
- '/sidecar/import/{filename}':
- post:
- consumes:
- - application/json
- description: |
- Imports a specific .csv file from the Storage Service via S3
- parameters:
- - description: Name of the object file to import from the Storage Service
- in: path
- name: filename
+ schema:
+ enum:
+ - database
+ - table
+ - view
+ - column
+ - user
+ - identifier
+ - concept
+ - unit
+ type: string
+ - in: body
+ name: body
required: true
+ schema:
+ properties:
+ field_value_pairs:
+ type: object
+ search_term:
+ example: air quality
+ type: string
+ t1:
+ example: 0
+ type: integer
+ t2:
+ example: 100
+ type: integer
+ type: object
produces:
- application/json
responses:
- '202':
- content: {}
- description: Imported the .csv
- '400':
- description: The Storage Service could not be contacted or .csv was not found.
- security:
- - bearerAuth: []
- - basicAuth: []
- summary: Imports a .csv from the Storage Service
+ '200':
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/IndexDto'
+ description: 'OK, contains the elements formatted as an array of JSON arrays'
+ summary: Gets the index
tags:
- - sidecar
+ - search-endpoint
components:
securitySchemes:
basicAuth:
@@ -5607,6 +5671,7 @@ components:
type: object
ImportDto:
required:
+ - header
- location
- separator
type: object
@@ -5614,16 +5679,17 @@ components:
location:
type: string
example: file.csv
+ header:
+ type: boolean
+ description: >-
+ If true, the first line contains the column names, otherwise it
+ contains only data
separator:
type: string
example: ','
quote:
type: string
example: '"'
- skip_lines:
- minimum: 0
- type: integer
- format: int64
line_termination:
type: string
example: \r\n
@@ -5961,8 +6027,6 @@ components:
- internal_name
- name
- quota
- - sidecar_host
- - sidecar_port
type: object
properties:
id:
@@ -5993,11 +6057,6 @@ components:
internal_name:
type: string
example: data-db
- sidecar_host:
- type: string
- sidecar_port:
- type: integer
- format: int32
ui_host:
type: string
ui_port:
@@ -6221,6 +6280,7 @@ components:
- id
- jdbc_method
- name
+ - operators
- registry
- version
type: object
@@ -6240,6 +6300,10 @@ components:
dialect:
type: string
example: org.hibernate.dialect.MariaDBDialect
+ operators:
+ type: array
+ items:
+ $ref: '#/components/schemas/OperatorDto'
driver_class:
type: string
example: org.mariadb.jdbc.Driver
@@ -6257,6 +6321,22 @@ components:
type: array
items:
$ref: '#/components/schemas/DataTypeDto'
+ OperatorDto:
+ required:
+ - display_name
+ - documentation
+ - value
+ type: object
+ properties:
+ value:
+ type: string
+ example: XOR
+ documentation:
+ type: string
+ example: 'https://mariadb.com/kb/en/xor/'
+ display_name:
+ type: string
+ example: XOR
PrimaryKeyDto:
required:
- column
@@ -6486,8 +6566,6 @@ components:
minLength: 0
type: string
example: Date
- alias:
- type: string
size:
type: integer
format: int64
@@ -8334,8 +8412,6 @@ components:
- privileged_password
- privileged_username
- quota
- - sidecar_host
- - sidecar_port
type: object
properties:
name:
@@ -8356,11 +8432,6 @@ components:
type: integer
description: Image ID
format: int64
- sidecar_host:
- type: string
- sidecar_port:
- type: integer
- format: int32
ui_host:
type: string
ui_port:
@@ -8657,11 +8728,6 @@ components:
port:
type: integer
format: int32
- sidecarHost:
- type: string
- sidecarPort:
- type: integer
- format: int32
uiHost:
type: string
uiPort:
@@ -8725,6 +8791,10 @@ components:
type: array
items:
$ref: '#/components/schemas/DataType'
+ operators:
+ type: array
+ items:
+ $ref: '#/components/schemas/Operator'
Creator:
type: object
properties:
@@ -9673,6 +9743,20 @@ components:
type: string
description:
type: string
+ Operator:
+ type: object
+ properties:
+ id:
+ type: integer
+ format: int64
+ displayName:
+ type: string
+ value:
+ type: string
+ documentation:
+ type: string
+ image:
+ $ref: '#/components/schemas/ContainerImage'
PrimaryKey:
type: object
properties:
@@ -9780,10 +9864,6 @@ components:
type: string
database:
$ref: '#/components/schemas/Database'
- columns:
- type: array
- items:
- $ref: '#/components/schemas/TableColumn'
identifiers:
type: array
items:
@@ -9804,6 +9884,10 @@ components:
avgRowLength:
type: integer
format: int64
+ columns:
+ type: array
+ items:
+ $ref: '#/components/schemas/TableColumn'
created:
type: string
format: date-time
@@ -10036,8 +10120,6 @@ components:
$ref: '#/components/schemas/View'
name:
type: string
- autoGenerated:
- type: boolean
internalName:
type: string
columnType:
diff --git a/.docs/.swagger/openapi-merge.json b/.docs/.swagger/openapi-merge.json
index af25a7582fc3673595a82f6b143a3e7b823a0aa9..6e41b75f580bb4e49a068f30665436632fca5acb 100644
--- a/.docs/.swagger/openapi-merge.json
+++ b/.docs/.swagger/openapi-merge.json
@@ -14,9 +14,6 @@
},
{
"inputFile": "./api-search.yaml"
- },
- {
- "inputFile": "./api-sidecar.yaml"
}
],
"output": "./api.yaml"
diff --git a/.docs/.swagger/swagger-generate.sh b/.docs/.swagger/swagger-generate.sh
index 8ea2981243601c51fa17f75570f38656cb301ff5..884c2adface7aa773fe83e429ecea7f3b5ab4eef 100644
--- a/.docs/.swagger/swagger-generate.sh
+++ b/.docs/.swagger/swagger-generate.sh
@@ -4,12 +4,11 @@ services[4000]=search
services[5000]=analyse
services[9093]=data
services[9099]=metadata
-services[3305]=sidecar
# requires https://github.com/mikefarah/yq/ -> v4.44.3
function retrieve () {
- if [[ "$2" == analyse ]] || [[ "$2" == search ]] || [[ "$2" == sidecar ]]; then
+ if [[ "$2" == analyse ]] || [[ "$2" == search ]]; then
echo "... retrieve json api from localhost:$1"
curl -sSL "http://localhost:$1/api-$2.json" | yq -p=json > "./.docs/.swagger/api-$2.yaml"
else
diff --git a/.docs/api/analyse-service.md b/.docs/api/analyse-service.md
index 3529f0f3df3482ecefcadd17951c641c60c3422a..6a6bb5f5064a96e78088d5aebf18e5e49816b813 100644
--- a/.docs/api/analyse-service.md
+++ b/.docs/api/analyse-service.md
@@ -6,12 +6,18 @@ author: Martin Weise
!!! debug "Debug Information"
- Image: [`registry.datalab.tuwien.ac.at/dbrepo/analyse-service:1.4.5`](https://hub.docker.com/r/dbrepo/analyse-service)
+ Image: [`registry.datalab.tuwien.ac.at/dbrepo/analyse-service:1.4.7`](https://hub.docker.com/r/dbrepo/analyse-service)
* Ports: 5000/tcp
* Prometheus: `http://<hostname>:5000/metrics`
* Health: `http://<hostname>:5000/health`
- * Swagger UI: `http://<hostname>:5000/swagger-ui/` <a href="./swagger/analyse" target="_blank">:fontawesome-solid-square-up-right: view online</a>
+ * Swagger UI: `http://<hostname>:5000/swagger-ui/` <a href="../../rest/" target="_blank">:fontawesome-solid-square-up-right: view online</a>
+
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/analyse-service 5000:80
+ ```
## Overview
diff --git a/.docs/api/auth-service.md b/.docs/api/auth-service.md
index 7b59ca1567e31b5e997baca36c4e3bbcce9f7650..93e87beaf280b5ed9b96a2aca508308098676173 100644
--- a/.docs/api/auth-service.md
+++ b/.docs/api/auth-service.md
@@ -11,6 +11,12 @@ author: Martin Weise
* Ports: 8080/tcp
* UI: `http://<hostname>:8080/`
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/auth-service 8080:80
+ ```
+
## Overview
By default, users are created using the [User Interface](../ui) and the sign-up page in the User Interface.
diff --git a/.docs/api/broker-service.md b/.docs/api/broker-service.md
index 41e2dc10b15ccd137a934cd9c162c85b32dffc22..373eb35b951305cdc75d634f253c805eee95df34 100644
--- a/.docs/api/broker-service.md
+++ b/.docs/api/broker-service.md
@@ -13,6 +13,12 @@ author: Martin Weise
* Prometheus: `http://<hostname>:15692/metrics`
* Management: `http://<hostname>:15672`
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/broker-service 15672:15672
+ ```
+
## Overview
It holds exchanges and topics responsible for holding AMQP messages for later consumption. We
diff --git a/.docs/api/dashboard-service.md b/.docs/api/dashboard-service.md
index 96db8260212b1b95081732f1fa386a0b92e2e4bf..60220229b3e0085f8bfbc2670a53ed334e2e4842 100644
--- a/.docs/api/dashboard-service.md
+++ b/.docs/api/dashboard-service.md
@@ -8,8 +8,14 @@ author: Martin Weise
Image: [`docker.io/bitnami/grafana:10.4.9-debian-12-r0`](https://hub.docker.com/r/bitnami/grafana)
- * Ports: `http://<hostname>/dashboard`
- * Prometheus: `http://<hostname>/dashboard/prometheus`
+ * Ports: `http://<hostname>:3000`
+ * Prometheus: `http://<hostname>:3000/prometheus`
+
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/broker-service 3000:3000
+ ```
## Overview
diff --git a/.docs/api/data-db.md b/.docs/api/data-db.md
index d5ba8d8361351ec7c52d2428f5e1304a64c6791e..aecabb9736a39bb987c9542b14bbd9b025697d17 100644
--- a/.docs/api/data-db.md
+++ b/.docs/api/data-db.md
@@ -9,11 +9,11 @@ author: Martin Weise
* Ports: 3306/tcp
* JDBC: `jdbc://mariadb:<hostname>:3306`
-!!! debug "Debug Information"
-
- Image: [`dbrepo/data-db-sidecar:1.4.5`](https://hub.docker.com/r/dbrepo/data-db-sidecar)
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
- * Ports: 8080/tcp
+ ```shell
+ kubectl [-n namespace] port-forward svc/data-db 3306:3306
+ ```
## Overview
@@ -22,20 +22,6 @@ Any number of MariaDB ata databases can be integrated into DBRepo, even non-empt
registered in the Metadata Database to be visible in the [User Interface](../ui) and usable from e.g. the Python
Library.
-## Architecture
-
-### Sidecar
-
-We deploy a sidecar that handles the CSV-file upload/download operations between
-the [Storage Service](../system-services-storage) and the Data Database using a Python Flask application and
-the [`boto3`](https://boto3.amazonaws.com/v1/documentation/api/latest/index.html) client until MariaDB supports S3
-natively.
-
-<figure markdown>
-
-<figcaption>Sidecar that handles the CSV-file upload/download.</figcaption>
-</figure>
-
## Data
The procedures require the user-generated databases to have the same collation (because of comparison operations).
diff --git a/.docs/api/data-service.md b/.docs/api/data-service.md
index 186732a472ba3218d0b65c3cc85e3653996040f0..64f03976132352cea195c6c231e3cc16ebc3d54b 100644
--- a/.docs/api/data-service.md
+++ b/.docs/api/data-service.md
@@ -6,7 +6,7 @@ author: Martin Weise
!!! debug "Debug Information"
- Image: [`registry.datalab.tuwien.ac.at/dbrepo/data-service:1.4.5`](https://hub.docker.com/r/dbrepo/data-service)
+ Image: [`registry.datalab.tuwien.ac.at/dbrepo/data-service:1.4.7`](https://hub.docker.com/r/dbrepo/data-service)
* Ports: 9093/tcp
* Info: `http://<hostname>:9093/actuator/info`
@@ -14,7 +14,13 @@ author: Martin Weise
- Readiness: `http://<hostname>:9093/actuator/health/readiness`
- Liveness: `http://<hostname>:9093/actuator/health/liveness`
* Prometheus: `http://<hostname>:9093/actuator/prometheus`
- * Swagger UI: `http://<hostname>:9093/swagger-ui/index.html` <a href="./swagger/data" target="_blank">:fontawesome-solid-square-up-right: view online</a>
+ * Swagger UI: `http://<hostname>:9093/swagger-ui/index.html` <a href="../../rest/" target="_blank">:fontawesome-solid-square-up-right: view online</a>
+
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/data-service 9093:80
+ ```
## Overview
diff --git a/.docs/api/identity-service.md b/.docs/api/identity-service.md
index fc075be448686769204908ff1c5d9ab586b23eec..3a1ae2bb5509d38fd653eebaa587976371eaabdd 100644
--- a/.docs/api/identity-service.md
+++ b/.docs/api/identity-service.md
@@ -10,6 +10,12 @@ author: Martin Weise
* Ports: 1389/tcp, 1636/tcp
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/identity-service 1389:389
+ ```
+
## Overview
This optional service holds the user identities which we simply call identities in the following. It is integrated into
diff --git a/.docs/api/metadata-db.md b/.docs/api/metadata-db.md
index 61a56ed1ac4f50ae2dcfd4b66e35f317f5bb9ded..ba93d051d0e00d3386680c93ccbfe1f4a5af2e7f 100644
--- a/.docs/api/metadata-db.md
+++ b/.docs/api/metadata-db.md
@@ -9,6 +9,12 @@ author: Martin Weise
* Ports: 3306/tcp
* JDBC: `jdbc://mariadb:<hostname>:3306`
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/metadata-db 3306:3306
+ ```
+
## Overview
The metadata database is the single, central source of truth within DBRepo and holds all metadata information for
diff --git a/.docs/api/metadata-service.md b/.docs/api/metadata-service.md
index 9d9c39ee25e62e14f610f5d84a1867af9a94e07f..a9218b4733dc0e1fe737bfe331d00a6eaec00656 100644
--- a/.docs/api/metadata-service.md
+++ b/.docs/api/metadata-service.md
@@ -6,7 +6,7 @@ author: Martin Weise
!!! debug "Debug Information"
- Image: [`registry.datalab.tuwien.ac.at/dbrepo/metadata-service:1.4.5`](https://hub.docker.com/r/dbrepo/metadata-service)
+ Image: [`registry.datalab.tuwien.ac.at/dbrepo/metadata-service:1.4.7`](https://hub.docker.com/r/dbrepo/metadata-service)
* Ports: 9099/tcp
* Info: `http://<hostname>:9099/actuator/info`
@@ -14,7 +14,13 @@ author: Martin Weise
- Readiness: `http://<hostname>:9099/actuator/health/readiness`
- Liveness: `http://<hostname>:9099/actuator/health/liveness`
* Prometheus: `http://<hostname>:9099/actuator/prometheus`
- * Swagger UI: `http://<hostname>:9099/swagger-ui/index.html`
+ * Swagger UI: `http://<hostname>:9099/swagger-ui/index.html` <a href="../../rest/" target="_blank">:fontawesome-solid-square-up-right: view online</a>
+
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/metadata-service 9099:80
+ ```
## Overview
diff --git a/.docs/api/metric-db.md b/.docs/api/metric-db.md
index 8ac9b611d99544eba5ee6738c416b12f8c2a1d47..f1fe9c11abdf8cd8fb97b19b4cc658be42c1c7ca 100644
--- a/.docs/api/metric-db.md
+++ b/.docs/api/metric-db.md
@@ -8,6 +8,14 @@ author: Martin Weise
Image: [`bitnami/prometheus:2.54.1-debian-12-r4`](https://hub.docker.com/r/bitnami/prometheus)
+ * Ports: 8080/tcp
+
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine on port `8080`:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/data-db 8080:80
+ ```
+
## Overview
The Metric Database is responsible for saving time-series data for the [Dashboard Service](../../api/dashboard-service).
@@ -140,8 +148,6 @@ The [Data Database Sidecar](#) metrics are:
| `dbrepo_search_update_database` | Time needed to update a database in the search database |
| `dbrepo_search_delete_database` | Time needed to delete a database in the search database |
-
-
## Limitations
!!! question "Do you miss functionality? Do these limitations affect you?"
diff --git a/.docs/api/search-service.md b/.docs/api/search-service.md
index 5c16b499552c32498e9e618284624d53ccf84641..ede6eefd657b29fed767ac84352de1a582b5c073 100644
--- a/.docs/api/search-service.md
+++ b/.docs/api/search-service.md
@@ -6,12 +6,18 @@ author: Martin Weise
!!! debug "Debug Information"
- Image: [`registry.datalab.tuwien.ac.at/dbrepo/search-service:1.4.5`](https://hub.docker.com/r/dbrepo/search-service)
+ Image: [`registry.datalab.tuwien.ac.at/dbrepo/search-service:1.4.7`](https://hub.docker.com/r/dbrepo/search-service)
* Ports: 4000/tcp
* Health: `http://<hostname>:4000/api/search/health`
* Prometheus: `http://<hostname>:4000/metrics`
- * Swagger UI: `http://<hostname>:4000/swagger-ui/`
+ * Swagger UI: `http://<hostname>:4000/swagger-ui/` <a href="../../rest/" target="_blank">:fontawesome-solid-square-up-right: view online</a>
+
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/search-service 4000:80
+ ```
## Overview
diff --git a/.docs/api/storage-service.md b/.docs/api/storage-service.md
index a8da4f0721f50cdbc515ca9b0ed240418529f269..939e3dbbcb07bab777118235bc1d97c4956c40af 100644
--- a/.docs/api/storage-service.md
+++ b/.docs/api/storage-service.md
@@ -8,8 +8,15 @@ author: Martin Weise
Image: [`docker.io/chrislusf/seaweedfs:3.59`](https://hub.docker.com/r/chrislusf/seaweedfs)
- * Ports: 9000/tcp
+ * Ports: 8888/tcp, 9000/tcp
* Prometheus: `http://<hostname>:9091/metrics`
+ * Filer UI: `http://<hostname>:8888`
+
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/storage-service-s3 9000:8333
+ ```
## Overview
diff --git a/.docs/api/ui.md b/.docs/api/ui.md
index d14303aa2cd7b33d48a743353bc6a82c53b0f55c..8753060f63a031e6438c43f96182c9cdef1ccc30 100644
--- a/.docs/api/ui.md
+++ b/.docs/api/ui.md
@@ -10,6 +10,12 @@ author: Martin Weise
* Ports: 3000/tcp
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/ui 3000:80
+ ```
+
The User Interface is configured in the `runtimeConfig` section of the `nuxt.config.ts` file during build time. For the
runtime, you need to override those values through environment variables or by mounting a `.env` file. As a small
example, you can configure the logo :material-numeric-1-circle-outline: in Figure 2. Make sure you mount the logo as
@@ -27,26 +33,15 @@ image as well, in this example we want to mount a custom logo `my_logo.png` into
```yaml title=".env"
NUXT_PUBLIC_TITLE="My overriden title"
- NUXT_PUBLIC_LOGO="/my_logo.png"
- NUXT_PUBLIC_ICON="/favicon.ico"
+ NUXT_PUBLIC_LOGO="https://mydomain/my_logo.png"
+ NUXT_PUBLIC_ICON="https://mydomain/my_favicon.ico"
...
```
- To work, you need to mount the `my_logo.png` file into the `dbrepo-ui` container via the `docker-compose.yml` file.
-
- ```yaml title="docker-compose.yml"
- services:
- dbrepo-ui:
- image: registry.datalab.tuwien.ac.at/dbrepo/ui:1.4.7
- volumes:
- - ./my_logo.png:/app/.output/public/my_logo.png
- - ./favicon.ico:/app/.output/public/favicon.ico
- environment:
- ...
- ...
- ```
-
- If you want to override more environment variables, extend the dictionary in `environment:`
+ To work, you need to serve the `my_logo.png` and `my_favicon.ico` from a separate webserver. Note that simply
+ copying the files into the Nuxt [`public/`](https://nuxt.com/docs/guide/directory-structure/public) directory will
+ not work as the content length is calculated only during build time. The development
+ team [#19263](https://github.com/nuxt/nuxt/issues/19263) does not plan to fix this.
=== "Kubernetes"
diff --git a/.docs/api/upload-service.md b/.docs/api/upload-service.md
index f8ad58ebcb1f626aa6064db682d3fffcd958c81a..97ca74d14be1c37e31878f4c0d54f76082a16e50 100644
--- a/.docs/api/upload-service.md
+++ b/.docs/api/upload-service.md
@@ -12,6 +12,12 @@ author: Martin Weise
* Prometheus: `http://<hostname>:1080/api/upload/metrics`
* API: `http://<hostname>:1080/api/upload`
+ To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+ ```shell
+ kubectl [-n namespace] port-forward svc/upload-service 1080:80
+ ```
+
## Overview
We use the [TUS](https://tus.io/) open protocol for resume-able file uploads which based entirely on HTTP. Even though
diff --git a/.docs/changelog.md b/.docs/changelog.md
index e7f12b284b67d0af3201031cd96c49eda62c2604..e39afc485135155b4b91def5b9f9878d5497cde5 100644
--- a/.docs/changelog.md
+++ b/.docs/changelog.md
@@ -2,7 +2,7 @@
author: Martin Weise
---
-## v1.4.7 (2024-10-21)
+## v1.4.7 (2024-11-06)
[:simple-gitlab: GitLab Release](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/tags/v1.4.7)
@@ -19,6 +19,8 @@ author: Martin Weise
#### Changes
+* Remove the Data Database Sidecar and replace it with Apache Spark
+ in [#458](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/issues/458).
* Allow anonymous users to create subsets for public databases
in [#449](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/issues/449).
* Show file upload progress
@@ -29,6 +31,8 @@ author: Martin Weise
#### Fixes
+* Preventing the semicolon `;` to be used in UI and fixed cryptic subset execution error messages
+ in [#456](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/issues/456).
* Multiple UI errors in [#453](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/issues/453).
* Fixed install script.sh
in [#444](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/issues/444)
diff --git a/.docs/index.md b/.docs/index.md
index f24d5c598e99e9a969b251cb0ba0854eb389f7a0..f1d1ced056fdd7003487d0f6a919b4690a26abdc 100644
--- a/.docs/index.md
+++ b/.docs/index.md
@@ -4,8 +4,10 @@ author: Martin Weise
[](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services){ tabindex=-1 }
[](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services){ tabindex=-1 }
-[](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services){ tabindex=-1 }
-[](https://hub.docker.com/u/dbrepo){ tabindex=-1 }
+[](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services){ tabindex=-1 }
+[](https://pypi.org/project/dbrepo/){ tabindex=-1 }
+[](https://hub.docker.com/u/dbrepo){ tabindex=-1 }
+[](https://artifacthub.io/packages/helm/dbrepo/dbrepo){ tabindex=-1 }
[](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services){ tabindex=-1 }
Documentation for version: [v1.4.7](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/releases).
@@ -31,11 +33,12 @@ Installing DBRepo is very easy or
## Who is using DBRepo?
- [TU Wien](https://dbrepo1.ec.tuwien.ac.at)
+- TU Graz
- TU Darmstadt
- [Universität Hamburg](https://dbrepo.fdm.uni-hamburg.de/)
- [Universiti Teknikal Malaysia Melaka](https://dbrepo.utem.edu.my/)
- University of the Philippines
-- [Universiti Sains Malaysia](https://dbrepo.wrfexpress.com/)
+- [Universiti Sains Malaysia](https://atmosfera.usm.my/dbrepo/)
## How can I try DBRepo?
diff --git a/.docs/installation.md b/.docs/installation.md
index 024d39bcd49cf68013c280552be3677bd8480e0a..4a0c6c6f433a1b0e7a766dcffae490e1a49e8792 100644
--- a/.docs/installation.md
+++ b/.docs/installation.md
@@ -29,7 +29,6 @@ settings.
- min. 8 vCPU cores
- min. 8GB free RAM memory
- min. 200GB free SSD storage
-- min. 100Mbit/s connection
Since DBRepo is intended to be a publicly available repository, an optional fixed/static IP-address with optional
SSL/TLS certificate is recommended. Follow the [secure install](#secure-install) guide.
diff --git a/.docs/kubernetes.md b/.docs/kubernetes.md
index 2384f61d0451435b0515e09b128f71d942039bee..72bb4bcc125e6b8d2a78e301211e3ee739a82aed 100644
--- a/.docs/kubernetes.md
+++ b/.docs/kubernetes.md
@@ -2,8 +2,6 @@
author: Martin Weise
---
-[](https://artifacthub.io/packages/helm/dbrepo/dbrepo){ tabindex=-1 }
-
## TL;DR
To install DBRepo in your existing cluster, download the
@@ -26,6 +24,15 @@ helm upgrade --install dbrepo \
* Kubernetes 3.8.0+
* PV provisioner support in the underlying infrastructure
+### Resource Quota
+
+* `requests.cpu=8`
+* `requests.memory=8Gi`
+* `requests.storage` >= 25
+* `pods` >= 50
+* `services` >= 50
+* `secrets` >= 50
+
## Limitations
1. The entire Helm deployment is rootless (=`runAsNonRoot=true`) except for
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f571fba1d16722ed56e3152dbe634272ebcbd284..d6c97103ae51b8e08ef231969cf650ae682afd8a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -59,15 +59,6 @@ build-analyse-service:
- "pip install pipenv"
- "pipenv install gunicorn && pipenv install --dev --system --deploy"
-build-data-db-sidecar:
- image: docker.io/python:3.11-alpine
- stage: build
- variables:
- PIPENV_PIPFILE: "./dbrepo-data-db/sidecar/Pipfile"
- script:
- - "pip install pipenv"
- - "pipenv install gunicorn && pipenv install --dev --system --deploy"
-
build-lib:
image: docker.io/python:3.11-alpine
stage: build
@@ -147,7 +138,6 @@ lint-docker-compose:
- "IGNORE_IMAGE=1 IGNORE_PORTS=1 bash .scripts/check-service.sh 'dbrepo-broker-service'"
- "IGNORE_PORTS=1 bash .scripts/check-service.sh 'dbrepo-dashboard-service'"
- "bash .scripts/check-service.sh 'dbrepo-data-db'"
- - "IGNORE_IMAGE=1 IGNORE_PORTS=1 bash .scripts/check-service.sh 'dbrepo-data-db-sidecar'"
- "IGNORE_IMAGE=1 IGNORE_PORTS=1 bash .scripts/check-service.sh 'dbrepo-data-service'"
- "IGNORE_VOLUMES=1 bash .scripts/check-service.sh 'dbrepo-gateway-service'"
- "IGNORE_VOLUMES=1 bash .scripts/check-service.sh 'dbrepo-identity-service'"
diff --git a/Pipfile b/Pipfile
new file mode 100644
index 0000000000000000000000000000000000000000..f0721bfdca857fc7072edafd32a0372e09e1168c
--- /dev/null
+++ b/Pipfile
@@ -0,0 +1,26 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+mkdocs = "==1.5.3"
+mkdocs-material = "==9.5.17"
+mkdocs-with-pdf = "==0.9.3"
+mkdocs-material-extensions = ">=1.0.3"
+py-dotenv = ">=0.1"
+python-dotenv = "==1.0.0"
+build = "==1.1.1"
+twine = "==5.0.0"
+furo = "==2024.1.29"
+requests = "==2.31.0"
+pika = "==1.3.2"
+pydantic = "==2.6.4"
+tuspy = "==1.0.3"
+mike = "==2.0.0"
+anybadge = "==1.14.0"
+
+[dev-packages]
+
+[requires]
+python_version = "3.11"
diff --git a/Pipfile.lock b/Pipfile.lock
new file mode 100644
index 0000000000000000000000000000000000000000..bf3eb9a4ce0a82df43ca1434743b85fd4a1fa88d
--- /dev/null
+++ b/Pipfile.lock
@@ -0,0 +1,2103 @@
+{
+ "_meta": {
+ "hash": {
+ "sha256": "c0f798e1103d6c20c3417ca7db612e28963f1b67de21172dd52ece1bb87f6816"
+ },
+ "pipfile-spec": 6,
+ "requires": {
+ "python_version": "3.11"
+ },
+ "sources": [
+ {
+ "name": "pypi",
+ "url": "https://pypi.org/simple",
+ "verify_ssl": true
+ }
+ ]
+ },
+ "default": {
+ "aiohappyeyeballs": {
+ "hashes": [
+ "sha256:75cf88a15106a5002a8eb1dab212525c00d1f4c0fa96e551c9fbe6f09a621586",
+ "sha256:8a7a83727b2756f394ab2895ea0765a0a8c475e3c71e98d43d76f22b4b435572"
+ ],
+ "markers": "python_version >= '3.8'",
+ "version": "==2.4.3"
+ },
+ "aiohttp": {
+ "hashes": [
+ "sha256:007ec22fbc573e5eb2fb7dec4198ef8f6bf2fe4ce20020798b2eb5d0abda6138",
+ "sha256:00819de9e45d42584bed046314c40ea7e9aea95411b38971082cad449392b08c",
+ "sha256:01948b1d570f83ee7bbf5a60ea2375a89dfb09fd419170e7f5af029510033d24",
+ "sha256:038f514fe39e235e9fef6717fbf944057bfa24f9b3db9ee551a7ecf584b5b480",
+ "sha256:03a42ac7895406220124c88911ebee31ba8b2d24c98507f4a8bf826b2937c7f2",
+ "sha256:05646ebe6b94cc93407b3bf34b9eb26c20722384d068eb7339de802154d61bc5",
+ "sha256:0631dd7c9f0822cc61c88586ca76d5b5ada26538097d0f1df510b082bad3411a",
+ "sha256:0b00807e2605f16e1e198f33a53ce3c4523114059b0c09c337209ae55e3823a8",
+ "sha256:0e1b370d8007c4ae31ee6db7f9a2fe801a42b146cec80a86766e7ad5c4a259cf",
+ "sha256:15ecd889a709b0080f02721255b3f80bb261c2293d3c748151274dfea93ac871",
+ "sha256:1b66ccafef7336a1e1f0e389901f60c1d920102315a56df85e49552308fc0486",
+ "sha256:1bbb122c557a16fafc10354b9d99ebf2f2808a660d78202f10ba9d50786384b9",
+ "sha256:1eb89d3d29adaf533588f209768a9c02e44e4baf832b08118749c5fad191781d",
+ "sha256:258c5dd01afc10015866114e210fb7365f0d02d9d059c3c3415382ab633fcbcb",
+ "sha256:2609e9ab08474702cc67b7702dbb8a80e392c54613ebe80db7e8dbdb79837c68",
+ "sha256:274cfa632350225ce3fdeb318c23b4a10ec25c0e2c880eff951a3842cf358ac1",
+ "sha256:28529e08fde6f12eba8677f5a8608500ed33c086f974de68cc65ab218713a59d",
+ "sha256:2b606353da03edcc71130b52388d25f9a30a126e04caef1fd637e31683033abd",
+ "sha256:30ca7c3b94708a9d7ae76ff281b2f47d8eaf2579cd05971b5dc681db8caac6e1",
+ "sha256:333cf6cf8e65f6a1e06e9eb3e643a0c515bb850d470902274239fea02033e9a8",
+ "sha256:3455522392fb15ff549d92fbf4b73b559d5e43dc522588f7eb3e54c3f38beee7",
+ "sha256:362f641f9071e5f3ee6f8e7d37d5ed0d95aae656adf4ef578313ee585b585959",
+ "sha256:3bcd391d083f636c06a68715e69467963d1f9600f85ef556ea82e9ef25f043f7",
+ "sha256:3dffb610a30d643983aeb185ce134f97f290f8935f0abccdd32c77bed9388b42",
+ "sha256:3fe407bf93533a6fa82dece0e74dbcaaf5d684e5a51862887f9eaebe6372cd79",
+ "sha256:413251f6fcf552a33c981c4709a6bba37b12710982fec8e558ae944bfb2abd38",
+ "sha256:438cd072f75bb6612f2aca29f8bd7cdf6e35e8f160bc312e49fbecab77c99e3a",
+ "sha256:4470c73c12cd9109db8277287d11f9dd98f77fc54155fc71a7738a83ffcc8ea8",
+ "sha256:45c3b868724137f713a38376fef8120c166d1eadd50da1855c112fe97954aed8",
+ "sha256:486f7aabfa292719a2753c016cc3a8f8172965cabb3ea2e7f7436c7f5a22a151",
+ "sha256:4f05e9727ce409358baa615dbeb9b969db94324a79b5a5cea45d39bdb01d82e6",
+ "sha256:50aed5155f819873d23520919e16703fc8925e509abbb1a1491b0087d1cd969e",
+ "sha256:50edbcad60d8f0e3eccc68da67f37268b5144ecc34d59f27a02f9611c1d4eec7",
+ "sha256:54ca74df1be3c7ca1cf7f4c971c79c2daf48d9aa65dea1a662ae18926f5bc8ce",
+ "sha256:578a4b875af3e0daaf1ac6fa983d93e0bbfec3ead753b6d6f33d467100cdc67b",
+ "sha256:597a079284b7ee65ee102bc3a6ea226a37d2b96d0418cc9047490f231dc09fe8",
+ "sha256:59bb3c54aa420521dc4ce3cc2c3fe2ad82adf7b09403fa1f48ae45c0cbde6628",
+ "sha256:5c6a5b8c7926ba5d8545c7dd22961a107526562da31a7a32fa2456baf040939f",
+ "sha256:64f6c17757251e2b8d885d728b6433d9d970573586a78b78ba8929b0f41d045a",
+ "sha256:679abe5d3858b33c2cf74faec299fda60ea9de62916e8b67e625d65bf069a3b7",
+ "sha256:741a46d58677d8c733175d7e5aa618d277cd9d880301a380fd296975a9cdd7bc",
+ "sha256:7789050d9e5d0c309c706953e5e8876e38662d57d45f936902e176d19f1c58ab",
+ "sha256:77abf6665ae54000b98b3c742bc6ea1d1fb31c394bcabf8b5d2c1ac3ebfe7f3b",
+ "sha256:79019094f87c9fb44f8d769e41dbb664d6e8fcfd62f665ccce36762deaa0e911",
+ "sha256:7b06b7843929e41a94ea09eb1ce3927865387e3e23ebe108e0d0d09b08d25be9",
+ "sha256:7e338c0523d024fad378b376a79faff37fafb3c001872a618cde1d322400a572",
+ "sha256:7ea7ffc6d6d6f8a11e6f40091a1040995cdff02cfc9ba4c2f30a516cb2633554",
+ "sha256:8105fd8a890df77b76dd3054cddf01a879fc13e8af576805d667e0fa0224c35d",
+ "sha256:84afcdea18eda514c25bc68b9af2a2b1adea7c08899175a51fe7c4fb6d551257",
+ "sha256:9294bbb581f92770e6ed5c19559e1e99255e4ca604a22c5c6397b2f9dd3ee42c",
+ "sha256:93429602396f3383a797a2a70e5f1de5df8e35535d7806c9f91df06f297e109b",
+ "sha256:9627cc1a10c8c409b5822a92d57a77f383b554463d1884008e051c32ab1b3742",
+ "sha256:998f3bd3cfc95e9424a6acd7840cbdd39e45bc09ef87533c006f94ac47296090",
+ "sha256:9c72109213eb9d3874f7ac8c0c5fa90e072d678e117d9061c06e30c85b4cf0e6",
+ "sha256:9fc1500fd2a952c5c8e3b29aaf7e3cc6e27e9cfc0a8819b3bce48cc1b849e4cc",
+ "sha256:a3f00003de6eba42d6e94fabb4125600d6e484846dbf90ea8e48a800430cc142",
+ "sha256:a45d85cf20b5e0d0aa5a8dca27cce8eddef3292bc29d72dcad1641f4ed50aa16",
+ "sha256:a7d8d14fe962153fc681f6366bdec33d4356f98a3e3567782aac1b6e0e40109a",
+ "sha256:a8fa23fe62c436ccf23ff930149c047f060c7126eae3ccea005f0483f27b2e28",
+ "sha256:aa6658732517ddabe22c9036479eabce6036655ba87a0224c612e1ae6af2087e",
+ "sha256:aafc8ee9b742ce75044ae9a4d3e60e3d918d15a4c2e08a6c3c3e38fa59b92d94",
+ "sha256:ab5a5a0c7a7991d90446a198689c0535be89bbd6b410a1f9a66688f0880ec026",
+ "sha256:acd48d5b80ee80f9432a165c0ac8cbf9253eaddb6113269a5e18699b33958dbb",
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+ "sha256:fe8bba2545427418efc1929c5c42852bdb4143eb8d0a46b09de88d1fe99258e7"
+ ],
+ "markers": "python_version >= '3.9'",
+ "version": "==1.16.0"
+ },
+ "zipp": {
+ "hashes": [
+ "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350",
+ "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"
+ ],
+ "markers": "python_version >= '3.8'",
+ "version": "==3.20.2"
+ },
+ "zopfli": {
+ "hashes": [
+ "sha256:0aa5f90d6298bda02a95bc8dc8c3c19004d5a4e44bda00b67ca7431d857b4b54",
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+ "sha256:eb45a34f23da4f8bc712b6376ca5396914b0b7c09adbb001dad964eb7f3132f8",
+ "sha256:ecb7572df5372abce8073df078207d9d1749f20b8b136089916a4a0868d56051",
+ "sha256:f12000a6accdd4bf0a3fa6eaa1b1c7a7bc80af0a2edf3f89d770d3dcce1d0e22",
+ "sha256:f7d69c1a7168ad0e9cb864e8663acb232986a0c9c9cb9801f56bf6214f53a54d",
+ "sha256:f815fcc2b2a457977724bad97fb4854022980f51ce7b136925e336b530545ae1",
+ "sha256:fc39f5c27f962ec8660d8d20c24762431131b5d8c672b44b0a54cf2b5bcde9b9"
+ ],
+ "version": "==0.2.3.post1"
+ }
+ },
+ "develop": {}
+}
diff --git a/README.md b/README.md
index 06f03b60102d1e66c3a270807b3d23fee9c866c4..f01d3f7d78f77b48fd2281facee8592b685497e5 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,11 @@
-
+
+
<img src="./dbrepo-ui/public/logo.png" width="200" alt="DBRepo — Repository for Data in Databases" />
diff --git a/dbrepo-analyse-service/Dockerfile b/dbrepo-analyse-service/Dockerfile
index 97b181c76e3e5207dc145ba2d02f45c78fb27e71..c71b3ed4ef29b8ac5b1a65d8e52208d1f3f24ff2 100644
--- a/dbrepo-analyse-service/Dockerfile
+++ b/dbrepo-analyse-service/Dockerfile
@@ -1,9 +1,11 @@
FROM python:3.11-alpine
LABEL org.opencontainers.image.authors="martin.weise@tuwien.ac.at"
-RUN apk add bash curl
-
-WORKDIR /home/alpine
+RUN apk --no-cache \
+ add \
+ bash \
+ curl \
+ openjdk8-jre
COPY Pipfile Pipfile.lock ./
@@ -13,14 +15,16 @@ RUN pip install pipenv && \
pipenv install gunicorn && \
pipenv install --system --deploy
-USER 1001
+RUN adduser -D analyse-service --uid 1000
WORKDIR /app
-COPY --chown=1001 ./api ./api
-COPY --chown=1001 ./as-yml ./as-yml
-COPY --chown=1001 ./clients ./clients
-COPY --chown=1001 ./*.py ./
+USER 1000
+
+COPY --chown=1000 ./api ./api
+COPY --chown=1000 ./as-yml ./as-yml
+COPY --chown=1000 ./clients ./clients
+COPY --chown=1000 ./*.py ./
# non-root port
EXPOSE 8080
diff --git a/dbrepo-analyse-service/Pipfile.lock b/dbrepo-analyse-service/Pipfile.lock
index bcff34a23efb2e4a660fb11c850aba569369e918..5b3e18df9a67bef696e1b68ecf30b3362e4e86dc 100644
--- a/dbrepo-analyse-service/Pipfile.lock
+++ b/dbrepo-analyse-service/Pipfile.lock
@@ -190,20 +190,20 @@
},
"boto3": {
"hashes": [
- "sha256:5970b62c1ec8177501e02520f0d41839ca5fc549b30bac4e8c0c0882ae776217",
- "sha256:670f811c65e3c5fe4ed8c8d69be0b44b1d649e992c0fc16de43816d1188f88f1"
+ "sha256:2d5e160b614db55fbee7981001c54476cb827c441cef65b2fcb2c52a62019909",
+ "sha256:7d9c359bbbc858a60b51c86328db813353c8bd1940212cdbd0a7da835291c2e1"
],
"index": "pypi",
"markers": "python_version >= '3.8'",
- "version": "==1.35.39"
+ "version": "==1.35.54"
},
"botocore": {
"hashes": [
- "sha256:781c547eb6a79c0e4b0bedd87b81fbfed957816b4841d33e20c8f1989c7c19ce",
- "sha256:cb7f851933b5ccc2fba4f0a8b846252410aa0efac5bfbe93b82d10801f5f8e90"
+ "sha256:131bb59ce59c8a939b31e8e647242d70cf11d32d4529fa4dca01feea1e891a76",
+ "sha256:9cca1811094b6cdc144c2c063a3ec2db6d7c88194b04d4277cd34fc8e3473aff"
],
"markers": "python_version >= '3.8'",
- "version": "==1.35.39"
+ "version": "==1.35.54"
},
"certifi": {
"hashes": [
@@ -407,42 +407,41 @@
},
"cryptography": {
"hashes": [
- "sha256:014f58110f53237ace6a408b5beb6c427b64e084eb451ef25a28308270086494",
- "sha256:1bbcce1a551e262dfbafb6e6252f1ae36a248e615ca44ba302df077a846a8806",
- "sha256:203e92a75716d8cfb491dc47c79e17d0d9207ccffcbcb35f598fbe463ae3444d",
- "sha256:27e613d7077ac613e399270253259d9d53872aaf657471473ebfc9a52935c062",
- "sha256:2bd51274dcd59f09dd952afb696bf9c61a7a49dfc764c04dd33ef7a6b502a1e2",
- "sha256:38926c50cff6f533f8a2dae3d7f19541432610d114a70808f0926d5aaa7121e4",
- "sha256:511f4273808ab590912a93ddb4e3914dfd8a388fed883361b02dea3791f292e1",
- "sha256:58d4e9129985185a06d849aa6df265bdd5a74ca6e1b736a77959b498e0505b85",
- "sha256:5b43d1ea6b378b54a1dc99dd8a2b5be47658fe9a7ce0a58ff0b55f4b43ef2b84",
- "sha256:61ec41068b7b74268fa86e3e9e12b9f0c21fcf65434571dbb13d954bceb08042",
- "sha256:666ae11966643886c2987b3b721899d250855718d6d9ce41b521252a17985f4d",
- "sha256:68aaecc4178e90719e95298515979814bda0cbada1256a4485414860bd7ab962",
- "sha256:7c05650fe8023c5ed0d46793d4b7d7e6cd9c04e68eabe5b0aeea836e37bdcec2",
- "sha256:80eda8b3e173f0f247f711eef62be51b599b5d425c429b5d4ca6a05e9e856baa",
- "sha256:8385d98f6a3bf8bb2d65a73e17ed87a3ba84f6991c155691c51112075f9ffc5d",
- "sha256:88cce104c36870d70c49c7c8fd22885875d950d9ee6ab54df2745f83ba0dc365",
- "sha256:9d3cdb25fa98afdd3d0892d132b8d7139e2c087da1712041f6b762e4f807cc96",
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- "sha256:fba1007b3ef89946dbbb515aeeb41e30203b004f0b4b00e5e16078b518563289"
+ "sha256:0c580952eef9bf68c4747774cde7ec1d85a6e61de97281f2dba83c7d2c806362",
+ "sha256:0f996e7268af62598f2fc1204afa98a3b5712313a55c4c9d434aef49cadc91d4",
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+ "sha256:53a583b6637ab4c4e3591a15bc9db855b8d9dee9a669b550f311480acab6eb08",
+ "sha256:63efa177ff54aec6e1c0aefaa1a241232dcd37413835a9b674b6e3f0ae2bfd3e",
+ "sha256:74f57f24754fe349223792466a709f8e0c093205ff0dca557af51072ff47ab18",
+ "sha256:7e1ce50266f4f70bf41a2c6dc4358afadae90e2a1e5342d3c08883df1675374f",
+ "sha256:81ef806b1fef6b06dcebad789f988d3b37ccaee225695cf3e07648eee0fc6b73",
+ "sha256:846da004a5804145a5f441b8530b4bf35afbf7da70f82409f151695b127213d5",
+ "sha256:8ac43ae87929a5982f5948ceda07001ee5e83227fd69cf55b109144938d96984",
+ "sha256:9762ea51a8fc2a88b70cf2995e5675b38d93bf36bd67d91721c309df184f49bd",
+ "sha256:a2a431ee15799d6db9fe80c82b055bae5a752bef645bba795e8e52687c69efe3",
+ "sha256:bf7a1932ac4176486eab36a19ed4c0492da5d97123f1406cf15e41b05e787d2e",
+ "sha256:c2e6fc39c4ab499049df3bdf567f768a723a5e8464816e8f009f121a5a9f4405",
+ "sha256:cbeb489927bd7af4aa98d4b261af9a5bc025bd87f0e3547e11584be9e9427be2",
+ "sha256:d03b5621a135bffecad2c73e9f4deb1a0f977b9a8ffe6f8e002bf6c9d07b918c",
+ "sha256:d56e96520b1020449bbace2b78b603442e7e378a9b3bd68de65c782db1507995",
+ "sha256:df6b6c6d742395dd77a23ea3728ab62f98379eff8fb61be2744d4679ab678f73",
+ "sha256:e1be4655c7ef6e1bbe6b5d0403526601323420bcf414598955968c9ef3eb7d16",
+ "sha256:f18c716be16bc1fea8e95def49edf46b82fccaa88587a45f8dc0ff6ab5d8e0a7",
+ "sha256:f46304d6f0c6ab8e52770addfa2fc41e6629495548862279641972b6215451cd",
+ "sha256:f7b178f11ed3664fd0e995a47ed2b5ff0a12d893e41dd0494f406d1cf555cab7"
],
"markers": "python_version >= '3.7'",
- "version": "==43.0.1"
+ "version": "==43.0.3"
},
"dbrepo": {
"hashes": [
- "sha256:84607677b0826bb9b2fa120aacdf56d16c8d9ae423f435b2bd2c22b1c965a33c"
+ "sha256:36316d520c23dcbd249b779ad596a979fe574321882a7d4b6c6934c62a5de57b"
],
- "markers": "python_version >= '3.11'",
"path": "./lib/dbrepo-1.4.7.tar.gz"
},
"events": {
@@ -503,131 +502,146 @@
},
"frozenlist": {
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],
"markers": "python_version >= '3.9'",
- "version": "==3.0.1"
+ "version": "==3.0.2"
},
"minio": {
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],
"index": "pypi",
"markers": "python_version >= '3.9'",
- "version": "==7.2.9"
+ "version": "==7.2.10"
},
"mistune": {
"hashes": [
@@ -958,63 +972,65 @@
},
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+ "sha256:e14e26956e6f1696070788252dcdff11b4aca4c3e8bd166e0df1bb8f315a67cb",
+ "sha256:e6988e90fcf617da2b5c78902fe8e668361b43b4fe26dbf2d7b0f8034d4cafb9",
+ "sha256:e711e02f49e176a01d0349d82cb5f05ba4db7d5e7e0defd026328e5cfb3226d3",
+ "sha256:ea4dedd6e394a9c180b33c2c872b92f7ce0f8e7ad93e9585312b0c5a04777a4a",
+ "sha256:ecc76a9ba2911d8d37ac01de72834d8849e55473457558e12995f4cd53e778e0",
+ "sha256:f55ba01150f52b1027829b50d70ef1dafd9821ea82905b63936668403c3b471e",
+ "sha256:f653490b33e9c3a4c1c01d41bc2aef08f9475af51146e4a7710c450cf9761598",
+ "sha256:fa2d1337dc61c8dc417fbccf20f6d1e139896a30721b7f1e832b2bb6ef4eb6c4"
],
"index": "pypi",
"markers": "python_version >= '3.10'",
- "version": "==2.1.2"
+ "version": "==2.1.3"
},
"opensearch-py": {
"hashes": [
@@ -1373,7 +1389,7 @@
"sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3",
"sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"
],
- "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+ "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
"version": "==2.9.0.post0"
},
"pytz": {
@@ -1461,112 +1477,112 @@
},
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+ "sha256:f16bc1334853e91ddaaa1217045dd7be166170beec337576818461268a3de67f",
+ "sha256:f19169781dddae7478a32301b499b2858bc52fc45a112955e798ee307e294977",
+ "sha256:fa3060d885657abc549b2a0f8e1b79699290e5d83845141717c6c90c2df38311",
+ "sha256:fa41a64ac5b08b292906e248549ab48b69c5428f3987b09689ab2441f267d04d",
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+ "sha256:fe00a9057d100e69b4ae4a094203a708d65b0f345ed546fdef86498bf5390982"
],
"markers": "python_version >= '3.8'",
- "version": "==0.20.0"
+ "version": "==0.20.1"
},
"s3transfer": {
"hashes": [
@@ -1578,18 +1594,18 @@
},
"setuptools": {
"hashes": [
- "sha256:35ab7fd3bcd95e6b7fd704e4a1539513edad446c097797f2985e0e4b960772f2",
- "sha256:d59a21b17a275fb872a9c3dae73963160ae079f1049ed956880cd7c09b120538"
+ "sha256:f2504966861356aa38616760c0f66568e535562374995367b4e69c7143cf6bcd",
+ "sha256:fba5dd4d766e97be1b1681d98712680ae8f2f26d7881245f2ce9e40714f1a686"
],
"markers": "python_version >= '3.8'",
- "version": "==75.1.0"
+ "version": "==75.3.0"
},
"six": {
"hashes": [
"sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926",
"sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"
],
- "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+ "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
"version": "==1.16.0"
},
"tinydb": {
@@ -1634,115 +1650,99 @@
},
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],
- "markers": "python_version >= '3.8'",
- "version": "==3.0.4"
+ "markers": "python_version >= '3.9'",
+ "version": "==3.1.1"
},
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},
"zope.event": {
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@@ -1754,46 +1754,46 @@
},
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}
},
"develop": {
@@ -2026,72 +2026,72 @@
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- "sha256:70a6756ce66cd6fe8486c775b30889f0dc4cb20c157aa8c35b45fd7868255c5c",
- "sha256:70d24936ca6c15a3bbc91ee9c7fc661132c6f4c9d42a23b31b6686c05073bde5",
- "sha256:71967c35828c9ff94e8c7d405469a1fb68257f686bca7c1ed85ed34e7c2529c4",
- "sha256:79644f68a6ff23b251cae1c82b01a0b51bc40c8468ca9585c6c4b1aeee570e0b",
- "sha256:87cd2e29067ea397a47e352efb13f976eb1b03e18c999270bb50589323294c6e",
- "sha256:8d4c6ea0f498c7c79111033a290d060c517853a7bcb2f46516f591dab628ddd3",
- "sha256:9134032f5aa445ae591c2ba6991d10136a1f533b1d2fa8f8c21126468c5025c6",
- "sha256:921fbe13492caf6a69528f09d5d7c7d518c8d0e7b9f6701b7719715f29a71e6e",
- "sha256:99670790f21a96665a35849990b1df447993880bb6463a0a1d757897f30da929",
- "sha256:9975442f2e7a5cfcf87299c26b5a45266ab0696348420049b9b94b2ad3d40234",
- "sha256:99ded130555c021d99729fabd4ddb91a6f4cc0707df4b1daf912c7850c373b13",
- "sha256:a3328c3e64ea4ab12b85999eb0779e6139295bbf5485f69d42cf794309e3d007",
- "sha256:a4fb91d5f72b7e06a14ff4ae5be625a81cd7e5f869d7a54578fc271d08d58ae3",
- "sha256:aa23ce39661a3e90eea5f99ec59b763b7d655c2cada10729ed920a38bfc2b167",
- "sha256:aac7501ae73d4a02f4b7ac8fcb9dc55342ca98ffb9ed9f2dfb8a25d53eda0e4d",
- "sha256:ab84a8b698ad5a6c365b08061920138e7a7dd9a04b6feb09ba1bfae68346ce6d",
- "sha256:b4adeb878a374126f1e5cf03b87f66279f479e01af0e9a654cf6d1509af46c40",
- "sha256:b9853509b4bf57ba7b1f99b9d866c422c9c5248799ab20e652bbb8a184a38181",
- "sha256:bb7d5fe92bd0dc235f63ebe9f8c6e0884f7360f88f3411bfed1350c872ef2054",
- "sha256:bca4c8abc50d38f9773c1ec80d43f3768df2e8576807d1656016b9d3eeaa96fd",
- "sha256:c222958f59b0ae091f4535851cbb24eb57fc0baea07ba675af718fb5302dddb2",
- "sha256:c30e42ea11badb147f0d2e387115b15e2bd8205a5ad70d6ad79cf37f6ac08c91",
- "sha256:c3a79f56dee9136084cf84a6c7c4341427ef36e05ae6415bf7d787c96ff5eaa3",
- "sha256:c51ef82302386d686feea1c44dbeef744585da16fcf97deea2a8d6c1556f519b",
- "sha256:c77326300b839c44c3e5a8fe26c15b7e87b2f32dfd2fc9fee1d13604347c9b38",
- "sha256:d33a785ea8354c480515e781554d3be582a86297e41ccbea627a5c632647f2cd",
- "sha256:d546cfa78844b8b9c1c0533de1851569a13f87449897bbc95d698d1d3cb2a30f",
- "sha256:da29ceabe3025a1e5a5aeeb331c5b1af686daab4ff0fb4f83df18b1180ea83e2",
- "sha256:df8c05a0f574d480947cba11b947dc41b1265d721c3777881da2fb8d3a1ddfba",
- "sha256:e266af4da2c1a4cbc6135a570c64577fd3e6eb204607eaff99d8e9b710003c6f",
- "sha256:e279f3db904e3b55f520f11f983cc8dc8a4ce9b65f11692d4718ed021ec58b83",
- "sha256:ea52bd218d4ba260399a8ae4bb6b577d82adfc4518b93566ce1fddd4a49d1dce",
- "sha256:ebec65f5068e7df2d49466aab9128510c4867e532e07cb6960075b27658dca38",
- "sha256:ec1e3b40b82236d100d259854840555469fad4db64f669ab817279eb95cd535c",
- "sha256:ee77c7bef0724165e795b6b7bf9c4c22a9b8468a6bdb9c6b4281293c6b22a90f",
- "sha256:f263b18692f8ed52c8de7f40a0751e79015983dbd77b16906e5b310a39d3ca21",
- "sha256:f7b26757b22faf88fcf232f5f0e62f6e0fd9e22a8a5d0d5016888cdfe1f6c1c4",
- "sha256:f7ddb920106bbbbcaf2a274d56f46956bf56ecbde210d88061824a95bdd94e92"
+ "sha256:00a1d69c112ff5149cabe60d2e2ee948752c975d95f1e1096742e6077affd376",
+ "sha256:023bf8ee3ec6d35af9c1c6ccc1d18fa69afa1cb29eaac57cb064dbb262a517f9",
+ "sha256:0294ca37f1ba500667b1aef631e48d875ced93ad5e06fa665a3295bdd1d95111",
+ "sha256:06babbb8f4e74b063dbaeb74ad68dfce9186c595a15f11f5d5683f748fa1d172",
+ "sha256:0809082ee480bb8f7416507538243c8863ac74fd8a5d2485c46f0f7499f2b491",
+ "sha256:0b3fb02fe73bed561fa12d279a417b432e5b50fe03e8d663d61b3d5990f29546",
+ "sha256:0b58c672d14f16ed92a48db984612f5ce3836ae7d72cdd161001cc54512571f2",
+ "sha256:0bcd1069e710600e8e4cf27f65c90c7843fa8edfb4520fb0ccb88894cad08b11",
+ "sha256:1032e178b76a4e2b5b32e19d0fd0abbce4b58e77a1ca695820d10e491fa32b08",
+ "sha256:11a223a14e91a4693d2d0755c7a043db43d96a7450b4f356d506c2562c48642c",
+ "sha256:12394842a3a8affa3ba62b0d4ab7e9e210c5e366fbac3e8b2a68636fb19892c2",
+ "sha256:182e6cd5c040cec0a1c8d415a87b67ed01193ed9ad458ee427741c7d8513d963",
+ "sha256:1d5b8007f81b88696d06f7df0cb9af0d3b835fe0c8dbf489bad70b45f0e45613",
+ "sha256:1f76846299ba5c54d12c91d776d9605ae33f8ae2b9d1d3c3703cf2db1a67f2c0",
+ "sha256:27fb4a050aaf18772db513091c9c13f6cb94ed40eacdef8dad8411d92d9992db",
+ "sha256:29155cd511ee058e260db648b6182c419422a0d2e9a4fa44501898cf918866cf",
+ "sha256:29fc0f17b1d3fea332f8001d4558f8214af7f1d87a345f3a133c901d60347c73",
+ "sha256:2b6b4c83d8e8ea79f27ab80778c19bc037759aea298da4b56621f4474ffeb117",
+ "sha256:2fdef0d83a2d08d69b1f2210a93c416d54e14d9eb398f6ab2f0a209433db19e1",
+ "sha256:3c65d37f3a9ebb703e710befdc489a38683a5b152242664b973a7b7b22348a4e",
+ "sha256:4f704f0998911abf728a7783799444fcbbe8261c4a6c166f667937ae6a8aa522",
+ "sha256:51b44306032045b383a7a8a2c13878de375117946d68dcb54308111f39775a25",
+ "sha256:53d202fd109416ce011578f321460795abfe10bb901b883cafd9b3ef851bacfc",
+ "sha256:58809e238a8a12a625c70450b48e8767cff9eb67c62e6154a642b21ddf79baea",
+ "sha256:5915fcdec0e54ee229926868e9b08586376cae1f5faa9bbaf8faf3561b393d52",
+ "sha256:5beb1ee382ad32afe424097de57134175fea3faf847b9af002cc7895be4e2a5a",
+ "sha256:5f8ae553cba74085db385d489c7a792ad66f7f9ba2ee85bfa508aeb84cf0ba07",
+ "sha256:5fbd612f8a091954a0c8dd4c0b571b973487277d26476f8480bfa4b2a65b5d06",
+ "sha256:6bd818b7ea14bc6e1f06e241e8234508b21edf1b242d49831831a9450e2f35fa",
+ "sha256:6f01ba56b1c0e9d149f9ac85a2f999724895229eb36bd997b61e62999e9b0901",
+ "sha256:73d2b73584446e66ee633eaad1a56aad577c077f46c35ca3283cd687b7715b0b",
+ "sha256:7bb92c539a624cf86296dd0c68cd5cc286c9eef2d0c3b8b192b604ce9de20a17",
+ "sha256:8165b796df0bd42e10527a3f493c592ba494f16ef3c8b531288e3d0d72c1f6f0",
+ "sha256:862264b12ebb65ad8d863d51f17758b1684560b66ab02770d4f0baf2ff75da21",
+ "sha256:8902dd6a30173d4ef09954bfcb24b5d7b5190cf14a43170e386979651e09ba19",
+ "sha256:8cf717ee42012be8c0cb205dbbf18ffa9003c4cbf4ad078db47b95e10748eec5",
+ "sha256:8ed9281d1b52628e81393f5eaee24a45cbd64965f41857559c2b7ff19385df51",
+ "sha256:99b41d18e6b2a48ba949418db48159d7a2e81c5cc290fc934b7d2380515bd0e3",
+ "sha256:9cb7fa111d21a6b55cbf633039f7bc2749e74932e3aa7cb7333f675a58a58bf3",
+ "sha256:a181e99301a0ae128493a24cfe5cfb5b488c4e0bf2f8702091473d033494d04f",
+ "sha256:a413a096c4cbac202433c850ee43fa326d2e871b24554da8327b01632673a076",
+ "sha256:a6b1e54712ba3474f34b7ef7a41e65bd9037ad47916ccb1cc78769bae324c01a",
+ "sha256:ade3ca1e5f0ff46b678b66201f7ff477e8fa11fb537f3b55c3f0568fbfe6e718",
+ "sha256:b0ac3d42cb51c4b12df9c5f0dd2f13a4f24f01943627120ec4d293c9181219ba",
+ "sha256:b369ead6527d025a0fe7bd3864e46dbee3aa8f652d48df6174f8d0bac9e26e0e",
+ "sha256:b57b768feb866f44eeed9f46975f3d6406380275c5ddfe22f531a2bf187eda27",
+ "sha256:b8d3a03d9bfcaf5b0141d07a88456bb6a4c3ce55c080712fec8418ef3610230e",
+ "sha256:bc66f0bf1d7730a17430a50163bb264ba9ded56739112368ba985ddaa9c3bd09",
+ "sha256:bf20494da9653f6410213424f5f8ad0ed885e01f7e8e59811f572bdb20b8972e",
+ "sha256:c48167910a8f644671de9f2083a23630fbf7a1cb70ce939440cd3328e0919f70",
+ "sha256:c481b47f6b5845064c65a7bc78bc0860e635a9b055af0df46fdf1c58cebf8e8f",
+ "sha256:c7c8b95bf47db6d19096a5e052ffca0a05f335bc63cef281a6e8fe864d450a72",
+ "sha256:c9b8e184898ed014884ca84c70562b4a82cbc63b044d366fedc68bc2b2f3394a",
+ "sha256:cc8ff50b50ce532de2fa7a7daae9dd12f0a699bfcd47f20945364e5c31799fef",
+ "sha256:d541423cdd416b78626b55f123412fcf979d22a2c39fce251b350de38c15c15b",
+ "sha256:dab4d16dfef34b185032580e2f2f89253d302facba093d5fa9dbe04f569c4f4b",
+ "sha256:dacbc52de979f2823a819571f2e3a350a7e36b8cb7484cdb1e289bceaf35305f",
+ "sha256:df57bdbeffe694e7842092c5e2e0bc80fff7f43379d465f932ef36f027179806",
+ "sha256:ed8fe9189d2beb6edc14d3ad19800626e1d9f2d975e436f84e19efb7fa19469b",
+ "sha256:f3ddf056d3ebcf6ce47bdaf56142af51bb7fad09e4af310241e9db7a3a8022e1",
+ "sha256:f8fe4984b431f8621ca53d9380901f62bfb54ff759a1348cd140490ada7b693c",
+ "sha256:fe439416eb6380de434886b00c859304338f8b19f6f54811984f3420a2e03858"
],
"index": "pypi",
"markers": "python_version >= '3.9'",
- "version": "==7.6.3"
+ "version": "==7.6.4"
},
"docker": {
"hashes": [
@@ -2125,12 +2125,12 @@
},
"minio": {
"hashes": [
- "sha256:a83c2fcd981944602a8dc11e8e07543ed9cda0a9462264e3f46a13171c56bccb",
- "sha256:fe5523d9c4a4d6cfc07e96905852841bccdb22b22770e1efca4bf5ae8b65774b"
+ "sha256:418c31ac79346a580df04a0e14db1becbc548a6e7cca61f9bc4ef3bcd336c449",
+ "sha256:5961c58192b1d70d3a2a362064b8e027b8232688998a6d1251dadbb02ab57a7d"
],
"index": "pypi",
"markers": "python_version >= '3.9'",
- "version": "==7.2.9"
+ "version": "==7.2.10"
},
"opensearch-py": {
"hashes": [
@@ -2217,7 +2217,7 @@
"sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3",
"sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"
],
- "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+ "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
"version": "==2.9.0.post0"
},
"requests": {
@@ -2243,7 +2243,7 @@
"sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926",
"sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"
],
- "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+ "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
"version": "==1.16.0"
},
"testcontainers-core": {
diff --git a/dbrepo-analyse-service/api/dto.py b/dbrepo-analyse-service/api/dto.py
index c3c6a22c04f19540755ff027abf899d520c2b2c4..319b06efa25b030e7638deca8fe6d0c72af065e6 100644
--- a/dbrepo-analyse-service/api/dto.py
+++ b/dbrepo-analyse-service/api/dto.py
@@ -27,6 +27,7 @@ class DataTypeDto(str, Enum):
MEDIUMINT = "mediumint"
MEDIUMTEXT = "mediumtext"
SET = "set"
+ SERIAL = "serial"
SMALLINT = "smallint"
TEXT = "text"
TIMESTAMP = "timestamp"
diff --git a/dbrepo-analyse-service/app.py b/dbrepo-analyse-service/app.py
index aa9a42096c43c87954f1e45c0db950e607a6bc31..99f1de1a160e3c83b55237b3eefab0c302ee75a9 100644
--- a/dbrepo-analyse-service/app.py
+++ b/dbrepo-analyse-service/app.py
@@ -218,14 +218,19 @@ swagger = Swagger(app, config=swagger_config, template=template)
app.config["JWT_ALGORITHM"] = "HS256"
app.config["JWT_PUBKEY"] = '-----BEGIN PUBLIC KEY-----\n' + os.getenv("JWT_PUBKEY",
"MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB") + '\n-----END PUBLIC KEY-----'
+app.config["ANALYSE_NROWS"] = int(os.getenv('ANALYSE_NROWS', '10000'))
app.config["AUTH_SERVICE_ENDPOINT"] = os.getenv("AUTH_SERVICE_ENDPOINT", "http://localhost/api/auth")
app.config["AUTH_SERVICE_CLIENT"] = os.getenv("AUTH_SERVICE_CLIENT", "dbrepo-client")
app.config["AUTH_SERVICE_CLIENT_SECRET"] = os.getenv("AUTH_SERVICE_CLIENT_SECRET", "MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG")
app.config["S3_ACCESS_KEY_ID"] = os.getenv('S3_ACCESS_KEY_ID', 'seaweedfsadmin')
app.config["S3_BUCKET"] = os.getenv('S3_BUCKET', 'dbrepo')
-app.config["S3_ENDPOINT"] = os.getenv('S3_ENDPOINT', 'http://localhost:9000')
+app.config["S3_ENDPOINT"] = os.getenv('S3_ENDPOINT', 'localhost:9000')
+app.config["S3_PROTO"] = os.getenv('S3_PROTO', 'http')
app.config["S3_SECRET_ACCESS_KEY"] = os.getenv('S3_SECRET_ACCESS_KEY', 'seaweedfsadmin')
-app.config["ANALYSE_NROWS"] = int(os.getenv('ANALYSE_NROWS', '10000'))
+app.config["SPARK_ENDPOINT"] = os.getenv('SPARK_ENDPOINT', 'local[2]')
+app.config["METADATA_SERVICE_ENDPOINT"] = os.getenv('METADATA_SERVICE_ENDPOINT', 'http://localhost')
+app.config["SYSTEM_USERNAME"] = os.getenv('SYSTEM_USERNAME', 'admin')
+app.config["SYSTEM_PASSWORD"] = os.getenv('SYSTEM_PASSWORD', 'admin')
app.json_encoder = LazyJSONEncoder
diff --git a/dbrepo-analyse-service/as-yml/import_dataset.yml b/dbrepo-analyse-service/as-yml/import_dataset.yml
new file mode 100644
index 0000000000000000000000000000000000000000..78f84f9e275a2ac436e00bb688cef9e925b9ecf6
--- /dev/null
+++ b/dbrepo-analyse-service/as-yml/import_dataset.yml
@@ -0,0 +1,62 @@
+tags:
+ - analyse-endpoint
+summary: "Determine datatypes"
+operationId: analyse_datatypes
+description: "Determines MySQL 8 datatypes of a given dataset. Requires role `table-semantic-analyse`."
