Merge branch 'release-1.4.4' into dev

.docker/docker-compose.yml

@@ -17,8 +17,8 @@ services:
     image: docker.io/bitnami/mariadb:11.1.3-debian-11-r6
     volumes:
       - metadata-db-data:/bitnami/mariadb
-      - ./dbrepo-metadata-db/setup-schema.sql:/docker-entrypoint-initdb.d/1_setup-schema.sql
-      - ./dbrepo-metadata-db/setup-data.sql:/docker-entrypoint-initdb.d/2_setup-data.sql
+      - ./dist/setup-schema.sql:/docker-entrypoint-initdb.d/1_setup-schema.sql
+      - ./dist/setup-data.sql:/docker-entrypoint-initdb.d/2_setup-data.sql
     ports:
       - "3306:3306"
     environment:
@@ -192,8 +192,6 @@ services:
     volumes:
       - ./dist/rabbitmq.conf:/etc/rabbitmq/rabbitmq.conf
       - ./dist/enabled_plugins:/etc/rabbitmq/enabled_plugins
-      - ./dist/cert.pem:/app/cert.pem
-      - ./dist/pubkey.pem:/app/pubkey.pem
       - ./dist/definitions.json:/app/definitions.json
       - broker-service-data:/bitnami/rabbitmq/mnesia
     depends_on:

.docs/examples/air.md

@@ -5,7 +5,7 @@ author: Martin Weise
 ## tl;dr
 
 [:fontawesome-solid-database:  Dataset](https://handle.stage.datacite.org/10.82556/gd17-aq82){ .md-button .md-button--primary target="_blank" }
-[:material-file-document:  Archive](https://doi.org/10.48436/mtha8-w2406){ .md-button .md-button--secondary target="_blank" }
+[:simple-grafana:  Dashboard](https://dbrepo1.ec.tuwien.ac.at/admin/grafana/d/FLB9eAv4z/airquality){ .md-button .md-button--secondary target="_blank" }
 
 ## Description
 
@@ -14,14 +14,25 @@ in Vienna, spanning the years from 1980 to 2021. The data was provided by the Um
 original form in this record. This record forms the basis of an analysis carried out in a bachelor's thesis at the TU 
 Wien.
 
-## Solution
+<figure markdown>
+![Grafana Dashboard](../../images/screenshots/air-dashboard.png)
+<figcaption>Figure 1: Grafana dashboard visualizing the dataset.</figcaption>
+</figure>
 
+The analysis was carried out in a Jupyter Notebook hosted by our IT-department
+[JupyterHub](https://science.datalab.tuwien.ac.at/) as part of TU Wien's virtual research environment.
 
 <figure markdown>
 ![Jupyter Notebook](../../images/screenshots/air-notebook.png){ .img-border }
-<figcaption>Figure 1: Jupyter Notebook accessing data on DBRepo using the Python Library.</figcaption>
+<figcaption>Figure 2: Jupyter Notebook accessing data on DBRepo using the Python Library.</figcaption>
 </figure>
 
+## Solution
+
+One of the first use-cases of importing external data into DBRepo which was provided as .csv flat file. We developed a
+database schema and a web scraper that scrapes live air quality data from the 
+[public map](https://luft.umweltbundesamt.at/pub/map_chart/index.pl) of the environment agency of Austria.
+
 ## DBRepo Features
 
 - [x] Import complex dataset

.docs/examples/survey.md

@@ -9,22 +9,25 @@ author: Martin Weise
 
 ## Description
 
-This digital record contains historical air pollution and air quality data from approximately 20 air monitoring stations
-in Vienna, spanning the years from 1980 to 2021. The data was provided by the Umweltbundesamt and is stored in its
-original form in this record. This record forms the basis of an analysis carried out in a bachelor's thesis at the TU 
-Wien.
+As part of a literature study, the research unit of data science has collected data on 47 Trusted Research Environments
+(TREs) who enable analysis of confidential data under strict security assertions who protect the data with technical, 
+organizational and legal measures from (accidentally) being leaked outside the facility. The literature study shows that
+47 TREs worldwide provide access to confidential data of which two-thirds provide data themselves (n=32, 68%), 
+predominantly via secure remote access (n=46, 98%).
 
