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Verified Commit 50a143fc authored by Martin Weise's avatar Martin Weise
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docs/deployment-docker-compose.md
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......@@ -26,6 +26,16 @@ technologies. The conceptualized microservices operate the basic database operat
Alternatively, you can also deploy DBRepo with [Helm](../deployment-helm/) in your virtual machine instead.
## Environment Values
| Key | Type | Default | Description |
|------------------------|--------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `DBREPO_CLIENT_ID` | string | `dbrepo-client` | Client ID of the keycloak client for API communication. |
| `DBREPO_CLIENT_SECRET` | string | `MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG` | Client secret of the keycloak client, this should be changed in the admin console of keycloak. |
| `JWT_ISSUER` | string | `http://localhost/api/auth/realms/dbrepo` | The issuer in the JWT `iss` field of the (decoded) token. Public deployments with hostnames other than localhost need to change that. The issuer always has the form `<PROTOCOL>://<HOSTNAME>/api/auth/realms/dbrepo`, e.g. change PROTOCOL to https for SSL/TLS deployments. |
| `JWT_PUBKEY` | string | `MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB` | Public key that can verify the JWT signature, this should be changed. |
| `JWT_CERT` | string | `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IJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB` | Public key that can verify the JWT signature, this should be changed. |
## Requirements
### Hardware
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docs/deployment-helm.md
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| `replicaCount` | int | `1` | Number of replicas (pods) to launch. |
| `nameOverride` | string | `""` | A name in place of the chart name for `app:` labels. |
| `fullnameOverride` | string | `""` | A name to substitute for the full names of resources. |
| `imagePullPolicy` | string | `Always` | Override for the image pull policy, e.g. `IfNotPresent` |
| `adminEmail` | string | `noreply@example.com` | E-mail address for OAI-PMH metadata. |
| `repositoryName` | string | `Database Repository` | Repository name for OAI-PMH metadata. |
| `hostname` | string | `example.com` | Domain name for the deployment, should not contain `https://` or any path. |
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docs/system-services-metadata.md
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!!! debug "Debug Information"
* Ports: 9092/tcp
* Info: `http://:9092/actuator/info`
* Health: `http://:9092/actuator/health`
* Prometheus: `http://:9092/actuator/prometheus`
* Swagger UI: `http://:9092/swagger-ui/index.html` <a href="/infrastructures/dbrepo/latest/swagger/database" target="_blank">:fontawesome-solid-square-up-right: view online</a>
* Ports: 9099/tcp
* Info: `http://:9099/actuator/info`
* Health: `http://:9099/actuator/health`
* Prometheus: `http://:9099/actuator/prometheus`
* Swagger UI: `http://:9099/swagger-ui/index.html` <a href="/infrastructures/dbrepo/latest/swagger/metadata" target="_blank">:fontawesome-solid-square-up-right: view online</a>
It creates the databases inside a Docker container and the Query Store. Currently, we only
support [MariaDB](https://mariadb.org/) images that allow table versioning with low programmatic effort.
This microservice manages:
!!! debug "Debug Information"
* Databases
* Users
* Metadata (PID, OAI-PMH)
* Queries, views
* Tables
* Ports: 9096/tcp
* Info: `http://:9096/actuator/info`
* Health: `http://:9096/actuator/health`
* Prometheus: `http://:9096/actuator/prometheus`
* Swagger UI: `http://:9096/swagger-ui/index.html` <a href="/infrastructures/dbrepo/latest/swagger/identifier" target="_blank">:fontawesome-solid-square-up-right: view online</a>
It creates the databases inside a Docker container and the Query Store. Currently, we only
support [MariaDB](https://mariadb.org/) images that allow table versioning with low programmatic effort.
This microservice is responsible for creating and resolving a *persistent identifier* (PID) attached to a query to
obtain the metadata attached to it and allow re-execution of a query. We store both the query and hashes of the query
......@@ -29,45 +29,11 @@ and result set to allow equality checks of the originally obtained result set an
the reference implementation we currently only use a numerical id column and plan to integrate *digital object
identifier* (DOI) through our institutional library soon.
!!! debug "Debug Information"
* Ports: 9099/tcp
* Info: `http://:9099/actuator/info`
* Health: `http://:9099/actuator/health`
* Prometheus: `http://:9099/actuator/prometheus`
* Swagger UI: `http://:9099/swagger-ui/index.html` <a href="/infrastructures/dbrepo/latest/swagger/metadata" target="_blank">:fontawesome-solid-square-up-right: view online</a>
This service provides an OAI-PMH endpoint for metadata crawler.
!!! debug "Debug Information"
* Ports: 9093/tcp
* Info: `http://:9093/actuator/info`
* Health: `http://:9093/actuator/health`
* Prometheus: `http://:9093/actuator/prometheus`
* Swagger UI: `http://:9093/swagger-ui/index.html` <a href="/infrastructures/dbrepo/latest/swagger/query" target="_blank">:fontawesome-solid-square-up-right: view online</a>
It provides an interface to insert data into the tables created by the Table Service. It also allows for view-only,
paginated and versioned query execution to the raw data and consumes messages in the message queue from the Broker
Service.
!!! debug "Debug Information"
* Ports: 9094/tcp
* Info: `http://:9094/actuator/info`
* Health: `http://:9094/actuator/health`
* Prometheus: `http://:9094/actuator/prometheus`
* Swagger UI: `http://:9094/swagger-ui/index.html` <a href="/infrastructures/dbrepo/latest/swagger/table" target="_blank">:fontawesome-solid-square-up-right: view online</a>
This microservice handles table operations inside a database that is managed by the Database Service. We
use [Hibernate](https://hibernate.org/orm/) for schema and data ingest operations.
!!! debug "Debug Information"
* Ports: 9098/tcp
* Info: `http://:9098/actuator/info`
* Health: `http://:9098/actuator/health`
* Prometheus: `http://:9098/actuator/prometheus`
* Swagger UI: `http://:9098/swagger-ui/index.html` <a href="/infrastructures/dbrepo/latest/swagger/user" target="_blank">:fontawesome-solid-square-up-right: view online</a>
This microservice handles user information.
docs/system-services-upload.md 0 → 100644
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---
author: Martin Weise
---
# Upload Service
!!! debug "Debug Information"
* Ports: 1080/tcp
Upload files using one of the official the TUSd clients:
* [NodeJS / JavaScript](https://github.com/tus/tus-js-client)
* [Java](https://github.com/tus/tus-java-client)
* [Python](https://github.com/tus/tus-py-client)
## Example (Python)
Uploads a file `file.csv` in 200 byte chunks.
```python
#!/bin/env python3
from tusclient import client
my_client = client.TusClient('http://localhost/api/upload/files')
uploader = my_client.uploader('/path/to/file.csv', chunk_size=200)
uploader.upload()
```
mkdocs.yml
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......@@ -19,6 +19,7 @@ nav:
- Broker Service: system-services-broker.md
- Gateway Service: system-services-gateway.md
- Metadata Service: system-services-metadata.md
- Upload Service: system-services-upload.md
- Databases:
- Data Database: system-databases-data.md
- Metadata Database: system-databases-metadata.md
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