+consumes:
+ - "application/json"
+produces:
+ - "application/json"
+parameters:
+ - name: filename
+ in: query
+ required: true
+ example: filename_s3_key
+ schema:
+ type: string
+ - name: separator
+ in: query
+ required: true
+ example: ","
+ schema:
+ type: string
+ - name: enum
+ in: query
+ required: false
+ example: "false"
+ schema:
+ type: boolean
+ - name: enum_tol
+ in: query
+ required: false
+ example: "2.5"
+ schema:
+ type: float
+responses:
+ 202:
+ description: Determined data types successfully
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/AnalysisDto'
+ 400:
+ description: "Failed to determine data types"
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/ErrorDto'
+ 404:
+ description: "Failed to find file in Storage Service"
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/ErrorDto'
+ 500:
+ description: "Unexpected system error"
+ content:
+ application/json:
+ schema:
+ $ref: '#/components/schemas/ErrorDto'
+security:
+ - bearerAuth: [ ]
+ - basicAuth: [ ]
diff --git a/dbrepo-analyse-service/clients/s3_client.py b/dbrepo-analyse-service/clients/s3_client.py
index e9f58ea40727a36dbb53dea5e759a1d32aac254f..18cdba1ec35acbcfbd029b43076de22ee1f97069 100644
--- a/dbrepo-analyse-service/clients/s3_client.py
+++ b/dbrepo-analyse-service/clients/s3_client.py
@@ -13,9 +13,8 @@ class S3Client:
endpoint_url = current_app.config['S3_ENDPOINT']
aws_access_key_id = current_app.config['S3_ACCESS_KEY_ID']
aws_secret_access_key = current_app.config['S3_SECRET_ACCESS_KEY']
- logging.info("retrieve file from S3, endpoint_url=%s, aws_access_key_id=%s, aws_secret_access_key=(hidden)",
- endpoint_url, aws_access_key_id)
- self.client = boto3.client(service_name='s3', endpoint_url=endpoint_url, aws_access_key_id=aws_access_key_id,
+ logging.info(f"retrieve file from S3, endpoint_url={current_app.config['S3_PROTO']}://{endpoint_url}, aws_access_key_id={aws_access_key_id}, aws_secret_access_key=(hidden)")
+ self.client = boto3.client(service_name='s3', endpoint_url=f"{current_app.config['S3_PROTO']}://{endpoint_url}", aws_access_key_id=aws_access_key_id,
aws_secret_access_key=aws_secret_access_key)
self.bucket_exists_or_exit(current_app.config['S3_BUCKET'])
diff --git a/dbrepo-analyse-service/determine_dt.py b/dbrepo-analyse-service/determine_dt.py
index fe3e6a0279042b4fbdd8fa2b508ff64efea17056..0358929165f20d6c53ed5547525b113dc42964ba 100644
--- a/dbrepo-analyse-service/determine_dt.py
+++ b/dbrepo-analyse-service/determine_dt.py
@@ -2,14 +2,13 @@
"""
@author: Martin Weise
"""
-import json
import logging
import io
import pandas
from numpy import dtype, max, min
from flask import current_app
-from pandas import DataFrame
+from pandas import DataFrame, NaT
from pandas.errors import EmptyDataError, ParserError
from api.dto import ColumnAnalysisDto, DataTypeDto, AnalysisDto
@@ -67,14 +66,14 @@ def determine_datatypes(filename, enum=False, enum_tol=0.0001, separator=',') ->
r = {}
for name, dataType in df.dtypes.items():
+ # trim leading/trailing whitespaces
+ column_name = name.strip()
col = ColumnAnalysisDto(type=DataTypeDto.TEXT, null_allowed=contains_null(df[name]))
- r[name] = col
+ r[column_name] = col
if dataType == dtype('float64'):
if pandas.to_numeric(df[name], errors='coerce').notnull().all():
logging.debug(f"mapped column {name} from float64 to decimal")
col.type = DataTypeDto.DECIMAL
- col.size = 40
- col.d = 10
else:
logging.debug(f"mapped column {name} from float64 to text")
col.type = DataTypeDto.TEXT
@@ -87,12 +86,15 @@ def determine_datatypes(filename, enum=False, enum_tol=0.0001, separator=',') ->
continue
logging.debug(f"mapped column {name} from int64 to bigint")
col.type = DataTypeDto.BIGINT
- col.size = 255
elif dataType == dtype('O'):
try:
pandas.to_datetime(df[name], format='mixed')
- logging.debug(f"mapped column {name} from O to timestamp")
- col.type = DataTypeDto.TIMESTAMP
+ if df[name].str.contains(':').any():
+ logging.debug(f"mapped column {name} from O to timestamp")
+ col.type = DataTypeDto.TIMESTAMP
+ continue
+ logging.debug(f"mapped column {name} from O to date")
+ col.type = DataTypeDto.DATE
continue
except ValueError:
pass
diff --git a/dbrepo-analyse-service/lib/dbrepo-1.4.7.tar.gz b/dbrepo-analyse-service/lib/dbrepo-1.4.7.tar.gz
index c652dbae4a60aae708eb6fe4e751977b97b72344..c85b1225ee9cc1f5386e58bced9b979ff160e982 100644
Binary files a/dbrepo-analyse-service/lib/dbrepo-1.4.7.tar.gz and b/dbrepo-analyse-service/lib/dbrepo-1.4.7.tar.gz differ
diff --git a/dbrepo-analyse-service/test/conftest.py b/dbrepo-analyse-service/test/conftest.py
index 424588bdfd7479ac742401d91858864f47639a9e..3418998a943a5891f34f0adea37987e8b46f1781 100644
--- a/dbrepo-analyse-service/test/conftest.py
+++ b/dbrepo-analyse-service/test/conftest.py
@@ -31,12 +31,7 @@ def session(request, app_context):
logging.debug("[fixture] starting container")
container.start()
# set the environment for the client
- endpoint = (
- "http://"
- + container.get_container_host_ip()
- + ":"
- + container.get_exposed_port(9000)
- )
+ endpoint = f"{container.get_container_host_ip()}:{container.get_exposed_port(9000)}"
logging.debug(f"[fixture] setting s3 endpoint {endpoint}")
app.config["S3_ENDPOINT"] = endpoint
client = container.get_client()
diff --git a/dbrepo-analyse-service/test/test_determine_dt.py b/dbrepo-analyse-service/test/test_determine_dt.py
index 0ac9dc4b8af211ec0beec82918d1873b687b3ca7..4be9e331d699649dc943bb75b25fdb5c657c93ce 100644
--- a/dbrepo-analyse-service/test/test_determine_dt.py
+++ b/dbrepo-analyse-service/test/test_determine_dt.py
@@ -7,7 +7,7 @@ from determine_dt import determine_datatypes
class DetermineDatatypesTest(unittest.TestCase):
- # @Test
+
def test_determine_datatypesDateTime_succeeds(self):
exp = AnalysisDto(separator=",", line_termination="\n", columns={
"Datum": {
@@ -36,8 +36,6 @@ class DetermineDatatypesTest(unittest.TestCase):
},
"Wert": {
"type": "decimal",
- "size": 40,
- "d": 10,
"null_allowed": False,
},
"Status": {
@@ -47,6 +45,7 @@ class DetermineDatatypesTest(unittest.TestCase):
},
})
+
# mock
S3Client().upload_file("datetime.csv", './data/test_dt/', 'dbrepo')
@@ -54,8 +53,6 @@ class DetermineDatatypesTest(unittest.TestCase):
response = determine_datatypes(filename="datetime.csv", separator=",")
self.assertEqual(exp, response)
- # @Test
-
def test_determine_datatypesDateTimeWithTimezone_succeeds(self):
exp = AnalysisDto(separator=",", line_termination="\n", columns={
"Datum": {
@@ -84,8 +81,6 @@ class DetermineDatatypesTest(unittest.TestCase):
},
"Wert": {
"type": "decimal",
- "size": 40,
- "d": 10,
"null_allowed": False,
},
"Status": {
@@ -102,8 +97,6 @@ class DetermineDatatypesTest(unittest.TestCase):
response = determine_datatypes(filename="datetime_tz.csv", separator=",")
self.assertEqual(exp, response)
- # @Test
-
def test_determine_datatypesDateTimeWithT_succeeds(self):
exp = AnalysisDto(separator=",", line_termination="\n", columns={
"Datum": {
@@ -132,8 +125,6 @@ class DetermineDatatypesTest(unittest.TestCase):
},
"Wert": {
"type": "decimal",
- "size": 40,
- "d": 10,
"null_allowed": False,
},
"Status": {
@@ -150,18 +141,14 @@ class DetermineDatatypesTest(unittest.TestCase):
response = determine_datatypes(filename="datetime_t.csv", separator=",")
self.assertEqual(exp, response)
- # @Test
def test_determine_datatypes_succeeds(self):
exp = AnalysisDto(separator=",", line_termination="\n", columns={
"int": {
"type": "bigint",
- "size": 255,
"null_allowed": False,
},
"float": {
"type": "decimal",
- "size": 40,
- "d": 10,
"null_allowed": False,
},
"string": {
@@ -171,7 +158,6 @@ class DetermineDatatypesTest(unittest.TestCase):
},
"boolean": {
"type": "bool",
- "size": None,
"null_allowed": False,
},
"bool": {
@@ -179,7 +165,7 @@ class DetermineDatatypesTest(unittest.TestCase):
"null_allowed": False,
},
"date": {
- "type": "timestamp",
+ "type": "date",
"null_allowed": False,
},
"time": {
@@ -200,7 +186,6 @@ class DetermineDatatypesTest(unittest.TestCase):
response = determine_datatypes(filename="datatypes.csv", separator=",")
self.assertEqual(exp, response)
- # @Test
def test_determine_datatypes_fileDoesNotExist_fails(self):
# test
@@ -213,7 +198,6 @@ class DetermineDatatypesTest(unittest.TestCase):
else:
self.fail("ExpectedException not raised")
- # @Test
def test_determine_datatypes_fileEmpty_succeeds(self):
# mock
@@ -224,7 +208,6 @@ class DetermineDatatypesTest(unittest.TestCase):
self.assertEqual({}, response.columns)
self.assertEqual(",", response.separator)
- # @Test
def test_determine_datatypes_separatorSemicolon_succeeds(self):
# mock
@@ -234,7 +217,6 @@ class DetermineDatatypesTest(unittest.TestCase):
response = determine_datatypes(filename="separator.csv", separator=";")
self.assertEqual(";", response.separator)
- # @Test
def test_determine_datatypes_separatorGuess_succeeds(self):
# mock
@@ -244,7 +226,6 @@ class DetermineDatatypesTest(unittest.TestCase):
response = determine_datatypes(filename="separator.csv")
self.assertEqual(";", response.separator)
- # @Test
def test_determine_datatypes_separatorGuessLargeDataset_succeeds(self):
# mock
@@ -254,12 +235,10 @@ class DetermineDatatypesTest(unittest.TestCase):
response = determine_datatypes(filename="large.csv")
self.assertEqual(",", response.separator)
- # @Test
def test_determine_datatypes_separatorGuessText_succeeds(self):
exp = AnalysisDto(separator=";", line_termination="\n", columns={
"id": {
"type": "bigint",
- "size": 255,
"null_allowed": False
},
"author": {
diff --git a/dbrepo-data-db/.gitignore b/dbrepo-data-db/.gitignore
deleted file mode 100644
index 78db1b98b3e0d6b9492d26f03be6ca91dd0f8af1..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/.gitignore
+++ /dev/null
@@ -1,127 +0,0 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-# Usually these files are written by a python script from a template
-# before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-# However, in case of collaboration, if having platform-specific dependencies or dependencies
-# having no cross-platform support, pipenv may install dependencies that don't work, or not
-# install all needed dependencies.
-#Pipfile.lock
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# SQLite db
-*.db
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
diff --git a/dbrepo-data-db/README.md b/dbrepo-data-db/README.md
deleted file mode 100644
index c2dfb1b0c65e7e97903457dfafc7ed7d913d2b94..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/README.md
+++ /dev/null
@@ -1,5 +0,0 @@
-# Data Database
-
-S3 Import
-
-https://mariadb.com/kb/en/s3-storage-engine-system-variables/
\ No newline at end of file
diff --git a/dbrepo-data-db/sidecar/Dockerfile b/dbrepo-data-db/sidecar/Dockerfile
deleted file mode 100644
index 3f849019a413d0add6166dd70a125a9e37be8730..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/sidecar/Dockerfile
+++ /dev/null
@@ -1,24 +0,0 @@
-FROM python:3.11-alpine
-LABEL org.opencontainers.image.authors="martin.weise@tuwien.ac.at"
-
-RUN apk add bash curl jq mariadb-client
-
-ENV PYTHONFAULTHANDLER=1
-
-COPY Pipfile Pipfile.lock ./
-
-RUN pip install pipenv && \
- pipenv install gunicorn && \
- pipenv install --system --deploy
-
-USER 1001
-
-WORKDIR /app
-
-COPY --chown=1001 ./clients ./clients
-COPY --chown=1001 ./ds-yml ./ds-yml
-COPY --chown=1001 ./app.py ./app.py
-
-EXPOSE 8080
-
-ENTRYPOINT [ "gunicorn", "--log-level", "DEBUG", "--workers", "4", "--bind", ":8080", "app:app" ]
diff --git a/dbrepo-data-db/sidecar/Pipfile b/dbrepo-data-db/sidecar/Pipfile
deleted file mode 100644
index 2bd2967cf6b96a3fb9cf86be7f46c589ca502154..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/sidecar/Pipfile
+++ /dev/null
@@ -1,27 +0,0 @@
-[[source]]
-url = "https://pypi.org/simple"
-verify_ssl = true
-name = "pypi"
-
-[packages]
-boto3 = "*"
-flasgger = "*"
-flask = "~=2.0"
-flask-cors = "~=4.0"
-flask-jwt-extended = "~=4.5"
-requests = "*"
-prometheus-flask-exporter = "*"
-flask-sqlalchemy = "~=3.0"
-python-dotenv = "~=1.0"
-sqlalchemy-utils = "*"
-gunicorn = "*"
-flask_httpauth = "*"
-jwt = "~=1.3"
-dataclasses = "*"
-
-[dev-packages]
-coverage = "*"
-pytest = "*"
-
-[requires]
-python_version = "3.11"
diff --git a/dbrepo-data-db/sidecar/Pipfile.lock b/dbrepo-data-db/sidecar/Pipfile.lock
deleted file mode 100644
index 12afdd063641de87d9b5a5f6630e36f7bd411714..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/sidecar/Pipfile.lock
+++ /dev/null
@@ -1,945 +0,0 @@
-{
- "_meta": {
- "hash": {
- "sha256": "3b1a231fb0354d787188ca7fb2a4c8de795a9e0767381deb7473682c54aae945"
- },
- "pipfile-spec": 6,
- "requires": {
- "python_version": "3.11"
- },
- "sources": [
- {
- "name": "pypi",
- "url": "https://pypi.org/simple",
- "verify_ssl": true
- }
- ]
- },
- "default": {
- "attrs": {
- "hashes": [
- "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30",
- "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"
- ],
- "markers": "python_version >= '3.7'",
- "version": "==23.2.0"
- },
- "blinker": {
- "hashes": [
- "sha256:c3f865d4d54db7abc53758a01601cf343fe55b84c1de4e3fa910e420b438d5b9",
- "sha256:e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182"
- ],
- "markers": "python_version >= '3.8'",
- "version": "==1.7.0"
- },
- "boto3": {
- "hashes": [
- "sha256:e0940e43810fe82f5b77442c751491fcc2768af7e7c3e8c15ea158e1ca9b586c",
- "sha256:f9166f485d64b012d46acd212fb29a45b195a85ff66a645b05b06d9f7572af36"
- ],
- "index": "pypi",
- "version": "==1.34.89"
- },
- "botocore": {
- "hashes": [
- "sha256:35205ed7db13058a3f7114c28e93058a8ff1490dfc6a5b5dff9c581c738fbf59",
- "sha256:6624b69bcdf2c5d0568b7bc9cbac13e605f370e7ea06710c61e2e2dc76831141"
- ],
- "markers": "python_version >= '3.8'",
- "version": "==1.34.89"
- },
- "certifi": {
- "hashes": [
- "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f",
- "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"
- ],
- "markers": "python_version >= '3.6'",
- "version": "==2024.2.2"
- },
- "cffi": {
- "hashes": [
- "sha256:0c9ef6ff37e974b73c25eecc13952c55bceed9112be2d9d938ded8e856138bcc",
- "sha256:131fd094d1065b19540c3d72594260f118b231090295d8c34e19a7bbcf2e860a",
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- ],
- "markers": "platform_python_implementation != 'PyPy'",
- "version": "==1.16.0"
- },
- "charset-normalizer": {
- "hashes": [
- "sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027",
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diff --git a/dbrepo-data-db/sidecar/README.md b/dbrepo-data-db/sidecar/README.md
deleted file mode 100644
index 83815a632f93ff66b7e50464ecd09b5135610746..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/sidecar/README.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# Data Database Sidecar
-
-Sidecar that downloads the .csv from the Upload Service to deposit on the same pod as the data-database.
-
-## Endpoints
-
-* Prometheus metrics [`/metrics`](http://localhost:8080/metrics)
-* Health check [`/health`](http://localhost:8080/health)
-* Swagger API [`/swagger-ui/`](http://localhost:8080/swagger-ui/)
\ No newline at end of file
diff --git a/dbrepo-data-db/sidecar/app.py b/dbrepo-data-db/sidecar/app.py
deleted file mode 100644
index 955e3d9c3d6cb3b9e8140bc0773607db9118a0e0..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/sidecar/app.py
+++ /dev/null
@@ -1,198 +0,0 @@
-import json
-import os
-import logging
-import requests
-
-from typing import Any, List
-from flasgger import LazyJSONEncoder, Swagger
-from flask import Flask, request, Response
-from flask_httpauth import HTTPBasicAuth, MultiAuth, HTTPTokenAuth
-from flasgger.utils import swag_from
-from json import dumps
-
-from clients.keycloak_client import KeycloakClient, User
-from clients.s3_client import S3Client
-from prometheus_flask_exporter import PrometheusMetrics
-
-logging.basicConfig(level=logging.DEBUG)
-
-from logging.config import dictConfig
-
-# logging configuration
-dictConfig({
- 'version': 1,
- 'formatters': {
- 'default': {
- 'format': '[%(asctime)s] %(levelname)s in %(module)s: %(message)s',
- },
- 'simple': {
- 'format': '[%(asctime)s] %(levelname)s: %(message)s',
- },
- },
- 'handlers': {'wsgi': {
- 'class': 'logging.StreamHandler',
- 'stream': 'ext://flask.logging.wsgi_errors_stream',
- 'formatter': 'simple' # default
- }},
- 'root': {
- 'level': 'DEBUG',
- 'handlers': ['wsgi']
- }
-})
-
-# create app object
-app = Flask(__name__)
-
-token_auth = HTTPTokenAuth(scheme='Bearer')
-basic_auth = HTTPBasicAuth()
-auth = MultiAuth(token_auth, basic_auth)
-
-metrics = PrometheusMetrics(app)
-metrics.info("app_info", "Application info", version="__APPVERSION__")
-app.config["SWAGGER"] = {"openapi": "3.0.1", "title": "Swagger UI", "uiversion": 3}
-
-swagger_config = {
- "headers": [],
- "specs": [
- {
- "endpoint": "api-sidecar",
- "route": "/api-sidecar.json",
- "rule_filter": lambda rule: rule.endpoint.startswith('actuator') or rule.endpoint.startswith('sidecar'),
- "model_filter": lambda tag: True, # all in
- }
- ],
- "static_url_path": "/flasgger_static",
- "swagger_ui": True,
- "specs_route": "/swagger-ui/",
-}
-
-template = {
- "openapi": "3.0.0",
- "components": {
- "securitySchemes": {
- "bearerAuth": {
- "type": "http",
- "scheme": "bearer",
- "bearerFormat": "JWT",
- "in": "header"
- },
- "basicAuth": {
- "type": "http",
- "scheme": "basic",
- "in": "header"
- }
- },
- },
- "info": {
- "title": "Database Repository Data Database sidecar API",
- "description": "Sidecar that downloads the import .csv file",
- "version": "__APPVERSION__",
- "contact": {
- "name": "Prof. Andreas Rauber",
- "email": "andreas.rauber@tuwien.ac.at"
- },
- "license": {
- "name": "Apache 2.0",
- "url": "https://www.apache.org/licenses/LICENSE-2.0"
- },
- },
- "externalDocs": {
- "description": "Sourcecode Documentation",
- "url": "https://www.ifs.tuwien.ac.at/infrastructures/dbrepo/__APPVERSION__/"
- },
- "servers": [
- {
- "url": "http://localhost:8080",
- "description": "Generated server url"
- },
- {
- "url": "https://test.dbrepo.tuwien.ac.at",
- "description": "Sandbox"
- }
- ]
-}
-
-swagger = Swagger(app, config=swagger_config, template=template)
-app.config["JWT_ALGORITHM"] = "HS256"
-app.config["JWT_PUBKEY"] = '-----BEGIN PUBLIC KEY-----\n' + os.getenv("JWT_PUBKEY",
- "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB") + '\n-----END PUBLIC KEY-----'
-app.config["AUTH_SERVICE_ENDPOINT"] = os.getenv("AUTH_SERVICE_ENDPOINT", "http://localhost/api/auth")
-app.config["AUTH_SERVICE_CLIENT"] = os.getenv("AUTH_SERVICE_CLIENT", "dbrepo-client")
-app.config["AUTH_SERVICE_CLIENT_SECRET"] = os.getenv("AUTH_SERVICE_CLIENT_SECRET", "MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG")
-app.config["S3_ACCESS_KEY_ID"] = os.getenv('S3_ACCESS_KEY_ID', 'seaweedfsadmin')
-app.config["S3_ENDPOINT"] = os.getenv('S3_ENDPOINT', 'http://localhost:9000')
-app.config["S3_FILE_PATH"] = os.getenv('S3_FILE_PATH', '/tmp')
-app.config["S3_SECRET_ACCESS_KEY"] = os.getenv('S3_SECRET_ACCESS_KEY', 'seaweedfsadmin')
-app.config["S3_BUCKET"] = os.getenv('S3_BUCKET', 'dbrepo')
-
-app.json_encoder = LazyJSONEncoder
-
-
-@token_auth.verify_token
-def verify_token(token: str):
- if token is None or token == "":
- return False
- try:
- client = KeycloakClient()
- return client.verify_jwt(access_token=token)
- except AssertionError:
- return False
-
-
-@basic_auth.verify_password
-def verify_password(username: str, password: str) -> Any:
- if username is None or username == "" or password is None or password == "":
- return False
- client = KeycloakClient()
- try:
- return client.verify_jwt(access_token=client.obtain_user_token(username=username, password=password))
- except AssertionError as error:
- logging.error(error)
- return False
- except requests.exceptions.ConnectionError as error:
- logging.error(f"Failed to connect to Authentication Service {error}")
- return False
-
-
-@token_auth.get_user_roles
-def get_user_roles(user: User) -> List[str]:
- return user.roles
-
-
-@basic_auth.get_user_roles
-def get_user_roles(user: User) -> List[str]:
- return user.roles
-
-
-@app.route("/health", methods=["GET"], endpoint="actuator_health")
-def health():
- logging.debug("endpoint health, body=%s", request)
- res = dumps({"status": "UP", "message": "Application is up and running"})
- return Response(res, mimetype="application/json"), 200
-
-
-@app.route("/sidecar/import/<string:filename>", methods=["POST"], endpoint="sidecar_import")
-@metrics.gauge(name='dbrepo_sidecar_import_dataset', description='Time needed to import dataset from S3')
-@auth.login_required(role=['import-database-data'])
-@swag_from("ds-yml/import.yml")
-def import_csv(filename):
- auth.current_user()
- logging.debug('endpoint import csv, filename=%s, body=%s', filename, request)
- s3_client = S3Client()
- response = s3_client.download_file(filename, app.config["S3_FILE_PATH"], app.config['S3_BUCKET'])
- if response is False:
- return Response(), 400
- return Response(json.dumps(response)), 202
-
-
-@app.route("/sidecar/export/<string:filename>", methods=["POST"], endpoint="sidecar_export")
-@metrics.gauge(name='dbrepo_sidecar_export_dataset', description='Time needed to export dataset to S3')
-@auth.login_required(role=['export-query-data', 'export-table-data'])
-@swag_from("ds-yml/export.yml")
-def import_csv(filename):
- logging.debug('endpoint export csv, filename=%s, body=%s', filename, request)
- s3_client = S3Client()
- response = s3_client.upload_file(filename, app.config["S3_FILE_PATH"], app.config['S3_BUCKET'])
- if response is False:
- return Response(), 400
- return Response(), 202
diff --git a/dbrepo-data-db/sidecar/clients/keycloak_client.py b/dbrepo-data-db/sidecar/clients/keycloak_client.py
deleted file mode 100644
index 9bd0b273bf9391d4b6976a96677608f85065a8ee..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/sidecar/clients/keycloak_client.py
+++ /dev/null
@@ -1,35 +0,0 @@
-import logging
-from dataclasses import dataclass
-import requests
-from flask import current_app
-from typing import List
-
-from jwt import jwk_from_pem, JWT
-
-
-@dataclass(init=True, eq=True)
-class User:
- username: str
- roles: List[str]
-
-
-class KeycloakClient:
-
- def obtain_user_token(self, username: str, password: str) -> str:
- response = requests.post(f"{current_app.config['KEYCLOAK_HOST']}/realms/dbrepo/protocol/openid-connect/token",
- data={
- "username": username,
- "password": password,
- "grant_type": "password",
- "client_id": current_app.config["AUTH_SERVICE_CLIENT"],
- "client_secret": current_app.config["KEYCLOAK_CLIENT_SECRET"]
- })
- body = response.json()
- if "access_token" not in body:
- raise AssertionError("Failed to obtain user token(s)")
- return response.json()["access_token"]
-
- def verify_jwt(self, access_token: str) -> User:
- public_key = jwk_from_pem(str(current_app.config["JWT_PUBKEY"]).encode('utf-8'))
- payload = JWT().decode(message=access_token, key=public_key, do_time_check=True)
- return User(username=payload.get('client_id'), roles=payload.get('realm_access')["roles"])
diff --git a/dbrepo-data-db/sidecar/clients/s3_client.py b/dbrepo-data-db/sidecar/clients/s3_client.py
deleted file mode 100644
index d34760f6230321a4219df43124d404c43c98e043..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/sidecar/clients/s3_client.py
+++ /dev/null
@@ -1,80 +0,0 @@
-import os
-import boto3
-import logging
-import sys
-
-from flask import current_app
-from botocore.exceptions import ClientError
-
-
-class S3Client:
-
- def __init__(self):
- endpoint_url = current_app.config['S3_ENDPOINT']
- aws_access_key_id = current_app.config['S3_ACCESS_KEY_ID']
- aws_secret_access_key = current_app.config['S3_SECRET_ACCESS_KEY']
- logging.info(
- f"retrieve file from S3, endpoint_url={endpoint_url}, aws_access_key_id={aws_access_key_id}, aws_secret_access_key=(hidden)")
- self.client = boto3.client(service_name='s3', endpoint_url=endpoint_url, aws_access_key_id=aws_access_key_id,
- aws_secret_access_key=aws_secret_access_key)
- self.bucket_exists_or_exit(current_app.config['S3_BUCKET'])
-
- def upload_file(self, filename, path, bucket) -> bool:
- """
- Uploads a file to the blob storage.
- Follows the official API https://boto3.amazonaws.com/v1/documentation/api/latest/guide/s3-uploading-files.html.
- :param filename: The filename.
- :param path: The path.
- :param bucket: The bucket.
- :return: True if the file was uploaded.
- """
- filepath = os.path.join(path, filename)
- try:
- self.client.upload_file(filepath, bucket, filename)
- logging.info(f"Uploaded .csv {filepath} with key {filename} into bucket {bucket}")
- return True
- except ClientError as e:
- logging.error(e)
- return False
-
- def download_file(self, filename, path, bucket) -> bool:
- """
- Downloads a file from the blob storage.
- Follows the official API https://boto3.amazonaws.com/v1/documentation/api/latest/guide/s3-example-download-file.html
- :param filename: The filename.
- :param path: The path.
- :param bucket: The bucket.
- :return: True if the file was downloaded and saved.
- """
- self.file_exists(bucket, filename)
- filepath = os.path.join(path, filename)
- try:
- self.client.download_file(bucket, filename, filepath)
- logging.info(f"Downloaded .csv with key {filename} into {filepath} from bucket {bucket}")
- return True
- except ClientError as e:
- logging.error(e)
- return False
-
- def file_exists(self, bucket, filename):
- try:
- self.client.head_object(Bucket=bucket, Key=filename)
- logging.debug(f"file with name {filename} exists in bucket with name {bucket}")
- except ClientError as e:
- if e.response["Error"]["Code"] == "404":
- logging.error(f"Failed to find key {filename} in bucket {bucket}")
- else:
- logging.error(
- f"Unexpected error when finding key {filename} in bucket {bucket}: {e.response['Error']['Code']}")
- raise e
-
- def bucket_exists_or_exit(self, bucket):
- try:
- self.client.head_bucket(Bucket=bucket)
- logging.debug(f"bucket {bucket} exists.")
- except ClientError as e:
- if e.response["Error"]["Code"] == "404":
- logging.error(f"Failed to find bucket {bucket}")
- else:
- logging.error(f"Unexpected error when finding bucket {bucket}: {e.response['Error']['Code']}")
- sys.exit(1)
diff --git a/dbrepo-data-db/sidecar/ds-yml/export.yml b/dbrepo-data-db/sidecar/ds-yml/export.yml
deleted file mode 100644
index 50b9e5710fec0b16396fd3b1ccc54384d9162b4b..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/sidecar/ds-yml/export.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-summary: Exports a .csv to the Storage Service
-description: |
- Exports a specific .csv file to the Storage Service via S3
-consumes:
- - application/json
-produces:
- - application/json
-parameters:
- - in: path
- name: filename
- description: Name of the object file to export to the Storage Service
- required: true
-security:
- - bearerAuth: [ ]
- - basicAuth: [ ]
-responses:
- 202:
- description: Exported the .csv
- content: { }
- 400:
- description: The Storage Service could not be contacted or .csv was not found.
-tags:
- - sidecar
-components:
- securitySchemes:
- basicAuth:
- type: http
- scheme: basic
- bearerAuth:
- type: http
- scheme: bearer
- bearerFormat: JWT
\ No newline at end of file
diff --git a/dbrepo-data-db/sidecar/ds-yml/health.yml b/dbrepo-data-db/sidecar/ds-yml/health.yml
deleted file mode 100644
index 6032625c66d25cb788ea0b5039e30dc24608927b..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/sidecar/ds-yml/health.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-summary: Return a healthcheck
-description: |
- Return UP if the instance is ready to serve connections.
-consumes:
- - application/json
-produces:
- - application/json
-parameters: [ ]
-
-responses:
- 200:
- description: OK, service is up and running
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Health"
- 404:
- description: Service is not yet ready
-tags:
- - actuator
-
-components:
- schemas:
- Health:
- title: Status object
- type: object
- properties:
- status:
- type: string
- example: UP
- required:
- - status
\ No newline at end of file
diff --git a/dbrepo-data-db/sidecar/ds-yml/import.yml b/dbrepo-data-db/sidecar/ds-yml/import.yml
deleted file mode 100644
index 87c6777127ffaf36caf42a567140148f09b7ee64..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/sidecar/ds-yml/import.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-summary: Imports a .csv from the Storage Service
-description: |
- Imports a specific .csv file from the Storage Service via S3
-consumes:
- - application/json
-produces:
- - application/json
-parameters:
- - in: path
- name: filename
- description: Name of the object file to import from the Storage Service
- required: true
-security:
- - bearerAuth: [ ]
- - basicAuth: [ ]
-responses:
- 202:
- description: Imported the .csv
- content: { }
- 400:
- description: The Storage Service could not be contacted or .csv was not found.
-tags:
- - sidecar
-components:
- securitySchemes:
- basicAuth:
- type: http
- scheme: basic
- bearerAuth:
- type: http
- scheme: bearer
- bearerFormat: JWT
\ No newline at end of file
diff --git a/dbrepo-data-db/sidecar/metrics.md b/dbrepo-data-db/sidecar/metrics.md
deleted file mode 100644
index 0aaa9e332bacdba4a977b0ed2bffab05b5d1eae6..0000000000000000000000000000000000000000
--- a/dbrepo-data-db/sidecar/metrics.md
+++ /dev/null
@@ -1,4 +0,0 @@
-| **Metric** | **Description** |
-|---------------------------------|---------------------------------------|
-| `dbrepo_sidecar_import_dataset` | Time needed to import dataset from S3 |
-| `dbrepo_sidecar_export_dataset` | Time needed to export dataset to S3 |
\ No newline at end of file
diff --git a/dbrepo-data-service/Dockerfile b/dbrepo-data-service/Dockerfile
index bd6d428695f2b85126a0a1b4dea604667510198c..f4e2be5b967ca109e858d6f17099ec67d341ac12 100644
--- a/dbrepo-data-service/Dockerfile
+++ b/dbrepo-data-service/Dockerfile
@@ -3,7 +3,7 @@ FROM dbrepo-metadata-service:build AS dependency
LABEL org.opencontainers.image.authors="martin.weise@tuwien.ac.at"
###### SECOND STAGE ######
-FROM maven:3-openjdk-17 AS build
+FROM maven:3-amazoncorretto-17 AS build
LABEL org.opencontainers.image.authors="martin.weise@tuwien.ac.at"
COPY ./pom.xml ./
@@ -28,6 +28,8 @@ RUN apk add --no-cache curl bash jq
WORKDIR /app
+RUN adduser -S -u 1001 data-service
+
USER 1001
COPY --from=build --chown=1001 ./rest-service/target/rest-service-*.jar ./data-service.jar
@@ -35,4 +37,6 @@ COPY --from=build --chown=1001 ./rest-service/target/rest-service-*.jar ./data-s
# non-root port
EXPOSE 8080
-ENTRYPOINT ["java", "-Dlog4j2.formatMsgNoLookups=true", "-jar", "./data-service.jar"]
\ No newline at end of file
+ENV JAVA_OPTS="-XX:+IgnoreUnrecognizedVMOptions --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.invoke=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/jdk.internal.ref=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/sun.nio.cs=ALL-UNNAMED --add-opens=java.base/sun.security.action=ALL-UNNAMED --add-opens=java.base/sun.util.calendar=ALL-UNNAMED --add-opens=java.security.jgss/sun.security.krb5=ALL-UNNAMED -Djdk.reflect.useDirectMethodHandle=false -Dio.netty.tryReflectionSetAccessible=true"
+
+ENTRYPOINT exec java $JAVA_OPTS -jar ./data-service.jar
\ No newline at end of file
diff --git a/dbrepo-data-service/metrics.md b/dbrepo-data-service/metrics.md
index 8219898284d6a830e52f3f2f3ee4ee80dd635e52..6d8a93935cc206423d53fb5259556cb57db95c31 100644
--- a/dbrepo-data-service/metrics.md
+++ b/dbrepo-data-service/metrics.md
@@ -16,4 +16,5 @@
| `dbrepo_table_schema_list` | Find tables |
| `dbrepo_table_statistic` | Get table statistic |
| `dbrepo_view_data` | Get view data |
+| `dbrepo_view_data_export` | Get view data |
| `dbrepo_view_schema_list` | Find views |
diff --git a/dbrepo-data-service/pom.xml b/dbrepo-data-service/pom.xml
index 6517de47460bdf48ad1f31397a1e67416e3dbc31..a6012b573bbfabf3d3b98643aeee28b8de71315b 100644
--- a/dbrepo-data-service/pom.xml
+++ b/dbrepo-data-service/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
- <version>3.0.13</version>
+ <version>3.3.5</version>
</parent>
<groupId>at.tuwien</groupId>
@@ -23,7 +23,7 @@
<module>report</module>
</modules>
- <url>https://www.ifs.tuwien.ac.at/infrastructures/dbrepo/</url>
+ <url>https://www.ifs.tuwien.ac.at/infrastructures/dbrepo/1.4.7/</url>
<developers>
<developer>
<name>Martin Weise</name>
@@ -34,11 +34,11 @@
<properties>
<java.version>17</java.version>
- <spring-cloud.version>4.0.2</spring-cloud.version>
+ <spring-cloud.version>4.1.4</spring-cloud.version>
<mapstruct.version>1.5.5.Final</mapstruct.version>
<rabbitmq.version>5.20.0</rabbitmq.version>
<jackson-datatype.version>2.15.0</jackson-datatype.version>
- <commons-io.version>2.15.0</commons-io.version>
+ <commons-io.version>2.17.0</commons-io.version>
<commons-validator.version>1.8.0</commons-validator.version>
<jacoco.version>0.8.12</jacoco.version>
<jwt.version>4.3.0</jwt.version>
@@ -54,13 +54,16 @@
<aws-s3.version>2.25.23</aws-s3.version>
<minio.version>8.5.7</minio.version>
<guava.version>33.3.0-jre</guava.version>
+ <spark.version>4.0.0-preview2</spark.version>
+ <scala.version>2.13</scala.version>
+ <antlr-runtime.version>3.5.2</antlr-runtime.version>
+ <micrometer.version>1.10.0</micrometer.version>
+ <!-- see https://github.com/apache/spark/blob/cde8e4a82e20a363861f451ebd5138efb3194ab8/pom.xml -->
+ <hadoop.version>3.4.0</hadoop.version>
+ <jakarta-servlet.version>5.0.0</jakarta-servlet.version>
</properties>
<dependencies>
- <dependency>
- <groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-starter-validation</artifactId>
- </dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
@@ -92,6 +95,44 @@
<artifactId>guava</artifactId>
<version>${guava.version}</version>
</dependency>
+ <!-- Spark -->
+ <dependency>
+ <groupId>org.apache.spark</groupId>
+ <artifactId>spark-core_${scala.version}</artifactId>
+ <version>${spark.version}</version>
+ <exclusions>
+ <exclusion>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-slf4j2-impl</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+ <dependency>
+ <groupId>org.antlr</groupId>
+ <artifactId>antlr-runtime</artifactId>
+ <version>${antlr-runtime.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.spark</groupId>
+ <artifactId>spark-sql_${scala.version}</artifactId>
+ <version>${spark.version}</version>
+ <exclusions>
+ <exclusion>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-slf4j2-impl</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+ <dependency>
+ <groupId>jakarta.servlet</groupId>
+ <artifactId>jakarta.servlet-api</artifactId>
+ <version>${jakarta-servlet.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.hadoop</groupId>
+ <artifactId>hadoop-aws</artifactId>
+ <version>${hadoop.version}</version>
+ </dependency>
<!-- Open API -->
<dependency>
<groupId>org.springdoc</groupId>
@@ -167,6 +208,11 @@
<artifactId>jackson-datatype-hibernate6</artifactId>
<version>${jackson-datatype.version}</version>
</dependency>
+ <dependency>
+ <groupId>com.github.jsqlparser</groupId>
+ <artifactId>jsqlparser</artifactId>
+ <version>${jsql.version}</version>
+ </dependency>
<!-- Authentication -->
<dependency>
<groupId>com.auth0</groupId>
@@ -202,11 +248,6 @@
<version>${aws-s3.version}</version>
</dependency>
<!-- Testing -->
- <dependency>
- <groupId>com.github.jsqlparser</groupId>
- <artifactId>jsqlparser</artifactId>
- <version>${jsql.version}</version>
- </dependency>
<dependency>
<groupId>at.tuwien</groupId>
<artifactId>dbrepo-metadata-service-test</artifactId>
@@ -240,11 +281,13 @@
<groupId>org.testcontainers</groupId>
<artifactId>minio</artifactId>
<version>${testcontainers.version}</version>
+ <scope>test</scope>
</dependency>
<dependency>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
+ <scope>test</scope>
</dependency>
</dependencies>
@@ -255,6 +298,7 @@
<filtering>true</filtering>
<includes>
<include>**/application*.yml</include>
+ <include>**/jars/*.jar</include>
</includes>
</resource>
</resources>
diff --git a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/AccessEndpoint.java b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/AccessEndpoint.java
index 4059a37a92ba138ef39a6f53365fd70558951e56..e5a25f174e8a41a942c9ded92cbfcf06e59e1713 100644
--- a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/AccessEndpoint.java
+++ b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/AccessEndpoint.java
@@ -16,6 +16,7 @@ import io.swagger.v3.oas.annotations.responses.ApiResponses;
import io.swagger.v3.oas.annotations.security.SecurityRequirement;
import jakarta.validation.Valid;
import jakarta.validation.constraints.NotBlank;
+import jakarta.validation.constraints.NotNull;
import lombok.extern.log4j.Log4j2;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
@@ -75,8 +76,8 @@ public class AccessEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> create(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("userId") UUID userId,
+ public ResponseEntity<Void> create(@NotNull @PathVariable("databaseId") Long databaseId,
+ @org.hibernate.validator.constraints.UUID @PathVariable("userId") UUID userId,
@Valid @RequestBody UpdateDatabaseAccessDto data)
throws NotAllowedException, DatabaseUnavailableException, DatabaseNotFoundException,
RemoteUnavailableException, UserNotFoundException, DatabaseMalformedException, MetadataServiceException {
@@ -131,8 +132,8 @@ public class AccessEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> update(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("userId") UUID userId,
+ public ResponseEntity<Void> update(@NotNull @PathVariable("databaseId") Long databaseId,
+ @org.hibernate.validator.constraints.UUID @PathVariable("userId") UUID userId,
@Valid @RequestBody UpdateDatabaseAccessDto access) throws NotAllowedException,
DatabaseUnavailableException, DatabaseNotFoundException, RemoteUnavailableException, UserNotFoundException,
DatabaseMalformedException, MetadataServiceException {
@@ -188,8 +189,8 @@ public class AccessEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> revoke(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("userId") UUID userId) throws NotAllowedException,
+ public ResponseEntity<Void> revoke(@NotNull @PathVariable("databaseId") Long databaseId,
+ @org.hibernate.validator.constraints.UUID @PathVariable("userId") UUID userId) throws NotAllowedException,
DatabaseUnavailableException, DatabaseNotFoundException, RemoteUnavailableException, UserNotFoundException,
DatabaseMalformedException, MetadataServiceException {
log.debug("endpoint revoke access to database, databaseId={}, userId={}", databaseId, userId);
diff --git a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/DatabaseEndpoint.java b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/DatabaseEndpoint.java
index 9cefc57fa2b70db65daee6d4bc1d1ddd6434aa24..50c503852bb7a7f92c05a6d144dde386faf32d5c 100644
--- a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/DatabaseEndpoint.java
+++ b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/DatabaseEndpoint.java
@@ -21,6 +21,7 @@ import io.swagger.v3.oas.annotations.responses.ApiResponses;
import io.swagger.v3.oas.annotations.security.SecurityRequirement;
import jakarta.validation.Valid;
import jakarta.validation.constraints.NotBlank;
+import jakarta.validation.constraints.NotNull;
import lombok.extern.log4j.Log4j2;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
@@ -131,7 +132,7 @@ public class DatabaseEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> update(@NotBlank @PathVariable("databaseId") Long databaseId,
+ public ResponseEntity<Void> update(@NotNull @PathVariable("databaseId") Long databaseId,
@Valid @RequestBody UpdateUserPasswordDto data)
throws DatabaseUnavailableException, DatabaseNotFoundException, RemoteUnavailableException,
DatabaseMalformedException, MetadataServiceException {
diff --git a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/SubsetEndpoint.java b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/SubsetEndpoint.java
index 1637878a6785f595a35643471aa2b2b71f027399..63962694f164a79e6268b579372f6324704f9fa7 100644
--- a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/SubsetEndpoint.java
+++ b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/SubsetEndpoint.java
@@ -146,7 +146,8 @@ public class SubsetEndpoint {
@RequestParam(required = false) Instant timestamp)
throws DatabaseUnavailableException, DatabaseNotFoundException, RemoteUnavailableException,
QueryNotFoundException, FormatNotAvailableException, StorageUnavailableException, QueryMalformedException,
- SidecarExportException, StorageNotFoundException, UserNotFoundException, MetadataServiceException {
+ StorageNotFoundException, UserNotFoundException, MetadataServiceException, ViewNotFoundException,
+ MalformedException {
String accept = httpServletRequest.getHeader("Accept");
log.debug("endpoint find subset in database, databaseId={}, subsetId={}, accept={}, timestamp={}", databaseId,
subsetId, accept, timestamp);
@@ -173,9 +174,8 @@ public class SubsetEndpoint {
return ResponseEntity.ok(query);
case "text/csv":
log.trace("accept header matches csv");
- final String filename = RandomStringUtils.randomAlphabetic(20).toLowerCase();
try {
- final ExportResourceDto resource = subsetService.export(database, query, timestamp, filename);
+ final ExportResourceDto resource = subsetService.export(database, query, timestamp);
final HttpHeaders headers = new HttpHeaders();
headers.add("Content-Disposition", "attachment; filename=\"" + resource.getFilename() + "\"");
log.trace("export table resulted in resource {}", resource);
@@ -240,9 +240,9 @@ public class SubsetEndpoint {
@RequestParam(required = false) Long size,
@RequestParam(required = false) Instant timestamp)
throws DatabaseUnavailableException, DatabaseNotFoundException, RemoteUnavailableException,
- QueryNotFoundException, StorageUnavailableException, QueryMalformedException, SidecarExportException,
- StorageNotFoundException, QueryStoreInsertException, TableMalformedException, PaginationException,
- QueryNotSupportedException, NotAllowedException, UserNotFoundException, MetadataServiceException {
+ QueryNotFoundException, StorageUnavailableException, QueryMalformedException, StorageNotFoundException,
+ QueryStoreInsertException, TableMalformedException, PaginationException, QueryNotSupportedException,
+ NotAllowedException, UserNotFoundException, MetadataServiceException {
log.debug("endpoint create subset in database, databaseId={}, data.statement={}, page={}, size={}, " +
"timestamp={}", databaseId, data.getStatement(), page, size,
timestamp);
diff --git a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
index 06afef015df02c8077ce312691e140916ea4e2f0..677e181b0a9d45cf8b95c298739880da4970da78 100644
--- a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
+++ b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
@@ -144,8 +144,8 @@ public class TableEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> delete(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("tableId") Long tableId)
+ public ResponseEntity<Void> delete(@NotNull @PathVariable("databaseId") Long databaseId,
+ @NotNull @PathVariable("tableId") Long tableId)
throws DatabaseUnavailableException, RemoteUnavailableException, TableNotFoundException,
QueryMalformedException, MetadataServiceException {
log.debug("endpoint delete table, databaseId={}, tableId={}", databaseId, tableId);
@@ -194,8 +194,8 @@ public class TableEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<QueryResultDto> getData(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("tableId") Long tableId,
+ public ResponseEntity<QueryResultDto> getData(@NotNull @PathVariable("databaseId") Long databaseId,
+ @NotNull @PathVariable("tableId") Long tableId,
@RequestParam(required = false) Instant timestamp,
@RequestParam(required = false) Long page,
@RequestParam(required = false) Long size,
@@ -237,7 +237,7 @@ public class TableEndpoint {
.headers(headers)
.build();
}
- final QueryResultDto dto = tableService.getData(table, timestamp, page, size);
+ final QueryResultDto dto = tableService.getPaginatedData(table, timestamp, page, size);
return ResponseEntity.ok()
.body(dto);
} catch (SQLException e) {
@@ -276,8 +276,8 @@ public class TableEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> insertRawTuple(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("tableId") Long tableId,
+ public ResponseEntity<Void> insertRawTuple(@NotNull @PathVariable("databaseId") Long databaseId,
+ @NotNull @PathVariable("tableId") Long tableId,
@Valid @RequestBody TupleDto data,
@NotNull Principal principal)
throws DatabaseUnavailableException, RemoteUnavailableException, TableNotFoundException,
@@ -328,8 +328,8 @@ public class TableEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> updateRawTuple(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("tableId") Long tableId,
+ public ResponseEntity<Void> updateRawTuple(@NotNull @PathVariable("databaseId") Long databaseId,
+ @NotNull @PathVariable("tableId") Long tableId,
@Valid @RequestBody TupleUpdateDto data,
@NotNull Principal principal)
throws DatabaseUnavailableException, RemoteUnavailableException, TableNotFoundException,
@@ -380,8 +380,8 @@ public class TableEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> deleteRawTuple(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("tableId") Long tableId,
+ public ResponseEntity<Void> deleteRawTuple(@NotNull @PathVariable("databaseId") Long databaseId,
+ @NotNull @PathVariable("tableId") Long tableId,
@Valid @RequestBody TupleDeleteDto data,
@NotNull Principal principal)
throws DatabaseUnavailableException, RemoteUnavailableException, TableNotFoundException,
@@ -503,7 +503,7 @@ public class TableEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<List<TableDto>> getSchema(@NotBlank @PathVariable("databaseId") Long databaseId)
+ public ResponseEntity<List<TableDto>> getSchema(@NotNull @PathVariable("databaseId") Long databaseId)
throws DatabaseUnavailableException, DatabaseNotFoundException, RemoteUnavailableException,
DatabaseMalformedException, TableNotFoundException, MetadataServiceException {
log.debug("endpoint inspect table schemas, databaseId={}", databaseId);
@@ -548,13 +548,12 @@ public class TableEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<InputStreamResource> exportDataset(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("tableId") Long tableId,
+ public ResponseEntity<InputStreamResource> exportDataset(@NotNull @PathVariable("databaseId") Long databaseId,
+ @NotNull @PathVariable("tableId") Long tableId,
@RequestParam(required = false) Instant timestamp,
Principal principal)
- throws DatabaseUnavailableException, RemoteUnavailableException, TableNotFoundException,
- NotAllowedException, StorageUnavailableException, QueryMalformedException, SidecarExportException,
- StorageNotFoundException, MetadataServiceException {
+ throws RemoteUnavailableException, TableNotFoundException, NotAllowedException, StorageUnavailableException,
+ QueryMalformedException, MetadataServiceException, MalformedException {
log.debug("endpoint export table data, databaseId={}, tableId={}, timestamp={}", databaseId, tableId, timestamp);
/* parameters */
if (timestamp == null) {
@@ -569,19 +568,13 @@ public class TableEndpoint {
}
metadataServiceGateway.getAccess(databaseId, UserUtil.getId(principal));
}
- try {
- final HttpHeaders headers = new HttpHeaders();
- final ExportResourceDto resource = tableService.exportDataset(table, timestamp);
- headers.add("Content-Disposition", "attachment; filename=\"" + resource.getFilename() + "\"");
- log.trace("export table resulted in resource {}", resource);
- return ResponseEntity.ok()
- .headers(headers)
- .body(resource.getResource());
-
- } catch (SQLException e) {
- log.error("Failed to establish connection to database: {}", e.getMessage());
- throw new DatabaseUnavailableException("Failed to establish connection to database", e);
- }
+ final HttpHeaders headers = new HttpHeaders();
+ final ExportResourceDto resource = tableService.exportDataset(table, timestamp);
+ headers.add("Content-Disposition", "attachment; filename=\"" + resource.getFilename() + "\"");
+ log.trace("export table resulted in resource {}", resource);
+ return ResponseEntity.ok()
+ .headers(headers)
+ .body(resource.getResource());
}
@PostMapping("/{tableId}/data/import")
@@ -614,13 +607,13 @@ public class TableEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> importDataset(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("tableId") Long tableId,
+ public ResponseEntity<Void> importDataset(@NotNull @PathVariable("databaseId") Long databaseId,
+ @NotNull @PathVariable("tableId") Long tableId,
@Valid @RequestBody ImportDto data,
@NotNull Principal principal)
- throws DatabaseUnavailableException, RemoteUnavailableException, TableNotFoundException,
- QueryMalformedException, StorageNotFoundException, SidecarImportException, NotAllowedException,
- MetadataServiceException {
+ throws RemoteUnavailableException, TableNotFoundException, NotAllowedException, MetadataServiceException,
+ StorageNotFoundException, MalformedException, StorageUnavailableException, QueryMalformedException,
+ DatabaseUnavailableException {
log.debug("endpoint insert table data, databaseId={}, tableId={}, data.location={}", databaseId, tableId, data.getLocation());
final PrivilegedTableDto table = metadataServiceGateway.getTableById(databaseId, tableId);
final DatabaseAccessDto access = metadataServiceGateway.getAccess(databaseId, UserUtil.getId(principal));
@@ -631,13 +624,13 @@ public class TableEndpoint {
}
try {
tableService.importDataset(table, data);
- metadataServiceGateway.updateTableStatistics(databaseId, tableId);
- return ResponseEntity.accepted()
- .build();
} catch (SQLException e) {
log.error("Failed to establish connection to database: {}", e.getMessage());
throw new DatabaseUnavailableException("Failed to establish connection to database", e);
}
+ metadataServiceGateway.updateTableStatistics(databaseId, tableId);
+ return ResponseEntity.accepted()
+ .build();
}
@GetMapping("/{tableId}/statistic")
@@ -666,8 +659,8 @@ public class TableEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<TableStatisticDto> statistic(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("tableId") Long tableId)
+ public ResponseEntity<TableStatisticDto> statistic(@NotNull @PathVariable("databaseId") Long databaseId,
+ @NotNull @PathVariable("tableId") Long tableId)
throws DatabaseUnavailableException, RemoteUnavailableException, TableNotFoundException,
MetadataServiceException, TableMalformedException, DatabaseNotFoundException {
log.debug("endpoint generate table statistic, databaseId={}, tableId={}", databaseId, tableId);
diff --git a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/ViewEndpoint.java b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/ViewEndpoint.java
index 9d0bd3b6adec78c34690073a46f35ab220386504..f0b1b891e73990b56510ec292643db96fbe6c1da 100644
--- a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/ViewEndpoint.java
+++ b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/endpoints/ViewEndpoint.java
@@ -6,7 +6,6 @@ import at.tuwien.api.database.ViewDto;
import at.tuwien.api.database.internal.PrivilegedDatabaseDto;
import at.tuwien.api.database.internal.PrivilegedViewDto;
import at.tuwien.api.database.query.QueryResultDto;
-import at.tuwien.api.database.table.internal.PrivilegedTableDto;
import at.tuwien.api.error.ApiErrorDto;
import at.tuwien.exception.*;
import at.tuwien.gateway.MetadataServiceGateway;
@@ -94,7 +93,7 @@ public class ViewEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<List<ViewDto>> getSchema(@NotBlank @PathVariable("databaseId") Long databaseId)
+ public ResponseEntity<List<ViewDto>> getSchema(@NotNull @PathVariable("databaseId") Long databaseId)
throws DatabaseUnavailableException, DatabaseNotFoundException, RemoteUnavailableException,
ViewNotFoundException, DatabaseMalformedException, MetadataServiceException {
log.debug("endpoint inspect view schemas, databaseId={}", databaseId);
@@ -182,8 +181,8 @@ public class ViewEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> delete(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("viewId") Long viewId)
+ public ResponseEntity<Void> delete(@NotNull @PathVariable("databaseId") Long databaseId,
+ @NotNull @PathVariable("viewId") Long viewId)
throws DatabaseUnavailableException, RemoteUnavailableException, ViewNotFoundException,
ViewMalformedException, MetadataServiceException {
log.debug("endpoint delete view, databaseId={}, viewId={}", databaseId, viewId);
@@ -237,8 +236,8 @@ public class ViewEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<QueryResultDto> getData(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("viewId") Long viewId,
+ public ResponseEntity<QueryResultDto> getData(@NotNull @PathVariable("databaseId") Long databaseId,
+ @NotNull @PathVariable("viewId") Long viewId,
@RequestParam(required = false) Long page,
@RequestParam(required = false) Long size,
@RequestParam(required = false) Instant timestamp,
@@ -318,12 +317,11 @@ public class ViewEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<InputStreamResource> exportDataset(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("viewId") Long viewId,
+ public ResponseEntity<InputStreamResource> exportDataset(@NotNull @PathVariable("databaseId") Long databaseId,
+ @NotNull @PathVariable("viewId") Long viewId,
Principal principal)
- throws DatabaseUnavailableException, RemoteUnavailableException, ViewNotFoundException,
- NotAllowedException, MetadataServiceException, StorageUnavailableException, QueryMalformedException,
- SidecarExportException, StorageNotFoundException {
+ throws RemoteUnavailableException, ViewNotFoundException, NotAllowedException, MetadataServiceException,
+ StorageUnavailableException, QueryMalformedException, MalformedException {
log.debug("endpoint export view data, databaseId={}, viewId={}", databaseId, viewId);
/* parameters */
final PrivilegedViewDto view = metadataServiceGateway.getViewById(databaseId, viewId);
@@ -334,19 +332,13 @@ public class ViewEndpoint {
}
metadataServiceGateway.getAccess(databaseId, UserUtil.getId(principal));
}
- try {
- final HttpHeaders headers = new HttpHeaders();
- final ExportResourceDto resource = viewService.exportDataset(view);
- headers.add("Content-Disposition", "attachment; filename=\"" + resource.getFilename() + "\"");
- log.trace("export table resulted in resource {}", resource);
- return ResponseEntity.ok()
- .headers(headers)
- .body(resource.getResource());
-
- } catch (SQLException e) {
- log.error("Failed to establish connection to database: {}", e.getMessage());
- throw new DatabaseUnavailableException("Failed to establish connection to database", e);
- }
+ final HttpHeaders headers = new HttpHeaders();
+ final ExportResourceDto resource = viewService.exportDataset(view);
+ headers.add("Content-Disposition", "attachment; filename=\"" + resource.getFilename() + "\"");
+ log.trace("export table resulted in resource {}", resource);
+ return ResponseEntity.ok()
+ .headers(headers)
+ .body(resource.getResource());
}
}
diff --git a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/handlers/ApiExceptionHandler.java b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/handlers/ApiExceptionHandler.java
index 6aa48b157082afe6686fccca36b375723cc3b44b..cf3f25fd2632e8427bf21afdc59634b4c46b91f6 100644
--- a/dbrepo-data-service/rest-service/src/main/java/at/tuwien/handlers/ApiExceptionHandler.java
+++ b/dbrepo-data-service/rest-service/src/main/java/at/tuwien/handlers/ApiExceptionHandler.java
@@ -45,6 +45,13 @@ public class ApiExceptionHandler extends ResponseEntityExceptionHandler {
return generic_handle(e.getClass(), e.getLocalizedMessage());
}
+ @Hidden
+ @ResponseStatus(code = HttpStatus.SERVICE_UNAVAILABLE)
+ @ExceptionHandler(AnalyseServiceException.class)
+ public ResponseEntity<ApiErrorDto> handle(AnalyseServiceException e) {
+ return generic_handle(e.getClass(), e.getLocalizedMessage());
+ }
+
@Hidden
@ResponseStatus(code = HttpStatus.BAD_GATEWAY)
@ExceptionHandler(AuthServiceConnectionException.class)
@@ -374,20 +381,6 @@ public class ApiExceptionHandler extends ResponseEntityExceptionHandler {
return generic_handle(e.getClass(), e.getLocalizedMessage());
}
- @Hidden
- @ResponseStatus(code = HttpStatus.SERVICE_UNAVAILABLE)
- @ExceptionHandler(SidecarExportException.class)
- public ResponseEntity<ApiErrorDto> handle(SidecarExportException e) {
- return generic_handle(e.getClass(), e.getLocalizedMessage());
- }
-
- @Hidden
- @ResponseStatus(code = HttpStatus.SERVICE_UNAVAILABLE)
- @ExceptionHandler(SidecarImportException.class)
- public ResponseEntity<ApiErrorDto> handle(SidecarImportException e) {
- return generic_handle(e.getClass(), e.getLocalizedMessage());
- }
-
@Hidden
@ResponseStatus(code = HttpStatus.BAD_REQUEST)
@ExceptionHandler(SortException.class)
diff --git a/dbrepo-data-service/rest-service/src/main/resources/application-local.yml b/dbrepo-data-service/rest-service/src/main/resources/application-local.yml
index 43cea9b9a538c7331562e7a068444d72826235a4..e12f578bdd6a8ab8a4aae4f33e338e70649dafd6 100644
--- a/dbrepo-data-service/rest-service/src/main/resources/application-local.yml
+++ b/dbrepo-data-service/rest-service/src/main/resources/application-local.yml
@@ -49,16 +49,18 @@ logging:
org.springframework.web.servlet.mvc.method.annotation.ExceptionHandlerExceptionResolver: debug
dbrepo:
endpoints:
- metadataService: http://localhost
- storageService: http://localhost/api/storage
- authService: http://localhost/api/auth
+ metadataService: "http://localhost:9099"
+ analyseService: "http://localhost"
+ storageService: "http://localhost:9000"
+ authService: "http://localhost:8080"
+ computeService: "local[2]"
s3:
- accessKeyId: seaweedfsadmin
- secretAccessKey: seaweedfsadmin
- bucket: dbrepo
+ accessKeyId: "seaweedfsadmin"
+ secretAccessKey: "seaweedfsadmin"
+ bucket: "dbrepo"
system:
- username: admin
- password: admin
+ username: "admin"
+ password: "admin"
jwt:
public_key: MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB
keycloak:
@@ -66,6 +68,3 @@ dbrepo:
password: admin
client: dbrepo-client
clientSecret: MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG
- defaultDateFormatId: 1
- defaultTimeFormatId: 4
- defaultTimestampFormatId: 3
diff --git a/dbrepo-data-service/rest-service/src/main/resources/application.yml b/dbrepo-data-service/rest-service/src/main/resources/application.yml
index 6684368fb250cdd4323278d329c5ce1fc2845d67..9bd16e6089443bfb2eb8972d7a8bc362661cb2a5 100644
--- a/dbrepo-data-service/rest-service/src/main/resources/application.yml
+++ b/dbrepo-data-service/rest-service/src/main/resources/application.yml
@@ -51,13 +51,14 @@ logging:
dbrepo:
endpoints:
metadataService: "${METADATA_SERVICE_ENDPOINT:http://metadata-service:8080}"
+ analyseService: "${ANALYSE_SERVICE_ENDPOINT:http://analyse-service:8080}"
storageService: "${S3_ENDPOINT:http://storage-service:9000}"
authService: "${AUTH_SERVICE_ENDPOINT:http://auth-service:8080}"
+ computeService: "${COMPUTE_SERVICE_ENDPOINT:local[2]}"
s3:
accessKeyId: "${S3_ACCESS_KEY_ID:seaweedfsadmin}"
secretAccessKey: "${S3_SECRET_ACCESS_KEY:seaweedfsadmin}"
bucket: "${S3_BUCKET:dbrepo}"
- filePath: "${S3_FILE_PATH:/tmp}"
system:
username: "${SYSTEM_USERNAME:admin}"
password: "${SYSTEM_PASSWORD:admin}"
@@ -69,7 +70,7 @@ dbrepo:
client: "${AUTH_SERVICE_CLIENT:dbrepo-client}"
clientSecret: "${AUTH_SERVICE_CLIENT_SECRET:MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG}"
sql:
- forbidden: "${NOT_SUPPORTED_KEYWORDS:\\*,AVG,BIT_AND,BIT_OR,BIT_XOR,COUNT,COUNTDISTINCT,GROUP_CONCAT,JSON_ARRAYAGG,JSON_OBJECTAGG,MAX,MIN,STD,STDDEV,STDDEV_POP,STDDEV_SAMP,SUM,VARIANCE,VAR_POP,VAR_SAMP,--}"
+ forbidden: "${NOT_SUPPORTED_KEYWORDS:AVG,BIT_AND,BIT_OR,BIT_XOR,COUNT,COUNTDISTINCT,GROUP_CONCAT,JSON_ARRAYAGG,JSON_OBJECTAGG,MAX,MIN,STD,STDDEV,STDDEV_POP,STDDEV_SAMP,SUM,VARIANCE,VAR_POP,VAR_SAMP,--}"
grant:
default:
read: "${GRANT_DEFAULT_READ:SELECT}"
@@ -81,6 +82,3 @@ dbrepo:
exchangeName: "${BROKER_EXCHANGE_NAME:dbrepo}"
routingKey: "${BROKER_ROUTING_KEY:#}"
connectionTimeout: ${CONNECTION_TIMEOUT:10000}
- defaultDateFormatId: "${DEFAULT_DATE_FORMAT_ID:3}"
- defaultTimeFormatId: "${DEFAULT_TIME_FORMAT_ID:4}"
- defaultTimestampFormatId: "${DEFAULT_TIMESTAMP_FORMAT_ID:1}"
diff --git a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/config/MariaDbConfig.java b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/config/MariaDbConfig.java
index 691d96006bb273bc257e6439b0f828cae70b9d58..38b33c4713031d2388ef6b6cf99b67ddc27776ce 100644
--- a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/config/MariaDbConfig.java
+++ b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/config/MariaDbConfig.java
@@ -6,7 +6,7 @@ import at.tuwien.api.database.internal.PrivilegedDatabaseDto;
import at.tuwien.api.database.query.QueryDto;
import at.tuwien.api.database.table.columns.ColumnTypeDto;
import at.tuwien.api.database.table.internal.PrivilegedTableDto;
-import lombok.extern.slf4j.Slf4j;
+import lombok.extern.log4j.Log4j2;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.io.ClassPathResource;
import org.springframework.jdbc.datasource.init.ResourceDatabasePopulator;
@@ -17,7 +17,7 @@ import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-@Slf4j
+@Log4j2
@Configuration
public class MariaDbConfig {
diff --git a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/SubsetEndpointUnitTest.java b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/SubsetEndpointUnitTest.java