 ## Solution
 
+We designed a database schema that allows collection of the data with correct primary key and foreign-key relationships.
+Three defined views allow for a simpler exploration of the study data. The analysis of the data was performed in TU
+Wien's virtual research environment using [JupyterHub](https://science.datalab.tuwien.ac.at/) as well as the chart
 
 <figure markdown>
-![Jupyter Notebook](../../images/screenshots/air-notebook.png){ .img-border }
+![Jupyter Notebook](../../images/screenshots/tre-notebook.png){ .img-border }
 <figcaption>Figure 1: Jupyter Notebook accessing data on DBRepo using the Python Library.</figcaption>
 </figure>
 
 ## DBRepo Features
 
-- [x] Import complex dataset
 - [x] System versioning
 - [x] Subset exploration
 - [x] Aggregated views
@@ -33,6 +36,6 @@ Wien.
 
 ## Acknowledgement
 
-This work was part of a cooperation with the [Umweltbundesamt](https://www.umweltbundesamt.at/).
+This work was part of a cooperation with the [Research Unit of Data Science](https://informatics.tuwien.ac.at/orgs/e194-04).
 
-<img src="../../images/logos/umweltbundesamt.png" width=100 />
\ No newline at end of file
+<img src="../../images/logos/ds-ifs.png" width=100 />
\ No newline at end of file

.docs/installation.md

@@ -44,7 +44,48 @@ are *not* recommended and not tested.
 
 ## Custom Install
 
-TBD
+In case you prefer a customized install, start by downloading the `docker-compose.yml` file used to define the services:
+
+```bash
+curl -O docker-compose.yml -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-1.4.4/.docker/docker-compose.yml
+```
+
+Create the folder `dist/` that hold necessary configuration files and download the Metadata Database schema and initial 
+data to display the created Data Database container:
+
+```bash
+mkdir -p dist
+curl -O dist/setup-schema.sql -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-1.4.4/dbrepo-metadata-db/setup-schema.sql
+curl -O dist/setup-data.sql -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-1.4.4/dbrepo-metadata-db/setup-data.sql
+```
+
+Download the Broker Service configuration files:
+
+```bash
+curl -O dist/rabbitmq.conf -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-1.4.4/dbrepo-broker-service/rabbitmq.conf
+curl -O dist/enabled_plugins -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-1.4.4/dbrepo-broker-service/enabled_plugins
+curl -O dist/definitions.json -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-1.4.4/dbrepo-broker-service/definitions.json
+```
+
+!!! warning "Default admin user credentials"
+
+    Note that you need to change the default user credentials `fda:fda` of the Broker Service by setting `users.0.name`
+    and `users.0.password_hash` of the `definitions.json` file. The `password_hash` can be created by executing 
+    `./helm/dbrepo/hack/generate-rabbitmq-pw.sh <your_password>`.
+
+Download the Gateway Service configuration file (or integrate it into your existing NGINX reverse proxy config):
+
+```bash
+curl -O dist/dbrepo.conf -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-1.4.4/dbrepo-gateway-service/dbrepo.conf
+```
+
+Download the S3 configuration for the Storage Service:
+
+```bash
+curl -O dist/s3_config.conf -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-1.4.4/dbrepo-storage-service/s3_config.conf
+```
+
+Continue the custom install by customizing the [User Interface](../api/ui).
 