index 9ab7082d0eb40da175947314c13b669de9f02476..5f302368eedec06766e77328fe4d738c28e9a168 100644
--- a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/SubsetEndpointUnitTest.java
+++ b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/SubsetEndpointUnitTest.java
@@ -107,9 +107,9 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
@Test
@WithAnonymousUser
public void findById_succeeds() throws DatabaseNotFoundException, RemoteUnavailableException, UserNotFoundException,
- DatabaseUnavailableException, StorageUnavailableException, NotAllowedException, QueryMalformedException,
- QueryNotFoundException, SidecarExportException, FormatNotAvailableException, StorageNotFoundException,
- SQLException, MetadataServiceException {
+ DatabaseUnavailableException, StorageUnavailableException, QueryMalformedException, QueryNotFoundException,
+ FormatNotAvailableException, StorageNotFoundException, SQLException, MetadataServiceException,
+ ViewNotFoundException, MalformedException {
/* mock */
when(metadataServiceGateway.getDatabaseById(DATABASE_3_ID))
@@ -124,7 +124,7 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
@Test
@WithAnonymousUser
public void findById_format_fails() throws DatabaseNotFoundException, RemoteUnavailableException, SQLException,
- UserNotFoundException, NotAllowedException, QueryNotFoundException, MetadataServiceException {
+ UserNotFoundException, QueryNotFoundException, MetadataServiceException {
/* mock */
when(metadataServiceGateway.getDatabaseById(DATABASE_3_ID))
@@ -141,9 +141,9 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
@Test
@WithAnonymousUser
public void findById_acceptCsv_succeeds() throws DatabaseNotFoundException, RemoteUnavailableException,
- UserNotFoundException, DatabaseUnavailableException, StorageUnavailableException, NotAllowedException,
- QueryMalformedException, QueryNotFoundException, SidecarExportException, FormatNotAvailableException,
- StorageNotFoundException, SQLException, MetadataServiceException {
+ UserNotFoundException, DatabaseUnavailableException, StorageUnavailableException, QueryMalformedException,
+ QueryNotFoundException, FormatNotAvailableException, StorageNotFoundException, SQLException,
+ MetadataServiceException, ViewNotFoundException, MalformedException {
final ExportResourceDto mock = ExportResourceDto.builder()
.filename("deadbeef")
.resource(new InputStreamResource(InputStream.nullInputStream()))
@@ -154,7 +154,7 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
.thenReturn(DATABASE_3_PRIVILEGED_DTO);
when(subsetService.findById(DATABASE_3_PRIVILEGED_DTO, QUERY_5_ID))
.thenReturn(QUERY_5_DTO);
- when(subsetService.export(any(PrivilegedDatabaseDto.class), any(QueryDto.class), any(Instant.class), anyString()))
+ when(subsetService.export(any(PrivilegedDatabaseDto.class), any(QueryDto.class), any(Instant.class)))
.thenReturn(mock);
/* test */
@@ -164,9 +164,9 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
@Test
@WithAnonymousUser
public void findById_timestamp_succeeds() throws DatabaseNotFoundException, RemoteUnavailableException,
- UserNotFoundException, DatabaseUnavailableException, StorageUnavailableException, NotAllowedException,
- QueryMalformedException, QueryNotFoundException, SidecarExportException, FormatNotAvailableException,
- StorageNotFoundException, SQLException, MetadataServiceException {
+ UserNotFoundException, DatabaseUnavailableException, StorageUnavailableException, QueryMalformedException,
+ QueryNotFoundException, FormatNotAvailableException, StorageNotFoundException, SQLException,
+ MetadataServiceException, ViewNotFoundException, MalformedException {
final ExportResourceDto mock = ExportResourceDto.builder()
.filename("deadbeef")
.resource(new InputStreamResource(InputStream.nullInputStream()))
@@ -177,7 +177,7 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
.thenReturn(DATABASE_3_PRIVILEGED_DTO);
when(subsetService.findById(DATABASE_3_PRIVILEGED_DTO, QUERY_5_ID))
.thenReturn(QUERY_5_DTO);
- when(subsetService.export(any(PrivilegedDatabaseDto.class), any(QueryDto.class), any(Instant.class), anyString()))
+ when(subsetService.export(any(PrivilegedDatabaseDto.class), any(QueryDto.class), any(Instant.class)))
.thenReturn(mock);
/* test */
@@ -202,7 +202,7 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
@Test
@WithAnonymousUser
public void findById_unavailable_fails() throws DatabaseNotFoundException, RemoteUnavailableException,
- MetadataServiceException, SQLException, UserNotFoundException, NotAllowedException, QueryNotFoundException {
+ MetadataServiceException, SQLException, UserNotFoundException, QueryNotFoundException {
/* mock */
when(metadataServiceGateway.getDatabaseById(DATABASE_3_ID))
@@ -221,8 +221,7 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
@WithAnonymousUser
public void findById_unavailableExport_fails() throws DatabaseNotFoundException, RemoteUnavailableException,
MetadataServiceException, SQLException, StorageUnavailableException, QueryMalformedException,
- SidecarExportException, StorageNotFoundException, UserNotFoundException, NotAllowedException,
- QueryNotFoundException {
+ StorageNotFoundException, UserNotFoundException, QueryNotFoundException, ViewNotFoundException, MalformedException {
final ExportResourceDto mock = ExportResourceDto.builder()
.filename("deadbeef")
.resource(new InputStreamResource(InputStream.nullInputStream()))
@@ -233,11 +232,11 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
.thenReturn(DATABASE_3_PRIVILEGED_DTO);
when(subsetService.findById(DATABASE_3_PRIVILEGED_DTO, QUERY_5_ID))
.thenReturn(QUERY_5_DTO);
- when(subsetService.export(any(PrivilegedDatabaseDto.class), any(QueryDto.class), any(Instant.class), anyString()))
+ when(subsetService.export(any(PrivilegedDatabaseDto.class), any(QueryDto.class), any(Instant.class)))
.thenReturn(mock);
doThrow(SQLException.class)
.when(subsetService)
- .export(eq(DATABASE_3_PRIVILEGED_DTO), eq(QUERY_5_DTO), any(Instant.class), anyString());
+ .export(eq(DATABASE_3_PRIVILEGED_DTO), eq(QUERY_5_DTO), any(Instant.class));
/* test */
assertThrows(DatabaseUnavailableException.class, () -> {
@@ -247,8 +246,8 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_1_USERNAME, authorities = {"execute-query"})
- public void create_noAccess_succeeds() throws UserNotFoundException, QueryStoreInsertException, TableMalformedException,
- NotAllowedException, SidecarExportException, QueryNotSupportedException, PaginationException,
+ public void create_noAccess_succeeds() throws UserNotFoundException, QueryStoreInsertException,
+ TableMalformedException, NotAllowedException, QueryNotSupportedException, PaginationException,
StorageNotFoundException, DatabaseUnavailableException, StorageUnavailableException,
QueryMalformedException, QueryNotFoundException, DatabaseNotFoundException, RemoteUnavailableException,
SQLException, MetadataServiceException {
@@ -270,7 +269,7 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
@WithMockUser(username = USER_1_USERNAME, authorities = {"execute-query"})
public void create_forbiddenKeyword_fails() {
final ExecuteStatementDto request = ExecuteStatementDto.builder()
- .statement("SELECT * FROM tbl")
+ .statement("SELECT COUNT(id) FROM tbl")
.build();
/* test */
@@ -282,7 +281,7 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_1_USERNAME, authorities = {"execute-query"})
public void create_noPageSize_succeeds() throws UserNotFoundException, QueryStoreInsertException,
- TableMalformedException, NotAllowedException, SidecarExportException, QueryNotSupportedException,
+ TableMalformedException, NotAllowedException, QueryNotSupportedException,
PaginationException, StorageNotFoundException, DatabaseUnavailableException, StorageUnavailableException,
QueryMalformedException, QueryNotFoundException, DatabaseNotFoundException, RemoteUnavailableException,
SQLException, MetadataServiceException {
@@ -343,7 +342,11 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_4_USERNAME)
- public void create_noRole_fails() throws DatabaseNotFoundException, RemoteUnavailableException, MetadataServiceException, UserNotFoundException, QueryStoreInsertException, TableMalformedException, NotAllowedException, SQLException, QueryNotFoundException, DatabaseUnavailableException, StorageUnavailableException, QueryMalformedException, SidecarExportException, QueryNotSupportedException, PaginationException, StorageNotFoundException {
+ public void create_noRole_fails() throws DatabaseNotFoundException, RemoteUnavailableException,
+ MetadataServiceException, UserNotFoundException, QueryStoreInsertException, TableMalformedException,
+ NotAllowedException, SQLException, QueryNotFoundException, DatabaseUnavailableException,
+ StorageUnavailableException, QueryMalformedException, QueryNotSupportedException, PaginationException,
+ StorageNotFoundException {
final ExecuteStatementDto request = ExecuteStatementDto.builder()
.statement(QUERY_5_STATEMENT)
.build();
@@ -360,7 +363,11 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
@Test
@WithAnonymousUser
- public void create_anonymous_succeeds() throws DatabaseNotFoundException, RemoteUnavailableException, MetadataServiceException, UserNotFoundException, QueryStoreInsertException, TableMalformedException, NotAllowedException, SQLException, QueryNotFoundException, DatabaseUnavailableException, StorageUnavailableException, QueryMalformedException, SidecarExportException, QueryNotSupportedException, PaginationException, StorageNotFoundException {
+ public void create_anonymous_succeeds() throws DatabaseNotFoundException, RemoteUnavailableException,
+ MetadataServiceException, UserNotFoundException, QueryStoreInsertException, TableMalformedException,
+ NotAllowedException, SQLException, QueryNotFoundException, DatabaseUnavailableException,
+ StorageUnavailableException, QueryMalformedException, QueryNotSupportedException, PaginationException,
+ StorageNotFoundException {
final ExecuteStatementDto request = ExecuteStatementDto.builder()
.statement(QUERY_5_STATEMENT)
.build();
@@ -645,9 +652,9 @@ public class SubsetEndpointUnitTest extends AbstractUnitTest {
}
protected void generic_findById(Long subsetId, MediaType accept, Instant timestamp) throws UserNotFoundException,
- DatabaseUnavailableException, StorageUnavailableException, NotAllowedException, QueryMalformedException,
- QueryNotFoundException, DatabaseNotFoundException, SidecarExportException, RemoteUnavailableException,
- FormatNotAvailableException, StorageNotFoundException, MetadataServiceException {
+ DatabaseUnavailableException, StorageUnavailableException, QueryMalformedException, QueryNotFoundException,
+ DatabaseNotFoundException, RemoteUnavailableException, FormatNotAvailableException,
+ StorageNotFoundException, MetadataServiceException, ViewNotFoundException, MalformedException {
/* mock */
when(mockHttpServletRequest.getHeader("Accept"))
diff --git a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/TableEndpointUnitTest.java b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/TableEndpointUnitTest.java
index cc4b957226a77fbe4f39aef09193b29def575959..29b7dfa67c0a01fb6ff9cbeac32d6b9a3430a5fd 100644
--- a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/TableEndpointUnitTest.java
+++ b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/TableEndpointUnitTest.java
@@ -2,6 +2,7 @@ package at.tuwien.endpoint;
import at.tuwien.ExportResourceDto;
import at.tuwien.api.database.DatabaseAccessDto;
+import at.tuwien.api.database.internal.PrivilegedDatabaseDto;
import at.tuwien.api.database.query.ImportDto;
import at.tuwien.api.database.query.QueryResultDto;
import at.tuwien.api.database.table.*;
@@ -276,7 +277,7 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
/* mock */
when(metadataServiceGateway.getTableById(DATABASE_3_ID, TABLE_8_ID))
.thenReturn(TABLE_8_PRIVILEGED_DTO);
- when(tableService.getData(eq(TABLE_8_PRIVILEGED_DTO), any(Instant.class), eq(0L), eq(10L)))
+ when(tableService.getPaginatedData(eq(TABLE_8_PRIVILEGED_DTO), any(Instant.class), eq(0L), eq(10L)))
.thenReturn(TABLE_8_DATA_DTO);
/* test */
@@ -299,7 +300,7 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
.thenReturn("HEAD");
when(tableService.getCount(eq(TABLE_8_PRIVILEGED_DTO), any(Instant.class)))
.thenReturn(3L);
- when(tableService.getData(eq(TABLE_8_PRIVILEGED_DTO), any(Instant.class), eq(0L), eq(10L)))
+ when(tableService.getPaginatedData(eq(TABLE_8_PRIVILEGED_DTO), any(Instant.class), eq(0L), eq(10L)))
.thenReturn(TABLE_8_DATA_DTO);
/* test */
@@ -355,7 +356,7 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
.thenReturn(TABLE_8_PRIVILEGED_DTO);
doThrow(SQLException.class)
.when(tableService)
- .getData(eq(TABLE_8_PRIVILEGED_DTO), any(Instant.class), eq(0L), eq(10L));
+ .getPaginatedData(eq(TABLE_8_PRIVILEGED_DTO), any(Instant.class), eq(0L), eq(10L));
/* test */
assertThrows(DatabaseUnavailableException.class, () -> {
@@ -393,7 +394,7 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
.thenReturn(TABLE_1_PRIVILEGED_DTO);
when(metadataServiceGateway.getAccess(DATABASE_1_ID, USER_2_ID))
.thenReturn(access);
- when(tableService.getData(eq(TABLE_1_PRIVILEGED_DTO), any(Instant.class), eq(0L), eq(10L)))
+ when(tableService.getPaginatedData(eq(TABLE_1_PRIVILEGED_DTO), any(Instant.class), eq(0L), eq(10L)))
.thenReturn(TABLE_1_DATA_DTO);
/* test */
@@ -1126,8 +1127,8 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
@Test
@WithAnonymousUser
public void exportData_succeeds() throws DatabaseUnavailableException, TableNotFoundException, NotAllowedException,
- StorageUnavailableException, QueryMalformedException, SidecarExportException, RemoteUnavailableException,
- StorageNotFoundException, SQLException, MetadataServiceException {
+ StorageUnavailableException, QueryMalformedException, RemoteUnavailableException, StorageNotFoundException,
+ SQLException, MetadataServiceException, MalformedException {
final ExportResourceDto mock = ExportResourceDto.builder()
.filename("deadbeef")
.resource(new InputStreamResource(InputStream.nullInputStream()))
@@ -1148,9 +1149,9 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
@ParameterizedTest
@WithMockUser(username = USER_2_USERNAME)
@MethodSource("anyAccess_parameters")
- public void exportData_private_succeeds(String name, DatabaseAccessDto access) throws DatabaseUnavailableException, TableNotFoundException, NotAllowedException,
- StorageUnavailableException, QueryMalformedException, SidecarExportException, RemoteUnavailableException,
- StorageNotFoundException, SQLException, MetadataServiceException {
+ public void exportData_private_succeeds(String name, DatabaseAccessDto access) throws TableNotFoundException,
+ NotAllowedException, StorageUnavailableException, QueryMalformedException, RemoteUnavailableException,
+ MetadataServiceException, MalformedException {
final ExportResourceDto mock = ExportResourceDto.builder()
.filename("deadbeef")
.resource(new InputStreamResource(InputStream.nullInputStream()))
@@ -1188,25 +1189,6 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
});
}
- @Test
- @WithMockUser(username = USER_1_USERNAME)
- public void exportData_unavailable_fails() throws TableNotFoundException, RemoteUnavailableException,
- MetadataServiceException, StorageUnavailableException, SQLException, QueryMalformedException,
- SidecarExportException, StorageNotFoundException {
-
- /* mock */
- when(metadataServiceGateway.getTableById(DATABASE_1_ID, TABLE_1_ID))
- .thenReturn(TABLE_1_PRIVILEGED_DTO);
- doThrow(SQLException.class)
- .when(tableService)
- .exportDataset(eq(TABLE_1_PRIVILEGED_DTO), any(Instant.class));
-
- /* test */
- assertThrows(DatabaseUnavailableException.class, () -> {
- tableEndpoint.exportDataset(DATABASE_1_ID, TABLE_1_ID, null, USER_1_PRINCIPAL);
- });
- }
-
@Test
@WithMockUser(username = USER_1_USERNAME, authorities = {"system"})
public void getSchema_succeeds() throws DatabaseUnavailableException, TableNotFoundException,
@@ -1264,11 +1246,10 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_1_USERNAME, authorities = {"insert-table-data"})
- public void importDataset_succeeds() throws DatabaseUnavailableException, TableNotFoundException,
- SidecarImportException, NotAllowedException, QueryMalformedException, RemoteUnavailableException,
- StorageNotFoundException, SQLException, MetadataServiceException {
+ public void importDataset_succeeds() throws TableNotFoundException, NotAllowedException, RemoteUnavailableException,
+ MetadataServiceException, StorageNotFoundException, MalformedException, StorageUnavailableException, DatabaseUnavailableException, QueryMalformedException, SQLException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination(null)
.location("deadbeef")
.build();
@@ -1294,7 +1275,7 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
@WithMockUser(username = USER_4_USERNAME)
public void importDataset_noRole_fails() {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
@@ -1310,7 +1291,7 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
public void importDataset_tableNotFound_fails() throws TableNotFoundException, RemoteUnavailableException,
MetadataServiceException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
@@ -1328,11 +1309,11 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_3_USERNAME, authorities = {"insert-table-data"})
- public void importDataset_unavailable_fails() throws RemoteUnavailableException, SidecarImportException,
- SQLException, QueryMalformedException, StorageNotFoundException, TableNotFoundException,
- MetadataServiceException, NotAllowedException {
+ public void importDataset_unavailable_fails() throws RemoteUnavailableException, TableNotFoundException,
+ MetadataServiceException, NotAllowedException, StorageNotFoundException, MalformedException,
+ StorageUnavailableException, SQLException, QueryMalformedException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
@@ -1354,11 +1335,11 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_3_USERNAME, authorities = {"insert-table-data"})
- public void importDataset_writeOwnAccess_fails() throws RemoteUnavailableException, SidecarImportException,
- SQLException, QueryMalformedException, StorageNotFoundException, TableNotFoundException,
- MetadataServiceException, NotAllowedException {
+ public void importDataset_writeOwnAccess_fails() throws RemoteUnavailableException, TableNotFoundException,
+ MetadataServiceException, NotAllowedException, StorageNotFoundException, MalformedException,
+ StorageUnavailableException, SQLException, QueryMalformedException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
@@ -1383,7 +1364,7 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
public void importDataset_readAccess_fails() throws TableNotFoundException, RemoteUnavailableException,
NotAllowedException, MetadataServiceException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
@@ -1403,10 +1384,10 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_1_USERNAME, authorities = {"insert-table-data"})
public void importDataset_writeOwnAccess_succeeds() throws TableNotFoundException, RemoteUnavailableException,
- NotAllowedException, DatabaseUnavailableException, SidecarImportException, QueryMalformedException,
- StorageNotFoundException, MetadataServiceException {
+ NotAllowedException, MetadataServiceException, StorageNotFoundException, MalformedException,
+ StorageUnavailableException, DatabaseUnavailableException, QueryMalformedException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
@@ -1426,7 +1407,7 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
public void importDataset_writeOwnAccessForeign_fails() throws TableNotFoundException, RemoteUnavailableException,
NotAllowedException, MetadataServiceException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
@@ -1445,11 +1426,11 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_3_USERNAME, authorities = {"insert-table-data"})
- public void importDataset_writeAllAccessForeign_succeeds() throws TableNotFoundException, RemoteUnavailableException,
- NotAllowedException, DatabaseUnavailableException, SidecarImportException, QueryMalformedException,
- StorageNotFoundException, MetadataServiceException {
+ public void importDataset_writeAllAccessForeign_succeeds() throws TableNotFoundException,
+ RemoteUnavailableException, NotAllowedException, MetadataServiceException, StorageNotFoundException,
+ MalformedException, StorageUnavailableException, DatabaseUnavailableException, QueryMalformedException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
@@ -1467,10 +1448,10 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME, authorities = {"insert-table-data"})
public void importDataset_privateForeign_succeeds() throws TableNotFoundException, RemoteUnavailableException,
- NotAllowedException, DatabaseUnavailableException, SidecarImportException, QueryMalformedException,
- StorageNotFoundException, MetadataServiceException {
+ NotAllowedException, MetadataServiceException, StorageNotFoundException, MalformedException,
+ StorageUnavailableException, DatabaseUnavailableException, QueryMalformedException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
@@ -1488,10 +1469,10 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME, authorities = {"insert-table-data"})
public void importDataset_private_succeeds() throws TableNotFoundException, RemoteUnavailableException,
- NotAllowedException, DatabaseUnavailableException, SidecarImportException, QueryMalformedException,
- StorageNotFoundException, MetadataServiceException {
+ NotAllowedException, MetadataServiceException, StorageNotFoundException, MalformedException,
+ StorageUnavailableException, DatabaseUnavailableException, QueryMalformedException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
@@ -1511,7 +1492,7 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
public void importDataset_privateForeign_fails() throws TableNotFoundException, RemoteUnavailableException,
NotAllowedException, MetadataServiceException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
@@ -1533,7 +1514,7 @@ public class TableEndpointUnitTest extends AbstractUnitTest {
public void importDataset_privateReadAccess_fails() throws TableNotFoundException, RemoteUnavailableException,
NotAllowedException, MetadataServiceException {
final ImportDto request = ImportDto.builder()
- .skipLines(1L)
+ .header(true)
.lineTermination("\\n")
.location("deadbeef")
.build();
diff --git a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/ViewEndpointUnitTest.java b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/ViewEndpointUnitTest.java
index fd1030c17bee1f169c01d33da8af86f339feecbe..1f4beb8afa988305d9faf8b178334d01e16b0063 100644
--- a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/ViewEndpointUnitTest.java
+++ b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/endpoint/ViewEndpointUnitTest.java
@@ -383,4 +383,56 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
});
}
+ @Test
+ @WithMockUser(username = USER_3_USERNAME, authorities = {"view-database-view-data"})
+ public void exportDataset_privateNoAccess_fails() throws RemoteUnavailableException, ViewNotFoundException,
+ NotAllowedException, MetadataServiceException {
+
+ /* mock */
+ when(metadataServiceGateway.getViewById(DATABASE_1_ID, VIEW_3_ID))
+ .thenReturn(VIEW_3_PRIVILEGED_DTO);
+ doThrow(NotAllowedException.class)
+ .when(metadataServiceGateway)
+ .getAccess(DATABASE_1_ID, USER_3_ID);
+
+ /* test */
+ assertThrows(NotAllowedException.class, () -> {
+ viewEndpoint.exportDataset(DATABASE_1_ID, VIEW_3_ID, USER_3_PRINCIPAL);
+ });
+ }
+
+ @Test
+ @WithMockUser(username = USER_1_USERNAME, authorities = {"view-database-view-data"})
+ public void exportDataset_viewNotFound_fails() throws RemoteUnavailableException, ViewNotFoundException,
+ MetadataServiceException {
+
+ /* mock */
+ doThrow(ViewNotFoundException.class)
+ .when(metadataServiceGateway)
+ .getViewById(DATABASE_1_ID, VIEW_1_ID);
+
+ /* test */
+ assertThrows(ViewNotFoundException.class, () -> {
+ viewEndpoint.exportDataset(DATABASE_1_ID, VIEW_1_ID, USER_4_PRINCIPAL);
+ });
+ }
+
+ @Test
+ @WithMockUser(username = USER_1_USERNAME, authorities = {"view-database-view-data"})
+ public void exportDataset_privateNoAccess_succeeds() throws RemoteUnavailableException, ViewNotFoundException,
+ NotAllowedException, MetadataServiceException {
+
+ /* mock */
+ when(metadataServiceGateway.getViewById(DATABASE_1_ID, VIEW_3_ID))
+ .thenReturn(VIEW_3_PRIVILEGED_DTO);
+ doThrow(NotAllowedException.class)
+ .when(metadataServiceGateway)
+ .getAccess(DATABASE_1_ID, USER_1_ID);
+
+ /* test */
+ assertThrows(NotAllowedException.class, () -> {
+ viewEndpoint.exportDataset(DATABASE_1_ID, VIEW_3_ID, USER_1_PRINCIPAL);
+ });
+ }
+
}
diff --git a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/gateway/DataDatabaseGatewayUnitTest.java b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/gateway/AnalyseServiceGatewayUnitTest.java
similarity index 68%
rename from dbrepo-data-service/rest-service/src/test/java/at/tuwien/gateway/DataDatabaseGatewayUnitTest.java
rename to dbrepo-data-service/rest-service/src/test/java/at/tuwien/gateway/AnalyseServiceGatewayUnitTest.java
index b00f871d5ca92797197e40b898ce95c94463b807..f0a7346ae744a5ea507754ae0efcb5f3f17c99b1 100644
--- a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/gateway/DataDatabaseGatewayUnitTest.java
+++ b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/gateway/AnalyseServiceGatewayUnitTest.java
@@ -16,7 +16,6 @@ import org.springframework.web.client.HttpClientErrorException;
import org.springframework.web.client.HttpServerErrorException;
import org.springframework.web.client.RestTemplate;
-import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.eq;
@@ -26,14 +25,14 @@ import static org.mockito.Mockito.when;
@Log4j2
@SpringBootTest
@ExtendWith(SpringExtension.class)
-public class DataDatabaseGatewayUnitTest extends AbstractUnitTest {
+public class AnalyseServiceGatewayUnitTest extends AbstractUnitTest {
@MockBean
@Qualifier("restTemplate")
private RestTemplate restTemplate;
@Autowired
- private DataDatabaseSidecarGateway dataDatabaseSidecarGateway;
+ private AnalyseServiceGateway dataDatabaseSidecarGateway;
@BeforeEach
public void beforeEach() {
@@ -41,8 +40,8 @@ public class DataDatabaseGatewayUnitTest extends AbstractUnitTest {
}
@Test
- public void importFile_succeeds() throws RemoteUnavailableException, StorageNotFoundException,
- SidecarImportException {
+ public void importDataset_succeeds() throws RemoteUnavailableException, StorageNotFoundException,
+ AnalyseServiceException {
/* mock */
when(restTemplate.exchange(anyString(), eq(HttpMethod.POST), eq(HttpEntity.EMPTY), eq(Void.class)))
@@ -50,11 +49,11 @@ public class DataDatabaseGatewayUnitTest extends AbstractUnitTest {
.build());
/* test */
- dataDatabaseSidecarGateway.importFile(CONTAINER_1_HOST, CONTAINER_1_PORT, "filename");
+ dataDatabaseSidecarGateway.importDataset(DATABASE_1_ID, TABLE_1_ID, "filename");
}
@Test
- public void importFile_unavailable_fails() {
+ public void importDataset_unavailable_fails() {
/* mock */
doThrow(HttpServerErrorException.class)
@@ -63,12 +62,12 @@ public class DataDatabaseGatewayUnitTest extends AbstractUnitTest {
/* test */
assertThrows(RemoteUnavailableException.class, () -> {
- dataDatabaseSidecarGateway.importFile(CONTAINER_1_HOST, CONTAINER_1_PORT, "filename");
+ dataDatabaseSidecarGateway.importDataset(DATABASE_1_ID, TABLE_1_ID, "filename");
});
}
@Test
- public void importFile_statusCode_fails() {
+ public void importDataset_statusCode_fails() {
/* mock */
when(restTemplate.exchange(anyString(), eq(HttpMethod.POST), eq(HttpEntity.EMPTY), eq(Void.class)))
@@ -76,13 +75,13 @@ public class DataDatabaseGatewayUnitTest extends AbstractUnitTest {
.build());
/* test */
- assertThrows(SidecarImportException.class, () -> {
- dataDatabaseSidecarGateway.importFile(CONTAINER_1_HOST, CONTAINER_1_PORT, "filename");
+ assertThrows(AnalyseServiceException.class, () -> {
+ dataDatabaseSidecarGateway.importDataset(DATABASE_1_ID, TABLE_1_ID, "filename");
});
}
@Test
- public void importFile_s3_fails() {
+ public void importDataset_s3_fails() {
/* mock */
doThrow(HttpClientErrorException.BadRequest.class)
@@ -91,13 +90,13 @@ public class DataDatabaseGatewayUnitTest extends AbstractUnitTest {
/* test */
assertThrows(StorageNotFoundException.class, () -> {
- dataDatabaseSidecarGateway.importFile(CONTAINER_1_HOST, CONTAINER_1_PORT, "filename");
+ dataDatabaseSidecarGateway.importDataset(DATABASE_1_ID, TABLE_1_ID, "filename");
});
}
@Test
- public void exportFile_succeeds() throws RemoteUnavailableException, StorageNotFoundException,
- SidecarExportException {
+ public void exportTable_succeeds() throws RemoteUnavailableException, StorageNotFoundException,
+ AnalyseServiceException {
/* mock */
when(restTemplate.exchange(anyString(), eq(HttpMethod.POST), eq(HttpEntity.EMPTY), eq(Void.class)))
@@ -105,11 +104,11 @@ public class DataDatabaseGatewayUnitTest extends AbstractUnitTest {
.build());
/* test */
- dataDatabaseSidecarGateway.exportFile(CONTAINER_1_HOST, CONTAINER_1_PORT, "filename");
+ dataDatabaseSidecarGateway.exportTable(DATABASE_1_ID, TABLE_1_ID);
}
@Test
- public void exportFile_unavailable_fails() {
+ public void exportTable_unavailable_fails() {
/* mock */
doThrow(HttpServerErrorException.class)
@@ -118,12 +117,12 @@ public class DataDatabaseGatewayUnitTest extends AbstractUnitTest {
/* test */
assertThrows(RemoteUnavailableException.class, () -> {
- dataDatabaseSidecarGateway.exportFile(CONTAINER_1_HOST, CONTAINER_1_PORT, "filename");
+ dataDatabaseSidecarGateway.exportTable(DATABASE_1_ID, TABLE_1_ID);
});
}
@Test
- public void exportFile_statusCode_fails() {
+ public void exportTable_statusCode_fails() {
/* mock */
when(restTemplate.exchange(anyString(), eq(HttpMethod.POST), eq(HttpEntity.EMPTY), eq(Void.class)))
@@ -131,13 +130,13 @@ public class DataDatabaseGatewayUnitTest extends AbstractUnitTest {
.build());
/* test */
- assertThrows(SidecarExportException.class, () -> {
- dataDatabaseSidecarGateway.exportFile(CONTAINER_1_HOST, CONTAINER_1_PORT, "filename");
+ assertThrows(AnalyseServiceException.class, () -> {
+ dataDatabaseSidecarGateway.exportTable(DATABASE_1_ID, TABLE_1_ID);
});
}
@Test
- public void exportFile_s3_fails() {
+ public void exportTable_s3_fails() {
/* mock */
doThrow(HttpClientErrorException.BadRequest.class)
@@ -146,7 +145,7 @@ public class DataDatabaseGatewayUnitTest extends AbstractUnitTest {
/* test */
assertThrows(StorageNotFoundException.class, () -> {
- dataDatabaseSidecarGateway.exportFile(CONTAINER_1_HOST, CONTAINER_1_PORT, "filename");
+ dataDatabaseSidecarGateway.exportTable(DATABASE_1_ID, TABLE_1_ID);
});
}
diff --git a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/gateway/MetadataServiceGatewayUnitTest.java b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/gateway/MetadataServiceGatewayUnitTest.java
index 44b01b1e9e2919721e446d7e183fbbcb739ea813..2730e94d9cb433b198681720a2d54d1de7fdef7a 100644
--- a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/gateway/MetadataServiceGatewayUnitTest.java
+++ b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/gateway/MetadataServiceGatewayUnitTest.java
@@ -62,8 +62,7 @@ public class MetadataServiceGatewayUnitTest extends AbstractUnitTest {
headers.set("X-Username", CONTAINER_1_PRIVILEGED_USERNAME);
headers.set("X-Password", CONTAINER_1_PRIVILEGED_PASSWORD);
headers.set("X-Database", DATABASE_1_INTERNALNAME);
- headers.set("X-Sidecar-Host", CONTAINER_1_SIDECAR_HOST);
- headers.set("X-Sidecar-Port", "" + CONTAINER_1_SIDECAR_PORT);
+ headers.set("X-Table", TABLE_1_INTERNALNAME);
/* mock */
when(restTemplate.exchange(anyString(), eq(HttpMethod.GET), eq(HttpEntity.EMPTY), eq(TableDto.class)))
@@ -79,8 +78,7 @@ public class MetadataServiceGatewayUnitTest extends AbstractUnitTest {
assertEquals(CONTAINER_1_PRIVILEGED_USERNAME, response.getDatabase().getContainer().getUsername());
assertEquals(CONTAINER_1_PRIVILEGED_PASSWORD, response.getDatabase().getContainer().getPassword());
assertEquals(DATABASE_1_INTERNALNAME, response.getDatabase().getInternalName());
- assertEquals(CONTAINER_1_SIDECAR_HOST, response.getDatabase().getContainer().getSidecarHost());
- assertEquals(CONTAINER_1_SIDECAR_PORT, response.getDatabase().getContainer().getSidecarPort());
+ assertEquals(TABLE_1_INTERNALNAME, response.getInternalName());
}
@Test
@@ -155,8 +153,7 @@ public class MetadataServiceGatewayUnitTest extends AbstractUnitTest {
headers.set("X-Username", CONTAINER_1_PRIVILEGED_USERNAME);
headers.set("X-Password", CONTAINER_1_PRIVILEGED_PASSWORD);
headers.set("X-Database", DATABASE_1_INTERNALNAME);
- headers.set("X-Sidecar-Host", CONTAINER_1_SIDECAR_HOST);
- headers.set("X-Sidecar-Port", "" + CONTAINER_1_SIDECAR_PORT);
+ headers.set("X-Table", TABLE_1_INTERNALNAME);
/* mock */
when(restTemplate.exchange(anyString(), eq(HttpMethod.GET), eq(HttpEntity.EMPTY), eq(TableDto.class)))
@@ -450,6 +447,7 @@ public class MetadataServiceGatewayUnitTest extends AbstractUnitTest {
headers.set("X-Username", CONTAINER_1_PRIVILEGED_USERNAME);
headers.set("X-Password", CONTAINER_1_PRIVILEGED_PASSWORD);
headers.set("X-Database", DATABASE_1_INTERNALNAME);
+ headers.set("X-View", VIEW_1_INTERNAL_NAME);
/* mock */
when(restTemplate.exchange(anyString(), eq(HttpMethod.GET), eq(HttpEntity.EMPTY), eq(ViewDto.class)))
diff --git a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/handlers/ApiExceptionHandlerTest.java b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/handlers/ApiExceptionHandlerTest.java
index ce56ce82da975f8f41d7233b0a017143044457ed..7dcb0343ac1c10f7e07af87405108cac8d6a6750 100644
--- a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/handlers/ApiExceptionHandlerTest.java
+++ b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/handlers/ApiExceptionHandlerTest.java
@@ -114,6 +114,24 @@ public class ApiExceptionHandlerTest extends AbstractUnitTest {
}
+ @Test
+ public void handle_AnalyseServiceException_succeeds() {
+ final AnalyseServiceException request = new AnalyseServiceException("msg");
+
+ /* test */
+ final ResponseEntity<ApiErrorDto> response = apiExceptionHandler.handle(request);
+ assertNotNull(response);
+ assertNotNull(request.getClass().getDeclaredAnnotation(ResponseStatus.class).code());
+ final HttpStatus httpStatus = request.getClass().getDeclaredAnnotation(ResponseStatus.class).code();
+ Assertions.assertNotEquals(httpStatus, HttpStatus.INTERNAL_SERVER_ERROR);
+ assertEquals(httpStatus, response.getStatusCode());
+ assertNotNull(response.getBody());
+ assertNotNull(response.getBody().getCode());
+ assertEquals(httpStatus, response.getBody().getStatus());
+ assertEquals("msg", response.getBody().getMessage());
+ }
+
+
@Test
public void handle_AuthServiceConnectionException_succeeds() {
final AuthServiceConnectionException request = new AuthServiceConnectionException("msg");
@@ -942,42 +960,6 @@ public class ApiExceptionHandlerTest extends AbstractUnitTest {
}
- @Test
- public void handle_SidecarExportException_succeeds() {
- final SidecarExportException request = new SidecarExportException("msg");
-
- /* test */
- final ResponseEntity<ApiErrorDto> response = apiExceptionHandler.handle(request);
- assertNotNull(response);
- assertNotNull(request.getClass().getDeclaredAnnotation(ResponseStatus.class).code());
- final HttpStatus httpStatus = request.getClass().getDeclaredAnnotation(ResponseStatus.class).code();
- Assertions.assertNotEquals(httpStatus, HttpStatus.INTERNAL_SERVER_ERROR);
- assertEquals(httpStatus, response.getStatusCode());
- assertNotNull(response.getBody());
- assertNotNull(response.getBody().getCode());
- assertEquals(httpStatus, response.getBody().getStatus());
- assertEquals("msg", response.getBody().getMessage());
- }
-
-
- @Test
- public void handle_SidecarImportException_succeeds() {
- final SidecarImportException request = new SidecarImportException("msg");
-
- /* test */
- final ResponseEntity<ApiErrorDto> response = apiExceptionHandler.handle(request);
- assertNotNull(response);
- assertNotNull(request.getClass().getDeclaredAnnotation(ResponseStatus.class).code());
- final HttpStatus httpStatus = request.getClass().getDeclaredAnnotation(ResponseStatus.class).code();
- Assertions.assertNotEquals(httpStatus, HttpStatus.INTERNAL_SERVER_ERROR);
- assertEquals(httpStatus, response.getStatusCode());
- assertNotNull(response.getBody());
- assertNotNull(response.getBody().getCode());
- assertEquals(httpStatus, response.getBody().getStatus());
- assertEquals("msg", response.getBody().getMessage());
- }
-
-
@Test
public void handle_SortException_succeeds() {
final SortException request = new SortException("msg");
diff --git a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/StorageServiceIntegrationTest.java b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/StorageServiceIntegrationTest.java
index d3432ad78b3ec1587619ff4cdf7ca2a8427f887b..7e7ec4a775af3164623b34cc15b43ae6ed67fb71 100644
--- a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/StorageServiceIntegrationTest.java
+++ b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/StorageServiceIntegrationTest.java
@@ -1,19 +1,22 @@
package at.tuwien.service;
import at.tuwien.ExportResourceDto;
-import at.tuwien.api.database.AccessTypeDto;
-import at.tuwien.config.MariaDbConfig;
-import at.tuwien.config.MariaDbContainerConfig;
import at.tuwien.config.S3Config;
-import at.tuwien.exception.DatabaseMalformedException;
+import at.tuwien.exception.MalformedException;
import at.tuwien.exception.StorageNotFoundException;
import at.tuwien.exception.StorageUnavailableException;
import at.tuwien.test.AbstractUnitTest;
import lombok.extern.log4j.Log4j2;
-import org.junit.jupiter.api.BeforeAll;
+import org.apache.commons.io.FileUtils;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.test.context.DynamicPropertyRegistry;
@@ -27,9 +30,14 @@ import software.amazon.awssdk.services.s3.S3Client;
import software.amazon.awssdk.services.s3.model.CreateBucketRequest;
import software.amazon.awssdk.services.s3.model.PutObjectRequest;
-import java.io.File;
-import java.io.InputStream;
+import java.io.*;
+import java.nio.charset.Charset;
import java.sql.SQLException;
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Stream;
import static org.junit.jupiter.api.Assertions.*;
@@ -48,6 +56,16 @@ public class StorageServiceIntegrationTest extends AbstractUnitTest {
@Autowired
private S3Config s3Config;
+ @Autowired
+ private SparkSession sparkSession;
+
+ public static Stream<Arguments> loadDataset_arguments() {
+ return Stream.of(
+ Arguments.arguments("withHeader", true, 4968),
+ Arguments.arguments("withoutHeader", false, 4969)
+ );
+ }
+
@Container
private static final MinIOContainer minIOContainer = new MinIOContainer("minio/minio:RELEASE.2024-06-06T09-36-42Z");
@@ -165,4 +183,82 @@ public class StorageServiceIntegrationTest extends AbstractUnitTest {
});
}
+ @Test
+ public void transformDataset_succeeds() throws StorageUnavailableException, IOException {
+ final Dataset<Row> request = sparkSession.read()
+ .option("header", "true")
+ .csv("./src/test/resources/csv/keyboard.csv");
+ final List<String> fileLines = FileUtils.readLines(new File("./src/test/resources/csv/keyboard.csv"), Charset.defaultCharset());
+
+ /* test */
+ final ExportResourceDto response = storageService.transformDataset(request);
+ assertNotNull(response.getFilename());
+ assertEquals("dataset.csv", response.getFilename());
+ assertNotNull(response.getResource());
+ final List<String> lines = new BufferedReader(new InputStreamReader(response.getResource().getInputStream()))
+ .lines()
+ .parallel()
+ .toList();
+ final String[] columNames = lines.get(0).split(",");
+ assertEquals(10, columNames.length);
+ assertArrayEquals(new String[]{"Shift key time", "Esc key time", "Ctrl key time", "Alt key time", "User ID", "Test date", "Gender", "Right hand", "Birth year", "Computer skill level"}, columNames);
+ assertEquals(4969, lines.size());
+ for (int i = 0; i < 4969; i++) {
+ assertEquals(fileLines.get(i), lines.get(i));
+ }
+ }
+
+ @Test
+ public void transformDataset_empty_succeeds() throws StorageUnavailableException, IOException {
+ final Dataset<Row> request = sparkSession.emptyDataFrame();
+
+ /* test */
+ final ExportResourceDto response = storageService.transformDataset(request);
+ assertNotNull(response.getFilename());
+ assertEquals("dataset.csv", response.getFilename());
+ assertNotNull(response.getResource());
+ final List<String> lines = new BufferedReader(new InputStreamReader(response.getResource().getInputStream()))
+ .lines()
+ .parallel()
+ .toList();
+ assertEquals(1, lines.size());
+ assertEquals("", lines.get(0));
+ }
+
+ @ParameterizedTest
+ @MethodSource("loadDataset_arguments")
+ public void generic_loadDataset(String name, Boolean withHeader, Integer expectedRows)
+ throws StorageUnavailableException, StorageNotFoundException, IOException, MalformedException {
+ final List<String> fileLines = FileUtils.readLines(new File("./src/test/resources/csv/keyboard.csv"), Charset.defaultCharset());
+ final String[] requestHeaders = new String[]{"Shift key time", "Esc key time", "Ctrl key time", "Alt key time", "User ID", "Test date", "Gender", "Right hand", "Birth year", "Computer skill level"};
+
+ /* mock */
+ s3Client.putObject(PutObjectRequest.builder()
+ .key("s3key")
+ .bucket(s3Config.getS3Bucket())
+ .build(), RequestBody.fromFile(new File("src/test/resources/csv/keyboard.csv")));
+
+ /* test */
+ final Dataset<Row> response = storageService.loadDataset(Arrays.asList(requestHeaders), "s3key", withHeader);
+ final List<Map<String, String>> rows = datasetToRows(response);
+ assertEquals(expectedRows, rows.size());
+ for (int i = 0; i < expectedRows; i++) {
+ assertEquals(fileLines.get(i + (withHeader ? 1 : 0)), String.join(",", rows.get(i).values()));
+ }
+ }
+
+ public List<Map<String, String>> datasetToRows(Dataset<Row> data) {
+ return data.collectAsList()
+ .stream()
+ .map(row -> {
+ final Map<String, String> map = new LinkedHashMap<>();
+ for (int i = 0; i < data.columns().length; i++) {
+ final String value = row.getString(i);
+ map.put(data.columns()[i], row.get(i) != null ? value : "");
+ }
+ return map;
+ })
+ .toList();
+ }
+
}
diff --git a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/SubsetServiceIntegrationTest.java b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/SubsetServiceIntegrationTest.java
index b33a76506c15b77df3e0243754ca57b6dfcd9ed4..63f69734f3b02183919bf6b73951e40cc20fc56a 100644
--- a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/SubsetServiceIntegrationTest.java
+++ b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/SubsetServiceIntegrationTest.java
@@ -8,15 +8,13 @@ import at.tuwien.config.MariaDbConfig;
import at.tuwien.config.MariaDbContainerConfig;
import at.tuwien.config.S3Config;
import at.tuwien.exception.*;
-import at.tuwien.gateway.DataDatabaseSidecarGateway;
+import at.tuwien.gateway.AnalyseServiceGateway;
import at.tuwien.gateway.MetadataServiceGateway;
import at.tuwien.test.AbstractUnitTest;
-import at.tuwien.utils.FileUtils;
-import com.google.common.hash.Hashing;
import lombok.extern.log4j.Log4j2;
import org.apache.commons.lang3.RandomStringUtils;
-import org.apache.commons.lang3.RandomUtils;
-import org.junit.jupiter.api.BeforeAll;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
@@ -28,11 +26,8 @@ import org.testcontainers.containers.MariaDBContainer;
import org.testcontainers.junit.jupiter.Container;
import org.testcontainers.junit.jupiter.Testcontainers;
-import java.io.File;
import java.io.IOException;
-import java.io.InputStream;
import java.math.BigInteger;
-import java.nio.charset.Charset;
import java.sql.SQLException;
import java.time.Instant;
import java.util.List;
@@ -56,7 +51,7 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
private MetadataServiceGateway metadataServiceGateway;
@MockBean
- private DataDatabaseSidecarGateway dataDatabaseSidecarGateway;
+ private AnalyseServiceGateway dataDatabaseSidecarGateway;
@MockBean
private StorageService storageService;
@@ -208,8 +203,8 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
}
@Test
- public void findAll_succeeds() throws SQLException, QueryNotFoundException, NotAllowedException,
- RemoteUnavailableException, MetadataServiceException, DatabaseNotFoundException, InterruptedException {
+ public void findAll_succeeds() throws SQLException, QueryNotFoundException, RemoteUnavailableException,
+ MetadataServiceException, DatabaseNotFoundException, InterruptedException {
/* test */
final List<QueryDto> response = findAll_generic(null);
@@ -219,7 +214,7 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
}
@Test
- public void findAll_onlyPersisted_succeeds() throws SQLException, QueryNotFoundException, NotAllowedException,
+ public void findAll_onlyPersisted_succeeds() throws SQLException, QueryNotFoundException,
RemoteUnavailableException, MetadataServiceException, DatabaseNotFoundException, InterruptedException {
/* test */
@@ -229,7 +224,7 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
}
@Test
- public void findAll_onlyNonPersisted_succeeds() throws SQLException, QueryNotFoundException, NotAllowedException,
+ public void findAll_onlyNonPersisted_succeeds() throws SQLException, QueryNotFoundException,
RemoteUnavailableException, MetadataServiceException, DatabaseNotFoundException, InterruptedException {
/* test */
@@ -240,8 +235,7 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
@Test
public void findById_succeeds() throws SQLException, QueryNotFoundException, UserNotFoundException,
- NotAllowedException, RemoteUnavailableException, MetadataServiceException, DatabaseNotFoundException,
- InterruptedException {
+ RemoteUnavailableException, MetadataServiceException, DatabaseNotFoundException, InterruptedException {
/* test */
findById_generic(QUERY_1_ID);
@@ -258,8 +252,8 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
@Test
public void persist_succeeds() throws SQLException, QueryStorePersistException, QueryNotFoundException,
- UserNotFoundException, NotAllowedException, RemoteUnavailableException, MetadataServiceException,
- DatabaseNotFoundException, InterruptedException {
+ UserNotFoundException, RemoteUnavailableException, MetadataServiceException, DatabaseNotFoundException,
+ InterruptedException {
/* mock */
when(metadataServiceGateway.getUserById(QUERY_2_CREATED_BY))
@@ -274,8 +268,8 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
@Test
public void persist_unPersist_succeeds() throws SQLException, QueryStorePersistException, QueryNotFoundException,
- UserNotFoundException, NotAllowedException, RemoteUnavailableException, MetadataServiceException,
- DatabaseNotFoundException, InterruptedException {
+ UserNotFoundException, RemoteUnavailableException, MetadataServiceException, DatabaseNotFoundException,
+ InterruptedException {
/* mock */
when(metadataServiceGateway.getUserById(QUERY_1_CREATED_BY))
@@ -309,8 +303,8 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
@Test
public void export_succeeds() throws SQLException, StorageUnavailableException, QueryMalformedException,
- SidecarExportException, MetadataServiceException, RemoteUnavailableException, IOException,
- StorageNotFoundException, InterruptedException {
+ RemoteUnavailableException, IOException, StorageNotFoundException, InterruptedException,
+ AnalyseServiceException, ViewNotFoundException, MalformedException {
/* mock */
MariaDbConfig.dropQueryStore(DATABASE_1_PRIVILEGED_DTO);
@@ -319,7 +313,7 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
export_generic();
}
- protected void findById_generic(Long queryId) throws NotAllowedException, RemoteUnavailableException, SQLException,
+ protected void findById_generic(Long queryId) throws RemoteUnavailableException, SQLException,
UserNotFoundException, QueryNotFoundException, MetadataServiceException, DatabaseNotFoundException,
InterruptedException {
@@ -340,7 +334,7 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
}
protected List<QueryDto> findAll_generic(Boolean filterPersisted) throws SQLException, QueryNotFoundException,
- NotAllowedException, RemoteUnavailableException, MetadataServiceException, DatabaseNotFoundException,
+ RemoteUnavailableException, MetadataServiceException, DatabaseNotFoundException,
InterruptedException {
/* pre-condition */
@@ -385,9 +379,9 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
assertEquals(0, response.size());
}
- protected void export_generic() throws StorageUnavailableException, SQLException,
- QueryMalformedException, SidecarExportException, MetadataServiceException, RemoteUnavailableException,
- StorageNotFoundException, IOException, InterruptedException {
+ protected void export_generic() throws StorageUnavailableException, SQLException, RemoteUnavailableException,
+ QueryMalformedException, StorageNotFoundException, IOException, InterruptedException,
+ AnalyseServiceException, ViewNotFoundException, MalformedException {
final String filename = RandomStringUtils.randomAlphanumeric(40).toLowerCase() + ".tmp";
EXPORT_RESOURCE_DTO.setFilename(filename);
@@ -397,12 +391,12 @@ public class SubsetServiceIntegrationTest extends AbstractUnitTest {
/* mock */
doNothing()
.when(dataDatabaseSidecarGateway)
- .exportFile(anyString(), anyInt(), eq(filename));
- when(storageService.getResource(anyString()))
+ .exportTable(anyLong(), anyLong());
+ when(storageService.transformDataset(any(Dataset.class)))
.thenReturn(EXPORT_RESOURCE_DTO);
/* test */
- final ExportResourceDto response = queryService.export(DATABASE_1_PRIVILEGED_DTO, QUERY_1_DTO, Instant.now(), filename);
+ final ExportResourceDto response = queryService.export(DATABASE_1_PRIVILEGED_DTO, QUERY_1_DTO, Instant.now());
assertEquals(filename, response.getFilename());
assertNotNull(response.getResource().getInputStream());
}
diff --git a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/TableServiceIntegrationTest.java b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/TableServiceIntegrationTest.java
index 7413b20462e7ba1968e9df86e4a83514f3835605..e24af574cb60f08c561e845e31fc2457a0004126 100644
--- a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/TableServiceIntegrationTest.java
+++ b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/TableServiceIntegrationTest.java
@@ -18,7 +18,7 @@ import at.tuwien.api.database.table.internal.TableCreateDto;
import at.tuwien.config.MariaDbConfig;
import at.tuwien.config.MariaDbContainerConfig;
import at.tuwien.exception.*;
-import at.tuwien.gateway.DataDatabaseSidecarGateway;
+import at.tuwien.gateway.AnalyseServiceGateway;
import at.tuwien.gateway.MetadataServiceGateway;
import at.tuwien.test.AbstractUnitTest;
import lombok.extern.log4j.Log4j2;
@@ -59,7 +59,7 @@ public class TableServiceIntegrationTest extends AbstractUnitTest {
private MetadataServiceGateway metadataServiceGateway;
@MockBean
- private DataDatabaseSidecarGateway dataDatabaseSidecarGateway;
+ private AnalyseServiceGateway dataDatabaseSidecarGateway;
@MockBean
private StorageService storageService;
@@ -675,10 +675,10 @@ public class TableServiceIntegrationTest extends AbstractUnitTest {
}
@Test
- public void getData_succeeds() throws SQLException, TableMalformedException {
+ public void getPaginatedData_succeeds() throws SQLException, TableMalformedException {
/* test */
- final QueryResultDto response = tableService.getData(TABLE_1_PRIVILEGED_DTO, null, 0L, 10L);
+ final QueryResultDto response = tableService.getPaginatedData(TABLE_1_PRIVILEGED_DTO, null, 0L, 10L);
assertEquals(TABLE_1_ID, response.getId());
final List<Map<String, Integer>> headers = response.getHeaders();
assertEquals(5, headers.size());
@@ -706,14 +706,14 @@ public class TableServiceIntegrationTest extends AbstractUnitTest {
}
@Test
- public void getData_notFound_fails() throws SQLException {
+ public void getPaginatedData_notFound_fails() throws SQLException {
/* mock */
MariaDbConfig.createDatabase(CONTAINER_1_PRIVILEGED_DTO, DATABASE_2_INTERNALNAME);
/* test */
assertThrows(TableMalformedException.class, () -> {
- tableService.getData(TABLE_5_PRIVILEGED_DTO, null, 0L, 10L);
+ tableService.getPaginatedData(TABLE_5_PRIVILEGED_DTO, null, 0L, 10L);
});
}
@@ -742,8 +742,9 @@ public class TableServiceIntegrationTest extends AbstractUnitTest {
}
@Test
- public void exportDataset_succeeds() throws SQLException, QueryMalformedException, RemoteUnavailableException,
- StorageNotFoundException, StorageUnavailableException, SidecarExportException {
+ public void exportTable_succeeds() throws QueryMalformedException, RemoteUnavailableException,
+ StorageNotFoundException, StorageUnavailableException, AnalyseServiceException, TableNotFoundException,
+ MalformedException {
final ExportResourceDto mock = ExportResourceDto.builder()
.filename("weather_aus.csv")
.resource(new InputStreamResource(InputStream.nullInputStream()))
@@ -752,7 +753,7 @@ public class TableServiceIntegrationTest extends AbstractUnitTest {
/* mock */
doNothing()
.when(dataDatabaseSidecarGateway)
- .exportFile(anyString(), anyInt(), eq("weather_aus.csv"));
+ .exportTable(anyLong(), anyLong());
when(storageService.getResource("weather_aus.csv"))
.thenReturn(mock);
diff --git a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/ViewServiceIntegrationTest.java b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/ViewServiceIntegrationTest.java
index 5f20464eb9f252164c037a2155cd661d24d9019a..670c9c66a5364e1c38ed15759d9aa5c2b04331da 100644
--- a/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/ViewServiceIntegrationTest.java
+++ b/dbrepo-data-service/rest-service/src/test/java/at/tuwien/service/ViewServiceIntegrationTest.java
@@ -105,8 +105,7 @@ public class ViewServiceIntegrationTest extends AbstractUnitTest {
}
@Test
- public void getSchemas_succeeds() throws ViewMalformedException, SQLException, ViewNotFoundException,
- DatabaseMalformedException, ViewSchemaException {
+ public void getSchemas_succeeds() throws SQLException, ViewNotFoundException, DatabaseMalformedException {
/* test */
final List<ViewDto> response = viewService.getSchemas(DATABASE_1_PRIVILEGED_DTO);
diff --git a/dbrepo-data-service/services/pom.xml b/dbrepo-data-service/services/pom.xml
index ab57ee97af68a230a6ffb39673b8b9b6eb3a2ace..ad3fcee0e03334b2e7ada029888cb54d23703c05 100644
--- a/dbrepo-data-service/services/pom.xml
+++ b/dbrepo-data-service/services/pom.xml
@@ -14,11 +14,6 @@
<version>1.4.7</version>
<dependencies>
- <dependency>
- <groupId>software.amazon.awssdk</groupId>
- <artifactId>auth</artifactId>
- <version>2.25.23</version>
- </dependency>
<dependency>
<groupId>at.tuwien</groupId>
<artifactId>dbrepo-data-service-querystore</artifactId>
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/auth/AuthTokenFilter.java b/dbrepo-data-service/services/src/main/java/at/tuwien/auth/AuthTokenFilter.java
index 35e55797ebffb688f801bfcf64163d3a4a630049..3140f77cb585ef3ba02937b514ed3a1cd36631da 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/auth/AuthTokenFilter.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/auth/AuthTokenFilter.java
@@ -11,7 +11,7 @@ import jakarta.servlet.FilterChain;
import jakarta.servlet.ServletException;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
-import lombok.extern.slf4j.Slf4j;
+import lombok.extern.log4j.Log4j2;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
import org.springframework.security.core.authority.SimpleGrantedAuthority;
@@ -31,7 +31,7 @@ import java.util.Arrays;
import java.util.Base64;
import java.util.stream.Collectors;
-@Slf4j
+@Log4j2
public class AuthTokenFilter extends OncePerRequestFilter {
@Value("${dbrepo.jwt.public_key}")
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/config/GatewayConfig.java b/dbrepo-data-service/services/src/main/java/at/tuwien/config/GatewayConfig.java
index 6ebd6744576fd034db2faf569ffb764e43d9c7f8..4bdb9cb89f9d93d14c34bb318667882e299f0201 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/config/GatewayConfig.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/config/GatewayConfig.java
@@ -19,6 +19,9 @@ public class GatewayConfig {
@Value("${dbrepo.endpoints.metadataService}")
private String metadataEndpoint;
+ @Value("${dbrepo.endpoints.analyseService}")
+ private String analyseEndpoint;
+
@Value("${dbrepo.system.username}")
private String systemUsername;
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/config/JacksonConfig.java b/dbrepo-data-service/services/src/main/java/at/tuwien/config/JacksonConfig.java
index d6a30b52508a71c5ff9f3ad33b7e90f8846caa90..94acf727d54bcd24b9c0e83890066ec057d8e5e1 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/config/JacksonConfig.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/config/JacksonConfig.java
@@ -5,13 +5,13 @@ import com.fasterxml.jackson.databind.SerializationFeature;
import com.fasterxml.jackson.datatype.hibernate6.Hibernate6Module;
import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import lombok.extern.slf4j.Slf4j;
+import lombok.extern.log4j.Log4j2;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import java.util.TimeZone;
-@Slf4j
+@Log4j2
@Configuration
public class JacksonConfig {
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/config/QueryConfig.java b/dbrepo-data-service/services/src/main/java/at/tuwien/config/QueryConfig.java
index 55888bda1ad9789cfca1eb097fb2d7716bdb555a..b6363911705d4778111879d8cce3dc30a0475992 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/config/QueryConfig.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/config/QueryConfig.java
@@ -13,13 +13,4 @@ public class QueryConfig {
@Value("${dbrepo.sql.forbidden}")
private String[] forbiddenKeywords;
- @Value("${dbrepo.defaultDateFormatId}")
- private Long defaultDateFormatId;
-
- @Value("${dbrepo.defaultTimeFormatId}")
- private Long defaultTimeFormatId;
-
- @Value("${dbrepo.defaultTimestampFormatId}")
- private Long defaultTimestampFormatId;
-
}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/config/S3Config.java b/dbrepo-data-service/services/src/main/java/at/tuwien/config/S3Config.java
index 10630c717fe153f230703d045b6a2bda63706b6a..c5aeb968d52468416c336264232e016e136bfc1a 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/config/S3Config.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/config/S3Config.java
@@ -1,7 +1,7 @@
package at.tuwien.config;
import lombok.Getter;
-import lombok.extern.slf4j.Slf4j;
+import lombok.extern.log4j.Log4j2;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@@ -13,7 +13,7 @@ import software.amazon.awssdk.services.s3.S3Client;
import java.net.URI;
-@Slf4j
+@Log4j2
@Getter
@Configuration
public class S3Config {
@@ -30,9 +30,6 @@ public class S3Config {
@Value("${dbrepo.s3.bucket}")
private String s3Bucket;
- @Value("${dbrepo.s3.filePath}")
- private String s3FilePath;
-
@Bean
public S3Client s3client() {
final AwsCredentialsProvider credentialsProvider = StaticCredentialsProvider.create(
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/config/SparkConfig.java b/dbrepo-data-service/services/src/main/java/at/tuwien/config/SparkConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..2a5ea780badcfee93ceb62aa102543dfd8b1912e
--- /dev/null
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/config/SparkConfig.java
@@ -0,0 +1,71 @@
+package at.tuwien.config;
+
+import lombok.Getter;
+import lombok.extern.log4j.Log4j2;
+import org.apache.spark.SparkConf;
+import org.apache.spark.sql.SparkSession;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+@Log4j2
+@Getter
+@Configuration
+public class SparkConfig {
+
+ @Value("${dbrepo.endpoints.computeService}")
+ private String computeEndpoint;
+
+ @Value("${dbrepo.endpoints.storageService}")
+ private String s3Endpoint;
+
+ @Value("${dbrepo.s3.accessKeyId}")
+ private String s3AccessKeyId;
+
+ @Value("${dbrepo.s3.secretAccessKey}")
+ private String s3SecretAccessKey;
+
+ @Bean
+ public Map<String, String> sparkOptions() {
+ return new LinkedHashMap<>() {{
+ put("spark.driver.extraJavaOptions", "-Divy.cache.dir=/tmp -Divy.home=/tmp");
+ put("spark.ui.enabled", "false");
+ }};
+ }
+
+ @Bean
+ public Map<String, String> hadoopOptions() {
+ return new LinkedHashMap<>() {{
+ put("fs.s3a.path.style.access", "true");
+ put("fs.s3a.endpoint", s3Endpoint);
+ put("fs.s3a.access.key", s3AccessKeyId);
+ put("fs.s3a.secret.key", s3SecretAccessKey);
+ }};
+ }
+
+ @Bean
+ public SparkConf sparkConf() {
+ final SparkConf config = new SparkConf()
+ .setMaster(computeEndpoint)
+ .setAppName("dbrepo-data-service");
+ sparkOptions()
+ .forEach(config::set);
+ return config;
+ }
+
+ @Bean
+ public SparkSession sparkSession() {
+ final SparkSession spark = SparkSession.builder()
+ .config(sparkConf())
+ .getOrCreate();
+ hadoopOptions()
+ .forEach((key, value) -> spark.sparkContext()
+ .hadoopConfiguration()
+ .set(key, value));
+ return spark;
+ }
+
+}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/AnalyseServiceGateway.java b/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/AnalyseServiceGateway.java
new file mode 100644
index 0000000000000000000000000000000000000000..0257f0b2c78ad4c2fff130ff1a96ef2fd6906677
--- /dev/null
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/AnalyseServiceGateway.java
@@ -0,0 +1,31 @@
+package at.tuwien.gateway;
+
+import at.tuwien.exception.*;
+
+public interface AnalyseServiceGateway {
+
+ /**
+ * Imports a given dataset name into the given database.
+ *
+ * @param databaseId The database id.
+ * @param tableId The table id.
+ * @param filename The dataset name.
+ * @throws StorageNotFoundException The dataset name was not found in the storage service.
+ * @throws RemoteUnavailableException Connection to the sidecar could not be established.
+ * @throws AnalyseServiceException The analyse service failed to import the dataset.
+ */
+ void importDataset(Long databaseId, Long tableId, String filename) throws StorageNotFoundException,
+ RemoteUnavailableException, AnalyseServiceException;
+
+ /**
+ * Exports a given dataset name from the given database.
+ *
+ * @param databaseId The database id.
+ * @param tableId The table id.
+ * @throws StorageNotFoundException The dataset name was not found in the storage service.
+ * @throws RemoteUnavailableException Connection to the sidecar could not be established.
+ * @throws AnalyseServiceException The analyse service failed to export the dataset.
+ */
+ void exportTable(Long databaseId, Long tableId) throws StorageNotFoundException,
+ RemoteUnavailableException, AnalyseServiceException;
+}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/DataDatabaseSidecarGateway.java b/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/DataDatabaseSidecarGateway.java
deleted file mode 100644
index 23dc08a55d366f6560bcbaafbf6c79a94dfc2af3..0000000000000000000000000000000000000000
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/DataDatabaseSidecarGateway.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package at.tuwien.gateway;
-
-import at.tuwien.exception.*;
-
-public interface DataDatabaseSidecarGateway {
-
- /**
- * Imports a given dataset name into the given database.
- * @param hostname The database hostname.
- * @param port The database port.
- * @param filename The dataset name.
- * @throws StorageNotFoundException The dataset name was not found in the storage service.
- * @throws RemoteUnavailableException Connection to the sidecar could not be established.
- * @throws SidecarImportException The sidecar failed to import the dataset.
- */
- void importFile(String hostname, Integer port, String filename) throws StorageNotFoundException,
- RemoteUnavailableException, SidecarImportException;
-
- /**
- * Exports a given dataset name from the given database.
- * @param hostname The database hostname.
- * @param port The database port.
- * @param filename The dataset name.
- * @throws StorageNotFoundException The dataset name was not found in the storage service.
- * @throws RemoteUnavailableException Connection to the sidecar could not be established.
- * @throws SidecarExportException The sidecar failed to export the dataset.
- */
- void exportFile(String hostname, Integer port, String filename) throws StorageNotFoundException,
- SidecarExportException, RemoteUnavailableException;
-}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/AnalyseServiceGatewayImpl.java b/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/AnalyseServiceGatewayImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..2ab9d0a0188d1c351584610a2b70287750e6e3c8
--- /dev/null
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/AnalyseServiceGatewayImpl.java
@@ -0,0 +1,85 @@
+package at.tuwien.gateway.impl;
+
+import at.tuwien.config.GatewayConfig;
+import at.tuwien.exception.AnalyseServiceException;
+import at.tuwien.exception.RemoteUnavailableException;
+import at.tuwien.exception.StorageNotFoundException;
+import at.tuwien.gateway.AnalyseServiceGateway;
+import lombok.extern.log4j.Log4j2;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpMethod;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Service;
+import org.springframework.web.client.HttpClientErrorException;
+import org.springframework.web.client.HttpServerErrorException;
+import org.springframework.web.client.RestTemplate;
+
+@Log4j2
+@Service
+public class AnalyseServiceGatewayImpl implements AnalyseServiceGateway {
+
+ private final RestTemplate restTemplate;
+ private final GatewayConfig gatewayConfig;
+
+ @Autowired
+ public AnalyseServiceGatewayImpl(RestTemplate restTemplate, GatewayConfig gatewayConfig) {
+ this.restTemplate = restTemplate;
+ this.gatewayConfig = gatewayConfig;
+ }
+
+ @Override
+ public void importDataset(Long databaseId, Long tableId, String filename) throws StorageNotFoundException,
+ RemoteUnavailableException, AnalyseServiceException {
+ final ResponseEntity<Void> response;
+ final String url = new StringBuilder(gatewayConfig.getAnalyseEndpoint())
+ .append("/api/analyse/import?database_id=")
+ .append(databaseId)
+ .append("&table_id=")
+ .append(tableId)
+ .append("&filename=")
+ .append(filename)
+ .toString();
+ log.debug("import file into data database: {}", url);
+ try {
+ response = restTemplate.exchange(url, HttpMethod.POST, HttpEntity.EMPTY, Void.class);
+ } catch (HttpServerErrorException e) {
+ log.error("Failed to import dataset with filename: {}: {}", filename, e.getMessage());
+ throw new RemoteUnavailableException("Failed to import dataset: " + e.getMessage(), e);
+ } catch (HttpClientErrorException.BadRequest e) {
+ log.error("Failed to import dataset with filename: {}: not found: {}", filename, e.getMessage());
+ throw new StorageNotFoundException("Failed to import dataset: not found: " + e.getMessage(), e);
+ }
+ if (!response.getStatusCode().equals(HttpStatus.ACCEPTED)) {
+ log.error("Failed to import dataset with filename: {}: service responded unsuccessful: {}", filename, response.getStatusCode());
+ throw new AnalyseServiceException("Failed to import dataset: service responded unsuccessful: " + response.getStatusCode());
+ }
+ }
+
+ @Override
+ public void exportTable(Long databaseId, Long tableId) throws StorageNotFoundException, RemoteUnavailableException,
+ AnalyseServiceException {
+ final ResponseEntity<Void> response;
+ final String url = new StringBuilder(gatewayConfig.getAnalyseEndpoint())
+ .append("/api/analyse/export?database_id=")
+ .append(databaseId)
+ .append("&table_id=")
+ .append(tableId)
+ .toString();
+ log.debug("export file from data database: {}", url);
+ try {
+ response = restTemplate.exchange(url, HttpMethod.POST, HttpEntity.EMPTY, Void.class);
+ } catch (HttpServerErrorException e) {
+ log.error("Failed to export dataset: {}", e.getMessage());
+ throw new RemoteUnavailableException("Failed to export dataset: " + e.getMessage(), e);
+ } catch (HttpClientErrorException.BadRequest e) {
+ log.error("Failed to export dataset: not found: {}", e.getMessage());
+ throw new StorageNotFoundException("Failed to export dataset: not found: " + e.getMessage(), e);
+ }
+ if (!response.getStatusCode().equals(HttpStatus.ACCEPTED)) {
+ log.error("Failed to export dataset: service responded unsuccessful: {}", response.getStatusCode());
+ throw new AnalyseServiceException("Failed to export dataset: service responded unsuccessful: " + response.getStatusCode());
+ }
+ }
+}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/DataDatabaseSidecarGatewayImpl.java b/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/DataDatabaseSidecarGatewayImpl.java
deleted file mode 100644
index 841aace47460c99a09a5d1cff0a26cf03bed1ce9..0000000000000000000000000000000000000000
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/DataDatabaseSidecarGatewayImpl.java
+++ /dev/null
@@ -1,66 +0,0 @@
-package at.tuwien.gateway.impl;
-
-import at.tuwien.exception.*;
-import at.tuwien.gateway.DataDatabaseSidecarGateway;
-import lombok.extern.slf4j.Slf4j;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.*;
-import org.springframework.stereotype.Service;
-import org.springframework.web.client.HttpClientErrorException;
-import org.springframework.web.client.HttpServerErrorException;
-import org.springframework.web.client.ResourceAccessException;
-import org.springframework.web.client.RestTemplate;
-
-@Slf4j
-@Service
-public class DataDatabaseSidecarGatewayImpl implements DataDatabaseSidecarGateway {
-
- private final RestTemplate restTemplate;
-
- @Autowired
- public DataDatabaseSidecarGatewayImpl(RestTemplate restTemplate) {
- this.restTemplate = restTemplate;
- }
-
- @Override
- public void importFile(String hostname, Integer port, String filename) throws StorageNotFoundException,
- RemoteUnavailableException, SidecarImportException {
- final ResponseEntity<Void> response;
- final String url = "http://" + hostname + ":" + port + "/sidecar/import/" + filename;
- log.debug("import file into data database sidecar");
- try {
- response = restTemplate.exchange(url, HttpMethod.POST, new HttpEntity<>(null), Void.class);
- } catch (HttpServerErrorException e) {
- log.error("Failed to import dataset with filename: {}: {}", filename, e.getMessage());
- throw new RemoteUnavailableException("Failed to import dataset: " + e.getMessage(), e);
- } catch (HttpClientErrorException.BadRequest e) {
- log.error("Failed to import dataset with filename: {}: not found: {}", filename, e.getMessage());
- throw new StorageNotFoundException("Failed to import dataset: not found: " + e.getMessage(), e);
- }
- if (!response.getStatusCode().equals(HttpStatus.ACCEPTED)) {
- log.error("Failed to import dataset with filename: {}: service responded unsuccessful: {}", filename, response.getStatusCode());
- throw new SidecarImportException("Failed to import dataset: service responded unsuccessful: " + response.getStatusCode());
- }
- }
-
- @Override
- public void exportFile(String hostname, Integer port, String filename) throws StorageNotFoundException,
- RemoteUnavailableException, SidecarExportException {
- final ResponseEntity<Void> response;
- final String url = "http://" + hostname + ":" + port + "/sidecar/export/" + filename;
- log.debug("export file from data database sidecar: {}", url);
- try {
- response = restTemplate.exchange(url, HttpMethod.POST, new HttpEntity<>(null), Void.class);
- } catch (HttpServerErrorException e) {
- log.error("Failed to export dataset with filename: {}: {}", filename, e.getMessage());
- throw new RemoteUnavailableException("Failed to export dataset: " + e.getMessage(), e);
- } catch (HttpClientErrorException.BadRequest e) {
- log.error("Failed to export dataset with filename: {}: not found: {}", filename, e.getMessage());
- throw new StorageNotFoundException("Failed to export dataset: not found: " + e.getMessage(), e);
- }
- if (!response.getStatusCode().equals(HttpStatus.ACCEPTED)) {
- log.error("Failed to export dataset with filename: {}: service responded unsuccessful: {}", filename, response.getStatusCode());
- throw new SidecarExportException("Failed to export dataset: service responded unsuccessful: " + response.getStatusCode());
- }
- }
-}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/KeycloakGatewayImpl.java b/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/KeycloakGatewayImpl.java
index 1d73f6219a77e05f33166e23f75e16cafebc3e6f..fe1b2e36116052f41952d93afe0f7c65fa408514 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/KeycloakGatewayImpl.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/KeycloakGatewayImpl.java
@@ -61,10 +61,10 @@ public class KeycloakGatewayImpl implements KeycloakGateway {
throw new AuthServiceConnectionException("Failed to obtain user token: " + e.getMessage(), e);
} catch (HttpClientErrorException.BadRequest e) {
if (e.getResponseBodyAsByteArray() != null && e.getResponseBodyAsByteArray().length > 0) {
- final KeycloakErrorDto error = e.getResponseBodyAs(KeycloakErrorDto.class);
- if (error != null && error.getError().equals("invalid_grant")) {
- log.error("Failed to obtain user token: {}", error.getErrorDescription());
- throw new AccountNotSetupException("Failed to obtain user token: " + error.getErrorDescription(), e);
+ final String error = e.getResponseBodyAsString();
+ if (error != null && error.contains("invalid_grant")) {
+ log.error("Failed to obtain user token: {}", error);
+ throw new AccountNotSetupException("Failed to obtain user token: " + error, e);
}
}
log.error("Failed to obtain user token: bad request");
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/MetadataServiceGatewayImpl.java b/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/MetadataServiceGatewayImpl.java
index 11a90afde703a353e9f5b539394806d6356fe73c..3c03f022b311bbbe1d161888cec1a10d07bae55a 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/MetadataServiceGatewayImpl.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/gateway/impl/MetadataServiceGatewayImpl.java
@@ -87,8 +87,10 @@ public class MetadataServiceGatewayImpl implements MetadataServiceGateway {
public PrivilegedDatabaseDto getDatabaseById(Long id) throws DatabaseNotFoundException, RemoteUnavailableException,
MetadataServiceException {
final ResponseEntity<PrivilegedDatabaseDto> response;
+ final String url = "/api/database/" + id;
+ log.debug("find privileged database from url: {}", url);
try {
- response = restTemplate.exchange("/api/database/" + id, HttpMethod.GET, HttpEntity.EMPTY,
+ response = restTemplate.exchange(url, HttpMethod.GET, HttpEntity.EMPTY,
PrivilegedDatabaseDto.class);
} catch (ResourceAccessException | HttpServerErrorException e) {
log.error("Failed to find database with id {}: {}", id, e.getMessage());
@@ -123,8 +125,10 @@ public class MetadataServiceGatewayImpl implements MetadataServiceGateway {
public PrivilegedDatabaseDto getDatabaseByInternalName(String internalName) throws DatabaseNotFoundException,
RemoteUnavailableException, MetadataServiceException {
final ResponseEntity<PrivilegedDatabaseDto[]> response;
+ final String url = "/api/database/";
+ log.debug("find privileged database from url: {}", url);
try {
- response = restTemplate.exchange("/api/database/", HttpMethod.GET, HttpEntity.EMPTY, PrivilegedDatabaseDto[].class);
+ response = restTemplate.exchange(url, HttpMethod.GET, HttpEntity.EMPTY, PrivilegedDatabaseDto[].class);
} catch (ResourceAccessException | HttpServerErrorException e) {
log.error("Failed to find database with internal name {}: {}", internalName, e.getMessage());
throw new RemoteUnavailableException("Failed to find database: " + e.getMessage(), e);
@@ -152,8 +156,10 @@ public class MetadataServiceGatewayImpl implements MetadataServiceGateway {
public PrivilegedTableDto getTableById(Long databaseId, Long id) throws TableNotFoundException,
RemoteUnavailableException, MetadataServiceException {
final ResponseEntity<TableDto> response;
+ final String url = "/api/database/" + databaseId + "/table/" + id;
+ log.debug("find privileged table from url: {}", url);
try {
- response = restTemplate.exchange("/api/database/" + databaseId + "/table/" + id, HttpMethod.GET, HttpEntity.EMPTY, TableDto.class);
+ response = restTemplate.exchange(url, HttpMethod.GET, HttpEntity.EMPTY, TableDto.class);
} catch (ResourceAccessException | HttpServerErrorException e) {
log.error("Failed to find table with id {}: {}", id, e.getMessage());
throw new RemoteUnavailableException("Failed to find table: " + e.getMessage(), e);
@@ -165,7 +171,7 @@ public class MetadataServiceGatewayImpl implements MetadataServiceGateway {
log.error("Failed to find table with id {}: service responded unsuccessful: {}", id, response.getStatusCode());
throw new MetadataServiceException("Failed to find table: service responded unsuccessful: " + response.getStatusCode());
}
- final List<String> expectedHeaders = List.of("X-Type", "X-Host", "X-Port", "X-Username", "X-Password", "X-Database", "X-Sidecar-Host", "X-Sidecar-Port");
+ final List<String> expectedHeaders = List.of("X-Type", "X-Host", "X-Port", "X-Username", "X-Password", "X-Database", "X-Table");
if (!response.getHeaders().keySet().containsAll(expectedHeaders)) {
log.error("Failed to find all privileged table headers");
log.debug("expected headers: {}", expectedHeaders);
@@ -183,8 +189,7 @@ public class MetadataServiceGatewayImpl implements MetadataServiceGateway {
table.getDatabase().getContainer().setUsername(response.getHeaders().get("X-Username").get(0));
table.getDatabase().getContainer().setPassword(response.getHeaders().get("X-Password").get(0));
table.getDatabase().setInternalName(response.getHeaders().get("X-Database").get(0));
- table.getDatabase().getContainer().setSidecarHost(response.getHeaders().get("X-Sidecar-Host").get(0));
- table.getDatabase().getContainer().setSidecarPort(Integer.parseInt(response.getHeaders().get("X-Sidecar-Port").get(0)));
+ table.setInternalName(response.getHeaders().get("X-Table").get(0));
log.debug("found privileged database username={}", table.getDatabase().getContainer().getUsername());
return table;
}
@@ -193,8 +198,10 @@ public class MetadataServiceGatewayImpl implements MetadataServiceGateway {
public PrivilegedViewDto getViewById(Long databaseId, Long id) throws RemoteUnavailableException,
ViewNotFoundException, MetadataServiceException {
final ResponseEntity<ViewDto> response;
+ final String url = "/api/database/" + databaseId + "/view/" + id;
+ log.debug("find privileged view from url: {}", url);
try {
- response = restTemplate.exchange("/api/database/" + databaseId + "/view/" + id, HttpMethod.GET, HttpEntity.EMPTY, ViewDto.class);
+ response = restTemplate.exchange(url, HttpMethod.GET, HttpEntity.EMPTY, ViewDto.class);
} catch (ResourceAccessException | HttpServerErrorException e) {
log.error("Failed to find view with id {}: {}", id, e.getMessage());
throw new RemoteUnavailableException("Failed to find view: " + e.getMessage(), e);
@@ -206,7 +213,7 @@ public class MetadataServiceGatewayImpl implements MetadataServiceGateway {
log.error("Failed to find view with id {}: service responded unsuccessful: {}", id, response.getStatusCode());
throw new MetadataServiceException("Failed to find view: service responded unsuccessful: " + response.getStatusCode());
}
- final List<String> expectedHeaders = List.of("X-Type", "X-Host", "X-Port", "X-Username", "X-Password", "X-Database");
+ final List<String> expectedHeaders = List.of("X-Type", "X-Host", "X-Port", "X-Username", "X-Password", "X-Database", "X-View");
if (!response.getHeaders().keySet().containsAll(expectedHeaders)) {
log.error("Failed to find all privileged view headers");
log.debug("expected headers: {}", expectedHeaders);
@@ -217,14 +224,15 @@ public class MetadataServiceGatewayImpl implements MetadataServiceGateway {
log.error("Failed to find view with id {}: body is empty", id);
throw new MetadataServiceException("Failed to find view with id " + id + ": body is empty");
}
- final PrivilegedViewDto table = metadataMapper.viewDtoToPrivilegedViewDto(response.getBody());
- table.getDatabase().getContainer().getImage().setJdbcMethod(response.getHeaders().get("X-Type").get(0));
- table.getDatabase().getContainer().setHost(response.getHeaders().get("X-Host").get(0));
- table.getDatabase().getContainer().setPort(Integer.parseInt(response.getHeaders().get("X-Port").get(0)));
- table.getDatabase().getContainer().setUsername(response.getHeaders().get("X-Username").get(0));
- table.getDatabase().getContainer().setPassword(response.getHeaders().get("X-Password").get(0));
- table.getDatabase().setInternalName(response.getHeaders().get("X-Database").get(0));
- return table;
+ final PrivilegedViewDto view = metadataMapper.viewDtoToPrivilegedViewDto(response.getBody());
+ view.getDatabase().getContainer().getImage().setJdbcMethod(response.getHeaders().get("X-Type").get(0));
+ view.getDatabase().getContainer().setHost(response.getHeaders().get("X-Host").get(0));
+ view.getDatabase().getContainer().setPort(Integer.parseInt(response.getHeaders().get("X-Port").get(0)));
+ view.getDatabase().getContainer().setUsername(response.getHeaders().get("X-Username").get(0));
+ view.getDatabase().getContainer().setPassword(response.getHeaders().get("X-Password").get(0));
+ view.getDatabase().setInternalName(response.getHeaders().get("X-Database").get(0));
+ view.setInternalName(response.getHeaders().get("X-View").get(0));
+ return view;
}
@Override
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/mapper/DataMapper.java b/dbrepo-data-service/services/src/main/java/at/tuwien/mapper/DataMapper.java
index 62b529976d029c0612e3849f032e0a1093270562..ff3ab95a44ed4f2e70284a28d7048275f29265ca 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/mapper/DataMapper.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/mapper/DataMapper.java
@@ -1,5 +1,6 @@
package at.tuwien.mapper;
+import at.tuwien.ExportResourceDto;
import at.tuwien.api.database.DatabaseDto;
import at.tuwien.api.database.ViewColumnDto;
import at.tuwien.api.database.ViewDto;
@@ -24,23 +25,26 @@ import at.tuwien.api.user.UserDto;
import at.tuwien.config.QueryConfig;
import at.tuwien.exception.QueryNotFoundException;
import at.tuwien.exception.TableNotFoundException;
-import com.github.dockerjava.zerodep.shaded.org.apache.commons.codec.binary.Hex;
import net.sf.jsqlparser.JSQLParserException;
import net.sf.jsqlparser.parser.CCJSqlParserManager;
import net.sf.jsqlparser.schema.Column;
import net.sf.jsqlparser.schema.Table;
import net.sf.jsqlparser.statement.select.*;
+import org.apache.hadoop.shaded.com.google.common.hash.Hashing;
+import org.apache.hadoop.shaded.org.apache.commons.codec.binary.Hex;
+import org.apache.hadoop.shaded.org.apache.commons.io.FileUtils;
+import org.apache.spark.Partition;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SaveMode;
import org.jetbrains.annotations.NotNull;
import org.mapstruct.Mapper;
import org.mapstruct.Mapping;
import org.mapstruct.Mappings;
-import org.testcontainers.shaded.com.google.common.hash.Hashing;
-import org.testcontainers.shaded.org.apache.commons.io.FileUtils;
+import org.springframework.core.io.InputStreamResource;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringReader;
+import java.io.*;
import java.math.BigInteger;
import java.nio.charset.StandardCharsets;
import java.sql.*;
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/mapper/MariaDbMapper.java b/dbrepo-data-service/services/src/main/java/at/tuwien/mapper/MariaDbMapper.java
index bfca2d923fc550a6420f1140a9a9fe6d3aae7e59..8a70a18a771b6853ba7e7c8ec3b07b70911c97cf 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/mapper/MariaDbMapper.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/mapper/MariaDbMapper.java
@@ -16,8 +16,10 @@ import org.mapstruct.Named;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
-import java.sql.Date;
-import java.sql.*;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Types;
import java.text.Normalizer;
import java.time.Instant;
import java.time.ZoneId;
@@ -491,23 +493,14 @@ public interface MariaDbMapper {
return "DROP TABLE `" + tableName + "`;";
}
- default String tableOrViewToRawExportQuery(String databaseName, String tableOrView, List<ColumnDto> columns,
- Instant timestamp, String filePath) {
- final StringBuilder statement = new StringBuilder("SELECT ");
- int[] idx = new int[]{0};
- columns.forEach(column -> {
- statement.append(idx[0] != 0 ? "," : "")
- .append("'")
- .append(column.getInternalName())
- .append("'");
- idx[0]++;
- });
- statement.append(" UNION ALL SELECT ");
+ default String tableOrViewToRawExportQuery(String databaseName, String tableOrView, List<String> columns,
+ Instant timestamp) {
+ final StringBuilder statement = new StringBuilder("(SELECT ");
int[] jdx = new int[]{0};
columns.forEach(column -> {
statement.append(jdx[0] != 0 ? "," : "")
.append("`")
- .append(column.getInternalName())
+ .append(column)
.append("`");
jdx[0]++;
});
@@ -522,10 +515,7 @@ public interface MariaDbMapper {
.append(mariaDbFormatter.format(timestamp))
.append("'");
}
- statement.append(" INTO OUTFILE '")
- .append(filePath)
- .append("' CHARACTER SET utf8 FIELDS TERMINATED BY ',' OPTIONALLY ENCLOSED BY '\"';");
- statement.append(";");
+ statement.append(") as tbl_alias");
log.debug("mapped table/view export query: {}", statement);
return statement.toString();
}
@@ -540,50 +530,38 @@ public interface MariaDbMapper {
return statement.toString();
}
- default String subsetToRawExportQuery(String viewName, Instant timestamp, String filePath) {
- final StringBuilder statement = new StringBuilder("SELECT * FROM `")
+ default String subsetToRawExportQuery(String viewName, Instant timestamp) {
+ final StringBuilder statement = new StringBuilder("(SELECT * FROM `")
.append(viewName)
.append("` FOR SYSTEM_TIME AS OF TIMESTAMP'")
.append(mariaDbFormatter.format(timestamp))
- .append("'")
- .append(" INTO OUTFILE '")
- .append(filePath)
- .append("' CHARACTER SET utf8 FIELDS TERMINATED BY ',' OPTIONALLY ENCLOSED BY '\"';");
+ .append("') as tbl");
log.debug("mapped export query: {}", statement);
return statement.toString();
}
- default String datasetToRawInsertQuery(String databaseName, PrivilegedTableDto table, ImportDto data) {
- final StringBuilder statement = new StringBuilder("LOAD DATA INFILE '")
- .append(data.getLocation())
- .append("' REPLACE INTO TABLE `")
- .append(databaseName)
+ default String temporaryTableToRawMergeQuery(String tmp, String table, List<String> columns) {
+ final StringBuilder statement = new StringBuilder("INSERT INTO `")
+ .append(table)
+ .append("` SELECT * FROM `")
+ .append(tmp)
+ .append("` ON DUPLICATE KEY UPDATE ");
+ final int[] idx = new int[]{0};
+ columns.forEach(column -> statement.append(idx[0]++ > 0 ? ", " : "")
+ .append("`")
+ .append(table)
.append("`.`")
- .append(table.getInternalName())
- .append("` CHARACTER SET utf8 FIELDS TERMINATED BY '")
- .append(data.getSeparator())
- .append("'");
- if (data.getQuote() != null) {
- statement.append(" OPTIONALLY ENCLOSED BY '")
- .append(data.getQuote())
- .append("'");
- }
- if (data.getLineTermination() != null) {
- statement.append(" LINES TERMINATED BY '")
- .append(data.getLineTermination())
- .append("'");
- }
- if (data.getSkipLines() != null) {
- statement.append(" IGNORE ")
- .append(data.getSkipLines())
- .append(" LINES");
- }
+ .append(column)
+ .append("` = `")
+ .append(tmp)
+ .append("`.`")
+ .append(column)
+ .append("`"));
statement.append(";");
log.trace("mapped insert statement: {}", statement);
return statement.toString();
}
-
default String tupleToRawDeleteQuery(PrivilegedTableDto table, TupleDeleteDto data) throws TableMalformedException {
log.trace("table csv to delete query, table.id={}, data.keys={}", table.getId(), data.getKeys());
if (table.getColumns().isEmpty()) {
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/service/StorageService.java b/dbrepo-data-service/services/src/main/java/at/tuwien/service/StorageService.java
index c1f546ce4462d60eb08b1f34683efd7f05dca0f9..b346a187a59756a934ed47c1168472c485252ffc 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/service/StorageService.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/service/StorageService.java
@@ -1,10 +1,16 @@
package at.tuwien.service;
import at.tuwien.ExportResourceDto;
+import at.tuwien.api.database.table.columns.ColumnDto;
+import at.tuwien.exception.MalformedException;
import at.tuwien.exception.StorageNotFoundException;
import at.tuwien.exception.StorageUnavailableException;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
+import java.io.IOException;
import java.io.InputStream;
+import java.util.List;
public interface StorageService {
@@ -59,6 +65,27 @@ public interface StorageService {
* @throws StorageUnavailableException The object failed to be loaded from the Storage Service.
* @throws StorageNotFoundException The key was not found in the Storage Service.
*/
- ExportResourceDto getResource(String bucket, String key) throws StorageUnavailableException, StorageNotFoundException;
+ ExportResourceDto getResource(String bucket, String key) throws StorageUnavailableException,
+ StorageNotFoundException;
+ /**
+ * Transforms the given dataset into a downloadable dataset.
+ *
+ * @param data The dataset.
+ * @throws StorageUnavailableException The object failed to be loaded from the Storage Service.
+ */
+ ExportResourceDto transformDataset(Dataset<Row> data) throws StorageUnavailableException;
+
+ /**
+ * Loads the dataset from the Storage Service with given key for a list of provided column names.
+ *
+ * @param columns The list of column names.
+ * @param key The key.
+ * @param withHeader If true, the first line contains the column names, otherwise it contains data only.
+ * @return The dataset.
+ * @throws StorageNotFoundException The key was not found in the Storage Service.
+ * @throws StorageUnavailableException The object failed to be loaded from the Storage Service.
+ */
+ Dataset<Row> loadDataset(List<String> columns, String key, Boolean withHeader) throws StorageNotFoundException,
+ StorageUnavailableException, MalformedException;
}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/service/SubsetService.java b/dbrepo-data-service/services/src/main/java/at/tuwien/service/SubsetService.java
index 56250a2917f2083d53bbeec51f6e3b1dae0e0cd1..938da8820c829113193be4e5fd95d2e20e0c0029 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/service/SubsetService.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/service/SubsetService.java
@@ -7,6 +7,9 @@ import at.tuwien.api.database.internal.PrivilegedDatabaseDto;
import at.tuwien.api.database.query.QueryDto;
import at.tuwien.api.database.query.QueryResultDto;
import at.tuwien.exception.*;
+import jakarta.validation.constraints.NotNull;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
import java.sql.SQLException;
import java.time.Instant;
@@ -99,23 +102,21 @@ public interface SubsetService {
QueryNotFoundException, RemoteUnavailableException, DatabaseNotFoundException, MetadataServiceException;
/**
- * Exports a subset by re-executing the query in a given database with given timestamp to a given filename.
+ * Exports a subset by re-executing the query in a given database with given timestamp to a given s3key.
*
* @param database The database.
* @param query The query.
* @param timestamp The timestamp.
- * @param filename The filename.
* @return The exported subset.
* @throws SQLException The connection to the database could not be established.
* @throws QueryMalformedException The mapped export query produced a database error.
- * @throws SidecarExportException The sidecar of the given database failed to communicate.
* @throws StorageNotFoundException The exported subset was not found from the key provided by the sidecar in the Storage Service.
* @throws StorageUnavailableException The communication to the Storage Service failed.
* @throws RemoteUnavailableException The privileged database information could not be found in the Metadata Service.
*/
- ExportResourceDto export(PrivilegedDatabaseDto database, QueryDto query, Instant timestamp, String filename)
- throws SQLException, QueryMalformedException, SidecarExportException, StorageNotFoundException,
- StorageUnavailableException, RemoteUnavailableException;
+ ExportResourceDto export(PrivilegedDatabaseDto database, QueryDto query, Instant timestamp) throws SQLException,
+ QueryMalformedException, StorageNotFoundException, StorageUnavailableException, RemoteUnavailableException,
+ ViewNotFoundException, MalformedException;
/**
* Executes a subset query without saving it.
@@ -180,4 +181,7 @@ public interface SubsetService {
* @throws QueryStoreGCException The query store failed to delete stale queries.
*/
void deleteStaleQueries(PrivilegedDatabaseDto database) throws SQLException, QueryStoreGCException;
+
+ Dataset<Row> getData(@NotNull PrivilegedDatabaseDto database, String viewName, Instant timestamp) throws ViewNotFoundException,
+ QueryMalformedException;
}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/service/TableService.java b/dbrepo-data-service/services/src/main/java/at/tuwien/service/TableService.java
index c93186f451c5b41d2c55924ce685d578b40bfbde..c70d1b703f714f9201aa8ffb972763aca1c72691 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/service/TableService.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/service/TableService.java
@@ -8,6 +8,9 @@ import at.tuwien.api.database.table.*;
import at.tuwien.api.database.table.internal.PrivilegedTableDto;
import at.tuwien.api.database.table.internal.TableCreateDto;
import at.tuwien.exception.*;
+import jakarta.validation.constraints.NotNull;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
import java.sql.SQLException;
import java.time.Instant;
@@ -17,10 +20,11 @@ public interface TableService {
/**
* Get table schemas from the information_schema in the data database.
+ *
* @param database The data database privileged object.
* @return List of tables, if successful.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
- * @throws TableNotFoundException The table could not be inspected in the data database.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @throws TableNotFoundException The table could not be inspected in the data database.
* @throws DatabaseMalformedException The database inspection was unsuccessful, likely due to a bug in the mapping.
*/
List<TableDto> getSchemas(PrivilegedDatabaseDto database) throws SQLException, TableNotFoundException,
@@ -28,22 +32,24 @@ public interface TableService {
/**
* Generate table statistic for a given table. Only numerical columns are calculated.
+ *
* @param table The table.
* @return The table statistic, if successful.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
* @throws TableMalformedException The table statistic generation was unsuccessful, likely due to a bug in the mapping.
- * @throws TableNotFoundException The table could not be inspected in the data database.
+ * @throws TableNotFoundException The table could not be inspected in the data database.
*/
TableStatisticDto getStatistics(PrivilegedTableDto table) throws SQLException, TableMalformedException,
TableNotFoundException;
/**
* Finds a table with given data database and table name.
- * @param database The data database.
+ *
+ * @param database The data database.
* @param tableName The table name.
* @return The table, if successful.
- * @throws TableNotFoundException The table could not be inspected in the data database.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @throws TableNotFoundException The table could not be inspected in the data database.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
* @throws QueryMalformedException The inspection query is malformed.
*/
TableDto find(PrivilegedDatabaseDto database, String tableName) throws TableNotFoundException, SQLException,
@@ -51,12 +57,13 @@ public interface TableService {
/**
* Creates a table in given data database with table definition.
+ *
* @param database The data database privileged object.
- * @param data The table definition.
+ * @param data The table definition.
* @return The created table, if successful.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
* @throws TableNotFoundException The table could not be inspected in the data database.
- * @throws TableExistsException The table name already exists in the information_schema.
+ * @throws TableExistsException The table name already exists in the information_schema.
* @throws TableNotFoundException The table could not be inspected in the data database.
*/
TableDto createTable(PrivilegedDatabaseDto database, TableCreateDto data) throws SQLException,
@@ -64,64 +71,71 @@ public interface TableService {
/**
* Drops a table in given table object.
+ *
* @param table The table object.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
* @throws QueryMalformedException The drop table query is malformed.
*/
void delete(PrivilegedTableDto table) throws SQLException, QueryMalformedException;
/**
* Obtains data from a table with given table object at timestamp, loaded as page number and length size.
- * @param table The table object.
+ *
+ * @param table The table object.
* @param timestamp The timestamp.
- * @param page The page number.
- * @param size The page size/length.
+ * @param page The page number.
+ * @param size The page size/length.
* @return The data.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
* @throws TableMalformedException The table schema is malformed, likely due to a bug in the application.
*/
- QueryResultDto getData(PrivilegedTableDto table, Instant timestamp, Long page, Long size) throws SQLException,
- TableMalformedException;
+ QueryResultDto getPaginatedData(PrivilegedTableDto table, Instant timestamp, Long page, Long size)
+ throws SQLException, TableMalformedException;
/**
* Obtains the table history for a given table object.
+ *
* @param table The table object.
- * @param size The maximum size.
+ * @param size The maximum size.
* @return The table history.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
* @throws TableNotFoundException The table could not be found in the data database.
*/
List<TableHistoryDto> history(PrivilegedTableDto table, Long size) throws SQLException, TableNotFoundException;
/**
* Obtains the table data tuples count at time.
- * @param table The table object.
+ *
+ * @param table The table object.
* @param timestamp The timestamp.
* @return Number of tuples, if successful.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
* @throws QueryMalformedException The count query is malformed, likely due to a bug in the application.
*/
Long getCount(PrivilegedTableDto table, Instant timestamp) throws SQLException,
QueryMalformedException;
/**
- * Imports a dataset by metadata into the sidecar of the target database by given table.
+ * Imports a dataset into the database by given table. By default, an <code>upsert</code> operation is performed
+ * that updates duplicate values (identified by their primary key) or inserts values if no duplicate is detected.
+ *
* @param table The table.
- * @param data The dataset metadata.
- * @throws SidecarImportException The sidecar of the target database failed to import the dataset.
- * @throws StorageNotFoundException The storage service was not able to find the dataset for import.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
- * @throws QueryMalformedException The import query is malformed, likely due to a bug in the application.
- * @throws RemoteUnavailableException Failed to establish connection to the sidecar.
+ * @param data The dataset metadata.
+ * @throws MalformedException The dataset is malformed.
+ * @throws StorageUnavailableException Failed to establish a connection with the Storage Service.
+ * @throws StorageNotFoundException The storage service was not able to find the dataset for import.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @throws QueryMalformedException The import query is malformed, likely due to a bug in the application.
*/
- void importDataset(PrivilegedTableDto table, ImportDto data) throws SidecarImportException,
- StorageNotFoundException, SQLException, QueryMalformedException, RemoteUnavailableException;
+ void importDataset(PrivilegedTableDto table, ImportDto data) throws MalformedException, StorageNotFoundException,
+ StorageUnavailableException, SQLException, QueryMalformedException;
/**
* Imports a dataset by metadata into the sidecar of the target database by given table.
+ *
* @param table The table.
- * @param data The dataset metadata.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @param data The dataset metadata.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
* @throws TableMalformedException The tuple is malformed and does not fit the table schema.
* @throws QueryMalformedException The delete query is malformed, likely due to a bug in the application.
*/
@@ -130,41 +144,52 @@ public interface TableService {
/**
* Creates a tuple in a table.
+ *
* @param table The table.
- * @param data The tuple.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
- * @throws QueryMalformedException The create query is malformed, likely due to a bug in the application.
- * @throws TableMalformedException The tuple is malformed and does not fit the table schema.
+ * @param data The tuple.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @throws QueryMalformedException The create query is malformed, likely due to a bug in the application.
+ * @throws TableMalformedException The tuple is malformed and does not fit the table schema.
* @throws StorageUnavailableException Failed to establish a connection with the Storage Service.
- * @throws StorageNotFoundException The storage service was not able to find the dataset for import.
+ * @throws StorageNotFoundException The storage service was not able to find the dataset for import.
*/
void createTuple(PrivilegedTableDto table, TupleDto data) throws SQLException,
QueryMalformedException, TableMalformedException, StorageUnavailableException, StorageNotFoundException;
/**
* Updates a tuple in a table.
+ *
* @param table The table.
- * @param data The tuple.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
+ * @param data The tuple.
+ * @throws SQLException Failed to parse SQL query, contains invalid syntax.
* @throws QueryMalformedException The update query is malformed, likely due to a bug in the application.
- * @throws TableMalformedException The tuple is malformed and does not fit the table schema.
+ * @throws TableMalformedException The tuple is malformed and does not fit the table schema.
*/
void updateTuple(PrivilegedTableDto table, TupleUpdateDto data) throws SQLException,
QueryMalformedException, TableMalformedException;
/**
* Exports a table at given system-versioning time.
- * @param table The table.
+ *
+ * @param table The table.
* @param timestamp The system-versioning time.
* @return The exported resource.
- * @throws SQLException Failed to parse SQL query, contains invalid syntax.
- * @throws SidecarExportException The sidecar of the target database failed to export the dataset.
- * @throws StorageNotFoundException The storage service was not able to find the dataset for export.
+ * @throws TableNotFoundException The table was not found in the data database.
+ * @throws QueryMalformedException The export query is malformed, likely due to a bug in the application.
* @throws StorageUnavailableException Failed to establish a connection with the Storage Service.
+ */
+ ExportResourceDto exportDataset(PrivilegedTableDto table, Instant timestamp) throws TableNotFoundException,
+ QueryMalformedException, StorageUnavailableException, MalformedException;
+
+ /**
+ * Get data from a given table at timestamp.
+ *
+ * @param table The table.
+ * @param timestamp The timestamp.
+ * @return The data.
+ * @throws TableNotFoundException The table was not found in the data database.
* @throws QueryMalformedException The export query is malformed, likely due to a bug in the application.
- * @throws RemoteUnavailableException Failed to establish connection to the sidecar.
*/
- ExportResourceDto exportDataset(PrivilegedTableDto table, Instant timestamp)
- throws SQLException, SidecarExportException, StorageNotFoundException, StorageUnavailableException,
- QueryMalformedException, RemoteUnavailableException;
+ Dataset<Row> getData(@NotNull PrivilegedTableDto table, Instant timestamp) throws TableNotFoundException,
+ QueryMalformedException;
}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/service/ViewService.java b/dbrepo-data-service/services/src/main/java/at/tuwien/service/ViewService.java
index 9151f868de9f271f9c73cc8f7da4fccf168b668d..26c04e401bb15945f1b438bd5af10beeccd470f7 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/service/ViewService.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/service/ViewService.java
@@ -6,7 +6,11 @@ import at.tuwien.api.database.ViewDto;
import at.tuwien.api.database.internal.PrivilegedDatabaseDto;
import at.tuwien.api.database.internal.PrivilegedViewDto;
import at.tuwien.api.database.query.QueryResultDto;
+import at.tuwien.api.database.table.internal.PrivilegedTableDto;
import at.tuwien.exception.*;
+import jakarta.validation.constraints.NotNull;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
import java.sql.SQLException;
import java.time.Instant;
@@ -16,11 +20,12 @@ public interface ViewService {
/**
* Gets the metadata schema for a given database.
+ *
* @param database The database.
* @return The list of view metadata.
- * @throws SQLException The connection to the data database was unsuccessful.
+ * @throws SQLException The connection to the data database was unsuccessful.
* @throws DatabaseMalformedException The columns that are referenced in the views are unknown to the Metadata Database. Call {@link TableService#getSchemas(PrivilegedDatabaseDto)} beforehand.
- * @throws ViewNotFoundException The view with given name was not found.
+ * @throws ViewNotFoundException The view with given name was not found.
*/
List<ViewDto> getSchemas(PrivilegedDatabaseDto database) throws SQLException, DatabaseMalformedException,
ViewNotFoundException;
@@ -52,33 +57,44 @@ public interface ViewService {
/**
* Deletes a view.
+ *
* @param view The view.
- * @throws SQLException The connection to the data database was unsuccessful.
+ * @throws SQLException The connection to the data database was unsuccessful.
* @throws ViewMalformedException The query is malformed and was rejected by the data database.
*/
void delete(PrivilegedViewDto view) throws SQLException, ViewMalformedException;
/**
* Counts tuples in a view at system-versioned timestamp.
- * @param view The view.
+ *
+ * @param view The view.
* @param timestamp The system-versioned timestamp.
* @return The number of tuples.
- * @throws SQLException The connection to the data database was unsuccessful.
+ * @throws SQLException The connection to the data database was unsuccessful.
* @throws QueryMalformedException The query is malformed and was rejected by the data database.
*/
Long count(PrivilegedViewDto view, Instant timestamp) throws SQLException, QueryMalformedException;
/**
* Exports view data into a dataset.
+ *
* @param view The view.
* @return The dataset.
- * @throws SQLException The connection to the data database was unsuccessful.
- * @throws QueryMalformedException The query is malformed and was rejected by the data database.
- * @throws SidecarExportException The sidecar of the target database failed to export the dataset.
- * @throws RemoteUnavailableException Failed to establish connection to the sidecar.
- * @throws StorageNotFoundException The storage service was not able to find the dataset for export.
+ * @throws QueryMalformedException The query is malformed and was rejected by the data database.
* @throws StorageUnavailableException Failed to establish a connection with the Storage Service.
+ * @throws ViewNotFoundException The view with given name was not found.
+ */
+ ExportResourceDto exportDataset(PrivilegedViewDto view) throws QueryMalformedException,
+ StorageUnavailableException, ViewNotFoundException, MalformedException;
+
+ /**
+ * Get data from a given view.
+ *
+ * @param view The view.
+ * @return The data.
+ * @throws ViewNotFoundException The view with given name was not found.
+ * @throws QueryMalformedException The query is malformed and was rejected by the data database.