 ## Architecture
 

dbrepo-broker-service/cert.pem

------BEGIN CERTIFICATE-----
-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
------END CERTIFICATE-----
\ No newline at end of file

dbrepo-broker-service/pubkey.pem

------BEGIN RSA PUBLIC KEY-----
-MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB
------END RSA PUBLIC KEY-----
\ No newline at end of file

dbrepo-broker-service/rabbitmq.conf

@@ -18,8 +18,8 @@ log.console.level = warning
 
 # Obviously your authentication server cannot vouch for itself, so you'll need another backend with at least one user in
 # it. You should probably use the internal database
-auth_backends.1 = rabbit_auth_backend_oauth2
-auth_backends.2 = rabbit_auth_backend_internal
+#auth_backends.1 = rabbit_auth_backend_oauth2
+auth_backends.1 = rabbit_auth_backend_internal
 
 # management.oauth_enabled = true
 # management.oauth_client_id = rabbitmq-client
@@ -28,10 +28,10 @@ auth_backends.2 = rabbit_auth_backend_internal
 # management.oauth_provider_url = http://localhost/api/auth/realms/dbrepo
 
 # OAuth 2.0 files
-auth_oauth2.resource_server_id = rabbitmq
-auth_oauth2.preferred_username_claims.1 = client_id
-auth_oauth2.default_key = t2OCeCheJ9uwoBbNQjG_nN6WKiLcceTIAZmiTbGODFM
-auth_oauth2.signing_keys.t2OCeCheJ9uwoBbNQjG_nN6WKiLcceTIAZmiTbGODFM = /app/cert.pem
-auth_oauth2.signing_keys.id2 = /app/pubkey.pem
-auth_oauth2.algorithms.1 = HS256
-auth_oauth2.algorithms.2 = RS256
+#auth_oauth2.resource_server_id = rabbitmq
+#auth_oauth2.preferred_username_claims.1 = client_id
+#auth_oauth2.default_key = t2OCeCheJ9uwoBbNQjG_nN6WKiLcceTIAZmiTbGODFM
+#auth_oauth2.signing_keys.t2OCeCheJ9uwoBbNQjG_nN6WKiLcceTIAZmiTbGODFM = /app/cert.pem
+#auth_oauth2.signing_keys.id2 = /app/pubkey.pem
+#auth_oauth2.algorithms.1 = HS256
+#auth_oauth2.algorithms.2 = RS256

docker-compose.yml

@@ -207,8 +207,6 @@ services:
     volumes:
       - ./dbrepo-broker-service/rabbitmq.conf:/etc/rabbitmq/rabbitmq.conf
       - ./dbrepo-broker-service/enabled_plugins:/etc/rabbitmq/enabled_plugins
-      - ./dbrepo-broker-service/cert.pem:/app/cert.pem
-      - ./dbrepo-broker-service/pubkey.pem:/app/pubkey.pem
       - ./dbrepo-broker-service/definitions.json:/app/definitions.json
       - broker-service-data:/bitnami/rabbitmq/mnesia
     depends_on:

helm/dbrepo/values.yaml

@@ -125,8 +125,6 @@ authservice:
 ## @section Data Database
 
 datadb:
-  global:
-    storageClass: test
   ## @param datadb.enabled Enable the Data Database.
   enabled: true
   ## @skip datadb.fullnameOverride

install.sh

@@ -63,8 +63,6 @@ curl -sSL -o ./dist/1_setup-schema.sql "https://gitlab.phaidra.org/fair-data-aus
 curl -sSL -o ./dist/2_setup-data.sql "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-metadata-db/setup-data.sql"
 curl -sSL -o ./dist/rabbitmq.conf "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-broker-service/rabbitmq.conf"
 curl -sSL -o ./dist/enabled_plugins "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-broker-service/enabled_plugins"
-curl -sSL -o ./dist/cert.pem "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-broker-service/cert.pem"
-curl -sSL -o ./dist/pubkey.pem "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-broker-service/pubkey.pem"
 curl -sSL -o ./dist/definitions.json "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-broker-service/definitions.json"
 curl -sSL -o ./dist/dbrepo.conf "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-gateway-service/dbrepo.conf"
 curl -sSL -o ./dist/opensearch_dashboards.yml "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/release-${VERSION}/dbrepo-search-db/opensearch_dashboards.yml"