*/
- ExportResourceDto exportDataset(PrivilegedViewDto view) throws SQLException, QueryMalformedException,
- SidecarExportException, RemoteUnavailableException, StorageNotFoundException, StorageUnavailableException;
+ Dataset<Row> getData(@NotNull PrivilegedViewDto view) throws ViewNotFoundException,
+ QueryMalformedException;
}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/HibernateConnector.java b/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/HibernateConnector.java
index 22bb599c6090cfe75f152d7f0a2a8f26e03c71b4..e2d085ae98c60b2ee0cc0b852fc9954b542d3413 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/HibernateConnector.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/HibernateConnector.java
@@ -3,15 +3,30 @@ package at.tuwien.service.impl;
import at.tuwien.api.container.internal.PrivilegedContainerDto;
import at.tuwien.api.database.internal.PrivilegedDatabaseDto;
import at.tuwien.api.database.table.internal.PrivilegedTableDto;
+import at.tuwien.config.S3Config;
+import at.tuwien.exception.QueryMalformedException;
+import at.tuwien.exception.TableNotFoundException;
import com.mchange.v2.c3p0.ComboPooledDataSource;
+import jakarta.validation.constraints.NotNull;
import lombok.extern.log4j.Log4j2;
+import org.apache.spark.SparkConf;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SparkSession;
+import org.apache.spark.sql.catalyst.ExtendedAnalysisException;
+import org.springframework.context.annotation.Bean;
import org.springframework.stereotype.Service;
+import java.time.Instant;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+
@Log4j2
@Service
public abstract class HibernateConnector {
- public static ComboPooledDataSource getPrivilegedDataSource(PrivilegedContainerDto container, String databaseName) {
+ public ComboPooledDataSource getPrivilegedDataSource(PrivilegedContainerDto container, String databaseName) {
final long start = System.currentTimeMillis();
final ComboPooledDataSource dataSource = new ComboPooledDataSource();
dataSource.setJdbcUrl(url(container, databaseName));
@@ -26,11 +41,35 @@ public abstract class HibernateConnector {
return dataSource;
}
- public static ComboPooledDataSource getPrivilegedDataSource(PrivilegedDatabaseDto database) {
+ public ComboPooledDataSource getPrivilegedDataSource(PrivilegedDatabaseDto database) {
return getPrivilegedDataSource(database.getContainer(), database.getInternalName());
}
- private static String url(PrivilegedContainerDto container, String databaseName) {
+ public Map<String, String> getPrivilegedDatabaseOptions(PrivilegedTableDto table) {
+ return new HashMap<>() {{
+ put("url", url(table.getDatabase().getContainer(), table.getDatabase().getInternalName()));
+ put("dbtable", table.getInternalName());
+ put("user", table.getDatabase().getContainer().getUsername());
+ put("password", table.getDatabase().getContainer().getPassword());
+ }};
+ }
+
+ public String getHibernateUrl(PrivilegedContainerDto container, String databaseName) {
+ final StringBuilder sb = new StringBuilder(url(container, databaseName))
+ .append("?currentSchema=")
+ .append(databaseName);
+ log.trace("mapped container to hibernate url: {}", sb.toString());
+ return sb.toString();
+ }
+
+ public String getSparkUrl(PrivilegedContainerDto container, String databaseName) {
+ final StringBuilder sb = new StringBuilder(url(container, databaseName))
+ .append("?sessionVariables=sql_mode='ANSI_QUOTES'");
+ log.trace("mapped container to spark url: {}", sb.toString());
+ return sb.toString();
+ }
+
+ private String url(PrivilegedContainerDto container, String databaseName) {
final StringBuilder stringBuilder = new StringBuilder("jdbc:")
.append(container.getImage().getJdbcMethod())
.append("://")
@@ -39,8 +78,6 @@ public abstract class HibernateConnector {
.append(container.getPort());
if (databaseName != null) {
stringBuilder.append("/")
- .append(databaseName)
- .append("?currentSchema=")
.append(databaseName);
}
return stringBuilder.toString();
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/StorageServiceS3Impl.java b/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/StorageServiceS3Impl.java
index 9a748d96dcfadcaa5c3b669cfb290b6803100db0..a3bcaed57885ac25588f72a69ab0979ffab144a7 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/StorageServiceS3Impl.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/StorageServiceS3Impl.java
@@ -2,18 +2,29 @@ package at.tuwien.service.impl;
import at.tuwien.ExportResourceDto;
import at.tuwien.config.S3Config;
+import at.tuwien.exception.MalformedException;
import at.tuwien.exception.StorageNotFoundException;
import at.tuwien.exception.StorageUnavailableException;
import at.tuwien.service.StorageService;
import lombok.extern.log4j.Log4j2;
+import org.apache.spark.sql.*;
+import org.apache.spark.sql.types.StructField;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.io.InputStreamResource;
import org.springframework.stereotype.Service;
import software.amazon.awssdk.services.s3.S3Client;
-import software.amazon.awssdk.services.s3.model.*;
+import software.amazon.awssdk.services.s3.model.GetObjectRequest;
+import software.amazon.awssdk.services.s3.model.NoSuchKeyException;
+import software.amazon.awssdk.services.s3.model.S3Exception;
-import java.io.IOException;
-import java.io.InputStream;
+import java.io.*;
+import java.nio.charset.Charset;
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import static scala.collection.JavaConverters.asScalaIteratorConverter;
@Log4j2
@Service
@@ -21,11 +32,13 @@ public class StorageServiceS3Impl implements StorageService {
private final S3Config s3Config;
private final S3Client s3Client;
+ private final SparkSession sparkSession;
@Autowired
- public StorageServiceS3Impl(S3Config s3Config, S3Client s3Client) {
+ public StorageServiceS3Impl(S3Config s3Config, S3Client s3Client, SparkSession sparkSession) {
this.s3Config = s3Config;
this.s3Client = s3Client;
+ this.sparkSession = sparkSession;
}
@Override
@@ -76,4 +89,87 @@ public class StorageServiceS3Impl implements StorageService {
.filename(key)
.build();
}
+
+ @Override
+ public ExportResourceDto transformDataset(Dataset<Row> dataset) throws StorageUnavailableException {
+ final List<Map<String, String>> inMemory = dataset.collectAsList()
+ .stream()
+ .map(row -> {
+ final Map<String, String> map = new LinkedHashMap<>();
+ for (int i = 0; i < dataset.columns().length; i++) {
+ map.put(dataset.columns()[i], row.get(i) != null ? String.valueOf(row.get(i)) : "");
+ }
+ return map;
+ })
+ .toList();
+ log.debug("collected dataset with {} row(s)", inMemory.size());
+ try {
+ final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+ try (Writer w = new OutputStreamWriter(byteArrayOutputStream, Charset.defaultCharset())) {
+ /* header */
+ w.write(String.join(",", Arrays.stream(dataset.schema().fields()).map(StructField::name).toList()));
+ w.write("\n");
+ /* rows */
+ for (Map<String, String> map : inMemory) {
+ w.write(String.join(",", map.values().stream().map(v -> {
+ if (v.contains(",")) {
+ v = "\"" + v + "\"";
+ }
+ return v;
+ })
+ .toList()));
+ w.write("\n");
+ }
+ w.flush();
+ }
+ return ExportResourceDto.builder()
+ .filename("dataset.csv")
+ .resource(new InputStreamResource(new ByteArrayInputStream(byteArrayOutputStream.toByteArray())))
+ .build();
+ } catch (IOException e) {
+ log.error("Failed to transform in-memory dataset: {}", e.getMessage());
+ throw new StorageUnavailableException("Failed to transform in-memory dataset: " + e.getMessage(), e);
+ }
+ }
+
+ @Override
+ public Dataset<Row> loadDataset(List<String> columns, String key, Boolean withHeader) throws StorageNotFoundException,
+ StorageUnavailableException, MalformedException {
+ final String path = "s3a://" + s3Config.getS3Bucket() + "/" + key;
+ log.debug("read dataset from s3 path: {} using header: {}", path, withHeader);
+ Dataset<Row> dataset;
+ try {
+ log.trace("spark session conf: {}", sparkSession.conf().getAllAsJava());
+ dataset = sparkSession.read()
+ .option("header", withHeader)
+ .csv(path);
+ } catch (Exception e) {
+ if (e instanceof AnalysisException) {
+ final AnalysisException exception = (AnalysisException) e;
+ if (exception.getSimpleMessage().contains("PATH_NOT_FOUND")) {
+ log.error("Failed to find dataset {} in storage service: {}", key, e.getMessage());
+ throw new StorageNotFoundException("Failed to find dataset in storage service: " + e.getMessage());
+ }
+ }
+ log.error("Failed to connect to storage service: {}", e.getMessage());
+ throw new StorageUnavailableException("Failed to connect to storage service: " + e.getMessage());
+ }
+ if (!withHeader) {
+ log.debug("no header provided: use table column names: {}", columns);
+ dataset = dataset.toDF(asScalaIteratorConverter(columns.iterator())
+ .asScala()
+ .toSeq());
+ }
+ /* determine header order in dataset */
+ if (dataset.schema().fields().length != columns.size()) {
+ log.error("Failed to transform dataset: field length {} and header length arrays differ {}", dataset.schema().fields().length, columns.size());
+ throw new MalformedException("Failed to transform dataset: field length and order length arrays differ");
+ }
+ /* reorder */
+ final List<Column> columnOrder = columns.stream()
+ .map(Column::new)
+ .toList();
+ log.trace("ordered columns: {}", columnOrder);
+ return dataset.select(columnOrder.toArray(new Column[0]));
+ }
}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/SubsetServiceMariaDbImpl.java b/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/SubsetServiceMariaDbImpl.java
index 8bfdc0089a9d31ce9faa8af40be151eb1044532f..55f513f339e05b79c32f904be182e0d8a5863a5c 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/SubsetServiceMariaDbImpl.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/SubsetServiceMariaDbImpl.java
@@ -3,6 +3,7 @@ package at.tuwien.service.impl;
import at.tuwien.ExportResourceDto;
import at.tuwien.api.SortTypeDto;
import at.tuwien.api.container.internal.PrivilegedContainerDto;
+import at.tuwien.api.database.ViewColumnDto;
import at.tuwien.api.database.internal.PrivilegedDatabaseDto;
import at.tuwien.api.database.query.QueryDto;
import at.tuwien.api.database.query.QueryResultDto;
@@ -10,29 +11,35 @@ import at.tuwien.api.database.table.columns.ColumnDto;
import at.tuwien.api.identifier.IdentifierDto;
import at.tuwien.api.identifier.IdentifierTypeDto;
import at.tuwien.api.user.UserDto;
-import at.tuwien.config.S3Config;
+import at.tuwien.config.SparkConfig;
import at.tuwien.exception.*;
-import at.tuwien.gateway.DataDatabaseSidecarGateway;
import at.tuwien.gateway.MetadataServiceGateway;
import at.tuwien.mapper.DataMapper;
import at.tuwien.mapper.MariaDbMapper;
import at.tuwien.mapper.MetadataMapper;
+import at.tuwien.service.SchemaService;
import at.tuwien.service.StorageService;
import at.tuwien.service.SubsetService;
import com.mchange.v2.c3p0.ComboPooledDataSource;
import io.micrometer.core.instrument.Counter;
+import jakarta.validation.constraints.NotNull;
import lombok.extern.log4j.Log4j2;
import net.sf.jsqlparser.JSQLParserException;
import org.apache.commons.lang3.RandomUtils;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SparkSession;
+import org.apache.spark.sql.catalyst.ExtendedAnalysisException;
+import org.sparkproject.guava.hash.Hashing;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
-import org.testcontainers.shaded.com.google.common.hash.Hashing;
import java.nio.charset.Charset;
import java.sql.*;
import java.time.Instant;
import java.util.LinkedList;
import java.util.List;
+import java.util.Properties;
import java.util.UUID;
@Log4j2
@@ -40,27 +47,27 @@ import java.util.UUID;
public class SubsetServiceMariaDbImpl extends HibernateConnector implements SubsetService {
private final Counter httpDataAccessCounter;
- private final S3Config s3Config;
private final DataMapper dataMapper;
+ private final SparkSession sparkSession;
private final MariaDbMapper mariaDbMapper;
+ private final SchemaService schemaService;
private final MetadataMapper metadataMapper;
private final StorageService storageService;
private final MetadataServiceGateway metadataServiceGateway;
- private final DataDatabaseSidecarGateway dataDatabaseSidecarGateway;
@Autowired
- public SubsetServiceMariaDbImpl(Counter httpDataAccessCounter, S3Config s3Config, DataMapper dataMapper,
- MariaDbMapper mariaDbMapper, MetadataMapper metadataMapper,
- StorageService storageService, MetadataServiceGateway metadataServiceGateway,
- DataDatabaseSidecarGateway dataDatabaseSidecarGateway) {
+ public SubsetServiceMariaDbImpl(Counter httpDataAccessCounter, DataMapper dataMapper, SparkSession sparkSession,
+ MariaDbMapper mariaDbMapper, SchemaService schemaService,
+ MetadataMapper metadataMapper, StorageService storageService,
+ MetadataServiceGateway metadataServiceGateway) {
this.httpDataAccessCounter = httpDataAccessCounter;
- this.s3Config = s3Config;
this.dataMapper = dataMapper;
+ this.sparkSession = sparkSession;
this.mariaDbMapper = mariaDbMapper;
+ this.schemaService = schemaService;
this.metadataMapper = metadataMapper;
this.storageService = storageService;
this.metadataServiceGateway = metadataServiceGateway;
- this.dataDatabaseSidecarGateway = dataDatabaseSidecarGateway;
}
@Override
@@ -171,14 +178,14 @@ public class SubsetServiceMariaDbImpl extends HibernateConnector implements Subs
}
@Override
- public ExportResourceDto export(PrivilegedDatabaseDto database, QueryDto query, Instant timestamp, String filename)
- throws SQLException, QueryMalformedException, SidecarExportException, StorageNotFoundException,
- StorageUnavailableException, RemoteUnavailableException {
- final String filePath = s3Config.getS3FilePath() + "/" + filename;
+ public ExportResourceDto export(PrivilegedDatabaseDto database, QueryDto query, Instant timestamp)
+ throws SQLException, QueryMalformedException, StorageNotFoundException, StorageUnavailableException,
+ RemoteUnavailableException, ViewNotFoundException, MalformedException {
final String viewName = "ex_" + Hashing.sha512()
.hashString(new String(RandomUtils.nextBytes(256), Charset.defaultCharset()), Charset.defaultCharset())
.toString()
.substring(0, 60);
+ final ExportResourceDto export;
final ComboPooledDataSource dataSource = getPrivilegedDataSource(database);
final Connection connection = dataSource.getConnection();
try {
@@ -186,15 +193,23 @@ public class SubsetServiceMariaDbImpl extends HibernateConnector implements Subs
long start = System.currentTimeMillis();
connection.prepareStatement(mariaDbMapper.subsetToRawTemporaryViewQuery(viewName, query.getQuery()))
.executeUpdate();
- log.debug("executed statement in {} ms", System.currentTimeMillis() - start);
+ log.debug("executed create view statement in {} ms", System.currentTimeMillis() - start);
start = System.currentTimeMillis();
- connection.prepareStatement(mariaDbMapper.subsetToRawExportQuery(viewName, timestamp, filePath))
- .executeUpdate();
- log.debug("executed statement in {} ms", System.currentTimeMillis() - start);
+ final List<String> columns = schemaService.inspectView(database, viewName)
+ .getColumns()
+ .stream()
+ .map(ViewColumnDto::getInternalName)
+ .toList();
+ log.debug("executed inspect view columns statement in {} ms", System.currentTimeMillis() - start);
+ start = System.currentTimeMillis();
+ final Dataset<Row> dataset = getData(database, viewName, timestamp)
+ .selectExpr(columns.toArray(new String[0]));
+ export = storageService.transformDataset(dataset);
+ log.debug("executed extract statement in {} ms", System.currentTimeMillis() - start);
start = System.currentTimeMillis();
connection.prepareStatement(mariaDbMapper.dropViewRawQuery(viewName))
.executeUpdate();
- log.debug("executed statement in {} ms", System.currentTimeMillis() - start);
+ log.debug("executed drop view statement in {} ms", System.currentTimeMillis() - start);
connection.commit();
} catch (SQLException e) {
connection.rollback();
@@ -203,9 +218,8 @@ public class SubsetServiceMariaDbImpl extends HibernateConnector implements Subs
} finally {
dataSource.close();
}
- dataDatabaseSidecarGateway.exportFile(database.getContainer().getSidecarHost(), database.getContainer().getSidecarPort(), filename);
httpDataAccessCounter.increment();
- return storageService.getResource(filename);
+ return export;
}
public QueryResultDto executeNonPersistent(PrivilegedDatabaseDto database, String statement,
@@ -350,4 +364,27 @@ public class SubsetServiceMariaDbImpl extends HibernateConnector implements Subs
}
}
+ @Override
+ public Dataset<Row> getData(@NotNull PrivilegedDatabaseDto database, String viewName, Instant timestamp)
+ throws ViewNotFoundException, QueryMalformedException {
+ log.debug("get data from view: {}", viewName);
+ try {
+ final Properties properties = new Properties();
+ properties.setProperty("user", database.getContainer().getUsername());
+ properties.setProperty("password", database.getContainer().getPassword());
+ return sparkSession.read()
+ .jdbc(getSparkUrl(database.getContainer(), database.getInternalName()),
+ mariaDbMapper.subsetToRawExportQuery(viewName, timestamp), properties);
+ } catch (Exception e) {
+ if (e instanceof ExtendedAnalysisException exception) {
+ if (exception.getSimpleMessage().contains("TABLE_OR_VIEW_NOT_FOUND")) {
+ log.error("Failed to find temporary view {}: {}", viewName, exception.getSimpleMessage());
+ throw new ViewNotFoundException("Failed to find temporary view " + viewName + ": " + exception.getSimpleMessage()) /* remove throwable on purpose, clutters the output */;
+ }
+ }
+ log.error("Failed to find get data from view: {}", e.getMessage());
+ throw new QueryMalformedException("Failed to find get data from view: " + e.getMessage(), e);
+ }
+ }
+
}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/TableServiceMariaDbImpl.java b/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/TableServiceMariaDbImpl.java
index 3ab02bbb016ff28469301a699f2ebd65bfd76f6c..531897706bc8971095127813694eb28825b12935 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/TableServiceMariaDbImpl.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/TableServiceMariaDbImpl.java
@@ -11,8 +11,8 @@ import at.tuwien.api.database.table.columns.ColumnTypeDto;
import at.tuwien.api.database.table.internal.PrivilegedTableDto;
import at.tuwien.api.database.table.internal.TableCreateDto;
import at.tuwien.config.S3Config;
+import at.tuwien.config.SparkConfig;
import at.tuwien.exception.*;
-import at.tuwien.gateway.DataDatabaseSidecarGateway;
import at.tuwien.mapper.DataMapper;
import at.tuwien.mapper.MariaDbMapper;
import at.tuwien.service.SchemaService;
@@ -21,12 +21,16 @@ import at.tuwien.service.TableService;
import at.tuwien.utils.MariaDbUtil;
import com.mchange.v2.c3p0.ComboPooledDataSource;
import io.micrometer.core.instrument.Counter;
+import jakarta.validation.constraints.NotNull;
import lombok.extern.log4j.Log4j2;
import org.apache.commons.lang3.RandomStringUtils;
+import org.apache.spark.sql.*;
+import org.apache.spark.sql.catalyst.ExtendedAnalysisException;
+import org.apache.spark.sql.types.StructField;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
-import java.io.File;
+import java.io.ByteArrayInputStream;
import java.sql.*;
import java.time.Instant;
import java.util.*;
@@ -36,25 +40,22 @@ import java.util.*;
public class TableServiceMariaDbImpl extends HibernateConnector implements TableService {
private final Counter httpDataAccessCounter;
- private final S3Config s3Config;
private final DataMapper dataMapper;
+ private final SparkSession sparkSession;
private final MariaDbMapper mariaDbMapper;
private final SchemaService schemaService;
private final StorageService storageService;
- private final DataDatabaseSidecarGateway dataDatabaseSidecarGateway;
@Autowired
- public TableServiceMariaDbImpl(Counter httpDataAccessCounter, S3Config s3Config, DataMapper dataMapper,
+ public TableServiceMariaDbImpl(Counter httpDataAccessCounter, DataMapper dataMapper, SparkSession sparkSession,
MariaDbMapper mariaDbMapper, SchemaService schemaService,
- StorageService storageService,
- DataDatabaseSidecarGateway dataDatabaseSidecarGateway) {
+ StorageService storageService) {
this.httpDataAccessCounter = httpDataAccessCounter;
- this.s3Config = s3Config;
this.dataMapper = dataMapper;
+ this.sparkSession = sparkSession;
this.mariaDbMapper = mariaDbMapper;
this.schemaService = schemaService;
this.storageService = storageService;
- this.dataDatabaseSidecarGateway = dataDatabaseSidecarGateway;
}
@Override
@@ -190,7 +191,7 @@ public class TableServiceMariaDbImpl extends HibernateConnector implements Table
}
@Override
- public QueryResultDto getData(PrivilegedTableDto table, Instant timestamp, Long page, Long size) throws SQLException,
+ public QueryResultDto getPaginatedData(PrivilegedTableDto table, Instant timestamp, Long page, Long size) throws SQLException,
TableMalformedException {
final ComboPooledDataSource dataSource = getPrivilegedDataSource(table.getDatabase());
final Connection connection = dataSource.getConnection();
@@ -273,20 +274,43 @@ public class TableServiceMariaDbImpl extends HibernateConnector implements Table
}
@Override
- public void importDataset(PrivilegedTableDto table, ImportDto data) throws StorageNotFoundException,
- SQLException, QueryMalformedException, RemoteUnavailableException, SidecarImportException {
- /* import .csv from blob storage to sidecar */
- dataDatabaseSidecarGateway.importFile(table.getDatabase().getContainer().getSidecarHost(), table.getDatabase().getContainer().getSidecarPort(), data.getLocation());
+ public void importDataset(PrivilegedTableDto table, ImportDto data) throws MalformedException,
+ StorageNotFoundException, StorageUnavailableException, SQLException, QueryMalformedException {
+ final List<String> columns = table.getColumns()
+ .stream()
+ .map(ColumnDto::getInternalName)
+ .toList();
+ final Dataset<Row> dataset = storageService.loadDataset(columns, data.getLocation(), data.getHeader());
+ final Properties properties = new Properties();
+ properties.setProperty("user", table.getDatabase().getContainer().getUsername());
+ properties.setProperty("password", table.getDatabase().getContainer().getPassword());
+ final String temporaryTable = table.getInternalName() + "_tmp";
+ try {
+ log.trace("import dataset to temporary table: {}", temporaryTable);
+ dataset.write()
+ .mode(SaveMode.Overwrite)
+ .option("header", data.getHeader())
+ .option("inferSchema", "true")
+ .jdbc(getSparkUrl(table.getDatabase().getContainer(), table.getDatabase().getInternalName()),
+ temporaryTable, properties);
+ } catch (Exception e) {
+ if (e instanceof AnalysisException exception) {
+ final String message = exception.getSimpleMessage()
+ .replaceAll(" Some\\(.*", "");
+ log.error("Failed to write dataset: schema malformed: {}", message);
+ throw new MalformedException("Failed to write dataset: schema malformed: " + message) /* remove throwable on purpose, clutters the output */;
+ }
+ log.error("Failed to write dataset: {}", e.getMessage());
+ throw new MalformedException("Failed to write dataset: " + e.getMessage()) /* remove throwable on purpose, clutters the output */;
+ }
/* import .csv from sidecar to database */
final ComboPooledDataSource dataSource = getPrivilegedDataSource(table.getDatabase());
final Connection connection = dataSource.getConnection();
try {
/* import tuple */
- data.setLocation(s3Config.getS3FilePath() + File.separator + data.getLocation());
- final long start = System.currentTimeMillis();
- connection.prepareStatement(mariaDbMapper.datasetToRawInsertQuery(table.getDatabase().getInternalName(), table, data))
+ connection.prepareStatement(mariaDbMapper.temporaryTableToRawMergeQuery(temporaryTable,
+ table.getInternalName(), table.getColumns().stream().map(c -> c.getInternalName()).toList()))
.execute();
- log.debug("executed statement in {} ms", System.currentTimeMillis() - start);
connection.commit();
} catch (SQLException e) {
connection.rollback();
@@ -420,31 +444,35 @@ public class TableServiceMariaDbImpl extends HibernateConnector implements Table
}
@Override
- public ExportResourceDto exportDataset(PrivilegedTableDto table, Instant timestamp) throws SQLException,
- StorageNotFoundException, StorageUnavailableException, QueryMalformedException, RemoteUnavailableException,
- SidecarExportException {
- final String fileName = RandomStringUtils.randomAlphabetic(40) + ".csv";
- final String filePath = s3Config.getS3FilePath() + "/" + fileName;
- final ComboPooledDataSource dataSource = getPrivilegedDataSource(table.getDatabase());
- final Connection connection = dataSource.getConnection();
+ public ExportResourceDto exportDataset(PrivilegedTableDto table, Instant timestamp) throws TableNotFoundException,
+ QueryMalformedException, StorageUnavailableException, MalformedException {
+ final Dataset<Row> dataset = getData(table, timestamp);
+ httpDataAccessCounter.increment();
+ return storageService.transformDataset(dataset);
+ }
+
+ @Override
+ public Dataset<Row> getData(@NotNull PrivilegedTableDto table, Instant timestamp) throws TableNotFoundException,
+ QueryMalformedException {
try {
- /* export to data database sidecar */
- final long start = System.currentTimeMillis();
- connection.prepareStatement(mariaDbMapper.tableOrViewToRawExportQuery(table.getDatabase().getInternalName(),
- table.getInternalName(), table.getColumns(), timestamp, filePath))
- .executeUpdate();
- log.debug("executed statement in {} ms", System.currentTimeMillis() - start);
- connection.commit();
- } catch (SQLException e) {
- connection.rollback();
- log.error("Failed to execute query: {}", e.getMessage());
- throw new QueryMalformedException("Failed to execute query: " + e.getMessage(), e);
- } finally {
- dataSource.close();
+ final Properties properties = new Properties();
+ properties.setProperty("user", table.getDatabase().getContainer().getUsername());
+ properties.setProperty("password", table.getDatabase().getContainer().getPassword());
+ return sparkSession.read()
+ .jdbc(getSparkUrl(table.getDatabase().getContainer(), table.getDatabase().getInternalName()),
+ mariaDbMapper.tableOrViewToRawExportQuery(table.getDatabase().getInternalName(),
+ table.getInternalName(), table.getColumns().stream()
+ .map(ColumnDto::getInternalName).toList(), timestamp), properties);
+ } catch (Exception e) {
+ if (e instanceof ExtendedAnalysisException exception) {
+ if (exception.getSimpleMessage().contains("TABLE_OR_VIEW_NOT_FOUND")) {
+ log.error("Failed to find table {}: {}", table.getInternalName(), exception.getSimpleMessage());
+ throw new TableNotFoundException("Failed to find table " + table.getInternalName() + ": " + exception.getSimpleMessage()) /* remove throwable on purpose, clutters the output */;
+ }
+ }
+ log.error("Failed to export dataset: {}", e.getMessage());
+ throw new QueryMalformedException("Failed to export dataset: " + e.getMessage(), e);
}
- dataDatabaseSidecarGateway.exportFile(table.getDatabase().getContainer().getSidecarHost(), table.getDatabase().getContainer().getSidecarPort(), fileName);
- httpDataAccessCounter.increment();
- return storageService.getResource(fileName);
}
}
diff --git a/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/ViewServiceMariaDbImpl.java b/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/ViewServiceMariaDbImpl.java
index 366cfa5faf5fabe34210b880d3fdca3659267a3a..77e065bc9354970252ae1318e1cb1c56770ac899 100644
--- a/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/ViewServiceMariaDbImpl.java
+++ b/dbrepo-data-service/services/src/main/java/at/tuwien/service/impl/ViewServiceMariaDbImpl.java
@@ -1,16 +1,18 @@
package at.tuwien.service.impl;
import at.tuwien.ExportResourceDto;
+import at.tuwien.api.database.ViewColumnDto;
import at.tuwien.api.database.ViewCreateDto;
import at.tuwien.api.database.ViewDto;
import at.tuwien.api.database.internal.PrivilegedDatabaseDto;
import at.tuwien.api.database.internal.PrivilegedViewDto;
import at.tuwien.api.database.query.QueryResultDto;
import at.tuwien.api.database.table.columns.ColumnDto;
+import at.tuwien.api.database.table.internal.PrivilegedTableDto;
import at.tuwien.config.QueryConfig;
import at.tuwien.config.S3Config;
+import at.tuwien.config.SparkConfig;
import at.tuwien.exception.*;
-import at.tuwien.gateway.DataDatabaseSidecarGateway;
import at.tuwien.mapper.DataMapper;
import at.tuwien.mapper.MariaDbMapper;
import at.tuwien.mapper.MetadataMapper;
@@ -20,8 +22,13 @@ import at.tuwien.service.ViewService;
import com.google.common.hash.Hashing;
import com.mchange.v2.c3p0.ComboPooledDataSource;
import io.micrometer.core.instrument.Counter;
+import jakarta.validation.constraints.NotNull;
import lombok.extern.log4j.Log4j2;
import org.apache.commons.lang3.RandomStringUtils;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SparkSession;
+import org.apache.spark.sql.catalyst.ExtendedAnalysisException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
@@ -34,35 +41,34 @@ import java.sql.SQLException;
import java.time.Instant;
import java.util.LinkedList;
import java.util.List;
+import java.util.Properties;
@Log4j2
@Service
public class ViewServiceMariaDbImpl extends HibernateConnector implements ViewService {
private final Counter httpDataAccessCounter;
- private final S3Config s3Config;
private final DataMapper dataMapper;
private final QueryConfig queryConfig;
+ private final SparkSession sparkSession;
private final MariaDbMapper mariaDbMapper;
private final SchemaService schemaService;
private final StorageService storageService;
private final MetadataMapper metadataMapper;
- private final DataDatabaseSidecarGateway dataDatabaseSidecarGateway;
@Autowired
- public ViewServiceMariaDbImpl(Counter httpDataAccessCounter, S3Config s3Config, DataMapper dataMapper,
- QueryConfig queryConfig, MariaDbMapper mariaDbMapper, SchemaService schemaService,
- StorageService storageService, MetadataMapper metadataMapper,
- DataDatabaseSidecarGateway dataDatabaseSidecarGateway) {
+ public ViewServiceMariaDbImpl(Counter httpDataAccessCounter, DataMapper dataMapper,
+ QueryConfig queryConfig, SparkSession sparkSession, MariaDbMapper mariaDbMapper,
+ SchemaService schemaService, StorageService storageService,
+ MetadataMapper metadataMapper) {
this.httpDataAccessCounter = httpDataAccessCounter;
- this.s3Config = s3Config;
this.dataMapper = dataMapper;
this.queryConfig = queryConfig;
+ this.sparkSession = sparkSession;
this.mariaDbMapper = mariaDbMapper;
this.schemaService = schemaService;
this.storageService = storageService;
this.metadataMapper = metadataMapper;
- this.dataDatabaseSidecarGateway = dataDatabaseSidecarGateway;
}
@Override
@@ -228,35 +234,35 @@ public class ViewServiceMariaDbImpl extends HibernateConnector implements ViewSe
}
@Override
- public ExportResourceDto exportDataset(PrivilegedViewDto view) throws SQLException, QueryMalformedException,
- SidecarExportException, RemoteUnavailableException, StorageNotFoundException, StorageUnavailableException {
- final String fileName = RandomStringUtils.randomAlphabetic(40) + ".csv";
- final String filePath = s3Config.getS3FilePath() + File.separator + fileName;
- final ComboPooledDataSource dataSource = getPrivilegedDataSource(view.getDatabase());
- final Connection connection = dataSource.getConnection();
+ public ExportResourceDto exportDataset(PrivilegedViewDto view) throws QueryMalformedException,
+ StorageUnavailableException, ViewNotFoundException, MalformedException {
+ final Dataset<Row> dataset = getData(view);
+ httpDataAccessCounter.increment();
+ return storageService.transformDataset(dataset);
+ }
+
+ @Override
+ public Dataset<Row> getData(@NotNull PrivilegedViewDto view) throws ViewNotFoundException,
+ QueryMalformedException {
try {
- /* export to data database sidecar */
- final List<ColumnDto> columns = view.getColumns()
- .stream()
- .map(metadataMapper::viewColumnDtoToColumnDto)
- .toList();
- final long start = System.currentTimeMillis();
- connection.prepareStatement(mariaDbMapper.tableOrViewToRawExportQuery(view.getDatabase().getInternalName(),
- view.getInternalName(), columns, null, filePath))
- .executeUpdate();
- log.debug("executed statement in {} ms", System.currentTimeMillis() - start);
- connection.commit();
- } catch (SQLException e) {
- connection.rollback();
- log.error("Failed to execute query: {}", e.getMessage());
- throw new QueryMalformedException("Failed to execute query: " + e.getMessage(), e);
- } finally {
- dataSource.close();
+ final Properties properties = new Properties();
+ properties.setProperty("user", view.getDatabase().getContainer().getUsername());
+ properties.setProperty("password", view.getDatabase().getContainer().getPassword());
+ return sparkSession.read()
+ .jdbc(getSparkUrl(view.getDatabase().getContainer(), view.getDatabase().getInternalName()),
+ mariaDbMapper.tableOrViewToRawExportQuery(view.getDatabase().getInternalName(),
+ view.getInternalName(), view.getColumns().stream()
+ .map(ViewColumnDto::getInternalName).toList(), Instant.now()), properties);
+ } catch (Exception e) {
+ if (e instanceof ExtendedAnalysisException exception) {
+ if (exception.getSimpleMessage().contains("TABLE_OR_VIEW_NOT_FOUND")) {
+ log.error("Failed to find view {}: {}", view.getInternalName(), exception.getSimpleMessage());
+ throw new ViewNotFoundException("Failed to find view " + view.getInternalName() + ": " + exception.getSimpleMessage()) /* remove throwable on purpose, clutters the output */;
+ }
+ }
+ log.error("Failed to export dataset: {}", e.getMessage());
+ throw new QueryMalformedException("Failed to export dataset: " + e.getMessage(), e);
}
- dataDatabaseSidecarGateway.exportFile(view.getDatabase().getContainer().getSidecarHost(),
- view.getDatabase().getContainer().getSidecarPort(), fileName);
- httpDataAccessCounter.increment();
- return storageService.getResource(fileName);
}
}
diff --git a/dbrepo-metadata-db/1_setup-schema.sql b/dbrepo-metadata-db/1_setup-schema.sql
index b6b3b7bf89a8140950f1bf11768911bcc9fb6977..58a4c6ff39002bedde3a0d4ed62a209a5d5d36a3 100644
--- a/dbrepo-metadata-db/1_setup-schema.sql
+++ b/dbrepo-metadata-db/1_setup-schema.sql
@@ -453,8 +453,8 @@ CREATE TABLE IF NOT EXISTS `mdb_related_identifiers`
id SERIAL,
pid BIGINT UNSIGNED NOT NULL,
value varchar(255) NOT NULL,
- type varchar(255) NOT NULL,
- relation varchar(255) NOT NULL,
+ type ENUM ('DOI','URL','URN','ARK','ARXIV','BIBCODE','EAN13','EISSN','HANDLE','IGSN','ISBN','ISTC','LISSN','LSID','PMID','PURL','UPC','W3ID') NOT NULL,
+ relation ENUM ('IS_CITED_BY','CITES','IS_SUPPLEMENT_TO','IS_SUPPLEMENTED_BY','IS_CONTINUED_BY','CONTINUES','IS_DESCRIBED_BY','DESCRIBES','HAS_METADATA','IS_METADATA_FOR','HAS_VERSION','IS_VERSION_OF','IS_NEW_VERSION_OF','IS_PREVIOUS_VERSION_OF','IS_PART_OF','HAS_PART','IS_PUBLISHED_IN','IS_REFERENCED_BY','REFERENCES','IS_DOCUMENTED_BY','DOCUMENTS','IS_COMPILED_BY','COMPILES','IS_VARIANT_FORM_OF','IS_ORIGINAL_FORM_OF','IS_IDENTICAL_TO','IS_REVIEWED_BY','REVIEWS','IS_DERIVED_FROM','IS_SOURCE_OF','IS_REQUIRED_BY','REQUIRES','IS_OBSOLETED_BY','OBSOLETES') NOT NULL,
PRIMARY KEY (id), /* must be a single id from persistent identifier concept */
FOREIGN KEY (pid) REFERENCES mdb_identifiers (id),
UNIQUE (pid, value)
@@ -535,6 +535,18 @@ CREATE TABLE IF NOT EXISTS `mdb_image_types`
UNIQUE (value)
) WITH SYSTEM VERSIONING;
+CREATE TABLE IF NOT EXISTS `mdb_image_operators`
+(
+ id SERIAL,
+ image_id BIGINT UNSIGNED NOT NULL,
+ display_name varchar(255) NOT NULL,
+ value varchar(255) NOT NULL,
+ documentation TEXT NOT NULL,
+ PRIMARY KEY (id),
+ FOREIGN KEY (image_id) REFERENCES `mdb_images` (`id`),
+ UNIQUE (value)
+ ) WITH SYSTEM VERSIONING;
+
COMMIT;
BEGIN;
@@ -619,6 +631,37 @@ VALUES (1, 'BIGINT(size)', 'bigint', 0, null, null, false, 1, null, null, null,
(1, 'VARCHAR(size)', 'varchar', 0, 65532, 255, true, null, null, null, null, null, null, null,
null, 'https://mariadb.com/kb/en/varchar/', false, true, false);
+INSERT INTO `mdb_image_operators` (image_id, display_name, value, documentation)
+VALUES (1, 'Equal operator', '=', 'https://mariadb.com/kb/en/assignment-operators-assignment-operator/'),
+ (1, 'NULL-safe equal operator', '<=>', 'https://mariadb.com/kb/en/null-safe-equal/'),
+ (1, 'Less-than operator', '<', 'https://mariadb.com/kb/en/less-than/'),
+ (1, 'Less than or equal operator', '<=', 'https://mariadb.com/kb/en/less-than-or-equal/'),
+ (1, 'Greater-than operator', '>', 'https://mariadb.com/kb/en/greater-than/'),
+ (1, 'Greater than or equal operator', '>=', 'https://mariadb.com/kb/en/greater-than-or-equal/'),
+ (1, 'Not equal operator', '!=', 'https://mariadb.com/kb/en/not-equal/'),
+ (1, 'Addition operator', '+', 'https://mariadb.com/kb/en/addition-operator/'),
+ (1, 'Division operator', '/', 'https://mariadb.com/kb/en/division-operator/'),
+ (1, 'Modulo operator', '%', 'https://mariadb.com/kb/en/modulo-operator/'),
+ (1, 'Multiplication operator', '*', 'https://mariadb.com/kb/en/multiplication-operator/'),
+ (1, 'Subtraction operator', '-', 'https://mariadb.com/kb/en/subtraction-operator-/'),
+ (1, 'LIKE', 'LIKE', 'https://mariadb.com/kb/en/like/'),
+ (1, 'NOT LIKE', 'NOT LIKE', 'https://mariadb.com/kb/en/not-like/'),
+ (1, 'IN', 'IN', 'https://mariadb.com/kb/en/in/'),
+ (1, 'NOT IN', 'NOT IN', 'https://mariadb.com/kb/en/not-in/'),
+ (1, 'IS', 'IS', 'https://mariadb.com/kb/en/is/'),
+ (1, 'IS NOT', 'IS NOT', 'https://mariadb.com/kb/en/is-not/'),
+ (1, 'IS NOT NULL', 'IS NOT NULL', 'https://mariadb.com/kb/en/is-not-null/'),
+ (1, 'IS NULL', 'IS NULL', 'https://mariadb.com/kb/en/is-null/'),
+ (1, 'ISNULL', 'ISNULL', 'https://mariadb.com/kb/en/isnull/'),
+ (1, 'REGEXP', 'REGEXP', 'https://mariadb.com/kb/en/regexp/'),
+ (1, 'NOT REGEXP', 'NOT REGEXP', 'https://mariadb.com/kb/en/not-regexp/'),
+ (1, 'Bitwise AND', '&', 'https://mariadb.com/kb/en/bitwise_and/'),
+ (1, 'Bitwise OR', '|', 'https://mariadb.com/kb/en/bitwise-or/'),
+ (1, 'Bitwise XOR', '^', 'https://mariadb.com/kb/en/bitwise-xor/'),
+ (1, 'Bitwise NOT', '~', 'https://mariadb.com/kb/en/bitwise-not/'),
+ (1, 'Left shift', '<<', 'https://mariadb.com/kb/en/shift-left/'),
+ (1, 'Right shift', '>>', 'https://mariadb.com/kb/en/shift-right/');
+
INSERT
INTO `mdb_ontologies` (prefix, uri, uri_pattern, sparql_endpoint, rdf_path)
VALUES ('om', 'http://www.ontology-of-units-of-measure.org/resource/om-2/',
diff --git a/dbrepo-metadata-service/Dockerfile b/dbrepo-metadata-service/Dockerfile
index 74e82043731ab8970c2d42b58032f2b5e5b00f3c..843c334a9acb3d24e061c42c72cb75c6068ef954 100644
--- a/dbrepo-metadata-service/Dockerfile
+++ b/dbrepo-metadata-service/Dockerfile
@@ -1,5 +1,5 @@
###### FIRST STAGE ######
-FROM maven:3-openjdk-17 AS build
+FROM maven:3-amazoncorretto-17 AS build
LABEL org.opencontainers.image.authors="martin.weise@tuwien.ac.at"
COPY ./pom.xml ./
diff --git a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/ContainerCreateDto.java b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/ContainerCreateDto.java
index 7080d2b5d96e2763a8ebf750eea27f9b08fa4a50..86b50bea70209334a41458c47610c07f44f1799f 100644
--- a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/ContainerCreateDto.java
+++ b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/ContainerCreateDto.java
@@ -20,7 +20,7 @@ public class ContainerCreateDto {
@Schema(example = "Air Quality")
private String name;
- @NotBlank
+ @NotNull
@JsonProperty("image_id")
@Schema(description = "Image ID")
private Long imageId;
@@ -32,14 +32,6 @@ public class ContainerCreateDto {
@Schema(description = "Port of container")
private Integer port;
- @NotBlank
- @JsonProperty("sidecar_host")
- private String sidecarHost;
-
- @NotNull
- @JsonProperty("sidecar_port")
- private Integer sidecarPort;
-
@JsonProperty("ui_host")
private String uiHost;
diff --git a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/ContainerDto.java b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/ContainerDto.java
index 7e46b80c1cfc745b158f6bffffd02bdd617a1987..8f745f9ee9795b1dc69dd92bdd0a660ee8e2b071 100644
--- a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/ContainerDto.java
+++ b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/ContainerDto.java
@@ -37,14 +37,6 @@ public class ContainerDto {
private Integer port;
- @NotBlank
- @JsonProperty("sidecar_host")
- private String sidecarHost;
-
- @NotNull
- @JsonProperty("sidecar_port")
- private Integer sidecarPort;
-
@JsonProperty("ui_host")
private String uiHost;
diff --git a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/image/ImageDto.java b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/image/ImageDto.java
index 743f1f2b0a8ab67795a58b060d6ef30597d36837..ea47c51e477e45359598076478fdce87b6c3ddc3 100644
--- a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/image/ImageDto.java
+++ b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/image/ImageDto.java
@@ -61,4 +61,7 @@ public class ImageDto {
@JsonProperty("data_types")
private List<DataTypeDto> dataTypes;
+ @NotNull
+ private List<OperatorDto> operators;
+
}
diff --git a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/image/OperatorDto.java b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/image/OperatorDto.java
new file mode 100644
index 0000000000000000000000000000000000000000..a954bf4a61d52a1d4ee3063cf7187f8865969554
--- /dev/null
+++ b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/image/OperatorDto.java
@@ -0,0 +1,32 @@
+package at.tuwien.api.container.image;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import io.swagger.v3.oas.annotations.media.Schema;
+import jakarta.validation.constraints.NotBlank;
+import jakarta.validation.constraints.NotNull;
+import lombok.*;
+import lombok.extern.jackson.Jacksonized;
+
+@Getter
+@Setter
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
+@Jacksonized
+@ToString
+public class OperatorDto {
+
+ @NotBlank
+ @JsonProperty("display_name")
+ @Schema(example = "XOR")
+ private String displayName;
+
+ @NotBlank
+ @Schema(example = "XOR")
+ private String value;
+
+ @NotNull
+ @Schema(example = "https://mariadb.com/kb/en/xor/")
+ private String documentation;
+
+}
diff --git a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/internal/PrivilegedContainerDto.java b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/internal/PrivilegedContainerDto.java
index 8bda16bf41630376ad105399ca1aca048d1514e6..3a7a375618d22c2fb3f85bb14d5494401d03dc04 100644
--- a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/internal/PrivilegedContainerDto.java
+++ b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/container/internal/PrivilegedContainerDto.java
@@ -37,14 +37,6 @@ public class PrivilegedContainerDto {
private Integer port;
- @NotBlank
- @JsonProperty("sidecar_host")
- private String sidecarHost;
-
- @NotNull
- @JsonProperty("sidecar_port")
- private Integer sidecarPort;
-
@JsonProperty("ui_host")
private String uiHost;
diff --git a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/query/ImportDto.java b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/query/ImportDto.java
index 043e3bc3eea9c0c438fb34f2e1b9427c0607bb18..1b31d9d6199c3f6ba2c24ae8a25c09dbd1cf0522 100644
--- a/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/query/ImportDto.java
+++ b/dbrepo-metadata-service/api/src/main/java/at/tuwien/api/database/query/ImportDto.java
@@ -1,11 +1,9 @@
package at.tuwien.api.database.query;
import com.fasterxml.jackson.annotation.JsonProperty;
-import io.swagger.v3.oas.annotations.Parameter;
import io.swagger.v3.oas.annotations.media.Schema;
import lombok.*;
-import jakarta.validation.constraints.Min;
import jakarta.validation.constraints.NotBlank;
import jakarta.validation.constraints.NotNull;
import lombok.extern.jackson.Jacksonized;
@@ -23,9 +21,9 @@ public class ImportDto {
@Schema(example = "file.csv")
private String location;
- @Min(value = 0L)
- @JsonProperty("skip_lines")
- private Long skipLines;
+ @NotNull
+ @Schema(description = "If true, the first line contains the column names, otherwise it contains only data")
+ private Boolean header;
@NotNull
@Schema(example = ",")
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/Container.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/Container.java
index 7545260ce1a83f2a39b7900e9b29de5e0a4bedde..168c0cc752079d259ac21b5da411d795cbd1cf46 100644
--- a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/Container.java
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/Container.java
@@ -43,12 +43,6 @@ public class Container {
@Column
private Integer port;
- @Column
- private String sidecarHost;
-
- @Column
- private Integer sidecarPort;
-
@Column
private String uiHost;
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/image/ContainerImage.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/image/ContainerImage.java
index 080a843aada9982608cb534c0e24027439e9d9c0..4a9e9a4b9f6a6552c1b4f8342da3248006e7ad34 100644
--- a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/image/ContainerImage.java
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/image/ContainerImage.java
@@ -71,7 +71,11 @@ public class ContainerImage {
private Instant lastModified;
@ToString.Exclude
- @OneToMany(fetch = FetchType.LAZY, mappedBy = "image")
+ @OneToMany(fetch = FetchType.LAZY, cascade = {CascadeType.ALL, CascadeType.PERSIST}, mappedBy = "image")
private List<DataType> dataTypes;
+ @ToString.Exclude
+ @OneToMany(fetch = FetchType.LAZY, cascade = {CascadeType.ALL, CascadeType.PERSIST}, mappedBy = "image")
+ private List<Operator> operators;
+
}
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/image/DataType.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/image/DataType.java
index a98da8d530e550cd12546d3bdfed8ad383461964..47872da89036300ed6ec9970821a77580322b630 100644
--- a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/image/DataType.java
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/image/DataType.java
@@ -68,7 +68,8 @@ public class DataType {
@Column(name = "is_buildable", nullable = false)
private Boolean buildable;
- @ManyToOne(fetch = FetchType.LAZY, cascade = {CascadeType.ALL, CascadeType.PERSIST})
+ @ToString.Exclude
+ @ManyToOne(fetch = FetchType.LAZY, cascade = {CascadeType.MERGE})
@JoinColumns({
@JoinColumn(name = "image_id", referencedColumnName = "id")
})
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/image/Operator.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/image/Operator.java
new file mode 100644
index 0000000000000000000000000000000000000000..418d54cb6446670123aa2b2acd4ed6e7b01e3ccc
--- /dev/null
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/container/image/Operator.java
@@ -0,0 +1,42 @@
+package at.tuwien.entities.container.image;
+
+import jakarta.persistence.*;
+import lombok.*;
+import org.hibernate.annotations.GenericGenerator;
+import org.springframework.data.jpa.domain.support.AuditingEntityListener;
+
+@Data
+@Entity
+@Builder
+@ToString
+@AllArgsConstructor
+@NoArgsConstructor
+@EntityListeners(AuditingEntityListener.class)
+@EqualsAndHashCode(onlyExplicitlyIncluded = true)
+@Table(name = "mdb_image_operators")
+public class Operator {
+
+ @Id
+ @EqualsAndHashCode.Include
+ @GeneratedValue(generator = "image-type-sequence")
+ @GenericGenerator(name = "image-type-sequence", strategy = "increment")
+ @Column(updatable = false, nullable = false)
+ public Long id;
+
+ @Column(name = "display_name", nullable = false)
+ private String displayName;
+
+ @Column(name = "value", nullable = false, unique = true)
+ private String value;
+
+ @Column(nullable = false)
+ private String documentation;
+
+ @ToString.Exclude
+ @ManyToOne(fetch = FetchType.LAZY, cascade = {CascadeType.MERGE})
+ @JoinColumns({
+ @JoinColumn(name = "image_id", referencedColumnName = "id")
+ })
+ private ContainerImage image;
+
+}
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/database/ViewColumn.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/database/ViewColumn.java
index 10ac29d8e65eaa15ba592919ac014e452a87a06a..201d7075e5f1df0b90c4c885ed76c2573e19d870 100644
--- a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/database/ViewColumn.java
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/database/ViewColumn.java
@@ -39,7 +39,7 @@ public class ViewColumn implements Comparable<ViewColumn> {
@Column(name = "internal_name", nullable = false, columnDefinition = "VARCHAR(64)")
private String internalName;
- @Column(nullable = false, columnDefinition = "ENUM('CHAR','VARCHAR','BINARY','VARBINARY','TINYBLOB','TINYTEXT','TEXT','BLOB','MEDIUMTEXT','MEDIUMBLOB','LONGTEXT','LONGBLOB','ENUM','SET','BIT','TINYINT','BOOL','SMALLINT','MEDIUMINT','INT','BIGINT','FLOAT','DOUBLE','DECIMAL','DATE','DATETIME','TIMESTAMP','TIME','YEAR')")
+ @Column(nullable = false, columnDefinition = "ENUM('CHAR','VARCHAR','BINARY','VARBINARY','TINYBLOB','TINYTEXT','TEXT','BLOB','MEDIUMTEXT','MEDIUMBLOB','LONGTEXT','LONGBLOB','ENUM','SET','SERIAL','BIT','TINYINT','BOOL','SMALLINT','MEDIUMINT','INT','BIGINT','FLOAT','DOUBLE','DECIMAL','DATE','DATETIME','TIMESTAMP','TIME','YEAR')")
@Enumerated(EnumType.STRING)
private TableColumnType columnType;
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/Creator.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/Creator.java
index f2452ac5598bce48c155a107038b931f7aeecdbd..f69f3c6d7177bd1f71cdaff66355971f9e2e1f8c 100644
--- a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/Creator.java
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/Creator.java
@@ -33,14 +33,14 @@ public class Creator {
@Column(name = "creator_name", nullable = false)
private String creatorName;
- @Column(columnDefinition = "enum('PERSONAL', 'ORGANIZATIONAL')")
+ @Column(columnDefinition = "ENUM('PERSONAL', 'ORGANIZATIONAL')")
@Enumerated(EnumType.STRING)
private NameType nameType;
@Column
private String nameIdentifier;
- @Column(columnDefinition = "enum('ROR', 'GRID', 'ISNI', 'ORCID')")
+ @Column(columnDefinition = "ENUM('ROR', 'GRID', 'ISNI', 'ORCID')")
@Enumerated(EnumType.STRING)
private NameIdentifierSchemeType nameIdentifierScheme;
@@ -53,7 +53,7 @@ public class Creator {
@Column
private String affiliationIdentifier;
- @Column(columnDefinition = "enum('ROR', 'GRID', 'ISNI')")
+ @Column(columnDefinition = "ENUM('ROR', 'GRID', 'ISNI')")
@Enumerated(EnumType.STRING)
private AffiliationIdentifierSchemeType affiliationIdentifierScheme;
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/Identifier.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/Identifier.java
index 6c8615f0d9d2bd5614de0049d480c117eebbad38..abf76758cc49fefe717f6546198559fa2b0e17af 100644
--- a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/Identifier.java
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/Identifier.java
@@ -66,7 +66,7 @@ public class Identifier implements Serializable {
@Column(nullable = false)
private String publisher;
- @Column(nullable = false, columnDefinition = "enum('DRAFT', 'PUBLISHED')")
+ @Column(nullable = false, columnDefinition = "ENUM('DRAFT', 'PUBLISHED')")
@Enumerated(EnumType.STRING)
private IdentifierStatusType status;
@@ -106,7 +106,7 @@ public class Identifier implements Serializable {
)
private List<License> licenses;
- @Column(name = "identifier_type", nullable = false, columnDefinition = "enum('SUBSET', 'DATABASE', 'VIEW', 'TABLE')")
+ @Column(name = "identifier_type", nullable = false, columnDefinition = "ENUM('SUBSET', 'DATABASE', 'VIEW', 'TABLE')")
@Enumerated(EnumType.STRING)
private IdentifierType type;
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierDescription.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierDescription.java
index 17376c1cb6b43e5960a33d16d4b9f29c689790b7..8544650a6c1b30ae06f3502fe91b33ce75783485 100644
--- a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierDescription.java
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierDescription.java
@@ -29,11 +29,11 @@ public class IdentifierDescription implements Serializable {
@Column(nullable = false, columnDefinition = "TEXT")
private String description;
- @Column(columnDefinition = "enum('ABSTRACT', 'METHODS', 'SERIES_INFORMATION', 'TABLE_OF_CONTENTS', 'TECHNICAL_INFO', 'OTHER')")
+ @Column(columnDefinition = "ENUM('ABSTRACT', 'METHODS', 'SERIES_INFORMATION', 'TABLE_OF_CONTENTS', 'TECHNICAL_INFO', 'OTHER')")
@Enumerated(EnumType.STRING)
private DescriptionType descriptionType;
- @Column(columnDefinition = "enum('AB','AA','AF','AK','SQ','AM','AR','AN','HY','AS','AV','AE','AY','AZ','BM','BA','EU','BE','BN','BH','BI','BS','BR','BG','MY','CA','KM','CH','CE','NY','ZH','CU','CV','KW','CO','CR','HR','CS','DA','DV','NL','DZ','EN','EO','ET','EE','FO','FJ','FI','FR','FF','GD','GL','LG','KA','DE','KI','EL','KL','GN','GU','HT','HA','HE','HZ','HI','HO','HU','IS','IO','IG','ID','IA','IE','IU','IK','GA','IT','JA','JV','KN','KR','KS','KK','RW','KV','KG','KO','KJ','KU','KY','LO','LA','LV','LB','LI','LN','LT','LU','MK','MG','MS','ML','MT','GV','MI','MR','MH','RO','MN','NA','NV','ND','NG','NE','SE','NO','NB','NN','II','OC','OJ','OR','OM','OS','PI','PA','PS','FA','PL','PT','QU','RM','RN','RU','SM','SG','SA','SC','SR','SN','SD','SI','SK','SL','SO','ST','NR','ES','SU','SW','SS','SV','TL','TY','TG','TA','TT','TE','TH','BO','TI','TO','TS','TN','TR','TK','TW','UG','UK','UR','UZ','VE','VI','VO','WA','CY','FY','WO','XH','YI','YO','ZA','ZU')")
+ @Column(columnDefinition = "ENUM('AB','AA','AF','AK','SQ','AM','AR','AN','HY','AS','AV','AE','AY','AZ','BM','BA','EU','BE','BN','BH','BI','BS','BR','BG','MY','CA','KM','CH','CE','NY','ZH','CU','CV','KW','CO','CR','HR','CS','DA','DV','NL','DZ','EN','EO','ET','EE','FO','FJ','FI','FR','FF','GD','GL','LG','KA','DE','KI','EL','KL','GN','GU','HT','HA','HE','HZ','HI','HO','HU','IS','IO','IG','ID','IA','IE','IU','IK','GA','IT','JA','JV','KN','KR','KS','KK','RW','KV','KG','KO','KJ','KU','KY','LO','LA','LV','LB','LI','LN','LT','LU','MK','MG','MS','ML','MT','GV','MI','MR','MH','RO','MN','NA','NV','ND','NG','NE','SE','NO','NB','NN','II','OC','OJ','OR','OM','OS','PI','PA','PS','FA','PL','PT','QU','RM','RN','RU','SM','SG','SA','SC','SR','SN','SD','SI','SK','SL','SO','ST','NR','ES','SU','SW','SS','SV','TL','TY','TG','TA','TT','TE','TH','BO','TI','TO','TS','TN','TR','TK','TW','UG','UK','UR','UZ','VE','VI','VO','WA','CY','FY','WO','XH','YI','YO','ZA','ZU')")
@Enumerated(EnumType.STRING)
private LanguageType language;
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierFunder.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierFunder.java
index 21977c19a9be256817b8966a472d1c90215d0e2c..cd08b9ccbe56045d18b477d17e34427163bae689 100644
--- a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierFunder.java
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierFunder.java
@@ -30,7 +30,7 @@ public class IdentifierFunder implements Serializable {
@Column(columnDefinition = "TEXT")
private String funderIdentifier;
- @Column(name="funder_identifier_type", columnDefinition = "enum('CROSSREF_FUNDER_ID', 'ROR', 'GND', 'ISNI', 'OTHER')")
+ @Column(name="funder_identifier_type", columnDefinition = "ENUM('CROSSREF_FUNDER_ID', 'ROR', 'GND', 'ISNI', 'OTHER')")
@Enumerated(EnumType.STRING)
private IdentifierFunderType funderIdentifierType;
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierTitle.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierTitle.java
index c5a62974b0e6b1788a7838dcb6623a446f53d1e2..72cc7c95ca87bdea83540c64d1ed32aee084bf88 100644
--- a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierTitle.java
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/IdentifierTitle.java
@@ -28,11 +28,11 @@ public class IdentifierTitle implements Serializable {
@Column(nullable = false, columnDefinition = "TEXT")
private String title;
- @Column(columnDefinition = "enum('ALTERNATIVE_TITLE', 'SUBTITLE', 'TRANSLATED_TITLE', 'OTHER')")
+ @Column(columnDefinition = "ENUM('ALTERNATIVE_TITLE', 'SUBTITLE', 'TRANSLATED_TITLE', 'OTHER')")
@Enumerated(EnumType.STRING)
private TitleType titleType;
- @Column(columnDefinition = "enum('AB','AA','AF','AK','SQ','AM','AR','AN','HY','AS','AV','AE','AY','AZ','BM','BA','EU','BE','BN','BH','BI','BS','BR','BG','MY','CA','KM','CH','CE','NY','ZH','CU','CV','KW','CO','CR','HR','CS','DA','DV','NL','DZ','EN','EO','ET','EE','FO','FJ','FI','FR','FF','GD','GL','LG','KA','DE','KI','EL','KL','GN','GU','HT','HA','HE','HZ','HI','HO','HU','IS','IO','IG','ID','IA','IE','IU','IK','GA','IT','JA','JV','KN','KR','KS','KK','RW','KV','KG','KO','KJ','KU','KY','LO','LA','LV','LB','LI','LN','LT','LU','MK','MG','MS','ML','MT','GV','MI','MR','MH','RO','MN','NA','NV','ND','NG','NE','SE','NO','NB','NN','II','OC','OJ','OR','OM','OS','PI','PA','PS','FA','PL','PT','QU','RM','RN','RU','SM','SG','SA','SC','SR','SN','SD','SI','SK','SL','SO','ST','NR','ES','SU','SW','SS','SV','TL','TY','TG','TA','TT','TE','TH','BO','TI','TO','TS','TN','TR','TK','TW','UG','UK','UR','UZ','VE','VI','VO','WA','CY','FY','WO','XH','YI','YO','ZA','ZU')")
+ @Column(columnDefinition = "ENUM('AB','AA','AF','AK','SQ','AM','AR','AN','HY','AS','AV','AE','AY','AZ','BM','BA','EU','BE','BN','BH','BI','BS','BR','BG','MY','CA','KM','CH','CE','NY','ZH','CU','CV','KW','CO','CR','HR','CS','DA','DV','NL','DZ','EN','EO','ET','EE','FO','FJ','FI','FR','FF','GD','GL','LG','KA','DE','KI','EL','KL','GN','GU','HT','HA','HE','HZ','HI','HO','HU','IS','IO','IG','ID','IA','IE','IU','IK','GA','IT','JA','JV','KN','KR','KS','KK','RW','KV','KG','KO','KJ','KU','KY','LO','LA','LV','LB','LI','LN','LT','LU','MK','MG','MS','ML','MT','GV','MI','MR','MH','RO','MN','NA','NV','ND','NG','NE','SE','NO','NB','NN','II','OC','OJ','OR','OM','OS','PI','PA','PS','FA','PL','PT','QU','RM','RN','RU','SM','SG','SA','SC','SR','SN','SD','SI','SK','SL','SO','ST','NR','ES','SU','SW','SS','SV','TL','TY','TG','TA','TT','TE','TH','BO','TI','TO','TS','TN','TR','TK','TW','UG','UK','UR','UZ','VE','VI','VO','WA','CY','FY','WO','XH','YI','YO','ZA','ZU')")
@Enumerated(EnumType.STRING)
private LanguageType language;
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/RelatedIdentifier.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/RelatedIdentifier.java
index a8006e626df74b2362ee9c6e98522a93939fdb6a..1bc3d269fa183f673b9f3c6912b290d36aebcc1c 100644
--- a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/RelatedIdentifier.java
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/identifier/RelatedIdentifier.java
@@ -29,11 +29,11 @@ public class RelatedIdentifier {
@Column(nullable = false)
private String value;
- @Column(columnDefinition = "enum('DOI','URL','URN','ARK','arXiv','bibcode','EAN13','EISSN','Handle','IGSN','ISBN','ISTC','LISSN','LSID','PMID','PURL','UPC','w3id')")
+ @Column(columnDefinition = "ENUM('DOI','URL','URN','ARK','ARXIV','BIBCODE','EAN13','EISSN','HANDLE','IGSN','ISBN','ISTC','LISSN','LSID','PMID','PURL','UPC','W3ID')")
@Enumerated(EnumType.STRING)
private RelatedType type;
- @Column(columnDefinition = "enum('IsCitedBy','Cites','IsSupplementTo','IsSupplementedBy','IsContinuedBy','Continues','IsDescribedBy','Describes','HasMetadata','IsMetadataFor','HasVersion','IsVersionOf','IsNewVersionOf','IsPreviousVersionOf','IsPartOf','HasPart','IsPublishedIn','IsReferencedBy','References','IsDocumentedBy','Documents','IsCompiledBy','Compiles','IsVariantFormOf','IsOriginalFormOf','IsIdenticalTo','IsReviewedBy','Reviews','IsDerivedFrom','IsSourceOf','IsRequiredBy','Requires','IsObsoletedBy','Obsoletes')")
+ @Column(columnDefinition = "ENUM('IS_CITED_BY','CITES','IS_SUPPLEMENT_TO','IS_SUPPLEMENTED_BY','IS_CONTINUED_BY','CONTINUES','IS_DESCRIBED_BY','DESCRIBES','HAS_METADATA','IS_METADATA_FOR','HAS_VERSION','IS_VERSION_OF','IS_NEW_VERSION_OF','IS_PREVIOUS_VERSION_OF','IS_PART_OF','HAS_PART','IS_PUBLISHED_IN','IS_REFERENCED_BY','REFERENCES','IS_DOCUMENTED_BY','DOCUMENTS','IS_COMPILED_BY','COMPILES','IS_VARIANT_FORM_OF','IS_ORIGINAL_FORM_OF','IS_IDENTICAL_TO','IS_REVIEWED_BY','REVIEWS','IS_DERIVED_FROM','IS_SOURCE_OF','IS_REQUIRED_BY','REQUIRES','IS_OBSOLETED_BY','OBSOLETES')")
@Enumerated(EnumType.STRING)
private RelationType relation;
diff --git a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/maintenance/BannerMessage.java b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/maintenance/BannerMessage.java
index f7d2abaafcfc7e14a6806c56821501d8f4af7080..de0d917b43c9a4b0b8aeba9ca71d329f7a0bf7a8 100644
--- a/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/maintenance/BannerMessage.java
+++ b/dbrepo-metadata-service/entities/src/main/java/at/tuwien/entities/maintenance/BannerMessage.java
@@ -27,7 +27,7 @@ public class BannerMessage {
@Column(updatable = false, nullable = false)
private Long id;
- @Column(nullable = false, columnDefinition = "enum('ERROR','WARNING','INFO')")
+ @Column(nullable = false, columnDefinition = "ENUM('ERROR','WARNING','INFO')")
@Enumerated(EnumType.STRING)
private BannerMessageType type;
diff --git a/dbrepo-metadata-service/pom.xml b/dbrepo-metadata-service/pom.xml
index a2de622dcacd12a615c2d8dc0f536df88ebc87dd..5ac480bce0defedbcebd245de9f7c5d62b13dd77 100644
--- a/dbrepo-metadata-service/pom.xml
+++ b/dbrepo-metadata-service/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
- <version>3.0.13</version>
+ <version>3.1.12</version>
</parent>
<groupId>at.tuwien</groupId>
diff --git a/dbrepo-metadata-service/repositories/src/main/java/at/tuwien/exception/SidecarExportException.java b/dbrepo-metadata-service/repositories/src/main/java/at/tuwien/exception/AnalyseServiceException.java
similarity index 53%
rename from dbrepo-metadata-service/repositories/src/main/java/at/tuwien/exception/SidecarExportException.java
rename to dbrepo-metadata-service/repositories/src/main/java/at/tuwien/exception/AnalyseServiceException.java
index 6000222a678be2f10a9c08634eb6dd6f05f64a13..44cd0d3dc812b8ac2ff2aa8e19ea022a6c93113e 100644
--- a/dbrepo-metadata-service/repositories/src/main/java/at/tuwien/exception/SidecarExportException.java
+++ b/dbrepo-metadata-service/repositories/src/main/java/at/tuwien/exception/AnalyseServiceException.java
@@ -3,18 +3,18 @@ package at.tuwien.exception;
import org.springframework.http.HttpStatus;
import org.springframework.web.bind.annotation.ResponseStatus;
-@ResponseStatus(code = HttpStatus.SERVICE_UNAVAILABLE, reason = "error.sidecar.export")
-public class SidecarExportException extends Exception {
+@ResponseStatus(code = HttpStatus.SERVICE_UNAVAILABLE, reason = "error.analyse.invalid")
+public class AnalyseServiceException extends Exception {
- public SidecarExportException(String message) {
+ public AnalyseServiceException(String message) {
super(message);
}
- public SidecarExportException(String message, Throwable thr) {
+ public AnalyseServiceException(String message, Throwable thr) {
super(message, thr);
}
- public SidecarExportException(Throwable thr) {
+ public AnalyseServiceException(Throwable thr) {
super(thr);
}
diff --git a/dbrepo-metadata-service/repositories/src/main/java/at/tuwien/exception/SidecarImportException.java b/dbrepo-metadata-service/repositories/src/main/java/at/tuwien/exception/SidecarImportException.java
deleted file mode 100644
index 4f44226c73e73a2f66ee0cb84944637629e0dd1b..0000000000000000000000000000000000000000
--- a/dbrepo-metadata-service/repositories/src/main/java/at/tuwien/exception/SidecarImportException.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package at.tuwien.exception;
-
-import org.springframework.http.HttpStatus;
-import org.springframework.web.bind.annotation.ResponseStatus;
-
-@ResponseStatus(code = HttpStatus.SERVICE_UNAVAILABLE, reason = "error.sidecar.import")
-public class SidecarImportException extends Exception {
-
- public SidecarImportException(String message) {
- super(message);
- }
-
- public SidecarImportException(String message, Throwable thr) {
- super(message, thr);
- }
-
- public SidecarImportException(Throwable thr) {
- super(thr);
- }
-
-}
diff --git a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/AccessEndpoint.java b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/AccessEndpoint.java
index f50f916ac4e2a900127244d619814d345c84b809..3b39857ee614cf55bc53aa9acec0a5e40a3afdc7 100644
--- a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/AccessEndpoint.java
+++ b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/AccessEndpoint.java
@@ -91,8 +91,8 @@ public class AccessEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<DatabaseAccessDto> create(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("userId") UUID userId,
+ public ResponseEntity<DatabaseAccessDto> create(@NotNull @PathVariable("databaseId") Long databaseId,
+ @org.hibernate.validator.constraints.UUID @PathVariable("userId") UUID userId,
@Valid @RequestBody UpdateDatabaseAccessDto data,
@NotNull Principal principal) throws NotAllowedException, DataServiceException,
DataServiceConnectionException, DatabaseNotFoundException, UserNotFoundException, AccessNotFoundException,
@@ -154,8 +154,8 @@ public class AccessEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> update(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("userId") UUID userId,
+ public ResponseEntity<Void> update(@NotNull @PathVariable("databaseId") Long databaseId,
+ @org.hibernate.validator.constraints.UUID @PathVariable("userId") UUID userId,
@Valid @RequestBody UpdateDatabaseAccessDto data,
@NotNull Principal principal) throws NotAllowedException,
DataServiceException, DataServiceConnectionException, DatabaseNotFoundException, UserNotFoundException,
@@ -199,8 +199,8 @@ public class AccessEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<DatabaseAccessDto> find(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("userId") UUID userId,
+ public ResponseEntity<DatabaseAccessDto> find(@NotNull @PathVariable("databaseId") Long databaseId,
+ @org.hibernate.validator.constraints.UUID @PathVariable("userId") UUID userId,
@NotNull Principal principal) throws DatabaseNotFoundException,
UserNotFoundException, AccessNotFoundException, NotAllowedException {
log.debug("endpoint get database access, databaseId={}, userId={}, principal.name={}", databaseId, userId,
@@ -256,8 +256,8 @@ public class AccessEndpoint {
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
})
- public ResponseEntity<Void> revoke(@NotBlank @PathVariable("databaseId") Long databaseId,
- @NotBlank @PathVariable("userId") UUID userId,
+ public ResponseEntity<Void> revoke(@NotNull @PathVariable("databaseId") Long databaseId,
+ @org.hibernate.validator.constraints.UUID @PathVariable("userId") UUID userId,
@NotNull Principal principal) throws NotAllowedException, DataServiceException,
DataServiceConnectionException, DatabaseNotFoundException, UserNotFoundException, AccessNotFoundException,
SearchServiceException, SearchServiceConnectionException {
diff --git a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/DatabaseEndpoint.java b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/DatabaseEndpoint.java
index d5c316fed960a8600352df7201871a370654c021..b270bdb20615ab725535242fac0982114e4e42db 100644
--- a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/DatabaseEndpoint.java
+++ b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/DatabaseEndpoint.java
@@ -448,6 +448,9 @@ public class DatabaseEndpoint {
@ApiResponses(value = {
@ApiResponse(responseCode = "200",
description = "Database found successfully",
+ headers = {@Header(name = "X-Username", description = "The authentication username", schema = @Schema(implementation = String.class)),
+ @Header(name = "X-Password", description = "The authentication password", schema = @Schema(implementation = String.class)),
+ @Header(name = "Access-Control-Expose-Headers", description = "Expose custom headers", schema = @Schema(implementation = String.class))},
content = {@Content(
mediaType = "application/json",
schema = @Schema(implementation = DatabaseDto.class))}),
diff --git a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/IdentifierEndpoint.java b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/IdentifierEndpoint.java
index 831e9cd28d7148b0eaec5b44c3cb4f3059726461..7f2e0ee93d25bd1a0b593803983fd870bc22214a 100644
--- a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/IdentifierEndpoint.java
+++ b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/IdentifierEndpoint.java
@@ -187,11 +187,6 @@ public class IdentifierEndpoint {
content = {@Content(
mediaType = "application/json",
schema = @Schema(implementation = ApiErrorDto.class))}),
- @ApiResponse(responseCode = "422",
- description = "Failed to retrieve from database sidecar",
- content = {@Content(
- mediaType = "application/json",
- schema = @Schema(implementation = ApiErrorDto.class))}),
@ApiResponse(responseCode = "502",
description = "Connection to data service failed",
content = {@Content(
diff --git a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
index 738e30d4e48aba2dc52703d0ca2bd3cb53b2b63a..ef897d06ee3701c5018fd7bc3e3ae8fd20de0bf0 100644
--- a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
+++ b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java
@@ -22,6 +22,7 @@ import at.tuwien.utils.UserUtil;
import at.tuwien.validation.EndpointValidator;
import io.micrometer.observation.annotation.Observed;
import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.headers.Header;
import io.swagger.v3.oas.annotations.media.ArraySchema;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
@@ -361,11 +362,19 @@ public class TableEndpoint {
@Transactional(readOnly = true)
@Observed(name = "dbrepo_tables_find")
@Operation(summary = "Find table",
- description = "Finds a table with id.",
+ description = "Finds a table with id. When the `system` role is present, the endpoint responds with additional connection metadata in the header.",
security = {@SecurityRequirement(name = "bearerAuth"), @SecurityRequirement(name = "basicAuth")})
@ApiResponses(value = {
@ApiResponse(responseCode = "200",
description = "Find table successfully",
+ headers = {@Header(name = "X-Username", description = "The authentication username", schema = @Schema(implementation = String.class)),
+ @Header(name = "X-Password", description = "The authentication password", schema = @Schema(implementation = String.class)),
+ @Header(name = "X-Host", description = "The database hostname", schema = @Schema(implementation = String.class)),
+ @Header(name = "X-Port", description = "The database port number", schema = @Schema(implementation = Integer.class)),
+ @Header(name = "X-Type", description = "The JDBC connection type", schema = @Schema(implementation = String.class)),
+ @Header(name = "X-Database", description = "The database internal name", schema = @Schema(implementation = String.class)),
+ @Header(name = "X-Table", description = "The table internal name", schema = @Schema(implementation = String.class)),
+ @Header(name = "Access-Control-Expose-Headers", description = "Expose custom headers", schema = @Schema(implementation = String.class))},
content = {@Content(
mediaType = "application/json",
schema = @Schema(implementation = TableDto.class))}),
@@ -405,9 +414,8 @@ public class TableEndpoint {
headers.set("X-Port", "" + table.getDatabase().getContainer().getPort());
headers.set("X-Type", table.getDatabase().getContainer().getImage().getJdbcMethod());
headers.set("X-Database", table.getDatabase().getInternalName());
- headers.set("X-Sidecar-Host", table.getDatabase().getContainer().getSidecarHost());
- headers.set("X-Sidecar-Port", "" + table.getDatabase().getContainer().getSidecarPort());
- headers.set("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database X-Sidecar-Host X-Sidecar-Port");
+ headers.set("X-Table", table.getInternalName());
+ headers.set("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database X-Table");
}
return ResponseEntity.status(HttpStatus.OK)
.headers(headers)
diff --git a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/ViewEndpoint.java b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/ViewEndpoint.java
index 79981ee6d1fdcaaa5344915f7a0f3d3c43514926..cfcc554885e171ac9d35ae3e9f1c24df59f258db 100644
--- a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/ViewEndpoint.java
+++ b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/ViewEndpoint.java
@@ -15,6 +15,7 @@ import at.tuwien.service.ViewService;
import at.tuwien.utils.UserUtil;
import io.micrometer.observation.annotation.Observed;
import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.headers.Header;
import io.swagger.v3.oas.annotations.media.ArraySchema;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
@@ -161,6 +162,14 @@ public class ViewEndpoint {
@ApiResponses(value = {
@ApiResponse(responseCode = "200",
description = "Find view successfully",
+ headers = {@Header(name = "X-Username", description = "The authentication username", schema = @Schema(implementation = String.class)),
+ @Header(name = "X-Password", description = "The authentication password", schema = @Schema(implementation = String.class)),
+ @Header(name = "X-Host", description = "The database hostname", schema = @Schema(implementation = String.class)),
+ @Header(name = "X-Port", description = "The database port number", schema = @Schema(implementation = Integer.class)),
+ @Header(name = "X-Type", description = "The JDBC connection type", schema = @Schema(implementation = String.class)),
+ @Header(name = "X-Database", description = "The database internal name", schema = @Schema(implementation = String.class)),
+ @Header(name = "X-View", description = "The view internal name", schema = @Schema(implementation = String.class)),
+ @Header(name = "Access-Control-Expose-Headers", description = "Expose custom headers", schema = @Schema(implementation = String.class))},
content = {@Content(
mediaType = "application/json",
schema = @Schema(implementation = ViewDto.class))}),
@@ -190,7 +199,8 @@ public class ViewEndpoint {
headers.set("X-Port", "" + view.getDatabase().getContainer().getPort());
headers.set("X-Type", view.getDatabase().getContainer().getImage().getJdbcMethod());
headers.set("X-Database", view.getDatabase().getInternalName());
- headers.set("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database");
+ headers.set("X-View", view.getInternalName());
+ headers.set("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database X-View");
}
return ResponseEntity.status(HttpStatus.OK)
.headers(headers)
diff --git a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/handlers/ApiExceptionHandler.java b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/handlers/ApiExceptionHandler.java
index bf655f071abee0fdd5fc390b76402e3165d04c37..5b5769583a8046356a216eb8510a4df971919718 100644
--- a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/handlers/ApiExceptionHandler.java
+++ b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/handlers/ApiExceptionHandler.java
@@ -30,6 +30,13 @@ public class ApiExceptionHandler extends ResponseEntityExceptionHandler {
return generic_handle(e.getClass(), e.getLocalizedMessage());
}
+ @Hidden
+ @ResponseStatus(code = HttpStatus.SERVICE_UNAVAILABLE)
+ @ExceptionHandler(AnalyseServiceException.class)
+ public ResponseEntity<ApiErrorDto> handle(AnalyseServiceException e) {
+ return generic_handle(e.getClass(), e.getLocalizedMessage());
+ }
+
@Hidden
@ResponseStatus(code = HttpStatus.BAD_GATEWAY)
@ExceptionHandler(AuthServiceConnectionException.class)
@@ -359,20 +366,6 @@ public class ApiExceptionHandler extends ResponseEntityExceptionHandler {
return generic_handle(e.getClass(), e.getLocalizedMessage());
}
- @Hidden
- @ResponseStatus(code = HttpStatus.SERVICE_UNAVAILABLE)
- @ExceptionHandler(SidecarExportException.class)
- public ResponseEntity<ApiErrorDto> handle(SidecarExportException e) {
- return generic_handle(e.getClass(), e.getLocalizedMessage());
- }
-
- @Hidden
- @ResponseStatus(code = HttpStatus.SERVICE_UNAVAILABLE)
- @ExceptionHandler(SidecarImportException.class)
- public ResponseEntity<ApiErrorDto> handle(SidecarImportException e) {
- return generic_handle(e.getClass(), e.getLocalizedMessage());
- }
-
@Hidden
@ResponseStatus(code = HttpStatus.BAD_REQUEST)
@ExceptionHandler(SortException.class)
diff --git a/dbrepo-metadata-service/rest-service/src/main/resources/application-local.yml b/dbrepo-metadata-service/rest-service/src/main/resources/application-local.yml
index 793a2b6021a270dfd6b23971e40675889b3e4980..00aad2593496910a1f4e82b4d6a611c260545ed2 100644
--- a/dbrepo-metadata-service/rest-service/src/main/resources/application-local.yml
+++ b/dbrepo-metadata-service/rest-service/src/main/resources/application-local.yml
@@ -6,7 +6,6 @@ spring:
password: dbrepo
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.MariaDBDialect
open-in-view: false
properties:
hibernate:
diff --git a/dbrepo-metadata-service/rest-service/src/main/resources/application.yml b/dbrepo-metadata-service/rest-service/src/main/resources/application.yml
index 13e207a8bdd4101e7e74b592ade00b7787fcce4b..2d79e7cfae29b68515a6f008fd1aaae2c53f0461 100644
--- a/dbrepo-metadata-service/rest-service/src/main/resources/application.yml
+++ b/dbrepo-metadata-service/rest-service/src/main/resources/application.yml
@@ -9,7 +9,6 @@ spring:
password: "${METADATA_DB_PASSWORD:dbrepo}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.MariaDBDialect
open-in-view: false
properties:
hibernate:
diff --git a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/ViewEndpointUnitTest.java b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/ViewEndpointUnitTest.java
index b4291ce902652eeeea7aa7e12f6aac26d444bbe1..5451efdd7567cff88f27f23f8ad9a8f10a563bbb 100644
--- a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/ViewEndpointUnitTest.java
+++ b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/endpoints/ViewEndpointUnitTest.java
@@ -60,8 +60,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithAnonymousUser
- public void findAll_publicAnonymous_succeeds() throws ViewNotFoundException, UserNotFoundException,
- AccessNotFoundException, DatabaseNotFoundException {
+ public void findAll_publicAnonymous_succeeds() throws UserNotFoundException, AccessNotFoundException,
+ DatabaseNotFoundException {
/* test */
findAll_generic(DATABASE_3_ID, DATABASE_3, null, null, null, null);
@@ -69,8 +69,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME, authorities = {"list-views"})
- public void findAll_publicHasRole_succeeds() throws ViewNotFoundException, UserNotFoundException,
- AccessNotFoundException, DatabaseNotFoundException {
+ public void findAll_publicHasRole_succeeds() throws UserNotFoundException, AccessNotFoundException,
+ DatabaseNotFoundException {
/* test */
findAll_generic(DATABASE_3_ID, DATABASE_3, USER_2_PRINCIPAL, USER_2_ID, USER_2, null);
@@ -78,8 +78,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME, authorities = {"list-views"})
- public void findAll_publicHasRoleHasAccess_succeeds() throws ViewNotFoundException, UserNotFoundException,
- AccessNotFoundException, DatabaseNotFoundException {
+ public void findAll_publicHasRoleHasAccess_succeeds() throws UserNotFoundException, AccessNotFoundException,
+ DatabaseNotFoundException {
/* test */
findAll_generic(DATABASE_3_ID, DATABASE_3, USER_2_PRINCIPAL, USER_2_ID, USER_2, DATABASE_3_USER_2_READ_ACCESS);
@@ -87,8 +87,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME)
- public void findAll_publicNoRole_succeeds() throws ViewNotFoundException, UserNotFoundException,
- AccessNotFoundException, DatabaseNotFoundException {
+ public void findAll_publicNoRole_succeeds() throws UserNotFoundException, AccessNotFoundException,
+ DatabaseNotFoundException {
/* test */
findAll_generic(DATABASE_3_ID, DATABASE_3, USER_2_PRINCIPAL, USER_2_ID, USER_2, null);
@@ -136,8 +136,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithAnonymousUser
- public void find_publicAnonymous_succeeds() throws ViewNotFoundException, UserNotFoundException,
- DatabaseNotFoundException, AccessNotFoundException {
+ public void find_publicAnonymous_succeeds() throws UserNotFoundException, DatabaseNotFoundException,
+ AccessNotFoundException, ViewNotFoundException {
/* test */
find_generic(DATABASE_3_ID, DATABASE_3, null, null, null, null);
@@ -145,8 +145,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME, authorities = {"find-database-view"})
- public void find_publicHasRole_succeeds() throws ViewNotFoundException, UserNotFoundException,
- DatabaseNotFoundException, AccessNotFoundException {
+ public void find_publicHasRole_succeeds() throws UserNotFoundException, DatabaseNotFoundException,
+ AccessNotFoundException, ViewNotFoundException {
/* test */
find_generic(DATABASE_3_ID, DATABASE_3, USER_2_PRINCIPAL, USER_2_ID, USER_2, DATABASE_2_USER_1_READ_ACCESS);
@@ -154,8 +154,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME)
- public void find_publicNoRole_succeeds() throws ViewNotFoundException, UserNotFoundException,
- DatabaseNotFoundException, AccessNotFoundException {
+ public void find_publicNoRole_succeeds() throws UserNotFoundException, DatabaseNotFoundException,
+ AccessNotFoundException, ViewNotFoundException {
/* test */
find_generic(DATABASE_3_ID, DATABASE_3, USER_2_PRINCIPAL, USER_2_ID, USER_2, DATABASE_2_USER_1_READ_ACCESS);
@@ -163,8 +163,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME)
- public void find_publicHasRoleHasAccess_succeeds() throws ViewNotFoundException, UserNotFoundException,
- DatabaseNotFoundException, AccessNotFoundException {
+ public void find_publicHasRoleHasAccess_succeeds() throws UserNotFoundException, DatabaseNotFoundException,
+ AccessNotFoundException, ViewNotFoundException {
/* test */
find_generic(DATABASE_3_ID, DATABASE_3, USER_2_PRINCIPAL, USER_2_ID, USER_2, DATABASE_2_USER_1_READ_ACCESS);
@@ -203,8 +203,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_3_USERNAME, authorities = {"delete-database-view"})
public void delete_publicOwner_succeeds() throws NotAllowedException, DataServiceException,
- DataServiceConnectionException, ViewNotFoundException, DatabaseNotFoundException, AccessNotFoundException,
- SearchServiceException, SearchServiceConnectionException {
+ DataServiceConnectionException, DatabaseNotFoundException, AccessNotFoundException,
+ SearchServiceException, SearchServiceConnectionException, ViewNotFoundException {
/* test */
delete_generic(DATABASE_3_ID, DATABASE_3, VIEW_5_ID, VIEW_5, USER_3_PRINCIPAL, USER_3_ID, USER_3, DATABASE_3_USER_1_WRITE_ALL_ACCESS);
@@ -216,7 +216,7 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithAnonymousUser
- public void findAll_privateAnonymous_succeeds() throws ViewNotFoundException, UserNotFoundException,
+ public void findAll_privateAnonymous_succeeds() throws UserNotFoundException,
AccessNotFoundException, DatabaseNotFoundException {
/* test */
@@ -225,7 +225,7 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME, authorities = {"list-views"})
- public void findAll_privateHasRole_succeeds() throws ViewNotFoundException, UserNotFoundException,
+ public void findAll_privateHasRole_succeeds() throws UserNotFoundException,
AccessNotFoundException, DatabaseNotFoundException {
/* test */
@@ -234,7 +234,7 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME, authorities = {"list-views"})
- public void findAll_privateHasRoleHasAccess_succeeds() throws ViewNotFoundException, UserNotFoundException,
+ public void findAll_privateHasRoleHasAccess_succeeds() throws UserNotFoundException,
AccessNotFoundException, DatabaseNotFoundException {
/* test */
@@ -243,7 +243,7 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME)
- public void findAll_privateNoRole_succeeds() throws ViewNotFoundException, UserNotFoundException,
+ public void findAll_privateNoRole_succeeds() throws UserNotFoundException,
AccessNotFoundException, DatabaseNotFoundException {
/* test */
@@ -292,8 +292,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithAnonymousUser
- public void find_privateAnonymous_succeeds() throws ViewNotFoundException, UserNotFoundException,
- DatabaseNotFoundException, AccessNotFoundException {
+ public void find_privateAnonymous_succeeds() throws UserNotFoundException, DatabaseNotFoundException,
+ AccessNotFoundException, ViewNotFoundException {
/* test */
find_generic(DATABASE_1_ID, DATABASE_1, null, null, null, null);
@@ -301,8 +301,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME, authorities = {"find-database-view"})
- public void find_privateHasRole_succeeds() throws ViewNotFoundException, UserNotFoundException,
- DatabaseNotFoundException, AccessNotFoundException {
+ public void find_privateHasRole_succeeds() throws UserNotFoundException, DatabaseNotFoundException,
+ AccessNotFoundException, ViewNotFoundException {
/* test */
find_generic(DATABASE_1_ID, DATABASE_1, USER_2_PRINCIPAL, USER_2_ID, USER_2, DATABASE_2_USER_1_READ_ACCESS);
@@ -310,8 +310,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME)
- public void find_privateNoRole_succeeds() throws ViewNotFoundException, UserNotFoundException,
- DatabaseNotFoundException, AccessNotFoundException {
+ public void find_privateNoRole_succeeds() throws UserNotFoundException, DatabaseNotFoundException,
+ AccessNotFoundException, ViewNotFoundException {
/* test */
find_generic(DATABASE_1_ID, DATABASE_1, USER_2_PRINCIPAL, USER_2_ID, USER_2, DATABASE_2_USER_1_READ_ACCESS);
@@ -319,8 +319,8 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_2_USERNAME)
- public void find_privateHasRoleHasAccess_succeeds() throws ViewNotFoundException, UserNotFoundException,
- DatabaseNotFoundException, AccessNotFoundException {
+ public void find_privateHasRoleHasAccess_succeeds() throws UserNotFoundException, DatabaseNotFoundException,
+ AccessNotFoundException, ViewNotFoundException {
/* test */
find_generic(DATABASE_1_ID, DATABASE_1, USER_2_PRINCIPAL, USER_2_ID, USER_2, DATABASE_2_USER_1_READ_ACCESS);
@@ -358,9 +358,9 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
@Test
@WithMockUser(username = USER_1_USERNAME, authorities = {"delete-database-view"})
- public void delete_privateOwner_succeeds() throws NotAllowedException, DataServiceException, DataServiceConnectionException,
- DatabaseNotFoundException, AccessNotFoundException, ViewNotFoundException, SearchServiceException,
- SearchServiceConnectionException {
+ public void delete_privateOwner_succeeds() throws NotAllowedException, DataServiceException,
+ DataServiceConnectionException, DatabaseNotFoundException, AccessNotFoundException, SearchServiceException,
+ SearchServiceConnectionException, ViewNotFoundException {
/* test */
delete_generic(DATABASE_1_ID, DATABASE_1, VIEW_1_ID, VIEW_1, USER_1_PRINCIPAL, USER_1_ID, USER_1, DATABASE_1_USER_1_WRITE_ALL_ACCESS);
@@ -476,7 +476,7 @@ public class ViewEndpointUnitTest extends AbstractUnitTest {
protected void delete_generic(Long databaseId, Database database, Long viewId, View view, Principal principal,
UUID userId, User user, DatabaseAccess access) throws NotAllowedException,
DataServiceException, DataServiceConnectionException, DatabaseNotFoundException, AccessNotFoundException,
- ViewNotFoundException, SearchServiceException, SearchServiceConnectionException {
+ SearchServiceException, SearchServiceConnectionException, ViewNotFoundException {
/* mock */
when(databaseService.findById(databaseId))
diff --git a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/mvc/AuthenticationPrivilegedIntegrationMvcTest.java b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/mvc/AuthenticationPrivilegedIntegrationMvcTest.java
index 474db3910bef5233d676bf387edd63afcd4aa5c6..6a01ae6fec9e06d679fc848af0b697fcfbeba3df 100644
--- a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/mvc/AuthenticationPrivilegedIntegrationMvcTest.java
+++ b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/mvc/AuthenticationPrivilegedIntegrationMvcTest.java
@@ -146,8 +146,7 @@ public class AuthenticationPrivilegedIntegrationMvcTest extends AbstractUnitTest
.andExpect(header().doesNotExist("X-Port"))
.andExpect(header().doesNotExist("X-Type"))
.andExpect(header().doesNotExist("X-Database"))
- .andExpect(header().doesNotExist("X-Sidecar-Host"))
- .andExpect(header().doesNotExist("X-Sidecar-Port"))
+ .andExpect(header().doesNotExist("X-Table"))
.andExpect(header().doesNotExist("Access-Control-Expose-Headers"))
.andExpect(status().isOk());
}
@@ -167,9 +166,8 @@ public class AuthenticationPrivilegedIntegrationMvcTest extends AbstractUnitTest
.andExpect(header().string("X-Port", "" + CONTAINER_1_PORT))
.andExpect(header().string("X-Type", IMAGE_1_JDBC))
.andExpect(header().string("X-Database", DATABASE_1_INTERNALNAME))
- .andExpect(header().string("X-Sidecar-Host", CONTAINER_1_SIDECAR_HOST))
- .andExpect(header().string("X-Sidecar-Port", "" + CONTAINER_1_SIDECAR_PORT))
- .andExpect(header().string("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database X-Sidecar-Host X-Sidecar-Port"))
+ .andExpect(header().string("X-Table", TABLE_1_INTERNALNAME))
+ .andExpect(header().string("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database X-Table"))
.andExpect(status().isOk());
}
@@ -186,9 +184,8 @@ public class AuthenticationPrivilegedIntegrationMvcTest extends AbstractUnitTest
.andExpect(header().string("X-Port", "" + CONTAINER_1_PORT))
.andExpect(header().string("X-Type", IMAGE_1_JDBC))
.andExpect(header().string("X-Database", DATABASE_1_INTERNALNAME))
- .andExpect(header().string("X-Sidecar-Host", CONTAINER_1_SIDECAR_HOST))
- .andExpect(header().string("X-Sidecar-Port", "" + CONTAINER_1_SIDECAR_PORT))
- .andExpect(header().string("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database X-Sidecar-Host X-Sidecar-Port"))
+ .andExpect(header().string("X-Table", TABLE_1_INTERNALNAME))
+ .andExpect(header().string("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database X-Table"))
.andExpect(status().isOk());
}
@@ -207,6 +204,7 @@ public class AuthenticationPrivilegedIntegrationMvcTest extends AbstractUnitTest
.andExpect(header().doesNotExist("X-Port"))
.andExpect(header().doesNotExist("X-Type"))
.andExpect(header().doesNotExist("X-Database"))
+ .andExpect(header().doesNotExist("X-View"))
.andExpect(header().doesNotExist("Access-Control-Expose-Headers"))
.andExpect(status().isOk());
}
@@ -226,7 +224,8 @@ public class AuthenticationPrivilegedIntegrationMvcTest extends AbstractUnitTest
.andExpect(header().string("X-Port", "" + CONTAINER_1_PORT))
.andExpect(header().string("X-Type", IMAGE_1_JDBC))
.andExpect(header().string("X-Database", DATABASE_1_INTERNALNAME))
- .andExpect(header().string("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database"))
+ .andExpect(header().string("X-View", VIEW_1_INTERNAL_NAME))
+ .andExpect(header().string("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database X-View"))
.andExpect(status().isOk());
}
@@ -243,7 +242,8 @@ public class AuthenticationPrivilegedIntegrationMvcTest extends AbstractUnitTest
.andExpect(header().string("X-Port", "" + CONTAINER_1_PORT))
.andExpect(header().string("X-Type", IMAGE_1_JDBC))
.andExpect(header().string("X-Database", DATABASE_1_INTERNALNAME))
- .andExpect(header().string("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database"))
+ .andExpect(header().string("X-View", VIEW_1_INTERNAL_NAME))
+ .andExpect(header().string("Access-Control-Expose-Headers", "X-Username X-Password X-Host X-Port X-Type X-Database X-View"))
.andExpect(status().isOk());
}
diff --git a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/service/DatabaseServicePersistenceTest.java b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/service/DatabaseServicePersistenceTest.java
index 51b6df4d27b7af3332e5cb592c627e1e2ae03995..436ccd18794fe1ba46e772c65c785ec4f1240f32 100644
--- a/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/service/DatabaseServicePersistenceTest.java
+++ b/dbrepo-metadata-service/rest-service/src/test/java/at/tuwien/service/DatabaseServicePersistenceTest.java
@@ -70,8 +70,6 @@ public class DatabaseServicePersistenceTest extends AbstractUnitTest {
assertEquals(CONTAINER_1_UI_HOST, response.getContainer().getUiHost());
assertEquals(CONTAINER_1_UI_PORT, response.getContainer().getUiPort());
assertEquals(CONTAINER_1_UI_ADDITIONAL_FLAGS, response.getContainer().getUiAdditionalFlags());
- assertEquals(CONTAINER_1_SIDECAR_HOST, response.getContainer().getSidecarHost());
- assertEquals(CONTAINER_1_SIDECAR_PORT, response.getContainer().getSidecarPort());
assertEquals(CONTAINER_1_PRIVILEGED_USERNAME, response.getContainer().getPrivilegedUsername());
assertEquals(CONTAINER_1_PRIVILEGED_PASSWORD, response.getContainer().getPrivilegedPassword());
assertNotNull(response.getContainer().getImage());
@@ -110,8 +108,6 @@ public class DatabaseServicePersistenceTest extends AbstractUnitTest {
assertEquals(CONTAINER_1_UI_HOST, response.getContainer().getUiHost());
assertEquals(CONTAINER_1_UI_PORT, response.getContainer().getUiPort());
assertEquals(CONTAINER_1_UI_ADDITIONAL_FLAGS, response.getContainer().getUiAdditionalFlags());
- assertEquals(CONTAINER_1_SIDECAR_HOST, response.getContainer().getSidecarHost());
- assertEquals(CONTAINER_1_SIDECAR_PORT, response.getContainer().getSidecarPort());
assertEquals(CONTAINER_1_PRIVILEGED_USERNAME, response.getContainer().getPrivilegedUsername());
assertEquals(CONTAINER_1_PRIVILEGED_PASSWORD, response.getContainer().getPrivilegedPassword());
assertNotNull(response.getContainer().getImage());
diff --git a/dbrepo-metadata-service/test/src/main/java/at/tuwien/test/AbstractUnitTest.java b/dbrepo-metadata-service/test/src/main/java/at/tuwien/test/AbstractUnitTest.java
index 3ab89a39051326901f9b4029689bf4be82bd177f..8e613cfa7cad69c2de42d96ccacee6957e5f7939 100644
--- a/dbrepo-metadata-service/test/src/main/java/at/tuwien/test/AbstractUnitTest.java
+++ b/dbrepo-metadata-service/test/src/main/java/at/tuwien/test/AbstractUnitTest.java
@@ -9,6 +9,7 @@ import java.util.List;
public abstract class AbstractUnitTest extends BaseTest {
public void genesis() {
+ IMAGE_1.setOperators(new LinkedList<>(IMAGE_1_OPERATORS));
CONTAINER_1.setDatabases(new LinkedList<>(List.of(DATABASE_1, DATABASE_2, DATABASE_3)));
CONTAINER_4.setDatabases(new LinkedList<>(List.of(DATABASE_4)));
/* USER_1 */
diff --git a/dbrepo-metadata-service/test/src/main/java/at/tuwien/test/BaseTest.java b/dbrepo-metadata-service/test/src/main/java/at/tuwien/test/BaseTest.java
index c6c0e4ec10150224ee4c21c6a1bf582649ba941e..7e6154be62dd72623c558816b1f679139b7f3a18 100644
--- a/dbrepo-metadata-service/test/src/main/java/at/tuwien/test/BaseTest.java
+++ b/dbrepo-metadata-service/test/src/main/java/at/tuwien/test/BaseTest.java
@@ -63,6 +63,7 @@ import at.tuwien.api.user.*;
import at.tuwien.api.user.internal.UpdateUserPasswordDto;
import at.tuwien.entities.container.Container;
import at.tuwien.entities.container.image.ContainerImage;
+import at.tuwien.entities.container.image.Operator;
import at.tuwien.entities.database.*;
import at.tuwien.entities.database.table.Table;
import at.tuwien.entities.database.table.columns.TableColumn;
@@ -953,6 +954,15 @@ public abstract class BaseTest {
.isDefault(IMAGE_1_IS_DEFAULT)
.build();
+ public final static List<Operator> IMAGE_1_OPERATORS = List.of(
+ Operator.builder()
+ .id(1L)
+ .image(IMAGE_1)
+ .displayName("XOR")
+ .value("XOR")
+ .documentation("https://mariadb.com/kb/en/xor/")
+ .build());
+
public final static Long CONTAINER_1_ID = 1L;
public final static ContainerImage CONTAINER_1_IMAGE = IMAGE_1;
public final static ImageDto CONTAINER_1_IMAGE_DTO = IMAGE_1_DTO;
@@ -966,8 +976,6 @@ public abstract class BaseTest {
public final static Integer CONTAINER_1_COUNT = 3;
public final static String CONTAINER_1_HOST = "localhost";
public final static Integer CONTAINER_1_PORT = 3308;
- public final static String CONTAINER_1_SIDECAR_HOST = "localhost";
- public final static Integer CONTAINER_1_SIDECAR_PORT = 33081;
public final static String CONTAINER_1_PRIVILEGED_USERNAME = "root";
public final static String CONTAINER_1_PRIVILEGED_PASSWORD = "dbrepo";
public final static Instant CONTAINER_1_CREATED = Instant.ofEpochSecond(1677399629L) /* 2023-02-26 08:20:29 (UTC) */;
@@ -986,8 +994,6 @@ public abstract class BaseTest {
.uiAdditionalFlags(CONTAINER_1_UI_ADDITIONAL_FLAGS)
.privilegedUsername(CONTAINER_1_PRIVILEGED_USERNAME)
.privilegedPassword(CONTAINER_1_PRIVILEGED_PASSWORD)
- .sidecarHost(CONTAINER_1_SIDECAR_HOST)
- .sidecarPort(CONTAINER_1_SIDECAR_PORT)
.build();
public final static ContainerDto CONTAINER_1_DTO = ContainerDto.builder()
@@ -1017,8 +1023,6 @@ public abstract class BaseTest {
.created(CONTAINER_1_CREATED)
.host(CONTAINER_1_HOST)
.port(CONTAINER_1_PORT)
- .sidecarHost(CONTAINER_1_SIDECAR_HOST)
- .sidecarPort(CONTAINER_1_SIDECAR_PORT)
.username(CONTAINER_1_PRIVILEGED_USERNAME)
.password(CONTAINER_1_PRIVILEGED_PASSWORD)
.build();
@@ -1031,8 +1035,6 @@ public abstract class BaseTest {
public final static String CONTAINER_2_IP = "172.30.0.6";
public final static String CONTAINER_2_HOST = "localhost";
public final static Integer CONTAINER_2_PORT = 3309;
- public final static String CONTAINER_2_SIDECAR_HOST = "localhost";
- public final static Integer CONTAINER_2_SIDECAR_PORT = 33091;
public final static Integer CONTAINER_2_QUOTA = 3;
public final static Integer CONTAINER_2_COUNT = 3;
public final static String CONTAINER_2_PRIVILEGED_USERNAME = "root";
@@ -1079,8 +1081,6 @@ public abstract class BaseTest {
public final static String CONTAINER_3_HOST = "localhost";
public final static Integer CONTAINER_3_PORT = 3310;
public final static Integer CONTAINER_3_QUOTA = 20;
- public final static String CONTAINER_3_SIDECAR_HOST = "localhost";
- public final static Integer CONTAINER_3_SIDECAR_PORT = 33101;
public final static String CONTAINER_3_PRIVILEGED_USERNAME = "root";
public final static String CONTAINER_3_PRIVILEGED_PASSWORD = "dbrepo";
public final static Instant CONTAINER_3_CREATED = Instant.ofEpochSecond(1677399672L) /* 2023-02-26 08:21:12 (UTC) */;
@@ -1107,8 +1107,6 @@ public abstract class BaseTest {
public final static String CONTAINER_4_HOST = "localhost";
public final static Integer CONTAINER_4_PORT = 3311;
public final static Integer CONTAINER_4_QUOTA = 0;
- public final static String CONTAINER_4_SIDECAR_HOST = "localhost";
- public final static Integer CONTAINER_4_SIDECAR_PORT = 33111;
public final static String CONTAINER_4_PRIVILEGED_USERNAME = "root";
public final static String CONTAINER_4_PRIVILEGED_PASSWORD = "dbrepo";
public final static Instant CONTAINER_4_CREATED = Instant.ofEpochSecond(1677399688L) /* 2023-02-26 08:21:28 (UTC) */;
diff --git a/dbrepo-metric-db/prometheus.yml b/dbrepo-metric-db/prometheus.yml
index 10df4f18959a0630be82ec22e44adbf13818f7bf..92ecf83adcbdb46179c74fc246143d1ca14a591a 100644
--- a/dbrepo-metric-db/prometheus.yml
+++ b/dbrepo-metric-db/prometheus.yml
@@ -16,7 +16,7 @@ scrape_configs:
- job_name: 'metrics scrape'
metrics_path: '/metrics'
static_configs:
- - targets: ['ui:3000', 'auth-service:9000', 'analyse-service:8080', 'search-service:8080', 'data-db-sidecar:8080', 'broker-service:15692', 'storage-service:9090', 'upload-service:8080', 'dashboard-service:3000']
+ - targets: ['ui:3000', 'compute-service:8080', 'auth-service:9000', 'analyse-service:8080', 'search-service:8080', 'data-db-sidecar:8080', 'broker-service:15692', 'storage-service:9090', 'upload-service:8080', 'dashboard-service:3000']
# - job_name: 'gateway scrape'
# metrics_path: '/metrics'
# static_configs:
diff --git a/dbrepo-search-service/Pipfile.lock b/dbrepo-search-service/Pipfile.lock
index 123e864f6dd050a838ae2c7e9137a4d7b3f1e27f..fc5839fcdb5054840363d5a4a010208af681d852 100644
--- a/dbrepo-search-service/Pipfile.lock
+++ b/dbrepo-search-service/Pipfile.lock
@@ -355,40 +355,40 @@
},
"cryptography": {
"hashes": [
- "sha256:014f58110f53237ace6a408b5beb6c427b64e084eb451ef25a28308270086494",
- "sha256:1bbcce1a551e262dfbafb6e6252f1ae36a248e615ca44ba302df077a846a8806",
- "sha256:203e92a75716d8cfb491dc47c79e17d0d9207ccffcbcb35f598fbe463ae3444d",
- "sha256:27e613d7077ac613e399270253259d9d53872aaf657471473ebfc9a52935c062",
- "sha256:2bd51274dcd59f09dd952afb696bf9c61a7a49dfc764c04dd33ef7a6b502a1e2",
- "sha256:38926c50cff6f533f8a2dae3d7f19541432610d114a70808f0926d5aaa7121e4",
- "sha256:511f4273808ab590912a93ddb4e3914dfd8a388fed883361b02dea3791f292e1",
- "sha256:58d4e9129985185a06d849aa6df265bdd5a74ca6e1b736a77959b498e0505b85",
- "sha256:5b43d1ea6b378b54a1dc99dd8a2b5be47658fe9a7ce0a58ff0b55f4b43ef2b84",
- "sha256:61ec41068b7b74268fa86e3e9e12b9f0c21fcf65434571dbb13d954bceb08042",
- "sha256:666ae11966643886c2987b3b721899d250855718d6d9ce41b521252a17985f4d",
- "sha256:68aaecc4178e90719e95298515979814bda0cbada1256a4485414860bd7ab962",
- "sha256:7c05650fe8023c5ed0d46793d4b7d7e6cd9c04e68eabe5b0aeea836e37bdcec2",
- "sha256:80eda8b3e173f0f247f711eef62be51b599b5d425c429b5d4ca6a05e9e856baa",
- "sha256:8385d98f6a3bf8bb2d65a73e17ed87a3ba84f6991c155691c51112075f9ffc5d",
- "sha256:88cce104c36870d70c49c7c8fd22885875d950d9ee6ab54df2745f83ba0dc365",
- "sha256:9d3cdb25fa98afdd3d0892d132b8d7139e2c087da1712041f6b762e4f807cc96",
- "sha256:a575913fb06e05e6b4b814d7f7468c2c660e8bb16d8d5a1faf9b33ccc569dd47",
- "sha256:ac119bb76b9faa00f48128b7f5679e1d8d437365c5d26f1c2c3f0da4ce1b553d",
- "sha256:c1332724be35d23a854994ff0b66530119500b6053d0bd3363265f7e5e77288d",
- "sha256:d03a475165f3134f773d1388aeb19c2d25ba88b6a9733c5c590b9ff7bbfa2e0c",
- "sha256:d75601ad10b059ec832e78823b348bfa1a59f6b8d545db3a24fd44362a1564cb",
- "sha256:de41fd81a41e53267cb020bb3a7212861da53a7d39f863585d13ea11049cf277",
- "sha256:e710bf40870f4db63c3d7d929aa9e09e4e7ee219e703f949ec4073b4294f6172",
- "sha256:ea25acb556320250756e53f9e20a4177515f012c9eaea17eb7587a8c4d8ae034",
- "sha256:f98bf604c82c416bc829e490c700ca1553eafdf2912a91e23a79d97d9801372a",
- "sha256:fba1007b3ef89946dbbb515aeeb41e30203b004f0b4b00e5e16078b518563289"
+ "sha256:0c580952eef9bf68c4747774cde7ec1d85a6e61de97281f2dba83c7d2c806362",
+ "sha256:0f996e7268af62598f2fc1204afa98a3b5712313a55c4c9d434aef49cadc91d4",
+ "sha256:1ec0bcf7e17c0c5669d881b1cd38c4972fade441b27bda1051665faaa89bdcaa",
+ "sha256:281c945d0e28c92ca5e5930664c1cefd85efe80e5c0d2bc58dd63383fda29f83",
+ "sha256:2ce6fae5bdad59577b44e4dfed356944fbf1d925269114c28be377692643b4ff",
+ "sha256:315b9001266a492a6ff443b61238f956b214dbec9910a081ba5b6646a055a805",
+ "sha256:443c4a81bb10daed9a8f334365fe52542771f25aedaf889fd323a853ce7377d6",
+ "sha256:4a02ded6cd4f0a5562a8887df8b3bd14e822a90f97ac5e544c162899bc467664",
+ "sha256:53a583b6637ab4c4e3591a15bc9db855b8d9dee9a669b550f311480acab6eb08",
+ "sha256:63efa177ff54aec6e1c0aefaa1a241232dcd37413835a9b674b6e3f0ae2bfd3e",
+ "sha256:74f57f24754fe349223792466a709f8e0c093205ff0dca557af51072ff47ab18",
+ "sha256:7e1ce50266f4f70bf41a2c6dc4358afadae90e2a1e5342d3c08883df1675374f",
+ "sha256:81ef806b1fef6b06dcebad789f988d3b37ccaee225695cf3e07648eee0fc6b73",
+ "sha256:846da004a5804145a5f441b8530b4bf35afbf7da70f82409f151695b127213d5",
+ "sha256:8ac43ae87929a5982f5948ceda07001ee5e83227fd69cf55b109144938d96984",
+ "sha256:9762ea51a8fc2a88b70cf2995e5675b38d93bf36bd67d91721c309df184f49bd",
+ "sha256:a2a431ee15799d6db9fe80c82b055bae5a752bef645bba795e8e52687c69efe3",
+ "sha256:bf7a1932ac4176486eab36a19ed4c0492da5d97123f1406cf15e41b05e787d2e",
+ "sha256:c2e6fc39c4ab499049df3bdf567f768a723a5e8464816e8f009f121a5a9f4405",
+ "sha256:cbeb489927bd7af4aa98d4b261af9a5bc025bd87f0e3547e11584be9e9427be2",
+ "sha256:d03b5621a135bffecad2c73e9f4deb1a0f977b9a8ffe6f8e002bf6c9d07b918c",
+ "sha256:d56e96520b1020449bbace2b78b603442e7e378a9b3bd68de65c782db1507995",
+ "sha256:df6b6c6d742395dd77a23ea3728ab62f98379eff8fb61be2744d4679ab678f73",
+ "sha256:e1be4655c7ef6e1bbe6b5d0403526601323420bcf414598955968c9ef3eb7d16",
+ "sha256:f18c716be16bc1fea8e95def49edf46b82fccaa88587a45f8dc0ff6ab5d8e0a7",
+ "sha256:f46304d6f0c6ab8e52770addfa2fc41e6629495548862279641972b6215451cd",
+ "sha256:f7b178f11ed3664fd0e995a47ed2b5ff0a12d893e41dd0494f406d1cf555cab7"
],
"markers": "python_version >= '3.7'",
- "version": "==43.0.1"
+ "version": "==43.0.3"
},
"dbrepo": {
"hashes": [
- "sha256:84607677b0826bb9b2fa120aacdf56d16c8d9ae423f435b2bd2c22b1c965a33c"
+ "sha256:36316d520c23dcbd249b779ad596a979fe574321882a7d4b6c6934c62a5de57b"
],
"path": "./lib/dbrepo-1.4.7.tar.gz"
},
@@ -458,86 +458,101 @@
},
"frozenlist": {
"hashes": [
- "sha256:04ced3e6a46b4cfffe20f9ae482818e34eba9b5fb0ce4056e4cc9b6e212d09b7",
- "sha256:0633c8d5337cb5c77acbccc6357ac49a1770b8c487e5b3505c57b949b4b82e98",
- "sha256:068b63f23b17df8569b7fdca5517edef76171cf3897eb68beb01341131fbd2ad",
- "sha256:0c250a29735d4f15321007fb02865f0e6b6a41a6b88f1f523ca1596ab5f50bd5",
- "sha256:1979bc0aeb89b33b588c51c54ab0161791149f2461ea7c7c946d95d5f93b56ae",
- "sha256:1a4471094e146b6790f61b98616ab8e44f72661879cc63fa1049d13ef711e71e",
- "sha256:1b280e6507ea8a4fa0c0a7150b4e526a8d113989e28eaaef946cc77ffd7efc0a",
- "sha256:1d0ce09d36d53bbbe566fe296965b23b961764c0bcf3ce2fa45f463745c04701",
- "sha256:20b51fa3f588ff2fe658663db52a41a4f7aa6c04f6201449c6c7c476bd255c0d",
- "sha256:23b2d7679b73fe0e5a4560b672a39f98dfc6f60df63823b0a9970525325b95f6",
- "sha256:23b701e65c7b36e4bf15546a89279bd4d8675faabc287d06bbcfac7d3c33e1e6",
- "sha256:2471c201b70d58a0f0c1f91261542a03d9a5e088ed3dc6c160d614c01649c106",
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],
"markers": "python_version >= '3.8'",
- "version": "==1.4.1"
+ "version": "==1.5.0"
},
"greenlet": {
"hashes": [
@@ -643,13 +658,6 @@
"markers": "python_version >= '3.7'",
"version": "==2.0.0"
},
- "isodate": {
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"itsdangerous": {
"hashes": [
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@@ -692,70 +700,70 @@
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],
"markers": "python_version >= '3.9'",
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+ "version": "==3.0.2"
},
"mistune": {
"hashes": [
@@ -865,62 +873,64 @@
},
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],
"markers": "python_version == '3.11'",
- "version": "==2.1.2"
+ "version": "==2.1.3"
},
"opensearch-py": {
"hashes": [
@@ -1344,12 +1354,12 @@
},
"rdflib": {
"hashes": [
- "sha256:0438920912a642c866a513de6fe8a0001bd86ef975057d6962c79ce4771687cd",
- "sha256:9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae"
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],
"index": "pypi",
"markers": "python_full_version >= '3.8.1' and python_full_version < '4.0.0'",
- "version": "==7.0.0"
+ "version": "==7.1.1"
},
"referencing": {
"hashes": [
@@ -1369,112 +1379,112 @@
},
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],
"markers": "python_version >= '3.8'",
- "version": "==0.20.0"
+ "version": "==0.20.1"
},
"six": {
"hashes": [
@@ -1486,58 +1496,66 @@
},
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+ "sha256:a86bfab2ef46d63300c0f06936bd6e6c0105faa11d509083ba8f2f9d237fb5b5",
+ "sha256:ac9dfa18ff2a67b09b372d5db8743c27966abf0e5344c555d86cc7199f7ad83a",
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+ "sha256:b11d0cfdd2b095e7b0686cf5fabeb9c67fae5b06d265d8180715b8cfa86522e3",
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+ "sha256:b5cc79df7f4bc3d11e4b542596c03826063092611e481fcf1c9dfee3c94355ef",
+ "sha256:b817d41d692bf286abc181f8af476c4fbef3fd05e798777492618378448ee689",
+ "sha256:b81ee3d84803fd42d0b154cb6892ae57ea6b7c55d8359a02379965706c7efe6c",
+ "sha256:be9812b766cad94a25bc63bec11f88c4ad3629a0cec1cd5d4ba48dc23860486b",
+ "sha256:c245b1fbade9c35e5bd3b64270ab49ce990369018289ecfde3f9c318411aaa07",
+ "sha256:c3f3631693003d8e585d4200730616b78fafd5a01ef8b698f6967da5c605b3fa",
+ "sha256:c4ae3005ed83f5967f961fd091f2f8c5329161f69ce8480aa8168b2d7fe37f06",
+ "sha256:c54a1e53a0c308a8e8a7dffb59097bff7facda27c70c286f005327f21b2bd6b1",
+ "sha256:d0ddd9db6e59c44875211bc4c7953a9f6638b937b0a88ae6d09eb46cced54eff",
+ "sha256:dc022184d3e5cacc9579e41805a681187650e170eb2fd70e28b86192a479dcaa",
+ "sha256:e32092c47011d113dc01ab3e1d3ce9f006a47223b18422c5c0d150af13a00687",
+ "sha256:f7b64e6ec3f02c35647be6b4851008b26cff592a95ecb13b6788a54ef80bbdd4",
+ "sha256:f942a799516184c855e1a32fbc7b29d7e571b52612647866d4ec1c3242578fcb",
+ "sha256:f9511d8dd4a6e9271d07d150fb2f81874a3c8c95e11ff9af3a2dfc35fe42ee44",
+ "sha256:fd3a55deef00f689ce931d4d1b23fa9f04c880a48ee97af488fd215cf24e2a6c",
+ "sha256:fddbe92b4760c6f5d48162aef14824add991aeda8ddadb3c31d56eb15ca69f8e",
+ "sha256:fdf3386a801ea5aba17c6410dd1dc8d39cf454ca2565541b5ac42a84e1e28f53"
],
"markers": "python_version >= '3.7'",
- "version": "==2.0.35"
+ "version": "==2.0.36"
},
"sqlalchemy-utils": {
"hashes": [
@@ -1605,11 +1623,11 @@
},
"werkzeug": {
"hashes": [
- "sha256:02c9eb92b7d6c06f31a782811505d2157837cea66aaede3e217c7c27c039476c",
- "sha256:34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306"
+ "sha256:8cd39dfbdfc1e051965f156163e2974e52c210f130810e9ad36858f0fd3edad4",
+ "sha256:a71124d1ef06008baafa3d266c02f56e1836a5984afd6dd6c9230669d60d9fb5"
],
- "markers": "python_version >= '3.8'",
- "version": "==3.0.4"
+ "markers": "python_version >= '3.9'",
+ "version": "==3.1.1"
},
"wrapt": {
"hashes": [
@@ -1689,107 +1707,91 @@
},
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+ "sha256:8ee427208c675f1b6e344a1f89376a9613fc30b52646a04ac0c1f6587c7e46ec",
+ "sha256:949681f68e0e3c25377462be4b658500e85ca24323d9619fdc41f68d46a1ffda",
+ "sha256:9e275792097c9f7e80741c36de3b61917aebecc08a67ae62899b074566ff8556",
+ "sha256:9fb815155aac6bfa8d86184079652c9715c812d506b22cfa369196ef4e99d1b4",
+ "sha256:a2a64e62c7a0edd07c1c917b0586655f3362d2c2d37d474db1a509efb96fea1c",
+ "sha256:a7ac5b4984c468ce4f4a553df281450df0a34aefae02e58d77a0847be8d1e11f",
+ "sha256:aa46dce75078fceaf7cecac5817422febb4355fbdda440db55206e3bd288cfb8",
+ "sha256:ae3476e934b9d714aa8000d2e4c01eb2590eee10b9d8cd03e7983ad65dfbfcba",
+ "sha256:b0341e6d9a0c0e3cdc65857ef518bb05b410dbd70d749a0d33ac0f39e81a4258",
+ "sha256:b40d1bf6e6f74f7c0a567a9e5e778bbd4699d1d3d2c0fe46f4b717eef9e96b95",
+ "sha256:b5c4804e4039f487e942c13381e6c27b4b4e66066d94ef1fae3f6ba8b953f383",
+ "sha256:b5d6a6c9602fd4598fa07e0389e19fe199ae96449008d8304bf5d47cb745462e",
+ "sha256:b5f1ac7359e17efe0b6e5fec21de34145caef22b260e978336f325d5c84e6938",
+ "sha256:c0167540094838ee9093ef6cc2c69d0074bbf84a432b4995835e8e5a0d984374",
+ "sha256:c180ac742a083e109c1a18151f4dd8675f32679985a1c750d2ff806796165b55",
+ "sha256:c73df5b6e8fabe2ddb74876fb82d9dd44cbace0ca12e8861ce9155ad3c886139",
+ "sha256:c7e177c619342e407415d4f35dec63d2d134d951e24b5166afcdfd1362828e17",
+ "sha256:cbad927ea8ed814622305d842c93412cb47bd39a496ed0f96bfd42b922b4a217",
+ "sha256:cc353841428d56b683a123a813e6a686e07026d6b1c5757970a877195f880c2d",
+ "sha256:cc7c92c1baa629cb03ecb0c3d12564f172218fb1739f54bf5f3881844daadc6d",
+ "sha256:cc7d768260f4ba4ea01741c1b5fe3d3a6c70eb91c87f4c8761bbcce5181beafe",
+ "sha256:d0eea830b591dbc68e030c86a9569826145df485b2b4554874b07fea1275a199",
+ "sha256:d216e5d9b8749563c7f2c6f7a0831057ec844c68b4c11cb10fc62d4fd373c26d",
+ "sha256:d401f07261dc5aa36c2e4efc308548f6ae943bfff20fcadb0a07517a26b196d8",
+ "sha256:d6324274b4e0e2fa1b3eccb25997b1c9ed134ff61d296448ab8269f5ac068c4c",
+ "sha256:d8a8b74d843c2638f3864a17d97a4acda58e40d3e44b6303b8cc3d3c44ae2d29",
+ "sha256:d9b6b28a57feb51605d6ae5e61a9044a31742db557a3b851a74c13bc61de5172",
+ "sha256:de599af166970d6a61accde358ec9ded821234cbbc8c6413acfec06056b8e860",
+ "sha256:e594b22688d5747b06e957f1ef822060cb5cb35b493066e33ceac0cf882188b7",
+ "sha256:e5b078134f48552c4d9527db2f7da0b5359abd49393cdf9794017baec7506170",
+ "sha256:eb6dce402734575e1a8cc0bb1509afca508a400a57ce13d306ea2c663bad1138",
+ "sha256:f1790a4b1e8e8e028c391175433b9c8122c39b46e1663228158e61e6f915bf06",
+ "sha256:f5efe0661b9fcd6246f27957f6ae1c0eb29bc60552820f01e970b4996e016004",
+ "sha256:f9cbfbc5faca235fbdf531b93aa0f9f005ec7d267d9d738761a4d42b744ea159",
+ "sha256:fbea1751729afe607d84acfd01efd95e3b31db148a181a441984ce9b3d3469da",
+ "sha256:fca4b4307ebe9c3ec77a084da3a9d1999d164693d16492ca2b64594340999988",
+ "sha256:ff5c6771c7e3511a06555afa317879b7db8d640137ba55d6ab0d0c50425cab75"
],
- "markers": "python_version >= '3.8'",
- "version": "==1.15.2"
+ "markers": "python_version >= '3.9'",
+ "version": "==1.17.1"
}
},
"develop": {
@@ -1914,72 +1916,72 @@
},
"coverage": {
"hashes": [
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- "sha256:99670790f21a96665a35849990b1df447993880bb6463a0a1d757897f30da929",
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- "sha256:99ded130555c021d99729fabd4ddb91a6f4cc0707df4b1daf912c7850c373b13",
- "sha256:a3328c3e64ea4ab12b85999eb0779e6139295bbf5485f69d42cf794309e3d007",
- "sha256:a4fb91d5f72b7e06a14ff4ae5be625a81cd7e5f869d7a54578fc271d08d58ae3",
- "sha256:aa23ce39661a3e90eea5f99ec59b763b7d655c2cada10729ed920a38bfc2b167",
- "sha256:aac7501ae73d4a02f4b7ac8fcb9dc55342ca98ffb9ed9f2dfb8a25d53eda0e4d",
- "sha256:ab84a8b698ad5a6c365b08061920138e7a7dd9a04b6feb09ba1bfae68346ce6d",
- "sha256:b4adeb878a374126f1e5cf03b87f66279f479e01af0e9a654cf6d1509af46c40",
- "sha256:b9853509b4bf57ba7b1f99b9d866c422c9c5248799ab20e652bbb8a184a38181",
- "sha256:bb7d5fe92bd0dc235f63ebe9f8c6e0884f7360f88f3411bfed1350c872ef2054",
- "sha256:bca4c8abc50d38f9773c1ec80d43f3768df2e8576807d1656016b9d3eeaa96fd",
- "sha256:c222958f59b0ae091f4535851cbb24eb57fc0baea07ba675af718fb5302dddb2",
- "sha256:c30e42ea11badb147f0d2e387115b15e2bd8205a5ad70d6ad79cf37f6ac08c91",
- "sha256:c3a79f56dee9136084cf84a6c7c4341427ef36e05ae6415bf7d787c96ff5eaa3",
- "sha256:c51ef82302386d686feea1c44dbeef744585da16fcf97deea2a8d6c1556f519b",
- "sha256:c77326300b839c44c3e5a8fe26c15b7e87b2f32dfd2fc9fee1d13604347c9b38",
- "sha256:d33a785ea8354c480515e781554d3be582a86297e41ccbea627a5c632647f2cd",
- "sha256:d546cfa78844b8b9c1c0533de1851569a13f87449897bbc95d698d1d3cb2a30f",
- "sha256:da29ceabe3025a1e5a5aeeb331c5b1af686daab4ff0fb4f83df18b1180ea83e2",
- "sha256:df8c05a0f574d480947cba11b947dc41b1265d721c3777881da2fb8d3a1ddfba",
- "sha256:e266af4da2c1a4cbc6135a570c64577fd3e6eb204607eaff99d8e9b710003c6f",
- "sha256:e279f3db904e3b55f520f11f983cc8dc8a4ce9b65f11692d4718ed021ec58b83",
- "sha256:ea52bd218d4ba260399a8ae4bb6b577d82adfc4518b93566ce1fddd4a49d1dce",
- "sha256:ebec65f5068e7df2d49466aab9128510c4867e532e07cb6960075b27658dca38",
- "sha256:ec1e3b40b82236d100d259854840555469fad4db64f669ab817279eb95cd535c",
- "sha256:ee77c7bef0724165e795b6b7bf9c4c22a9b8468a6bdb9c6b4281293c6b22a90f",
- "sha256:f263b18692f8ed52c8de7f40a0751e79015983dbd77b16906e5b310a39d3ca21",
- "sha256:f7b26757b22faf88fcf232f5f0e62f6e0fd9e22a8a5d0d5016888cdfe1f6c1c4",
- "sha256:f7ddb920106bbbbcaf2a274d56f46956bf56ecbde210d88061824a95bdd94e92"
+ "sha256:00a1d69c112ff5149cabe60d2e2ee948752c975d95f1e1096742e6077affd376",
+ "sha256:023bf8ee3ec6d35af9c1c6ccc1d18fa69afa1cb29eaac57cb064dbb262a517f9",
+ "sha256:0294ca37f1ba500667b1aef631e48d875ced93ad5e06fa665a3295bdd1d95111",
+ "sha256:06babbb8f4e74b063dbaeb74ad68dfce9186c595a15f11f5d5683f748fa1d172",
+ "sha256:0809082ee480bb8f7416507538243c8863ac74fd8a5d2485c46f0f7499f2b491",
+ "sha256:0b3fb02fe73bed561fa12d279a417b432e5b50fe03e8d663d61b3d5990f29546",
+ "sha256:0b58c672d14f16ed92a48db984612f5ce3836ae7d72cdd161001cc54512571f2",
+ "sha256:0bcd1069e710600e8e4cf27f65c90c7843fa8edfb4520fb0ccb88894cad08b11",
+ "sha256:1032e178b76a4e2b5b32e19d0fd0abbce4b58e77a1ca695820d10e491fa32b08",
+ "sha256:11a223a14e91a4693d2d0755c7a043db43d96a7450b4f356d506c2562c48642c",
+ "sha256:12394842a3a8affa3ba62b0d4ab7e9e210c5e366fbac3e8b2a68636fb19892c2",
+ "sha256:182e6cd5c040cec0a1c8d415a87b67ed01193ed9ad458ee427741c7d8513d963",
+ "sha256:1d5b8007f81b88696d06f7df0cb9af0d3b835fe0c8dbf489bad70b45f0e45613",
+ "sha256:1f76846299ba5c54d12c91d776d9605ae33f8ae2b9d1d3c3703cf2db1a67f2c0",
+ "sha256:27fb4a050aaf18772db513091c9c13f6cb94ed40eacdef8dad8411d92d9992db",
+ "sha256:29155cd511ee058e260db648b6182c419422a0d2e9a4fa44501898cf918866cf",
+ "sha256:29fc0f17b1d3fea332f8001d4558f8214af7f1d87a345f3a133c901d60347c73",
+ "sha256:2b6b4c83d8e8ea79f27ab80778c19bc037759aea298da4b56621f4474ffeb117",
+ "sha256:2fdef0d83a2d08d69b1f2210a93c416d54e14d9eb398f6ab2f0a209433db19e1",
+ "sha256:3c65d37f3a9ebb703e710befdc489a38683a5b152242664b973a7b7b22348a4e",
+ "sha256:4f704f0998911abf728a7783799444fcbbe8261c4a6c166f667937ae6a8aa522",
+ "sha256:51b44306032045b383a7a8a2c13878de375117946d68dcb54308111f39775a25",
+ "sha256:53d202fd109416ce011578f321460795abfe10bb901b883cafd9b3ef851bacfc",
+ "sha256:58809e238a8a12a625c70450b48e8767cff9eb67c62e6154a642b21ddf79baea",
+ "sha256:5915fcdec0e54ee229926868e9b08586376cae1f5faa9bbaf8faf3561b393d52",
+ "sha256:5beb1ee382ad32afe424097de57134175fea3faf847b9af002cc7895be4e2a5a",
+ "sha256:5f8ae553cba74085db385d489c7a792ad66f7f9ba2ee85bfa508aeb84cf0ba07",
+ "sha256:5fbd612f8a091954a0c8dd4c0b571b973487277d26476f8480bfa4b2a65b5d06",
+ "sha256:6bd818b7ea14bc6e1f06e241e8234508b21edf1b242d49831831a9450e2f35fa",
+ "sha256:6f01ba56b1c0e9d149f9ac85a2f999724895229eb36bd997b61e62999e9b0901",
+ "sha256:73d2b73584446e66ee633eaad1a56aad577c077f46c35ca3283cd687b7715b0b",
+ "sha256:7bb92c539a624cf86296dd0c68cd5cc286c9eef2d0c3b8b192b604ce9de20a17",
+ "sha256:8165b796df0bd42e10527a3f493c592ba494f16ef3c8b531288e3d0d72c1f6f0",
+ "sha256:862264b12ebb65ad8d863d51f17758b1684560b66ab02770d4f0baf2ff75da21",
+ "sha256:8902dd6a30173d4ef09954bfcb24b5d7b5190cf14a43170e386979651e09ba19",
+ "sha256:8cf717ee42012be8c0cb205dbbf18ffa9003c4cbf4ad078db47b95e10748eec5",
+ "sha256:8ed9281d1b52628e81393f5eaee24a45cbd64965f41857559c2b7ff19385df51",
+ "sha256:99b41d18e6b2a48ba949418db48159d7a2e81c5cc290fc934b7d2380515bd0e3",
+ "sha256:9cb7fa111d21a6b55cbf633039f7bc2749e74932e3aa7cb7333f675a58a58bf3",
+ "sha256:a181e99301a0ae128493a24cfe5cfb5b488c4e0bf2f8702091473d033494d04f",
+ "sha256:a413a096c4cbac202433c850ee43fa326d2e871b24554da8327b01632673a076",
+ "sha256:a6b1e54712ba3474f34b7ef7a41e65bd9037ad47916ccb1cc78769bae324c01a",
+ "sha256:ade3ca1e5f0ff46b678b66201f7ff477e8fa11fb537f3b55c3f0568fbfe6e718",
+ "sha256:b0ac3d42cb51c4b12df9c5f0dd2f13a4f24f01943627120ec4d293c9181219ba",
+ "sha256:b369ead6527d025a0fe7bd3864e46dbee3aa8f652d48df6174f8d0bac9e26e0e",
+ "sha256:b57b768feb866f44eeed9f46975f3d6406380275c5ddfe22f531a2bf187eda27",
+ "sha256:b8d3a03d9bfcaf5b0141d07a88456bb6a4c3ce55c080712fec8418ef3610230e",
+ "sha256:bc66f0bf1d7730a17430a50163bb264ba9ded56739112368ba985ddaa9c3bd09",
+ "sha256:bf20494da9653f6410213424f5f8ad0ed885e01f7e8e59811f572bdb20b8972e",
+ "sha256:c48167910a8f644671de9f2083a23630fbf7a1cb70ce939440cd3328e0919f70",
+ "sha256:c481b47f6b5845064c65a7bc78bc0860e635a9b055af0df46fdf1c58cebf8e8f",
+ "sha256:c7c8b95bf47db6d19096a5e052ffca0a05f335bc63cef281a6e8fe864d450a72",
+ "sha256:c9b8e184898ed014884ca84c70562b4a82cbc63b044d366fedc68bc2b2f3394a",
+ "sha256:cc8ff50b50ce532de2fa7a7daae9dd12f0a699bfcd47f20945364e5c31799fef",
+ "sha256:d541423cdd416b78626b55f123412fcf979d22a2c39fce251b350de38c15c15b",
+ "sha256:dab4d16dfef34b185032580e2f2f89253d302facba093d5fa9dbe04f569c4f4b",
+ "sha256:dacbc52de979f2823a819571f2e3a350a7e36b8cb7484cdb1e289bceaf35305f",
+ "sha256:df57bdbeffe694e7842092c5e2e0bc80fff7f43379d465f932ef36f027179806",
+ "sha256:ed8fe9189d2beb6edc14d3ad19800626e1d9f2d975e436f84e19efb7fa19469b",
+ "sha256:f3ddf056d3ebcf6ce47bdaf56142af51bb7fad09e4af310241e9db7a3a8022e1",
+ "sha256:f8fe4984b431f8621ca53d9380901f62bfb54ff759a1348cd140490ada7b693c",
+ "sha256:fe439416eb6380de434886b00c859304338f8b19f6f54811984f3420a2e03858"
],
"index": "pypi",
"markers": "python_version >= '3.9'",
- "version": "==7.6.3"
+ "version": "==7.6.4"
},
"idna": {
"hashes": [
diff --git a/dbrepo-search-service/init/Pipfile.lock b/dbrepo-search-service/init/Pipfile.lock
index 75bdbc29f92ce91ebd3bca121e904cd2bc05174b..de0064f408e2aefd4f4478c641e3ae6520d18fba 100644
--- a/dbrepo-search-service/init/Pipfile.lock
+++ b/dbrepo-search-service/init/Pipfile.lock
@@ -282,7 +282,7 @@
},
"dbrepo": {
"hashes": [
- "sha256:84607677b0826bb9b2fa120aacdf56d16c8d9ae423f435b2bd2c22b1c965a33c"
+ "sha256:36316d520c23dcbd249b779ad596a979fe574321882a7d4b6c6934c62a5de57b"
],
"path": "./lib/dbrepo-1.4.7.tar.gz"
},
@@ -311,86 +311,101 @@
},
"frozenlist": {
"hashes": [
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],
"markers": "python_version >= '3.8'",
- "version": "==1.4.1"
+ "version": "==1.5.0"
},
"idna": {
"hashes": [
@@ -408,13 +423,6 @@
"markers": "python_version >= '3.7'",
"version": "==2.0.0"
},
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"itsdangerous": {
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@@ -433,70 +441,70 @@
},
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],
"markers": "python_version >= '3.9'",
- "version": "==3.0.1"
+ "version": "==3.0.2"
},
"multidict": {
"hashes": [
@@ -598,62 +606,64 @@
},
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+ "sha256:e14e26956e6f1696070788252dcdff11b4aca4c3e8bd166e0df1bb8f315a67cb",
+ "sha256:e6988e90fcf617da2b5c78902fe8e668361b43b4fe26dbf2d7b0f8034d4cafb9",
+ "sha256:e711e02f49e176a01d0349d82cb5f05ba4db7d5e7e0defd026328e5cfb3226d3",
+ "sha256:ea4dedd6e394a9c180b33c2c872b92f7ce0f8e7ad93e9585312b0c5a04777a4a",
+ "sha256:ecc76a9ba2911d8d37ac01de72834d8849e55473457558e12995f4cd53e778e0",
+ "sha256:f55ba01150f52b1027829b50d70ef1dafd9821ea82905b63936668403c3b471e",
+ "sha256:f653490b33e9c3a4c1c01d41bc2aef08f9475af51146e4a7710c450cf9761598",
+ "sha256:fa2d1337dc61c8dc417fbccf20f6d1e139896a30721b7f1e832b2bb6ef4eb6c4"
],
"markers": "python_version == '3.11'",
- "version": "==2.1.2"
+ "version": "==2.1.3"
},
"opensearch-py": {
"hashes": [
@@ -986,12 +996,12 @@
},
"rdflib": {
"hashes": [
- "sha256:0438920912a642c866a513de6fe8a0001bd86ef975057d6962c79ce4771687cd",
- "sha256:9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae"
+ "sha256:164de86bd3564558802ca983d84f6616a4a1a420c7a17a8152f5016076b2913e",
+ "sha256:e590fa9a2c34ba33a667818b5a84be3fb8a4d85868f8038f17912ec84f912a25"
],
"index": "pypi",
"markers": "python_full_version >= '3.8.1' and python_full_version < '4.0.0'",
- "version": "==7.0.0"
+ "version": "==7.1.1"
},
"requests": {
"hashes": [
@@ -1066,11 +1076,11 @@
},
"werkzeug": {
"hashes": [
- "sha256:02c9eb92b7d6c06f31a782811505d2157837cea66aaede3e217c7c27c039476c",
- "sha256:34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306"
+ "sha256:8cd39dfbdfc1e051965f156163e2974e52c210f130810e9ad36858f0fd3edad4",
+ "sha256:a71124d1ef06008baafa3d266c02f56e1836a5984afd6dd6c9230669d60d9fb5"
],
- "markers": "python_version >= '3.8'",
- "version": "==3.0.4"
+ "markers": "python_version >= '3.9'",
+ "version": "==3.1.1"
},
"wrapt": {
"hashes": [
@@ -1150,178 +1160,162 @@
},
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+ "sha256:73d2b73584446e66ee633eaad1a56aad577c077f46c35ca3283cd687b7715b0b",
+ "sha256:7bb92c539a624cf86296dd0c68cd5cc286c9eef2d0c3b8b192b604ce9de20a17",
+ "sha256:8165b796df0bd42e10527a3f493c592ba494f16ef3c8b531288e3d0d72c1f6f0",
+ "sha256:862264b12ebb65ad8d863d51f17758b1684560b66ab02770d4f0baf2ff75da21",
+ "sha256:8902dd6a30173d4ef09954bfcb24b5d7b5190cf14a43170e386979651e09ba19",
+ "sha256:8cf717ee42012be8c0cb205dbbf18ffa9003c4cbf4ad078db47b95e10748eec5",
+ "sha256:8ed9281d1b52628e81393f5eaee24a45cbd64965f41857559c2b7ff19385df51",
+ "sha256:99b41d18e6b2a48ba949418db48159d7a2e81c5cc290fc934b7d2380515bd0e3",
+ "sha256:9cb7fa111d21a6b55cbf633039f7bc2749e74932e3aa7cb7333f675a58a58bf3",
+ "sha256:a181e99301a0ae128493a24cfe5cfb5b488c4e0bf2f8702091473d033494d04f",
+ "sha256:a413a096c4cbac202433c850ee43fa326d2e871b24554da8327b01632673a076",
+ "sha256:a6b1e54712ba3474f34b7ef7a41e65bd9037ad47916ccb1cc78769bae324c01a",
+ "sha256:ade3ca1e5f0ff46b678b66201f7ff477e8fa11fb537f3b55c3f0568fbfe6e718",
+ "sha256:b0ac3d42cb51c4b12df9c5f0dd2f13a4f24f01943627120ec4d293c9181219ba",
+ "sha256:b369ead6527d025a0fe7bd3864e46dbee3aa8f652d48df6174f8d0bac9e26e0e",
+ "sha256:b57b768feb866f44eeed9f46975f3d6406380275c5ddfe22f531a2bf187eda27",
+ "sha256:b8d3a03d9bfcaf5b0141d07a88456bb6a4c3ce55c080712fec8418ef3610230e",
+ "sha256:bc66f0bf1d7730a17430a50163bb264ba9ded56739112368ba985ddaa9c3bd09",
+ "sha256:bf20494da9653f6410213424f5f8ad0ed885e01f7e8e59811f572bdb20b8972e",
+ "sha256:c48167910a8f644671de9f2083a23630fbf7a1cb70ce939440cd3328e0919f70",
+ "sha256:c481b47f6b5845064c65a7bc78bc0860e635a9b055af0df46fdf1c58cebf8e8f",
+ "sha256:c7c8b95bf47db6d19096a5e052ffca0a05f335bc63cef281a6e8fe864d450a72",
+ "sha256:c9b8e184898ed014884ca84c70562b4a82cbc63b044d366fedc68bc2b2f3394a",
+ "sha256:cc8ff50b50ce532de2fa7a7daae9dd12f0a699bfcd47f20945364e5c31799fef",
+ "sha256:d541423cdd416b78626b55f123412fcf979d22a2c39fce251b350de38c15c15b",
+ "sha256:dab4d16dfef34b185032580e2f2f89253d302facba093d5fa9dbe04f569c4f4b",
+ "sha256:dacbc52de979f2823a819571f2e3a350a7e36b8cb7484cdb1e289bceaf35305f",
+ "sha256:df57bdbeffe694e7842092c5e2e0bc80fff7f43379d465f932ef36f027179806",
+ "sha256:ed8fe9189d2beb6edc14d3ad19800626e1d9f2d975e436f84e19efb7fa19469b",
+ "sha256:f3ddf056d3ebcf6ce47bdaf56142af51bb7fad09e4af310241e9db7a3a8022e1",
+ "sha256:f8fe4984b431f8621ca53d9380901f62bfb54ff759a1348cd140490ada7b693c",
+ "sha256:fe439416eb6380de434886b00c859304338f8b19f6f54811984f3420a2e03858"
],
"index": "pypi",
"markers": "python_version >= '3.9'",
- "version": "==7.6.3"
+ "version": "==7.6.4"
},
"iniconfig": {
"hashes": [
diff --git a/dbrepo-search-service/init/lib/dbrepo-1.4.7.tar.gz b/dbrepo-search-service/init/lib/dbrepo-1.4.7.tar.gz
index c652dbae4a60aae708eb6fe4e751977b97b72344..c85b1225ee9cc1f5386e58bced9b979ff160e982 100644
Binary files a/dbrepo-search-service/init/lib/dbrepo-1.4.7.tar.gz and b/dbrepo-search-service/init/lib/dbrepo-1.4.7.tar.gz differ
diff --git a/dbrepo-search-service/lib/dbrepo-1.4.7.tar.gz b/dbrepo-search-service/lib/dbrepo-1.4.7.tar.gz
index c652dbae4a60aae708eb6fe4e751977b97b72344..c85b1225ee9cc1f5386e58bced9b979ff160e982 100644
Binary files a/dbrepo-search-service/lib/dbrepo-1.4.7.tar.gz and b/dbrepo-search-service/lib/dbrepo-1.4.7.tar.gz differ
diff --git a/dbrepo-ui/bun.lockb b/dbrepo-ui/bun.lockb
index 3f85eb8de9c7a334e2a6a89d3cbcf75254751610..20aecae3f32b90faac1b0e97a01889f10f5c9aa7 100755
Binary files a/dbrepo-ui/bun.lockb and b/dbrepo-ui/bun.lockb differ
diff --git a/dbrepo-ui/components/subset/Builder.vue b/dbrepo-ui/components/subset/Builder.vue
index a6f53c6e4f0dba0ef1f8935c9112dc1e2d1d0df2..3a3cd3a142dce81172d23d1ee979515514c0326a 100644
--- a/dbrepo-ui/components/subset/Builder.vue
+++ b/dbrepo-ui/components/subset/Builder.vue
@@ -44,7 +44,7 @@
v-if="isView"
class="mt-1"
dense>
- <v-col md="8">
+ <v-col lg="8">
<v-text-field
v-model="view.name"
:disabled="isExecuted"
@@ -74,7 +74,7 @@
<v-row
v-if="isView"
dense>
- <v-col md="8">
+ <v-col lg="8">
<v-select
v-model="view.is_public"
:items="visibilities"
@@ -95,7 +95,7 @@
<v-window-item
value="0">
<v-row dense>
- <v-col md="4">
+ <v-col lg="4">
<v-select
v-model="table"
:disabled="isExecuted"
@@ -109,7 +109,7 @@
:hint="$t('pages.view.subpages.create.table.hint')"
:rules="[v => !!v || $t('validation.required')]" />
</v-col>
- <v-col md="4">
+ <v-col lg="4">
<v-select
v-model="select"
item-title="internal_name"
@@ -143,7 +143,7 @@
</v-col>
</v-row>
<v-row v-if="select.length > 0">
- <v-col md="8">
+ <v-col lg="8">
<v-btn
v-if="clauses.length === 0"
size="small"
@@ -157,15 +157,15 @@
<div class="mb-5">
<v-row v-if="clauses.length > 0">
<v-col
- md="8"
+ lg="8"
class="text-center">
- <pre>WHERE</pre>
+ <pre>FILTER</pre>
</v-col>
</v-row>
<div v-for="(clause, idx) in clauses" :key="idx">
<v-row
v-if="clause.type === 'where'">
- <v-col md="3">
+ <v-col lg="3">
<v-select
v-model="clause.params[0]"
:disabled="clausesDisabled"
@@ -177,16 +177,36 @@
:hint="$t('pages.subset.subpages.create.filter.column.hint')"
:items="select" />
</v-col>
- <v-col md="1">
+ <v-col lg="2">
<v-select
v-model="clause.params[1]"
:disabled="clausesDisabled"
+ item-title="value"
+ item-value="value"
persistent-hint
- :label="$t('pages.subset.subpages.create.filter.operator.label')"
- :hint="$t('pages.subset.subpages.create.filter.operator.hint')"
- :items="operators" />
+ :label="operatorHint(clause.params[1])"
+ :hint="$t('pages.subset.subpages.create.filter.operator.label')"
+ :items="operators">
+ <template
+ v-slot:append>
+ <NuxtLink
+ target="_blank"
+ :href="documentationLink(clause.params[1])">
+ <v-tooltip
+ location="bottom">
+ <template
+ v-slot:activator="{ props }">
+ <v-icon
+ v-bind="props"
+ icon="mdi-help-circle-outline" />
+ </template>
+ {{ $t('navigation.help') }}
+ </v-tooltip>
+ </NuxtLink>
+ </template>
+ </v-select>
</v-col>
- <v-col md="3">
+ <v-col lg="3">
<v-text-field
v-model="clause.params[2]"
:disabled="clausesDisabled"
@@ -194,7 +214,7 @@
:label="$t('pages.subset.subpages.create.filter.value.label')"
:hint="$t('pages.subset.subpages.create.filter.value.hint')" />
</v-col>
- <v-col md="1">
+ <v-col lg="1">
<v-btn
:disabled="clausesDisabled"
class="mt-4"
@@ -208,7 +228,7 @@
<v-row
v-else>
<v-col
- md="8"
+ lg="8"
class="text-center">
<pre>{{ clause.type.toUpperCase() }}</pre>
</v-col>
@@ -308,48 +328,6 @@ export default {
{ title: this.$t('toolbars.database.public'), value: true },
{ title: this.$t('toolbars.database.private'), value: false },
],
- operators: [
- '=',
- '<',
- '>',
- '<=',
- '>=',
- '<>',
- '!=',
- 'like',
- 'not like',
- 'between',
- 'not between',
- 'ilike',
- 'not ilike',
- 'exists',
- 'not exist',
- 'rlike',
- 'not rlike',
- 'regexp',
- 'not regexp',
- 'match',
- '&',
- '|',
- '^',
- '<<',
- '>>',
- '~',
- '~=',
- '~*',
- '!~',
- '!~*',
- '#',
- '&&',
- '@>',
- '<@',
- '||',
- '&<',
- '&>',
- '-|-',
- '@@',
- '!!'
- ],
tableDetails: null,
resultId: null,
valid: false,
@@ -375,6 +353,12 @@ export default {
columnNames () {
return this.columns && this.columns.map(s => s.internal_name)
},
+ operators () {
+ if (!this.database) {
+ return []
+ }
+ return this.database.container.image.operators
+ },
columns () {
if (!this.table) {
return []
@@ -451,13 +435,13 @@ export default {
return true
}
}
- return false
+ return this.sql.includes(';')
},
canExecute () {
if (this.isView) {
return this.view.name !== null && this.view.is_public !== null && this.view.query !== null
}
- return this.query.raw !== null
+ return this.sql !== null && !this.sql.includes(';')
},
inputVariant () {
const runtimeConfig = useRuntimeConfig()
@@ -523,13 +507,13 @@ export default {
await this.$router.push(`/database/${this.$route.params.database_id}/subset/${subset.id}/data`)
this.loadingQuery = false
})
- .catch(({code}) => {
+ .catch(({code, message}) => {
this.loadingQuery = false
const toast = useToastInstance()
if (typeof code !== 'string') {
return
}
- toast.error(this.$t(code))
+ toast.error(`${this.$t(code)}: ${message}`)
})
},
createView () {
@@ -618,6 +602,20 @@ export default {
} else {
this.select = []
}
+ },
+ documentationLink (value) {
+ const filter = this.operators.filter(o => o.value === value)
+ if (filter.length !== 1) {
+ return null
+ }
+ return filter[0].documentation
+ },
+ operatorHint (value) {
+ const filter = this.operators.filter(o => o.value === value)
+ if (filter.length !== 1) {
+ return null
+ }
+ return filter[0].display_name
}
}
}
diff --git a/dbrepo-ui/components/table/TableImport.vue b/dbrepo-ui/components/table/TableImport.vue
index 84c1011c9b24842c7bb1ed563919af61f6211833..14d4dae70a45f07fe716335edaff597ed2bbc79a 100644
--- a/dbrepo-ui/components/table/TableImport.vue
+++ b/dbrepo-ui/components/table/TableImport.vue
@@ -32,18 +32,17 @@
</v-row>
<v-row dense>
<v-col md="8">
- <v-text-field
- v-model.number="tableImport.skip_lines"
- :rules="[
- v => isNonNegativeInteger(v) || $t('validation.integer')
- ]"
- type="number"
+ <v-select
+ v-model="tableImport.header"
+ :items="headers"
+ item-title="key"
+ item-value="value"
required
clearable
persistent-hint
:variant="inputVariant"
:hint="$t('pages.table.subpages.import.skip.hint')"
- :label="$t('pages.table.subpages.import.skip.label')"/>
+ :label="$t('pages.table.subpages.import.skip.label')" />
</v-col>
</v-row>
<v-row dense>
@@ -265,7 +264,6 @@
</template>
<script>
-import { isNonNegativeInteger } from '@/utils'
import { useCacheStore } from '@/stores/cache'
export default {
@@ -304,7 +302,7 @@ export default {
quote: '"',
separator: ',',
line_termination: '\\n',
- skip_lines: 1
+ header: true
},
separators: [
{key: ',', value: ','},
@@ -315,6 +313,10 @@ export default {
{key: 'Double "', value: '"'},
{key: 'Single \'', value: '\''}
],
+ headers: [
+ {key: 'First line is header', value: true},
+ {key: 'Data only', value: false}
+ ],
lineTerminationItems: [
{name: '\\r\\n (Windows)', value: '\r\n'},
{name: '\\n (UNIX)', value: '\n'},
@@ -329,7 +331,7 @@ export default {
this.setQueryParamSafely('quote')
this.setQueryParamSafely('separator')
this.setQueryParamSafely('line_termination')
- this.setQueryParamSafely('skip_lines')
+ this.setQueryParamSafely('header', true)
if (this.$route.query.location) {
this.step = 2
this.validStep2 = true
@@ -407,13 +409,16 @@ export default {
}
},
methods: {
- isNonNegativeInteger,
submit() {
this.$refs.form.validate()
},
- setQueryParamSafely(name) {
+ setQueryParamSafely(name, parse_bool = false) {
if (this.$route.query[name]) {
- this.tableImport[name] = this.$route.query[name]
+ var value = this.$route.query[name]
+ if (parse_bool) {
+ value = this.$route.query[name] === 'true'
+ }
+ this.tableImport[name] = value
}
},
importCsv() {
@@ -485,7 +490,7 @@ export default {
this.columns = Object.entries(columns)
.map(([name, analyse]) => {
return {
- name: name,
+ name: name.trim(),
type: analyse.type,
null_allowed: analyse.null_allowed,
primary_key: false,
@@ -507,7 +512,7 @@ export default {
filename,
line_termination: line_termination === '\\n' ? '\n' : JSON.stringify(line_termination).replaceAll('"', ''),
separator: this.tableImport.separator,
- skip_lines: this.tableImport.skip_lines,
+ header: this.tableImport.header,
quote: this.tableImport.quote,
})
this.loading = false
diff --git a/dbrepo-ui/composables/identifier-service.ts b/dbrepo-ui/composables/identifier-service.ts
index 96e5610c8c11161b0a4c1687e630204f80e53554..f85c48dc21f1428ea0656a00861eb260e48c0cf5 100644
--- a/dbrepo-ui/composables/identifier-service.ts
+++ b/dbrepo-ui/composables/identifier-service.ts
@@ -288,7 +288,7 @@ export const useIdentifierService = (): any => {
if (!data) {
return null
}
- return data.doi !== null ? 'DOI' : 'URI'
+ return data.doi ? 'DOI' : 'URI'
}
function creatorToCreatorJsonLd(creator: CreatorDto) {
diff --git a/dbrepo-ui/dto/index.ts b/dbrepo-ui/dto/index.ts
index 74b3911764fbd3da5d41d5d72cd269d79ee3963d..7658b4d1715af0b26d0b43bfd16493c84a02d391 100644
--- a/dbrepo-ui/dto/index.ts
+++ b/dbrepo-ui/dto/index.ts
@@ -75,18 +75,18 @@ interface ImageDto {
version: string;
dialect: string;
driver_class: string;
- date_formats: ImageDateDto[];
+ data_types: DataTypeDto[];
+ operators: OperatorDto[];
jdbc_method: string;
default_port: number;
}
-interface ImageDateDto {
+interface OperatorDto {
id: number;
- example: string;
- database_format: string;
- unix_format: string;
- has_time: boolean;
- created_at: Date;
+ image_id: number;
+ display_name: string;
+ documentation: string;
+ value: string;
}
interface TableBriefDto {
diff --git a/dbrepo-ui/locales/en-US.json b/dbrepo-ui/locales/en-US.json
index 3a3846e2efdb70cb02793834c3e018ea9c189f08..46ab9b93a4466d78671b08dc78ef091a8c267d87 100644
--- a/dbrepo-ui/locales/en-US.json
+++ b/dbrepo-ui/locales/en-US.json
@@ -1,5 +1,6 @@
{
"navigation": {
+ "logo": "Logo",
"information": "Information",
"search": "Search",
"container": "Engines",
@@ -365,8 +366,8 @@
}
},
"skip": {
- "label": "Skip Rows",
- "hint": "Optional. Number of rows to skip, e.g. when the first one contains header and no data"
+ "label": "Column Headers",
+ "hint": "Required. First line contains only data"
},
"storage": {
"text": "Dataset from Storage Service"
@@ -920,17 +921,17 @@
"query": {
"title": "Query"
},
- "query-hash": {
- "prefix": "sha256",
- "title": "Query Hash"
+ "hash": {
+ "title": "Hash",
+ "prefix": "sha256"
},
"executed": {
"title": "Created"
},
- "result-hash": {
- "title": "Result Hash"
+ "result": {
+ "title": "Result"
},
- "result-rows": {
+ "rows": {
"title": "Result Rows"
},
"tabs": {
@@ -946,7 +947,7 @@
},
"expert": {
"text": "Expert",
- "warn": "It is not recommended to use comments, aggregation functions and the following operations"
+ "warn": "It is not recommended to use comments, aggregation functions, the semicolon and the following operations"
},
"name": {
"label": ""
@@ -1075,6 +1076,7 @@
},
"axios": {
"connection": "Failed to contact backend",
+ "malformed": "Malformed request",
"timeout": "Connection timed out"
},
"concept": {
diff --git a/dbrepo-ui/nuxt.config.ts b/dbrepo-ui/nuxt.config.ts
index 8def4012d992f9f998969ec2b247398706ec5db4..be6fb2940f66b5ae026427b7a4eae964d05fa714 100644
--- a/dbrepo-ui/nuxt.config.ts
+++ b/dbrepo-ui/nuxt.config.ts
@@ -27,6 +27,7 @@ export default defineNuxtConfig({
charset: 'utf-8',
viewport: 'width=device-width, initial-scale=1',
meta: [
+ {'ref': 'icon', type: 'image/x-icon', href: '/favicon.ico'},
{'http-equiv': 'Content-Security-Policy', content: 'upgrade-insecure-requests'}
],
htmlAttrs: {
@@ -86,7 +87,7 @@ export default defineNuxtConfig({
prefix: '/'
},
database: {
- unsupported: '*,AVG,BIT_AND,BIT_OR,BIT_XOR,COUNT,COUNTDISTINCT,GROUP_CONCAT,JSON_ARRAYAGG,JSON_OBJECTAGG,MAX,MIN,STD,STDDEV,STDDEV_POP,STDDEV_SAMP,SUM,VARIANCE,VAR_POP,VAR_SAMP,--',
+ unsupported: 'AVG,BIT_AND,BIT_OR,BIT_XOR,COUNT,COUNTDISTINCT,GROUP_CONCAT,JSON_ARRAYAGG,JSON_OBJECTAGG,MAX,MIN,STD,STDDEV,STDDEV_POP,STDDEV_SAMP,SUM,VARIANCE,VAR_POP,VAR_SAMP,--',
image: {
width: 200,
height: 200
diff --git a/dbrepo-ui/pages/database/[database_id]/subset/[subset_id]/info.vue b/dbrepo-ui/pages/database/[database_id]/subset/[subset_id]/info.vue
index 01620ea35eebf78969c6353b9ccaa0e7e9fdfb05..0d59b1ed25e405db59c50e3f492d9122f9fbf5ae 100644
--- a/dbrepo-ui/pages/database/[database_id]/subset/[subset_id]/info.vue
+++ b/dbrepo-ui/pages/database/[database_id]/subset/[subset_id]/info.vue
@@ -50,9 +50,9 @@
<pre>{{ subset.query }}</pre>
</v-list-item>
<v-list-item
- :title="$t('pages.subset.query-hash.title')"
+ :title="`${$t('pages.subset.query.title')} ${$t('pages.subset.hash.title')}`"
density="compact">
- <pre>{{ $t('pages.subset.query-hash.prefix') }}{{ subset.query_hash }}</pre>
+ <pre>{{ $t('pages.subset.hash.prefix') }}:{{ subset.query_hash }}</pre>
</v-list-item>
<v-list-item
v-if="executionUTC"
@@ -61,9 +61,9 @@
{{ executionUTC }}
</v-list-item>
<v-list-item
- :title="$t('pages.subset.result-hash.title')"
+ :title="`${$t('pages.subset.result.title')} ${$t('pages.subset.hash.title')}`"
density="compact">
- <pre>{{ result_hash }}</pre>
+ <pre>{{ $t('pages.subset.hash.prefix') }}:{{ result_hash }}</pre>
</v-list-item>
<v-list-item
:title="$t('pages.subset.result-rows.title')"
@@ -215,7 +215,7 @@ export default {
if (!this.subset.result_hash) {
return '(none)'
}
- return `sha256:${this.subset.result_hash}`
+ return this.subset.result_hash
},
publisher () {
if (this.database.publisher === null) {
diff --git a/dbrepo-ui/pages/database/[database_id]/table/[table_id]/data.vue b/dbrepo-ui/pages/database/[database_id]/table/[table_id]/data.vue
index e9173726e96af147ab849aa2fcd4515484c03825..1be05e4bf1e08a26d44ff833588b1a3cca9e85ac 100644
--- a/dbrepo-ui/pages/database/[database_id]/table/[table_id]/data.vue
+++ b/dbrepo-ui/pages/database/[database_id]/table/[table_id]/data.vue
@@ -344,8 +344,8 @@ export default {
},
download () {
this.downloadLoading = true
+ const tableService = useTableService()
if (!this.version) {
- const tableService = useTableService()
tableService.exportData(this.$route.params.database_id, this.$route.params.table_id)
.then((data) => {
this.downloadLoading = false
@@ -359,18 +359,15 @@ export default {
.catch(({code}) => {
this.downloadLoading = false
const toast = useToastInstance()
- if (typeof code !== 'string') {
- return
- }
toast.error(this.$t(code))
})
.finally(() => {
this.downloadLoading = false
})
} else {
- const tableService = useTableService()
tableService.exportData(this.$route.params.database_id, this.$route.params.table_id, this.versionISO)
.then((data) => {
+ this.downloadLoading = false
const url = URL.createObjectURL(data)
const link = document.createElement('a')
link.href = url
@@ -378,8 +375,10 @@ export default {
document.body.appendChild(link)
link.click()
})
- .catch(() => {
+ .catch(({code}) => {
this.downloadLoading = false
+ const toast = useToastInstance()
+ toast.error(this.$t(code))
})
.finally(() => {
this.downloadLoading = false
@@ -420,9 +419,6 @@ export default {
console.debug('date columns are', this.dateColumns)
} catch ({code}) {
const toast = useToastInstance()
- if (typeof code !== 'string') {
- return
- }
toast.error(this.$t(code))
}
this.loading = false
@@ -439,8 +435,10 @@ export default {
this.total = count
this.loadingCount = false
})
- .catch((error) => {
+ .catch(({code}) => {
this.loadingCount = false
+ const toast = useToastInstance()
+ toast.error(this.$t(code))
})
},
loadData({ page, itemsPerPage, sortBy }) {
@@ -470,9 +468,6 @@ export default {
this.error = true
this.loadingData = false
const toast = useToastInstance()
- if (typeof code !== 'string' || typeof message !== 'string') {
- return
- }
toast.error(this.$t(code) + ": " + message)
})
},
diff --git a/dbrepo-ui/pages/database/[database_id]/table/create/dataset.vue b/dbrepo-ui/pages/database/[database_id]/table/create/dataset.vue
index c54314abcba4d714426e4990527d1a53b3a287d6..d77ea941349d44e419c055466055fe7c16a704ad 100644
--- a/dbrepo-ui/pages/database/[database_id]/table/create/dataset.vue
+++ b/dbrepo-ui/pages/database/[database_id]/table/create/dataset.vue
@@ -234,7 +234,6 @@ export default {
rules: {
required: value => !!value || 'validation.required'
},
- dateFormats: [],
tables: [],
tableCreate: {
name: null,
@@ -246,7 +245,7 @@ export default {
quote: '"',
separator: ',',
line_termination: null,
- skip_lines: 1
+ header: true
},
loading: false,
url: null,
@@ -303,29 +302,11 @@ export default {
return this.$vuetify.theme.global.name.toLowerCase().endsWith('contrast') ? runtimeConfig.public.variant.button.contrast : runtimeConfig.public.variant.button.normal
}
},
- mounted() {
- this.loadDateFormats()
- },
methods: {
notEmpty,
submit() {
this.$refs.form.validate()
},
- async loadDateFormats() {
- this.loading = true
- const databaseService = useDatabaseService()
- databaseService.findOne(this.$route.params.database_id)
- .then((database) => {
- this.dateFormats = database.container.image.date_formats
- this.loading = false
- })
- .catch(() => {
- this.loading = false
- })
- .finally(() => {
- this.loading = false
- })
- },
createEmptyTableAndImport({success, columns, constraints}) {
if (!success) {
return
@@ -356,13 +337,13 @@ export default {
this.loading = false
})
},
- onAnalyse({columns, filename, line_termination, separator, skip_lines, quote, null_element, true_element, false_element}) {
+ onAnalyse({columns, filename, line_termination, separator, header, quote}) {
console.debug('analysed', columns)
this.tableCreate.columns = columns
this.tableImport.location = filename
this.tableImport.line_termination = line_termination
this.tableImport.separator = separator
- this.tableImport.skip_lines = skip_lines
+ this.tableImport.header = header
this.tableImport.quote = quote
if (filename) {
this.step = 4
diff --git a/dbrepo-ui/utils/index.ts b/dbrepo-ui/utils/index.ts
index 995c03a82795545858c477326a57ef93296c4d5b..95380474e1ad2608c2862ec3414eca0d8d7f7a67 100644
--- a/dbrepo-ui/utils/index.ts
+++ b/dbrepo-ui/utils/index.ts
@@ -1056,6 +1056,14 @@ export function axiosErrorToApiError(error: AxiosError): ApiErrorDto {
message: error.message
}
return errorObj
+ } else if (error.code === 'ERR_BAD_REQUEST') {
+ /* timeout */
+ const errorObj: ApiErrorDto = {
+ status: error.code,
+ code: 'error.axios.malformed',
+ message: error.message
+ }
+ return errorObj
}
if (error.response?.data) {
const errorObj: ApiErrorDto = (error.response?.data as ApiErrorDto)
diff --git a/docker-compose.yml b/docker-compose.yml
index e8cec6aa893092b08fe98a1dc352fa4d5c378aa0..fd5cc586138c3e5ac65dceddcd21f311bf66ab9f 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -194,8 +194,10 @@ services:
JWT_PUBKEY: "${JWT_PUBKEY:-MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB}"
S3_ACCESS_KEY_ID: "${S3_ACCESS_KEY_ID:-seaweedfsadmin}"
S3_BUCKET: "${S3_BUCKET:-dbrepo}"
- S3_ENDPOINT: "${S3_ENDPOINT:-http://storage-service:9000}"
+ S3_ENDPOINT: "${S3_ENDPOINT:-storage-service:9000}"
+ S3_PROTO: "${S3_PROTO:-http}"
S3_SECRET_ACCESS_KEY: "${S3_SECRET_ACCESS_KEY:-seaweedfsadmin}"
+ METADATA_SERVICE_ENDPOINT: ${METADATA_SERVICE_ENDPOINT:-http://metadata-service:8080}
SYSTEM_USERNAME: "${SYSTEM_USERNAME:-admin}"
SYSTEM_PASSWORD: "${SYSTEM_PASSWORD:-admin}"
volumes:
@@ -290,32 +292,6 @@ services:
timeout: 5s
retries: 12
- dbrepo-data-db-sidecar:
- restart: "no"
- container_name: dbrepo-data-db-sidecar
- hostname: data-db-sidecar
- image: dbrepo-data-db-sidecar:latest
- build:
- context: ./dbrepo-data-db/sidecar
- network: host
- ports:
- - "3305:8080"
- environment:
- S3_ACCESS_KEY_ID: "${S3_ACCESS_KEY_ID:-seaweedfsadmin}"
- S3_BUCKET: "${S3_BUCKET:-dbrepo}"
- S3_ENDPOINT: "${S3_ENDPOINT:-http://storage-service:9000}"
- S3_FILE_PATH: "${S3_FILE_PATH:-/tmp}"
- S3_SECRET_ACCESS_KEY: "${S3_SECRET_ACCESS_KEY:-seaweedfsadmin}"
- volumes:
- - "${SHARED_FILESYSTEM:-/tmp}:/tmp"
- healthcheck:
- test: curl -sSL localhost:8080/health | grep 'UP' || exit 1
- interval: 10s
- timeout: 5s
- retries: 12
- logging:
- driver: json-file
-
dbrepo-ui:
restart: "no"
container_name: dbrepo-ui
@@ -551,6 +527,7 @@ services:
BROKER_USERNAME: "${SYSTEM_USERNAME:-admin}"
BROKER_VIRTUALHOST: "${BROKER_VIRTUALHOST:-dbrepo}"
CONNECTION_TIMEOUT: ${CONNECTION_TIMEOUT:-60000}
+ COMPUTE_SERVICE_ENDPOINT: "${COMPUTE_SERVICE_ENDPOINT:-local[2]}"
EXCHANGE_NAME: "${EXCHANGE_NAME:-dbrepo}"
METADATA_SERVICE_ENDPOINT: "${METADATA_SERVICE_ENDPOINT:-http://metadata-service:8080}"
GRANT_DEFAULT_READ: "${GRANT_DEFAULT_READ:-SELECT}"
@@ -568,6 +545,7 @@ services:
S3_FILE_PATH: "${S3_FILE_PATH:-/tmp}"
S3_IMPORT_BUCKET: "${S3_IMPORT_BUCKET:-dbrepo-upload}"
S3_SECRET_ACCESS_KEY: "${S3_SECRET_ACCESS_KEY:-seaweedfsadmin}"
+ SPARK_USER: "${COMPUTE_SERVICE_USERNAME:-spark}"
SYSTEM_USERNAME: "${SYSTEM_USERNAME:-admin}"
SYSTEM_PASSWORD: "${SYSTEM_PASSWORD:-admin}"
healthcheck:
diff --git a/helm/dbrepo-mariadb-galera/.gitignore b/helm/dbrepo-mariadb-galera/.gitignore
deleted file mode 100644
index 613d851d27fbfa390c201b7ed8591da3e04bec35..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/.gitignore
+++ /dev/null
@@ -1,6 +0,0 @@
-# generated
-*.crt
-*.key
-*.srl
-*.csr
-build/*
\ No newline at end of file
diff --git a/helm/dbrepo-mariadb-galera/.helmignore b/helm/dbrepo-mariadb-galera/.helmignore
deleted file mode 100644
index b9029e8dea3ccab2aabc5c3a8d9226e9bb9ac827..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/.helmignore
+++ /dev/null
@@ -1,30 +0,0 @@
-# Dev
-values.dev.yaml
-Chart.tpl.yaml
-hack/
-# MacOS
-.DS_Store
-# Common VCS dirs
-.git/
-.gitignore
-.bzr/
-.bzrignore
-.hg/
-.hgignore
-.svn/
-# Generated
-build/
-artifacthub-repo.yml
-# Common backup files
-*.swp
-*.bak
-*.tmp
-*.orig
-*~
-# Various IDEs
-.project
-.idea/
-*.tmproj
-.vscode/
-# Make
-Makefile
diff --git a/helm/dbrepo-mariadb-galera/Chart.lock b/helm/dbrepo-mariadb-galera/Chart.lock
deleted file mode 100644
index fb510b79ee5efe30a1091eb91b09a163f7e6c4e9..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/Chart.lock
+++ /dev/null
@@ -1,6 +0,0 @@
-dependencies:
-- name: mariadb-galera
- repository: https://charts.bitnami.com/bitnami
- version: 10.1.3
-digest: sha256:ec9ea7a577993779d520b0c93990fb04847f96e41f2bd503141ba66338340985
-generated: "2024-09-14T01:42:48.297778184+04:00"
diff --git a/helm/dbrepo-mariadb-galera/Chart.yaml b/helm/dbrepo-mariadb-galera/Chart.yaml
deleted file mode 100644
index 4be4337885fe446add1835f3a5296bc2a42f9583..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/Chart.yaml
+++ /dev/null
@@ -1,23 +0,0 @@
-annotations:
- licenses: Apache-2.0
-apiVersion: v2
-name: dbrepo-mariadb-galera
-description: Helm Chart for installing DBRepo Data Database
-sources:
- - https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services
-type: application
-version: "1.4.6"
-appVersion: "1.4.6"
-keywords:
- - dbrepo
-maintainers:
- - name: Martin Weise
- email: martin.weise@tuwien.ac.at
-home: https://www.ifs.tuwien.ac.at/infrastructures/dbrepo/
-icon: https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/dbrepo-ui/public/favicon.png
-dependencies:
- - name: mariadb-galera
- alias: database
- version: 10.1.3 # app version: 11.1.3
- repository: https://charts.bitnami.com/bitnami
- condition: database.enabled
\ No newline at end of file
diff --git a/helm/dbrepo-mariadb-galera/README.md b/helm/dbrepo-mariadb-galera/README.md
deleted file mode 100644
index c5aa55100a7959b5a7bc888519e4d7ccbdaefb5e..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/README.md
+++ /dev/null
@@ -1,6 +0,0 @@
-# DBRepo MariaDB Helm chart
-
-tbd
-
-## Parameters
-
diff --git a/helm/dbrepo-mariadb-galera/charts/mariadb-galera-10.1.3.tgz b/helm/dbrepo-mariadb-galera/charts/mariadb-galera-10.1.3.tgz
deleted file mode 100644
index c906aaf7634b20f0eaf9358b435b01086bdc4f55..0000000000000000000000000000000000000000
Binary files a/helm/dbrepo-mariadb-galera/charts/mariadb-galera-10.1.3.tgz and /dev/null differ
diff --git a/helm/dbrepo-mariadb-galera/templates/_compatibility.tpl b/helm/dbrepo-mariadb-galera/templates/_compatibility.tpl
deleted file mode 100644
index 6fc2aa8fa45e3bf7a8cfdb5312515aa2c27a0491..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/templates/_compatibility.tpl
+++ /dev/null
@@ -1,42 +0,0 @@
-{{/*
-Copyright Broadcom, Inc. All Rights Reserved.
-SPDX-License-Identifier: APACHE-2.0
-*/}}
-
-{{/* vim: set filetype=mustache: */}}
-
-{{/*
-Return true if the detected platform is Openshift
-Usage:
-{{- include "common.compatibility.isOpenshift" . -}}
-*/}}
-{{- define "common.compatibility.isOpenshift" -}}
-{{- if .Capabilities.APIVersions.Has "security.openshift.io/v1" -}}
-{{- true -}}
-{{- end -}}
-{{- end -}}
-
-{{/*
-Render a compatible securityContext depending on the platform. By default it is maintained as it is. In other platforms like Openshift we remove default user/group values that do not work out of the box with the restricted-v1 SCC
-Usage:
-{{- include "common.compatibility.renderSecurityContext" (dict "secContext" .Values.containerSecurityContext "context" $) -}}
-*/}}
-{{- define "common.compatibility.renderSecurityContext" -}}
-{{- $adaptedContext := .secContext -}}
-
-{{- if (((.context.Values.global).compatibility).openshift) -}}
- {{- if or (eq .context.Values.global.compatibility.openshift.adaptSecurityContext "force") (and (eq .context.Values.global.compatibility.openshift.adaptSecurityContext "auto") (include "common.compatibility.isOpenshift" .context)) -}}
- {{/* Remove incompatible user/group values that do not work in Openshift out of the box */}}
- {{- $adaptedContext = omit $adaptedContext "fsGroup" "runAsUser" "runAsGroup" -}}
- {{- if not .secContext.seLinuxOptions -}}
- {{/* If it is an empty object, we remove it from the resulting context because it causes validation issues */}}
- {{- $adaptedContext = omit $adaptedContext "seLinuxOptions" -}}
- {{- end -}}
- {{- end -}}
-{{- end -}}
-{{/* Remove fields that are disregarded when running the container in privileged mode */}}
-{{- if $adaptedContext.privileged -}}
- {{- $adaptedContext = omit $adaptedContext "capabilities" "seLinuxOptions" -}}
-{{- end -}}
-{{- omit $adaptedContext "enabled" | toYaml -}}
-{{- end -}}
\ No newline at end of file
diff --git a/helm/dbrepo-mariadb-galera/templates/_helpers.tpl b/helm/dbrepo-mariadb-galera/templates/_helpers.tpl
deleted file mode 100644
index b17e44d2dfa6f6e7a09c3ab58b35794c46791c71..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/templates/_helpers.tpl
+++ /dev/null
@@ -1,62 +0,0 @@
-{{/*
-Expand the name of the chart.
-*/}}
-{{- define "kubernetes.name" -}}
-{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
-{{- end }}
-
-{{/*
-Create a default fully qualified app name.
-We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
-If release name contains chart name it will be used as a full name.
-*/}}
-{{- define "kubernetes.fullname" -}}
-{{- if .Values.fullnameOverride }}
-{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }}
-{{- else }}
-{{- $name := default .Chart.Name .Values.nameOverride }}
-{{- if contains $name .Release.Name }}
-{{- .Release.Name | trunc 63 | trimSuffix "-" }}
-{{- else }}
-{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" }}
-{{- end }}
-{{- end }}
-{{- end }}
-
-{{/*
-Create chart name and version as used by the chart label.
-*/}}
-{{- define "kubernetes.chart" -}}
-{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
-{{- end }}
-
-{{/*
-Common labels
-*/}}
-{{- define "kubernetes.labels" -}}
-helm.sh/chart: {{ include "kubernetes.chart" . }}
-{{ include "kubernetes.selectorLabels" . }}
-{{- if .Chart.AppVersion }}
-app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
-{{- end }}
-app.kubernetes.io/managed-by: {{ .Release.Service }}
-{{- end }}
-
-{{/*
-Selector labels
-*/}}
-{{- define "kubernetes.selectorLabels" -}}
-app.kubernetes.io/name: {{ include "kubernetes.name" . }}
-app.kubernetes.io/instance: {{ .Release.Name }}
-{{- end }}
-
-{{/*
-Create the name of the service account to use
-*/}}
-{{- define "kubernetes.serviceAccountName" -}}
-{{- if .Values.serviceAccount.create }}
-{{- default (include "kubernetes.fullname" .) .Values.serviceAccount.name }}
-{{- else }}
-{{- default "default" .Values.serviceAccount.name }}
-{{- end }}
-{{- end }}
diff --git a/helm/dbrepo-mariadb-galera/templates/_names.tpl b/helm/dbrepo-mariadb-galera/templates/_names.tpl
deleted file mode 100644
index cea9dae390ea083c43da813edeefa5441c007f0e..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/templates/_names.tpl
+++ /dev/null
@@ -1,6 +0,0 @@
-{{/*
-Allow the release namespace to be overridden for multi-namespace deployments in combined charts.
-*/}}
-{{- define "common.names.namespace" -}}
-{{- default .Release.Namespace .Values.namespaceOverride | trunc 63 | trimSuffix "-" -}}
-{{- end -}}
\ No newline at end of file
diff --git a/helm/dbrepo-mariadb-galera/templates/configmap.yaml b/helm/dbrepo-mariadb-galera/templates/configmap.yaml
deleted file mode 100644
index 066a0d1afbbc5d46cd00a1f5315195365aef0c66..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/templates/configmap.yaml
+++ /dev/null
@@ -1,580 +0,0 @@
-apiVersion: v1
-kind: ConfigMap
-metadata:
- name: database-setup
- namespace: {{ .Values.namespace }}
-data:
- {{- with .Values.database.extraInitDbScripts }}
- {{ toYaml . | nindent 2 }}
- {{- end }}
- 02-setup-data.sql: |
- BEGIN;
- INSERT INTO `mdb_containers` (name, internal_name, image_id, host, port, sidecar_host, sidecar_port, privileged_username, privileged_password)
- VALUES ('MariaDB 11.1.3', 'mariadb_11_1_3', 1, 'data-db', 3306, 'data-db', 8080, 'root', 'dbrepo');
- COMMIT;
- 01-setup-schema.sql: |
- BEGIN;
-
- CREATE TABLE IF NOT EXISTS `mdb_users`
- (
- id character varying(36) NOT NULL,
- username character varying(255) NOT NULL,
- firstname character varying(255),
- lastname character varying(255),
- email character varying(255) NOT NULL,
- orcid character varying(255),
- affiliation character varying(255),
- mariadb_password character varying(255) NOT NULL,
- theme character varying(255) NOT NULL default ('light'),
- language character varying(3) NOT NULL default ('en'),
- PRIMARY KEY (id),
- UNIQUE (username),
- UNIQUE (email)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_images`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- registry character varying(255) NOT NULL DEFAULT 'docker.io',
- name character varying(255) NOT NULL,
- version character varying(255) NOT NULL,
- default_port integer NOT NULL,
- dialect character varying(255) NOT NULL,
- driver_class character varying(255) NOT NULL,
- jdbc_method character varying(255) NOT NULL,
- is_default BOOLEAN NOT NULL DEFAULT FALSE,
- created timestamp NOT NULL DEFAULT NOW(),
- last_modified timestamp,
- PRIMARY KEY (id),
- UNIQUE (name, version),
- UNIQUE (is_default)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_images_date`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- iid bigint NOT NULL,
- database_format character varying(255) NOT NULL,
- unix_format character varying(255) NOT NULL,
- example character varying(255) NOT NULL,
- has_time boolean NOT NULL,
- created_at timestamp NOT NULL DEFAULT NOW(),
- PRIMARY KEY (id),
- FOREIGN KEY (iid) REFERENCES mdb_images (id),
- UNIQUE (database_format, unix_format, example)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_containers`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- internal_name character varying(255) NOT NULL,
- name character varying(255) NOT NULL,
- host character varying(255) NOT NULL,
- port integer NOT NULL default 3306,
- ui_host character varying(255) NOT NULL default host,
- ui_port integer NOT NULL default port,
- ui_additional_flags text,
- sidecar_host character varying(255),
- sidecar_port integer,
- image_id bigint NOT NULL,
- created timestamp NOT NULL DEFAULT NOW(),
- last_modified timestamp,
- privileged_username character varying(255) NOT NULL,
- privileged_password character varying(255) NOT NULL,
- quota integer NOT NULL DEFAULT 50,
- PRIMARY KEY (id),
- FOREIGN KEY (image_id) REFERENCES mdb_images (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_data`
- (
- ID bigint NOT NULL AUTO_INCREMENT,
- PROVENANCE text,
- FileEncoding text,
- FileType character varying(100),
- Version text,
- Seperator text,
- PRIMARY KEY (ID)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_licenses`
- (
- identifier character varying(255) NOT NULL,
- uri text NOT NULL,
- description text NOT NULL,
- PRIMARY KEY (identifier),
- UNIQUE (uri(200))
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_databases`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- cid bigint NOT NULL,
- name character varying(255) NOT NULL,
- internal_name character varying(255) NOT NULL,
- exchange_name character varying(255) NOT NULL,
- description text,
- engine character varying(20),
- is_public boolean NOT NULL DEFAULT TRUE,
- image longblob,
- created_by character varying(36),
- owned_by character varying(36),
- contact_person character varying(36),
- created timestamp NOT NULL DEFAULT NOW(),
- last_modified timestamp,
- PRIMARY KEY (id),
- FOREIGN KEY (cid) REFERENCES mdb_containers (id) /* currently we only support one-to-one */,
- FOREIGN KEY (created_by) REFERENCES mdb_users (id),
- FOREIGN KEY (owned_by) REFERENCES mdb_users (id),
- FOREIGN KEY (contact_person) REFERENCES mdb_users (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_databases_subjects`
- (
- dbid BIGINT NOT NULL,
- subjects character varying(255) NOT NULL,
- PRIMARY KEY (dbid, subjects)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_tables`
- (
- ID bigint NOT NULL AUTO_INCREMENT,
- tDBID bigint NOT NULL,
- tName VARCHAR(64) NOT NULL,
- internal_name VARCHAR(64) NOT NULL,
- queue_name VARCHAR(255) NOT NULL,
- routing_key VARCHAR(255),
- tDescription VARCHAR(2048),
- num_rows BIGINT,
- data_length BIGINT,
- max_data_length BIGINT,
- avg_row_length BIGINT,
- `separator` CHAR(1),
- quote CHAR(1),
- element_null VARCHAR(50),
- skip_lines BIGINT,
- element_true VARCHAR(50),
- element_false VARCHAR(50),
- Version TEXT,
- created timestamp NOT NULL DEFAULT NOW(),
- versioned boolean not null default true,
- created_by character varying(36) NOT NULL,
- owned_by character varying(36) NOT NULL,
- last_modified timestamp,
- PRIMARY KEY (ID),
- UNIQUE (tDBID, internal_name),
- FOREIGN KEY (tDBID) REFERENCES mdb_databases (id),
- FOREIGN KEY (created_by) REFERENCES mdb_users (id),
- FOREIGN KEY (owned_by) REFERENCES mdb_users (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_columns`
- (
- ID BIGINT NOT NULL AUTO_INCREMENT,
- tID BIGINT NOT NULL,
- dfID BIGINT,
- cName VARCHAR(64),
- internal_name VARCHAR(64) NOT NULL,
- Datatype ENUM ('CHAR','VARCHAR','BINARY','VARBINARY','TINYBLOB','TINYTEXT','TEXT','BLOB','MEDIUMTEXT','MEDIUMBLOB','LONGTEXT','LONGBLOB','ENUM','SET','BIT','TINYINT','BOOL','SMALLINT','MEDIUMINT','INT','BIGINT','FLOAT','DOUBLE','DECIMAL','DATE','DATETIME','TIMESTAMP','TIME','YEAR'),
- length BIGINT NULL,
- ordinal_position INTEGER NOT NULL,
- index_length BIGINT NULL,
- description VARCHAR(2048),
- size BIGINT,
- d BIGINT,
- auto_generated BOOLEAN DEFAULT false,
- is_null_allowed BOOLEAN NOT NULL DEFAULT true,
- val_min NUMERIC NULL,
- val_max NUMERIC NULL,
- mean NUMERIC NULL,
- median NUMERIC NULL,
- std_dev Numeric NULL,
- created timestamp NOT NULL DEFAULT NOW(),
- last_modified timestamp,
- FOREIGN KEY (tID) REFERENCES mdb_tables (ID) ON DELETE CASCADE,
- PRIMARY KEY (ID)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_columns_enums`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- column_id bigint NOT NULL,
- value CHARACTER VARYING(255) NOT NULL,
- FOREIGN KEY (column_id) REFERENCES mdb_columns (ID) ON DELETE CASCADE,
- PRIMARY KEY (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_columns_sets`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- column_id bigint NOT NULL,
- value CHARACTER VARYING(255) NOT NULL,
- FOREIGN KEY (column_id) REFERENCES mdb_columns (ID) ON DELETE CASCADE,
- PRIMARY KEY (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_columns_nom`
- (
- tID bigint,
- cID bigint,
- maxlength INTEGER,
- last_modified timestamp,
- created timestamp NOT NULL DEFAULT NOW(),
- FOREIGN KEY (tID, cID) REFERENCES mdb_columns (tID, ID),
- PRIMARY KEY (tID, cID)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_columns_cat`
- (
- tID bigint,
- cID bigint,
- num_cat INTEGER,
- -- cat_array TEXT[],
- last_modified timestamp,
- created timestamp NOT NULL DEFAULT NOW(),
- FOREIGN KEY (tID, cID) REFERENCES mdb_columns (tID, ID),
- PRIMARY KEY (tID, cID)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_constraints_foreign_key`
- (
- fkid BIGINT NOT NULL AUTO_INCREMENT,
- tid BIGINT NOT NULL,
- rtid BIGINT NOT NULL,
- name VARCHAR(255) NOT NULL,
- on_update VARCHAR(50) NULL,
- on_delete VARCHAR(50) NULL,
- position INT NULL,
- PRIMARY KEY (fkid),
- FOREIGN KEY (tid) REFERENCES mdb_tables (id) ON DELETE CASCADE,
- FOREIGN KEY (rtid) REFERENCES mdb_tables (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_constraints_primary_key`
- (
- pkid BIGINT NOT NULL AUTO_INCREMENT,
- tID BIGINT NOT NULL,
- cid BIGINT NOT NULL,
- PRIMARY KEY (pkid),
- FOREIGN KEY (tID) REFERENCES mdb_tables (id) ON DELETE CASCADE,
- FOREIGN KEY (cid) REFERENCES mdb_columns (id) ON DELETE CASCADE
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_constraints_foreign_key_reference`
- (
- id BIGINT NOT NULL AUTO_INCREMENT,
- fkid BIGINT NOT NULL,
- cid BIGINT NOT NULL,
- rcid BIGINT NOT NULL,
- PRIMARY KEY (id),
- UNIQUE (fkid, cid, rcid),
- FOREIGN KEY (fkid) REFERENCES mdb_constraints_foreign_key (fkid) ON UPDATE CASCADE,
- FOREIGN KEY (cid) REFERENCES mdb_columns (id),
- FOREIGN KEY (rcid) REFERENCES mdb_columns (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_constraints_unique`
- (
- uid BIGINT NOT NULL AUTO_INCREMENT,
- name VARCHAR(255) NOT NULL,
- tid BIGINT NOT NULL,
- position INT NULL,
- PRIMARY KEY (uid),
- FOREIGN KEY (tid) REFERENCES mdb_tables (id) ON DELETE CASCADE
- );
-
- CREATE TABLE IF NOT EXISTS `mdb_constraints_unique_columns`
- (
- id BIGINT NOT NULL AUTO_INCREMENT,
- uid BIGINT NOT NULL,
- cid BIGINT NOT NULL,
- PRIMARY KEY (id),
- FOREIGN KEY (uid) REFERENCES mdb_constraints_unique (uid),
- FOREIGN KEY (cid) REFERENCES mdb_columns (id) ON DELETE CASCADE
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_constraints_checks`
- (
- id BIGINT NOT NULL AUTO_INCREMENT,
- tid BIGINT NOT NULL,
- checks VARCHAR(255) NOT NULL,
- PRIMARY KEY (id),
- FOREIGN KEY (tid) REFERENCES mdb_tables (id) ON DELETE CASCADE
- ) WITH SYSTEM VERSIONING;
-
-
- CREATE TABLE IF NOT EXISTS `mdb_concepts`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- uri text not null,
- name VARCHAR(255) null,
- description TEXT null,
- created timestamp NOT NULL DEFAULT NOW(),
- PRIMARY KEY (id),
- UNIQUE (uri(200))
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_units`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- uri text not null,
- name VARCHAR(255) null,
- description TEXT null,
- created timestamp NOT NULL DEFAULT NOW(),
- PRIMARY KEY (id),
- UNIQUE (uri(200))
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_columns_concepts`
- (
- id bigint NOT NULL,
- cID bigint NOT NULL,
- created timestamp NOT NULL DEFAULT NOW(),
- PRIMARY KEY (id, cid),
- FOREIGN KEY (cID) REFERENCES mdb_columns (ID)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_columns_units`
- (
- id bigint NOT NULL,
- cID bigint NOT NULL,
- created timestamp NOT NULL DEFAULT NOW(),
- PRIMARY KEY (id, cID),
- FOREIGN KEY (cID) REFERENCES mdb_columns (ID)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_view`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- vdbid bigint NOT NULL,
- vName VARCHAR(64) NOT NULL,
- internal_name VARCHAR(64) NOT NULL,
- Query TEXT NOT NULL,
- query_hash VARCHAR(255) NOT NULL,
- Public BOOLEAN NOT NULL,
- InitialView BOOLEAN NOT NULL,
- created timestamp NOT NULL DEFAULT NOW(),
- last_modified timestamp,
- created_by character varying(36) NOT NULL,
- PRIMARY KEY (id),
- FOREIGN KEY (vdbid) REFERENCES mdb_databases (id),
- FOREIGN KEY (created_by) REFERENCES mdb_users (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_banner_messages`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- type ENUM ('ERROR', 'WARNING', 'INFO') NOT NULL default 'INFO',
- message TEXT NOT NULL,
- link TEXT NULL,
- link_text VARCHAR(255) NULL,
- display_start timestamp NULL,
- display_end timestamp NULL,
- PRIMARY KEY (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_ontologies`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- prefix VARCHAR(8) NOT NULL,
- uri TEXT NOT NULL,
- uri_pattern TEXT,
- sparql_endpoint TEXT NULL,
- rdf_path TEXT NULL,
- last_modified timestamp,
- created timestamp NOT NULL DEFAULT NOW(),
- UNIQUE (prefix),
- UNIQUE (uri(200)),
- PRIMARY KEY (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_view_columns`
- (
- id BIGINT NOT NULL AUTO_INCREMENT,
- view_id BIGINT NOT NULL,
- dfID BIGINT,
- name VARCHAR(64),
- internal_name VARCHAR(64) NOT NULL,
- column_type ENUM ('CHAR','VARCHAR','BINARY','VARBINARY','TINYBLOB','TINYTEXT','TEXT','BLOB','MEDIUMTEXT','MEDIUMBLOB','LONGTEXT','LONGBLOB','ENUM','SET','BIT','TINYINT','BOOL','SMALLINT','MEDIUMINT','INT','BIGINT','FLOAT','DOUBLE','DECIMAL','DATE','DATETIME','TIMESTAMP','TIME','YEAR'),
- ordinal_position INTEGER NOT NULL,
- size BIGINT,
- d BIGINT,
- auto_generated BOOLEAN DEFAULT false,
- is_null_allowed BOOLEAN NOT NULL DEFAULT true,
- PRIMARY KEY (id),
- FOREIGN KEY (view_id) REFERENCES mdb_view (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_identifiers`
- (
- id BIGINT NOT NULL AUTO_INCREMENT,
- dbid BIGINT NOT NULL,
- qid BIGINT,
- vid BIGINT,
- tid BIGINT,
- publisher VARCHAR(255) NOT NULL,
- language VARCHAR(2),
- publication_year INTEGER NOT NULL,
- publication_month INTEGER,
- publication_day INTEGER,
- identifier_type ENUM ('DATABASE', 'SUBSET', 'VIEW', 'TABLE') NOT NULL,
- status ENUM ('DRAFT', 'PUBLISHED') NOT NULL DEFAULT ('PUBLISHED'),
- query TEXT,
- query_normalized TEXT,
- query_hash VARCHAR(255),
- execution TIMESTAMP,
- result_hash VARCHAR(255),
- result_number BIGINT,
- doi VARCHAR(255),
- created TIMESTAMP NOT NULL DEFAULT NOW(),
- created_by VARCHAR(36) NOT NULL,
- last_modified TIMESTAMP,
- PRIMARY KEY (id), /* must be a single id from persistent identifier concept */
- FOREIGN KEY (dbid) REFERENCES mdb_databases (id),
- FOREIGN KEY (created_by) REFERENCES mdb_users (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_identifier_licenses`
- (
- pid bigint NOT NULL,
- license_id VARCHAR(255) NOT NULL,
- PRIMARY KEY (pid, license_id),
- FOREIGN KEY (pid) REFERENCES mdb_identifiers (id),
- FOREIGN KEY (license_id) REFERENCES mdb_licenses (identifier)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_identifier_titles`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- pid bigint NOT NULL,
- title text NOT NULL,
- title_type ENUM ('ALTERNATIVE_TITLE', 'SUBTITLE', 'TRANSLATED_TITLE', 'OTHER'),
- language VARCHAR(2),
- PRIMARY KEY (id),
- FOREIGN KEY (pid) REFERENCES mdb_identifiers (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_identifier_funders`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- pid bigint NOT NULL,
- funder_name VARCHAR(255) NOT NULL,
- funder_identifier TEXT,
- funder_identifier_type ENUM ('CROSSREF_FUNDER_ID', 'GRID', 'ISNI', 'ROR', 'OTHER'),
- scheme_uri text,
- award_number VARCHAR(255),
- award_title text,
- language VARCHAR(255),
- PRIMARY KEY (id),
- FOREIGN KEY (pid) REFERENCES mdb_identifiers (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_identifier_descriptions`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- pid bigint NOT NULL,
- description text NOT NULL,
- description_type ENUM ('ABSTRACT', 'METHODS', 'SERIES_INFORMATION', 'TABLE_OF_CONTENTS', 'TECHNICAL_INFO', 'OTHER'),
- language VARCHAR(2),
- PRIMARY KEY (id),
- FOREIGN KEY (pid) REFERENCES mdb_identifiers (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_related_identifiers`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- pid bigint NOT NULL,
- value varchar(255) NOT NULL,
- type varchar(255) NOT NULL,
- relation varchar(255) NOT NULL,
- PRIMARY KEY (id), /* must be a single id from persistent identifier concept */
- FOREIGN KEY (pid) REFERENCES mdb_identifiers (id),
- UNIQUE (pid, value)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_identifier_creators`
- (
- id bigint NOT NULL AUTO_INCREMENT,
- pid bigint NOT NULL,
- given_names text,
- family_name text,
- creator_name VARCHAR(255) NOT NULL,
- name_type ENUM ('PERSONAL', 'ORGANIZATIONAL') default 'PERSONAL',
- name_identifier text,
- name_identifier_scheme ENUM ('ROR', 'GRID', 'ISNI', 'ORCID'),
- name_identifier_scheme_uri text,
- affiliation VARCHAR(255),
- affiliation_identifier text,
- affiliation_identifier_scheme ENUM ('ROR', 'GRID', 'ISNI'),
- affiliation_identifier_scheme_uri text,
- PRIMARY KEY (id),
- FOREIGN KEY (pid) REFERENCES mdb_identifiers (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_update`
- (
- uUserID character varying(255) NOT NULL,
- uDBID bigint NOT NULL,
- created timestamp NOT NULL DEFAULT NOW(),
- PRIMARY KEY (uUserID, uDBID),
- FOREIGN KEY (uDBID) REFERENCES mdb_databases (id)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_access`
- (
- aUserID character varying(255) NOT NULL,
- aDBID bigint REFERENCES mdb_databases (id),
- attime TIMESTAMP,
- download BOOLEAN,
- created timestamp NOT NULL DEFAULT NOW(),
- PRIMARY KEY (aUserID, aDBID)
- ) WITH SYSTEM VERSIONING;
-
- CREATE TABLE IF NOT EXISTS `mdb_have_access`
- (
- user_id character varying(36) NOT NULL,
- database_id bigint REFERENCES mdb_databases (id),
- access_type ENUM ('READ', 'WRITE_OWN', 'WRITE_ALL') NOT NULL,
- created timestamp NOT NULL DEFAULT NOW(),
- PRIMARY KEY (user_id, database_id),
- FOREIGN KEY (user_id) REFERENCES mdb_users (id)
- ) WITH SYSTEM VERSIONING;
-
- COMMIT;
- BEGIN;
-
- INSERT INTO `mdb_licenses` (identifier, uri, description)
- VALUES ('CC0-1.0', 'https://creativecommons.org/publicdomain/zero/1.0/legalcode',
- 'CC0 waives copyright interest in a work you''ve created and dedicates it to the world-wide public domain. Use CC0 to opt out of copyright entirely and ensure your work has the widest reach.'),
- ('CC-BY-4.0', 'https://creativecommons.org/licenses/by/4.0/legalcode',
- 'The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited.');
-
- INSERT INTO `mdb_images` (name, registry, version, default_port, dialect, driver_class, jdbc_method)
- VALUES ('mariadb', 'docker.io', '11.1.3', 3306, 'org.hibernate.dialect.MariaDBDialect', 'org.mariadb.jdbc.Driver',
- 'mariadb');
-
- INSERT INTO `mdb_images_date` (iid, database_format, unix_format, example, has_time)
- VALUES (1, '%Y-%c-%d %H:%i:%S.%f', 'yyyy-MM-dd HH:mm:ss.SSSSSS', '2022-01-30 13:44:25.499', true),
- (1, '%Y-%c-%d %H:%i:%S', 'yyyy-MM-dd HH:mm:ss', '2022-01-30 13:44:25', true),
- (1, '%Y-%c-%d', 'yyyy-MM-dd', '2022-01-30', false),
- (1, '%H:%i:%S', 'HH:mm:ss', '13:44:25', true),
- (1, '%d.%c.%Y', 'dd.MM.yyyy', '30.01.2022', false);
-
- INSERT INTO `mdb_ontologies` (prefix, uri, uri_pattern, sparql_endpoint, rdf_path)
- VALUES ('om', 'http://www.ontology-of-units-of-measure.org/resource/om-2/',
- 'http://www.ontology-of-units-of-measure.org/resource/om-2/.*', null, 'rdf/om-2.0.rdf'),
- ('wd', 'http://www.wikidata.org/', 'http://www.wikidata.org/entity/.*', 'https://query.wikidata.org/sparql',
- null),
- ('mo', 'http://purl.org/ontology/mo/', 'http://purl.org/ontology/mo/.*', null, null),
- ('dc', 'http://purl.org/dc/elements/1.1/', null, null, null),
- ('xsd', 'http://www.w3.org/2001/XMLSchema#', null, null, null),
- ('tl', 'http://purl.org/NET/c4dm/timeline.owl#', null, null, null),
- ('foaf', 'http://xmlns.com/foaf/0.1/', null, null, null),
- ('schema', 'http://schema.org/', null, null, null),
- ('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#', null, null, null),
- ('rdfs', 'http://www.w3.org/2000/01/rdf-schema#', null, null, null),
- ('owl', 'http://www.w3.org/2002/07/owl#', null, null, null),
- ('prov', 'http://www.w3.org/ns/prov#', null, null, null),
- ('db', 'http://dbpedia.org', 'http://dbpedia.org/ontology/.*', 'http://dbpedia.org/sparql', null);
- COMMIT;
-
diff --git a/helm/dbrepo-mariadb-galera/templates/secret.yaml b/helm/dbrepo-mariadb-galera/templates/secret.yaml
deleted file mode 100644
index fc5a2a7c5ddaa757c9fc29dc75b24d787a3c0656..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/templates/secret.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-apiVersion: v1
-kind: Secret
-metadata:
- name: sidecar-secret
- namespace: {{ .Values.namespace }}
-stringData:
- S3_ACCESS_KEY_ID: "{{ .Values.s3.auth.adminAccessKeyId }}"
- S3_SECRET_ACCESS_KEY: "{{ .Values.s3.auth.adminSecretAccessKey }}"
- S3_STORAGE_ENDPOINT: "{{ .Values.s3.endpoint }}"
diff --git a/helm/dbrepo-mariadb-galera/values.schema.json b/helm/dbrepo-mariadb-galera/values.schema.json
deleted file mode 100644
index 336e7dc1e5fb1f7455ebb7cea7593df6cd016a90..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/values.schema.json
+++ /dev/null
@@ -1,301 +0,0 @@
-{
- "$schema": "https://json-schema.org/draft/2020-12/schema",
- "properties": {
- "database": {
- "properties": {
- "db": {
- "properties": {
- "name": {
- "type": "string"
- }
- },
- "type": "object"
- },
- "enabled": {
- "type": "boolean"
- },
- "extraInitDbScripts": {
- "properties": {},
- "type": "object"
- },
- "extraVolumeMounts": {
- "items": {
- "properties": {
- "mountPath": {
- "type": "string"
- },
- "name": {
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "extraVolumes": {
- "items": {
- "properties": {
- "emptyDir": {
- "properties": {},
- "type": "object"
- },
- "name": {
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "fullnameOverride": {
- "type": "string"
- },
- "galera": {
- "properties": {
- "mariabackup": {
- "properties": {
- "password": {
- "type": "string"
- },
- "user": {
- "type": "string"
- }
- },
- "type": "object"
- }
- },
- "type": "object"
- },
- "host": {
- "type": "string"
- },
- "initdbScriptsConfigMap": {
- "type": "string"
- },
- "jdbcExtraArgs": {
- "type": "string"
- },
- "metrics": {
- "properties": {
- "enabled": {
- "type": "boolean"
- }
- },
- "type": "object"
- },
- "persistence": {
- "properties": {
- "enabled": {
- "type": "boolean"
- }
- },
- "type": "object"
- },
- "replicaCount": {
- "type": "integer"
- },
- "rootUser": {
- "properties": {
- "password": {
- "type": "string"
- },
- "user": {
- "type": "string"
- }
- },
- "type": "object"
- },
- "service": {
- "properties": {
- "extraPorts": {
- "items": {
- "properties": {
- "name": {
- "type": "string"
- },
- "port": {
- "type": "integer"
- },
- "protocol": {
- "type": "string"
- },
- "targetPort": {
- "type": "integer"
- }
- },
- "type": "object"
- },
- "type": "array"
- }
- },
- "type": "object"
- },
- "sidecars": {
- "items": {
- "properties": {
- "envFrom": {
- "items": {
- "properties": {
- "secretRef": {
- "properties": {
- "name": {
- "type": "string"
- }
- },
- "type": "object"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "image": {
- "type": "string"
- },
- "imagePullPolicy": {
- "type": "string"
- },
- "livenessProbe": {
- "properties": {
- "exec": {
- "properties": {
- "command": {
- "items": {
- "type": "string"
- },
- "type": "array"
- }
- },
- "type": "object"
- },
- "initialDelaySeconds": {
- "type": "integer"
- },
- "periodSeconds": {
- "type": "integer"
- }
- },
- "type": "object"
- },
- "name": {
- "type": "string"
- },
- "ports": {
- "items": {
- "properties": {
- "containerPort": {
- "type": "integer"
- },
- "name": {
- "type": "string"
- },
- "protocol": {
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "readinessProbe": {
- "properties": {
- "exec": {
- "properties": {
- "command": {
- "items": {
- "type": "string"
- },
- "type": "array"
- }
- },
- "type": "object"
- },
- "initialDelaySeconds": {
- "type": "integer"
- },
- "periodSeconds": {
- "type": "integer"
- }
- },
- "type": "object"
- },
- "securityContext": {
- "properties": {
- "allowPrivilegeEscalation": {
- "type": "boolean"
- },
- "capabilities": {
- "properties": {
- "drop": {
- "items": {
- "type": "string"
- },
- "type": "array"
- }
- },
- "type": "object"
- },
- "runAsGroup": {
- "type": "integer"
- },
- "runAsNonRoot": {
- "type": "boolean"
- },
- "runAsUser": {
- "type": "integer"
- },
- "seccompProfile": {
- "properties": {
- "type": {
- "type": "string"
- }
- },
- "type": "object"
- }
- },
- "type": "object"
- },
- "volumeMounts": {
- "items": {
- "properties": {
- "mountPath": {
- "type": "string"
- },
- "name": {
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- }
- },
- "type": "object"
- },
- "type": "array"
- }
- },
- "type": "object"
- },
- "s3": {
- "properties": {
- "auth": {
- "properties": {
- "adminAccessKeyId": {
- "type": "string"
- },
- "adminSecretAccessKey": {
- "type": "string"
- }
- },
- "type": "object"
- },
- "endpoint": {
- "type": "string"
- }
- },
- "type": "object"
- }
- },
- "type": "object"
-}
diff --git a/helm/dbrepo-mariadb-galera/values.yaml b/helm/dbrepo-mariadb-galera/values.yaml
deleted file mode 100644
index f5026a3b5bdeb9f1ce83e1b4b79cb5e87bef6122..0000000000000000000000000000000000000000
--- a/helm/dbrepo-mariadb-galera/values.yaml
+++ /dev/null
@@ -1,107 +0,0 @@
-# Copyright the DBRepo developers
-# SPDX-License-Identifier: APACHE-2.0
-
-## @param namespaceOverride The namespace to install the chart
-
-s3:
- endpoint: http://storage-service-s3:8333
- auth:
- adminAccessKeyId: seaweedfsadmin
- adminSecretAccessKey: seaweedfsadmin
-
-database:
- ## @param database.enabled Enable the Metadata Database.
- enabled: true
- ## @skip database.fullnameOverride
- fullnameOverride: data-db
- ## @param database.host The hostname for the microservices.
- host: data-db
- rootUser:
- ## @param database.rootUser.user The root username.
- user: root
- ## @param database.rootUser.password The root user password.
- password: dbrepo
- db:
- ## @param database.db.name The database name.
- name: dbrepo
- galera:
- mariabackup:
- ## @param database.galera.mariabackup.user The database backup username.
- user: backup
- ## @param database.galera.mariabackup.password The database backup user password
- password: backup
- ## @param database.jdbcExtraArgs The extra arguments for JDBC connections in the microservices.
- jdbcExtraArgs: ""
- metrics:
- ## @skip database.metrics.enabled The Prometheus settings.
- enabled: false
- ## @skip database.initdbScriptsConfigMap The initial database scripts.
- initdbScriptsConfigMap: database-setup
- ## @param database.extraInitDbScripts Additional init.db scripts that are executed on the first start.
- extraInitDbScripts: { }
- # 03-additional-data.sql: |
- # BEGIN;
- # INSERT INTO `mdb_containers` (name, internal_name, image_id, host, port, sidecar_host, sidecar_port, privileged_username, privileged_password)
- # VALUES ('MariaDB Galera TEST', 'mariadb_11_1_3', 1, 'data-db', 3306, 'data-db', 80, 'root', 'dbrepo');
- # COMMIT;
- ## @param database.replicaCount The number of cluster nodes, should be uneven i.e. 2n+1
- replicaCount: 3
- persistence:
- ## @param database.persistence.enabled Enable persistent storage.
- enabled: true
- ## @skip database.service
- service:
- extraPorts:
- - name: "sidecar"
- port: 8080
- targetPort: 8080
- protocol: TCP
- ## @skip database.sidecars
- sidecars:
- - name: sidecar
- image: registry.datalab.tuwien.ac.at/dbrepo/data-db-sidecar:1.4.5
- imagePullPolicy: Always
- securityContext:
- runAsUser: 1001
- runAsGroup: 0
- runAsNonRoot: true
- allowPrivilegeEscalation: false
- seccompProfile:
- type: RuntimeDefault
- capabilities:
- drop:
- - ALL
- ports:
- - name: "sidecar"
- containerPort: 8080
- protocol: TCP
- envFrom:
- - secretRef:
- name: data-service-secret
- livenessProbe:
- exec:
- command:
- - /bin/bash
- - -ec
- - "curl -sSL localhost:8080/health | grep 'UP' || exit 1"
- initialDelaySeconds: 120
- periodSeconds: 30
- readinessProbe:
- exec:
- command:
- - /bin/bash
- - -ec
- - "curl -sSL localhost:8080/health | grep 'UP' || exit 1"
- initialDelaySeconds: 30
- periodSeconds: 30
- volumeMounts:
- - name: s3
- mountPath: /s3
- ## @skip database.extraVolumeMounts
- extraVolumeMounts:
- - name: s3
- mountPath: /s3
- ## @skip database.extraVolumes
- extraVolumes:
- - name: s3
- emptyDir: { }
diff --git a/helm/dbrepo/Chart.lock b/helm/dbrepo/Chart.lock
index 0937dd527af328b079b719db542efa264c410368..29ab55f1a1530f3b401b38d623e873c27a581fa0 100644
--- a/helm/dbrepo/Chart.lock
+++ b/helm/dbrepo/Chart.lock
@@ -5,9 +5,9 @@ dependencies:
- name: keycloak
repository: https://charts.bitnami.com/bitnami
version: 21.6.1
-- name: dbrepo-mariadb-galera
- repository: file://../dbrepo-mariadb-galera
- version: 1.4.7
+- name: mariadb-galera
+ repository: https://charts.bitnami.com/bitnami
+ version: 10.1.3
- name: mariadb-galera
repository: https://charts.bitnami.com/bitnami
version: 10.1.3
@@ -29,5 +29,5 @@ dependencies:
- name: prometheus
repository: https://charts.bitnami.com/bitnami
version: 1.3.22
-digest: sha256:840d2ea4b1e36fe8fa399fc4170b6274a3de161c13a4a1a3b18ce3107ab71f79
-generated: "2024-10-01T07:48:55.174297756+02:00"
+digest: sha256:54cb4dc867a23b7b265fba49608a0aaa8add75ec697c2446fbf013169c4489cd
+generated: "2024-11-02T18:34:23.0903882+01:00"
diff --git a/helm/dbrepo/Chart.yaml b/helm/dbrepo/Chart.yaml
index 9e09e7f8e37033cc9c8ff2fa4f1776f43212c59c..301352c6b26405e04f34e8ce0ef217cc83402cde 100644
--- a/helm/dbrepo/Chart.yaml
+++ b/helm/dbrepo/Chart.yaml
@@ -26,11 +26,11 @@ dependencies:
version: 21.6.1 # app version: 24.0.5
repository: https://charts.bitnami.com/bitnami
condition: authservice.enabled
- - name: dbrepo-mariadb-galera
+ - name: mariadb-galera
alias: datadb
- version: 1.4.7
- repository: file://../dbrepo-mariadb-galera
- condition: datadb.enabled
+ version: 10.1.3 # app version: 11.1.3
+ repository: https://charts.bitnami.com/bitnami
+ condition: database.enabled
- name: mariadb-galera
alias: metadatadb
version: 10.1.3 # app version: 11.1.3
diff --git a/helm/dbrepo/charts/dbrepo-mariadb-galera-1.4.6.tgz b/helm/dbrepo/charts/dbrepo-mariadb-galera-1.4.6.tgz
deleted file mode 100644
index 4af22ff6e998199f69a8e1ff43fd96c3f55aa8ec..0000000000000000000000000000000000000000
Binary files a/helm/dbrepo/charts/dbrepo-mariadb-galera-1.4.6.tgz and /dev/null differ
diff --git a/helm/dbrepo/templates/analyse-secret.yaml b/helm/dbrepo/templates/analyse-secret.yaml
index 49aa8938296b07342350f9749d9b62d078acbdb9..8baf598c936095b8e11d10a81538172b8a1e8901 100644
--- a/helm/dbrepo/templates/analyse-secret.yaml
+++ b/helm/dbrepo/templates/analyse-secret.yaml
@@ -6,8 +6,6 @@ metadata:
name: analyse-service-secret
namespace: {{ include "common.names.namespace" . | quote }}
stringData:
- ADMIN_USERNAME: "{{ .Values.identityservice.users }}"
- ADMIN_PASSWORD: "{{ .Values.identityservice.userPasswords }}"
AUTH_SERVICE_ADMIN: "{{ .Values.authservice.auth.adminUser }}"
AUTH_SERVICE_ADMIN_PASSWORD: "{{ .Values.authservice.auth.adminPassword }}"
AUTH_SERVICE_CLIENT: "{{ .Values.authservice.client.id }}"
@@ -20,4 +18,7 @@ stringData:
S3_BUCKET: "{{ .Values.storageservice.s3.bucket }}"
S3_ENDPOINT: "{{ .Values.analyseservice.s3.endpoint }}"
S3_SECRET_ACCESS_KEY: "{{ .Values.storageservice.s3.auth.adminSecretAccessKey }}"
+ METADATA_SERVICE_ENDPOINT: "{{ .Values.metadataservice.endpoint }}"
+ SYSTEM_USERNAME: "{{ .Values.identityservice.users }}"
+ SYSTEM_PASSWORD: "{{ .Values.identityservice.userPasswords }}"
{{- end }}
diff --git a/helm/dbrepo/templates/data-deployment.yaml b/helm/dbrepo/templates/data-deployment.yaml
index fae3250738ef0952f974a2ec1fa4498c03f9d231..3e3c308bf0369e80c0db93abee7d13d2c4cda268 100644
--- a/helm/dbrepo/templates/data-deployment.yaml
+++ b/helm/dbrepo/templates/data-deployment.yaml
@@ -33,7 +33,7 @@ spec:
securityContext: {{- include "common.compatibility.renderSecurityContext" (dict "secContext" .Values.dataservice.containerSecurityContext "context" $) | nindent 12 }}
{{- end }}
ports:
- - containerPort: 80
+ - containerPort: 8080
protocol: TCP
envFrom:
- secretRef:
diff --git a/helm/dbrepo/templates/data-secret.yaml b/helm/dbrepo/templates/data-secret.yaml
index dd40e3e649ab6b679510871184e4ee7e09d11c31..12d269718304abf7905fab9a0aae1b4e937e356f 100644
--- a/helm/dbrepo/templates/data-secret.yaml
+++ b/helm/dbrepo/templates/data-secret.yaml
@@ -24,9 +24,6 @@ stringData:
GATEWAY_SERVICE_ENDPOINT: "{{ .Values.gateway }}"
GRANT_DEFAULT_READ: "{{ .Values.dataservice.grant.read }}"
GRANT_DEFAULT_WRITE: "{{ .Values.dataservice.grant.write }}"
- DEFAULT_DATE_FORMAT_ID: "{{ .Values.dataservice.default.date }}"
- DEFAULT_TIME_FORMAT_ID: "{{ .Values.dataservice.default.time }}"
- DEFAULT_TIMESTAMP_FORMAT_ID: "{{ .Values.dataservice.default.timestamp }}"
JWT_PUBKEY: "{{ .Values.authservice.jwt.pubkey }}"
LOG_LEVEL: "{{ ternary "trace" "info" .Values.dataservice.image.debug }}"
METADATA_SERVICE_ENDPOINT: "{{ .Values.metadataservice.endpoint }}"
diff --git a/helm/dbrepo/templates/metadata-configmap.yaml b/helm/dbrepo/templates/metadata-configmap.yaml
index 893f255627c17b9ddf0a3ad765527857b3f9982b..bdd2cdbcf8540fa4e9dd0fdcbd59c7dfab91e0f0 100644
--- a/helm/dbrepo/templates/metadata-configmap.yaml
+++ b/helm/dbrepo/templates/metadata-configmap.yaml
@@ -11,8 +11,8 @@ data:
{{- end }}
02-setup-data.sql: |
BEGIN;
- INSERT INTO `mdb_containers` (name, internal_name, image_id, host, port, sidecar_host, sidecar_port, privileged_username, privileged_password)
- VALUES ('mariadb:11.1.3-debian-11-r6', 'mariadb_11_1_3', 1, 'data-db', 3306, 'data-db', 8080, 'root', 'dbrepo');
+ INSERT INTO `mdb_containers` (name, internal_name, image_id, host, port, privileged_username, privileged_password)
+ VALUES ('mariadb:11.1.3-debian-11-r6', 'mariadb_11_1_3', 1, 'data-db', 3306, '{{ .Values.datadb.rootUser.user }}', '{{ .Values.datadb.rootUser.password }}');
COMMIT;
01-setup-schema.sql: |
BEGIN;
@@ -161,14 +161,13 @@ data:
tID BIGINT UNSIGNED NOT NULL,
cName VARCHAR(64),
internal_name VARCHAR(64) NOT NULL,
- Datatype ENUM ('CHAR','VARCHAR','BINARY','VARBINARY','TINYBLOB','TINYTEXT','TEXT','BLOB','MEDIUMTEXT','MEDIUMBLOB','LONGTEXT','LONGBLOB','ENUM','SET','BIT','TINYINT','BOOL','SMALLINT','MEDIUMINT','INT','BIGINT','FLOAT','DOUBLE','DECIMAL','DATE','DATETIME','TIMESTAMP','TIME','YEAR'),
+ Datatype ENUM ('CHAR','VARCHAR','BINARY','VARBINARY','TINYBLOB','TINYTEXT','TEXT','BLOB','MEDIUMTEXT','MEDIUMBLOB','LONGTEXT','LONGBLOB','ENUM','SET','SERIAL','BIT','TINYINT','BOOL','SMALLINT','MEDIUMINT','INT','BIGINT','FLOAT','DOUBLE','DECIMAL','DATE','DATETIME','TIMESTAMP','TIME','YEAR'),
length BIGINT UNSIGNED NULL,
ordinal_position INTEGER NOT NULL,
index_length BIGINT UNSIGNED NULL,
description VARCHAR(2048),
size BIGINT UNSIGNED,
d BIGINT UNSIGNED,
- auto_generated BOOLEAN DEFAULT false,
is_null_allowed BOOLEAN NOT NULL DEFAULT true,
val_min NUMERIC NULL,
val_max NUMERIC NULL,
@@ -225,7 +224,7 @@ data:
CREATE TABLE IF NOT EXISTS `mdb_constraints_foreign_key`
(
- fkid BIGINT UNSIGNED NOT NULL AUTO_INCREMENT,
+ fkid SERIAL,
tid BIGINT UNSIGNED NOT NULL,
rtid BIGINT UNSIGNED NOT NULL,
name VARCHAR(255) NOT NULL,
@@ -262,7 +261,7 @@ data:
CREATE TABLE IF NOT EXISTS `mdb_constraints_unique`
(
- uid BIGINT UNSIGNED NOT NULL AUTO_INCREMENT,
+ uid SERIAL,
name VARCHAR(255) NOT NULL,
tid BIGINT UNSIGNED NOT NULL,
position INT NULL,
@@ -379,17 +378,16 @@ data:
(
id SERIAL,
view_id BIGINT UNSIGNED NOT NULL,
- dfID BIGINT UNSIGNED,
name VARCHAR(64),
internal_name VARCHAR(64) NOT NULL,
column_type ENUM ('CHAR','VARCHAR','BINARY','VARBINARY','TINYBLOB','TINYTEXT','TEXT','BLOB','MEDIUMTEXT','MEDIUMBLOB','LONGTEXT','LONGBLOB','ENUM','SET','BIT','TINYINT','BOOL','SMALLINT','MEDIUMINT','INT','BIGINT','FLOAT','DOUBLE','DECIMAL','DATE','DATETIME','TIMESTAMP','TIME','YEAR'),
ordinal_position INTEGER NOT NULL,
size BIGINT UNSIGNED,
d BIGINT UNSIGNED,
- auto_generated BOOLEAN DEFAULT false,
is_null_allowed BOOLEAN NOT NULL DEFAULT true,
PRIMARY KEY (id),
- FOREIGN KEY (view_id) REFERENCES mdb_view (id) ON DELETE CASCADE
+ FOREIGN KEY (view_id) REFERENCES mdb_view (id) ON DELETE CASCADE,
+ UNIQUE (view_id, internal_name)
) WITH SYSTEM VERSIONING;
CREATE TABLE IF NOT EXISTS `mdb_identifiers`
@@ -470,10 +468,10 @@ data:
CREATE TABLE IF NOT EXISTS `mdb_related_identifiers`
(
id SERIAL,
- pid BIGINT UNSIGNED NOT NULL,
- value varchar(255) NOT NULL,
- type varchar(255) NOT NULL,
- relation varchar(255) NOT NULL,
+ pid BIGINT UNSIGNED NOT NULL,
+ value varchar(255) NOT NULL,
+ type ENUM ('DOI','URL','URN','ARK','ARXIV','BIBCODE','EAN13','EISSN','HANDLE','IGSN','ISBN','ISTC','LISSN','LSID','PMID','PURL','UPC','W3ID') NOT NULL,
+ relation ENUM ('IS_CITED_BY','CITES','IS_SUPPLEMENT_TO','IS_SUPPLEMENTED_BY','IS_CONTINUED_BY','CONTINUES','IS_DESCRIBED_BY','DESCRIBES','HAS_METADATA','IS_METADATA_FOR','HAS_VERSION','IS_VERSION_OF','IS_NEW_VERSION_OF','IS_PREVIOUS_VERSION_OF','IS_PART_OF','HAS_PART','IS_PUBLISHED_IN','IS_REFERENCED_BY','REFERENCES','IS_DOCUMENTED_BY','DOCUMENTS','IS_COMPILED_BY','COMPILES','IS_VARIANT_FORM_OF','IS_ORIGINAL_FORM_OF','IS_IDENTICAL_TO','IS_REVIEWED_BY','REVIEWS','IS_DERIVED_FROM','IS_SOURCE_OF','IS_REQUIRED_BY','REQUIRES','IS_OBSOLETED_BY','OBSOLETES') NOT NULL,
PRIMARY KEY (id), /* must be a single id from persistent identifier concept */
FOREIGN KEY (pid) REFERENCES mdb_identifiers (id),
UNIQUE (pid, value)
@@ -543,8 +541,10 @@ data:
d_default INT UNSIGNED,
d_required BOOLEAN COMMENT 'When setting NULL, the service assumes the data type has no d',
d_step INT UNSIGNED,
- hint TEXT,
+ type_hint TEXT,
+ data_hint TEXT,
documentation TEXT NOT NULL,
+ is_generated BOOLEAN NOT NULL,
is_quoted BOOLEAN NOT NULL,
is_buildable BOOLEAN NOT NULL,
PRIMARY KEY (id),
@@ -567,67 +567,74 @@ data:
'mariadb');
INSERT INTO `mdb_image_types` (image_id, display_name, value, size_min, size_max, size_default, size_required,
- size_step, d_min, d_max, d_default, d_required, d_step, hint, documentation, is_quoted,
- is_buildable)
- VALUES (1, 'BIGINT(size)', 'bigint', 0, null, null, false, 1, null, null, null, null, null, null,
- 'https://mariadb.com/kb/en/bigint/', false, true),
- (1, 'BINARY(size)', 'binary', 0, 255, 255, true, 1, null, null, null, null, null, 'size in Bytes',
- 'https://mariadb.com/kb/en/binary/', false, true),
- (1, 'BIT(size)', 'bit', 0, 64, null, false, 1, null, null, null, null, null, null,
- 'https://mariadb.com/kb/en/bit/', false, true),
- (1, 'BLOB(size)', 'blob', 0, 65535, null, false, 1, null, null, null, null, null, 'size in Bytes',
- 'https://mariadb.com/kb/en/blob/', false, false),
- (1, 'BOOL', 'bool', null, null, null, null, null, null, null, null, null, null, null,
- 'https://mariadb.com/kb/en/bool/', false, true),
- (1, 'CHAR(size)', 'char', 0, 255, 255, false, 1, null, null, null, null, null, null,
- 'https://mariadb.com/kb/en/char/', false, true),
+ size_step, d_min, d_max, d_default, d_required, d_step, type_hint, data_hint,
+ documentation, is_quoted, is_buildable, is_generated)
+ VALUES (1, 'BIGINT(size)', 'bigint', 0, null, null, false, 1, null, null, null, null, null, null, null,
+ 'https://mariadb.com/kb/en/bigint/', false, true, false),
+ (1, 'BINARY(size)', 'binary', 0, 255, 255, true, 1, null, null, null, null, null, 'size in Bytes', null,
+ 'https://mariadb.com/kb/en/binary/', false, true, false),
+ (1, 'BIT(size)', 'bit', 0, 64, null, false, 1, null, null, null, null, null, null, null,
+ 'https://mariadb.com/kb/en/bit/', false, true, false),
+ (1, 'BLOB(size)', 'blob', 0, 65535, null, false, 1, null, null, null, null, null, 'size in Bytes', null,
+ 'https://mariadb.com/kb/en/blob/', false, false, false),
+ (1, 'BOOL', 'bool', null, null, null, null, null, null, null, null, null, null, null, null,
+ 'https://mariadb.com/kb/en/bool/', false, true, false),
+ (1, 'CHAR(size)', 'char', 0, 255, 255, false, 1, null, null, null, null, null, null, null,
+ 'https://mariadb.com/kb/en/char/', false, true, false),
(1, 'DATE', 'date', null, null, null, null, null, null, null, null, null, null,
- 'min. 1000-01-01, max. 9999-12-31', 'https://mariadb.com/kb/en/date/', true, true),
+ 'min. 1000-01-01, max. 9999-12-31', 'e.g. YYYY-MM-DD, YY-MM-DD, YYMMDD, YYYY/MM/DD',
+ 'https://mariadb.com/kb/en/date/', true, true, false),
(1, 'DATETIME(fsp)', 'datetime', 0, 6, null, null, 1, null, null, null, null, null,
'fsp=microsecond precision, min. 1000-01-01 00:00:00.0, max. 9999-12-31 23:59:59.9',
- 'https://mariadb.com/kb/en/datetime/', true, true),
- (1, 'DECIMAL(size, d)', 'decimal', 0, 65, null, false, 1, 0, 38, null, false, null, null,
- 'https://mariadb.com/kb/en/decimal/', false, true),
- (1, 'DOUBLE(size, d)', 'double', null, null, null, false, null, null, null, null, false, null, null,
- 'https://mariadb.com/kb/en/double/', false, true),
+ 'e.g. YYYY-MM-DD HH:MM:SS, YY-MM-DD HH:MM:SS, YYYYMMDDHHMMSS, YYMMDDHHMMSS, YYYYMMDD, YYMMDD',
+ 'https://mariadb.com/kb/en/datetime/', true, true, false),
+ (1, 'DECIMAL(size, d)', 'decimal', 0, 65, null, false, 1, 0, 38, null, false, null, null, null,
+ 'https://mariadb.com/kb/en/decimal/', false, true, false),
+ (1, 'DOUBLE(size, d)', 'double', null, null, null, false, null, null, null, null, false, null, null, null,
+ 'https://mariadb.com/kb/en/double/', false, true, false),
(1, 'ENUM(v1,v2,...)', 'enum', null, null, null, null, null, null, null, null, null, null, null,
- 'https://mariadb.com/kb/en/enum/', true, true),
- (1, 'FLOAT(size)', 'float', null, null, null, false, null, null, null, null, null, null, null,
- 'https://mariadb.com/kb/en/float/', false, true),
- (1, 'INT(size)', 'int', null, null, null, false, null, null, null, null, null, null, 'size in Bytes',
- 'https://mariadb.com/kb/en/int/', false, true),
- (1, 'LONGBLOB', 'longblob', null, null, null, null, null, null, null, null, null, null, 'max. 3.999 GiB',
- 'https://mariadb.com/kb/en/longblob/', false, true),
- (1, 'LONGTEXT', 'longtext', null, null, null, null, null, null, null, null, null, null, 'max. 3.999 GiB',
- 'https://mariadb.com/kb/en/longtext/', true, true),
+ 'e.g. value1, value2, ...', 'https://mariadb.com/kb/en/enum/', true, true, false),
+ (1, 'FLOAT(size)', 'float', null, null, null, false, null, null, null, null, null, null, null, null,
+ 'https://mariadb.com/kb/en/float/', false, true, false),
+ (1, 'INT(size)', 'int', null, null, null, false, null, null, null, null, null, null, 'size in Bytes', null,
+ 'https://mariadb.com/kb/en/int/', false, true, false),
+ (1, 'LONGBLOB', 'longblob', null, null, null, null, null, null, null, null, null, null, 'max. 3.999 GiB', null,
+ 'https://mariadb.com/kb/en/longblob/', false, true, false),
+ (1, 'LONGTEXT', 'longtext', null, null, null, null, null, null, null, null, null, null, 'max. 3.999 GiB', null,
+ 'https://mariadb.com/kb/en/longtext/', true, true, false),
(1, 'MEDIUMBLOB', 'mediumblob', null, null, null, null, null, null, null, null, null, null, 'max. 15.999 MiB',
- 'https://mariadb.com/kb/en/mediumblob/', false, true),
- (1, 'MEDIUMINT', 'mediumint', null, null, null, null, null, null, null, null, null, null, 'size in Bytes',
- 'https://mariadb.com/kb/en/mediumint/', false, true),
+ null, 'https://mariadb.com/kb/en/mediumblob/', false, true, false),
+ (1, 'MEDIUMINT', 'mediumint', null, null, null, null, null, null, null, null, null, null, 'size in Bytes', null,
+ 'https://mariadb.com/kb/en/mediumint/', false, true, false),
(1, 'MEDIUMTEXT', 'mediumtext', null, null, null, null, null, null, null, null, null, null, 'size in Bytes',
- 'https://mariadb.com/kb/en/mediumtext/', true, true),
+ null, 'https://mariadb.com/kb/en/mediumtext/', true, true, false),
+ (1, 'SERIAL', 'serial', null, null, null, null, null, null, null, null, null, null, null,
+ null, 'https://mariadb.com/kb/en/bigint/', true, true, true),
(1, 'SET(v1,v2,...)', 'set', null, null, null, null, null, null, null, null, null, null, null,
- 'https://mariadb.com/kb/en/set/', true, true),
+ 'e.g. value1, value2, ...', 'https://mariadb.com/kb/en/set/', true, true, false),
(1, 'SMALLINT(size)', 'smallint', 0, null, null, false, null, null, null, null, null, null, 'size in Bytes',
- 'https://mariadb.com/kb/en/smallint/', false, true),
- (1, 'TEXT(size)', 'text', 0, null, null, false, null, null, null, null, null, null, 'size in Bytes',
- 'https://mariadb.com/kb/en/text/', true, true),
+ null, 'https://mariadb.com/kb/en/smallint/', false, true, false),
+ (1, 'TEXT(size)', 'text', 0, null, null, false, null, null, null, null, null, null, 'size in Bytes', null,
+ 'https://mariadb.com/kb/en/text/', true, true, false),
(1, 'TIME(fsp)', 'time', 0, 6, 0, false, null, null, null, null, null, null,
- 'fsp=microsecond precision, min. 0, max. 6', 'https://mariadb.com/kb/en/time/', true, true),
+ 'fsp=microsecond precision, min. 0, max. 6', 'e.g. HH:MM:SS, HH:MM, HHMMSS, H:M:S',
+ 'https://mariadb.com/kb/en/time/', true, true, false),
(1, 'TIMESTAMP(fsp)', 'timestamp', 0, 6, 0, false, null, null, null, null, null, null,
- 'fsp=microsecond precision, min. 0, max. 6', 'https://mariadb.com/kb/en/timestamp/', true, true),
- (1, 'TINYBLOB', 'tinyblob', null, null, null, null, null, null, null, null, null, null,
- 'fsp=microsecond precision, min. 0, max. 6', 'https://mariadb.com/kb/en/timestamp/', false, true),
- (1, 'TINYINT(size)', 'tinyint', 0, null, null, false, null, null, null, null, null, null,
- 'size in Bytes', 'https://mariadb.com/kb/en/tinyint/', false, true),
- (1, 'TINYTEXT', 'tinytext', null, null, null, null, null, null, null, null, null, null,
- 'max. 255 characters', 'https://mariadb.com/kb/en/tinytext/', true, true),
- (1, 'YEAR', 'year', 2, 4, null, false, 2, null, null, null, null, null, 'min. 1901, max. 2155',
- 'https://mariadb.com/kb/en/year/', false, true),
- (1, 'VARBINARY(size)', 'varbinary', 0, null, null, true, null, null, null, null, null, null,
- null, 'https://mariadb.com/kb/en/varbinary/', false, true),
- (1, 'VARCHAR(size)', 'varchar', 0, 65532, 255, true, null, null, null, null, null, null,
- null, 'https://mariadb.com/kb/en/varchar/', false, true);
+ 'fsp=microsecond precision, min. 0, max. 6',
+ 'e.g. YYYY-MM-DD HH:MM:SS, YY-MM-DD HH:MM:SS, YYYYMMDDHHMMSS, YYMMDDHHMMSS, YYYYMMDD, YYMMDD',
+ 'https://mariadb.com/kb/en/timestamp/', true, true, false),
+ (1, 'TINYBLOB', 'tinyblob', null, null, null, null, null, null, null, null, null, null, null,
+ 'fsp=microsecond precision, min. 0, max. 6', 'https://mariadb.com/kb/en/timestamp/', false, true, false),
+ (1, 'TINYINT(size)', 'tinyint', 0, null, null, false, null, null, null, null, null, null, null,
+ 'size in Bytes', 'https://mariadb.com/kb/en/tinyint/', false, true, false),
+ (1, 'TINYTEXT', 'tinytext', null, null, null, null, null, null, null, null, null, null, null,
+ 'max. 255 characters', 'https://mariadb.com/kb/en/tinytext/', true, true, false),
+ (1, 'YEAR', 'year', 2, 4, null, false, 2, null, null, null, null, null, 'min. 1901, max. 2155', 'e.g. YYYY, YY',
+ 'https://mariadb.com/kb/en/year/', false, true, false),
+ (1, 'VARBINARY(size)', 'varbinary', 0, null, null, true, null, null, null, null, null, null, null,
+ null, 'https://mariadb.com/kb/en/varbinary/', false, true, false),
+ (1, 'VARCHAR(size)', 'varchar', 0, 65532, 255, true, null, null, null, null, null, null, null,
+ null, 'https://mariadb.com/kb/en/varchar/', false, true, false);
INSERT
INTO `mdb_ontologies` (prefix, uri, uri_pattern, sparql_endpoint, rdf_path)
diff --git a/helm/dbrepo/templates/metadata-deployment.yaml b/helm/dbrepo/templates/metadata-deployment.yaml
index 46c96a331d55d330054cff0d43b7e956f816762c..9919e301dc700c6e98867c9861b4cc2be01efd25 100644
--- a/helm/dbrepo/templates/metadata-deployment.yaml
+++ b/helm/dbrepo/templates/metadata-deployment.yaml
@@ -33,7 +33,7 @@ spec:
securityContext: {{- include "common.compatibility.renderSecurityContext" (dict "secContext" .Values.metadataservice.containerSecurityContext "context" $) | nindent 12 }}
{{- end }}
ports:
- - containerPort: 80
+ - containerPort: 8080
protocol: TCP
envFrom:
- secretRef:
diff --git a/helm/dbrepo/values.schema.json b/helm/dbrepo/values.schema.json
index a8e7bbbf743a45c32d8a3a43c8785f4c279fc0ba..6f83a1d170836312b1cc2aaea8428143d4f9154d 100644
--- a/helm/dbrepo/values.schema.json
+++ b/helm/dbrepo/values.schema.json
@@ -516,16 +516,18 @@
"properties": {
"database": {
"properties": {
- "auth": {
+ "galera": {
"properties": {
- "replicationPassword": {
- "type": "string"
- },
- "replicationUser": {
- "type": "string"
- },
- "rootPassword": {
- "type": "string"
+ "mariabackup": {
+ "properties": {
+ "password": {
+ "type": "string"
+ },
+ "user": {
+ "type": "string"
+ }
+ },
+ "type": "object"
}
},
"type": "object"
@@ -546,10 +548,13 @@
},
"type": "object"
},
- "secondary": {
+ "rootUser": {
"properties": {
- "replicaCount": {
- "type": "integer"
+ "password": {
+ "type": "string"
+ },
+ "user": {
+ "type": "string"
}
},
"type": "object"
diff --git a/helm/dbrepo/values.yaml b/helm/dbrepo/values.yaml
index 68c2e4e06fed820f6c5858efdce9bcf97550fada..36dceda681fad0ad39f201437b91aab5e740aada 100644
--- a/helm/dbrepo/values.yaml
+++ b/helm/dbrepo/values.yaml
@@ -27,7 +27,7 @@ clusterDomain: cluster.local
## @section Metadata Database
metadatadb:
- ## @param metadatadb.enabled Enable the Metadata Database.
+ ## @param metadatadb.enabled Enable the Metadata datadb.
enabled: true
## @skip metadatadb.fullnameOverride
fullnameOverride: metadata-db
@@ -122,32 +122,39 @@ authservice:
## @section Data Database
datadb:
- ## @param datadb.enabled Enable the Data Database.
- enabled: true
## @skip datadb.fullnameOverride
fullnameOverride: data-db
- database:
- image:
- ## @param datadb.database.image.debug Set the logging level to `trace`. Otherwise, set to `info`.
- debug: false
- metrics:
- ## @skip datadb.database.metrics.enabled
- enabled: true
- ## @skip datadb.database.secondary
- secondary:
- replicaCount: 2
- auth:
- ## @param datadb.auth.rootPassword The root user password.
- rootPassword: dbrepo
- ## @param datadb.auth.replicationUser The database replication user password
- replicationUser: replication
- ## @param datadb.auth.replicationPassword The database replication user password
- replicationPassword: replication
+ ## @param datadb.host The hostname for the microservices.
+ host: data-db
+ rootUser:
+ ## @param datadb.rootUser.user The root username.
+ user: root
+ ## @param datadb.rootUser.password The root user password.
+ password: dbrepo
+ db:
+ ## @param datadb.db.name The database name.
+ name: dbrepo
+ galera:
+ mariabackup:
+ ## @param datadb.galera.mariabackup.user The database backup username.
+ user: backup
+ ## @param datadb.galera.mariabackup.password The database backup user password
+ password: backup
+ ## @param datadb.jdbcExtraArgs The extra arguments for JDBC connections in the microservices.
+ jdbcExtraArgs: ""
+ metrics:
+ ## @skip datadb.metrics.enabled The Prometheus settings.
+ enabled: false
+ ## @param datadb.replicaCount The number of cluster nodes, should be uneven i.e. 2n+1
+ replicaCount: 3
+ persistence:
+ ## @param datadb.persistence.enabled Enable persistent storage.
+ enabled: true
## @section Search Database
searchdb:
- ## @param searchdb.enabled Enable the Data Database.
+ ## @param searchdb.enabled Enable the Data datadb.
enabled: true
## @skip searchdb.fullnameOverride
fullnameOverride: search-db
@@ -335,8 +342,10 @@ analyseservice:
## @param analyseservice.endpoint The url of the endpoint.
endpoint: http://analyse-service
s3:
- ## @param analyseservice.s3.endpoint The S3-capable endpoint the microservice connects to.
- endpoint: http://storage-service-s3:8333
+ ## @param analyseservice.s3.proto The protocol of the storage service endpoint.
+ proto: http
+ ## @param analyseservice.s3.endpoint The hostname and port of the storage service endpoint.
+ endpoint: storage-service-s3:8333
## @param analyseservice.replicaCount The number of replicas.
replicaCount: 2
@@ -490,13 +499,6 @@ dataservice:
read: SELECT
## @param dataservice.grant.write The default database permissions for users with write access.
write: SELECT, CREATE, CREATE VIEW, CREATE ROUTINE, CREATE TEMPORARY TABLES, LOCK TABLES, INDEX, TRIGGER, INSERT, UPDATE, DELETE
- default:
- ## @param dataservice.default.date The default date format id for dates. Default: YYYY-MM-dd (e.g. 2024-06-15).
- date: 3
- ## @param dataservice.default.time The default date format id for times. Default: HH:mm:ss (e.g. 14:23:42).
- time: 4
- ## @param dataservice.default.timestamp The default date format id for timestamps. Default: YYYY-MM-dd HH:mm:ss (e.g. 2024-06-15 14:23:42).
- timestamp: 1
rabbitmq:
## @param dataservice.rabbitmq.consumerConcurrentMin The minimal number of RabbitMQ consumers.
consumerConcurrentMin: 2
@@ -649,6 +651,9 @@ identityservice:
adminPassword: admin
## @skip identityservice.global.configUserEnabled
configUserEnabled: false
+ containerSecurityContext:
+ ## @skip identityservice.containerSecurityContext.enabled
+ enabled: true
## @param identityservice.users The admin username for internal authentication.
users: admin
## @param identityservice.userPasswords The admin user password for internal authentication.
@@ -767,7 +772,7 @@ ui:
## @param ui.public.broker.extra Extra metadata displayed.
extra: ""
database:
- ## @param ui.public.database.extra Extra metadata displayed.
+ ## @param ui.public.datadb.extra Extra metadata displayed.
extra: ""
## @skip ui.public.links
links:
diff --git a/lib/python/dbrepo/RestClient.py b/lib/python/dbrepo/RestClient.py
index 8e0e782bb88055e8bc34a8ae8afb46aea0cb30f7..b80daff7d0a7a1d2d92fcdd60e90fe3fa9b5d2da 100644
--- a/lib/python/dbrepo/RestClient.py
+++ b/lib/python/dbrepo/RestClient.py
@@ -1102,7 +1102,7 @@ class RestClient:
f'201 (CREATED): {response.text}')
def import_table_data(self, database_id: int, table_id: int, file_name_or_data_frame: str | DataFrame,
- separator: str = ",", quote: str = "\"", skip_lines: int = 0,
+ separator: str = ",", quote: str = "\"", header: bool = False,
line_encoding: str = "\n") -> None:
"""
Import a csv dataset from a file into a table in a database with given database id and table id. ATTENTION:
@@ -1114,7 +1114,7 @@ class RestClient:
:param file_name_or_data_frame: The path of the file that is imported on the storage service or pandas dataframe.
:param separator: The csv column separator. Optional.
:param quote: The column data quotation character. Optional.
- :param skip_lines: The number of lines to skip. Optional. Default: 0.
+ :param header: If `True`, the first line contains column names, otherwise the first line is data. Optional. Default: `False`.
:param line_encoding: The encoding of the line termination. Optional. Default: CR (Windows).
:raises MalformedError: If the payload is rejected by the service (e.g. LOB could not be imported).
@@ -1134,7 +1134,7 @@ class RestClient:
url = f'/api/database/{database_id}/table/{table_id}/data/import'
response = self._wrapper(method="post", url=url, force_auth=True,
payload=Import(location=filename, separator=separator, quote=quote,
- skip_lines=skip_lines, line_termination=line_encoding))
+ header=header, line_termination=line_encoding))
if response.status_code == 202:
return
if response.status_code == 400:
diff --git a/lib/python/dbrepo/api/dto.py b/lib/python/dbrepo/api/dto.py
index fc97c2b8d731b064e2d8ff7a77e458e727f95f3c..4de986e87080d207dbd68f8293f31be4004753d6 100644
--- a/lib/python/dbrepo/api/dto.py
+++ b/lib/python/dbrepo/api/dto.py
@@ -52,8 +52,6 @@ class CreateContainer(BaseModel):
name: str
host: str
image_id: int
- sidecar_host: str
- sidecar_port: int
privileged_username: str
privileged_password: str
ui_host: Optional[str] = None
@@ -94,8 +92,6 @@ class Container(BaseModel):
port: int
image: Image
created: Timestamp
- sidecar_host: Optional[str] = None
- sidecar_port: Optional[int] = None
ui_host: Optional[str] = None
ui_port: Optional[int] = None
@@ -478,8 +474,8 @@ class DeleteData(BaseModel):
class Import(BaseModel):
location: str
separator: str
+ header: bool
quote: Optional[str] = None
- skip_lines: Optional[int] = None
line_termination: Optional[str] = None
diff --git a/make/dev.mk b/make/dev.mk
index 76c05989eb224c0ca0625f4d380f6467b8688f2f..e95dee62fe4c0f3bd933dd8058e4329c49d5bb1e 100644
--- a/make/dev.mk
+++ b/make/dev.mk
@@ -2,6 +2,8 @@
.PHONY: start-dev
start-dev: build-images ## Start the development deployment.
+ docker container stop dbrepo-gateway-service || true
+ docker container rm dbrepo-gateway-service || true
docker compose up -d
diff --git a/make/rel.mk b/make/rel.mk
index 042b93d5680b93115202bd207538821c952d8f28..f32f34dc22b0e2f1497e59e739b01377a556265b 100644
--- a/make/rel.mk
+++ b/make/rel.mk
@@ -3,7 +3,6 @@
.PHONY: tag-images
tag-images: build-images ## Tag the docker images.
docker tag dbrepo-analyse-service:latest "${REPOSITORY_URL}/analyse-service:${APP_VERSION}"
- docker tag dbrepo-auth-service:latest "${REPOSITORY_URL}/auth-service:${APP_VERSION}"
docker tag dbrepo-dashboard-service:latest "${REPOSITORY_URL}/dashboard-service:${APP_VERSION}"
docker tag dbrepo-ui:latest "${REPOSITORY_URL}/ui:${APP_VERSION}"
docker tag dbrepo-data-service:latest "${REPOSITORY_URL}/data-service:${APP_VERSION}"
@@ -17,7 +16,6 @@ tag-images: build-images ## Tag the docker images.
.PHONY: release-images
release-images: tag-images ## Release the docker images.
docker push "${REPOSITORY_URL}/analyse-service:${APP_VERSION}"
- docker push "${REPOSITORY_URL}/auth-service:${APP_VERSION}"
docker push "${REPOSITORY_URL}/dashboard-service:${APP_VERSION}"
docker push "${REPOSITORY_URL}/ui:${APP_VERSION}"
docker push "${REPOSITORY_URL}/data-service:${APP_VERSION}"
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 659eb487ea25bbc048959ecd8755ea65bfa84f06..0000000000000000000000000000000000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,18 +0,0 @@
-mkdocs==1.5.3
-mkdocs-material==9.5.17
-mkdocs-with-pdf==0.9.3
-mkdocs-material-extensions>=1.0.3
-requests>=2.27.0
-py-dotenv>=0.1
-python-dotenv==1.0.0
-requests==2.31.0
-build==1.1.1
-setuptools==69.2.0
-twine==5.0.0
-furo==2024.1.29
-requests==2.31.0
-pika==1.3.2
-pydantic==2.6.4
-tuspy==1.0.3
-mike==2.0.0
-anybadge==1.14.0
\ No newline at end of file