Updated all images and documented their environment variables

dockerhub/_footer.md

+# License
+
+View [license information](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/blob/master/LICENSE)
+for the software contained in this image.
+
+As with all Docker images, these likely also contain other software which may be under other licenses (such as Bash, etc
+from the base distribution, along with any direct or indirect dependencies of the primary software being contained).
+
+As for any pre-built image usage, it is the image user's responsibility to ensure that any use of this image complies
+with any relevant licenses for all software contained within.
\ No newline at end of file

dockerhub/_header.md

@@ -11,6 +11,7 @@
 
 # Supported tags and respective `Dockerfile` links
 
+* [`1.1.1`](https://hub.docker.com/repository/docker/dbrepo/REPOSITORY/tags?page=1&ordering=last_updated&name=1.1.1)
 * [`latest`](https://hub.docker.com/repository/docker/dbrepo/REPOSITORY/tags?page=1&ordering=last_updated&name=latest)
 
 # Quick reference (cont.)
@@ -30,5 +31,7 @@
 
 # What is DBRepo?
 
-tbd
+We present a database repository system that allows researchers to ingest data into a central, versioned repository
+through common interfaces, provides efficient access to arbitrary subsets of data even when the underlying data store is
+evolving, allows reproducing of query results and supports findable-, accessible-, interoperable- and reusable (FAIR) data.
 

dockerhub/client/Dockerhub.py

@@ -28,11 +28,12 @@ class Dockerhub:
 
     def modify_description(self, repository):
         header = self.__read__(self.workpath + "/_header.md").replace('REPOSITORY', repository)
+        footer = self.__read__(self.workpath + "/_footer.md").replace('REPOSITORY', repository)
         body = self.__read__(self.workpath + "/fda-" + repository + ".md")
         response = rq.patch(self.baseurl + "/v2/repositories/" + self.username + "/" + repository + "/", headers=self.headers,
             json={
                 "description": "Official repository of DBRepo.",
-                "full_description": header + "\n\n" + body,
+                "full_description": header + "\n\n" + body + "\n\n" + footer,
                 "registry": self.registry
             })
         if response.status_code == 200:

dockerhub/fda-analyse-service.md

@@ -4,6 +4,13 @@
 $ docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp -p 5000:5000
 ```
 
+## Customization
+
+Change the default behavior by setting the following environment variables to different values:
+
+* `EUREKA_SERVER` default: http://discovery-service:9090/eureka/, needs to point to
+  the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service).
+
 ## Swagger Endpoints
 
 * **OpenAPI**:

dockerhub/fda-authentication-service.md

@@ -4,6 +4,83 @@
 $ docker run -p 9097:9097 -e SPRING_PROFILES_ACTIVE=docker
 ```
 
+## Customization
+
+Change the default behavior by setting the following environment variables to different values:
+
+* `METADATA_DB`, default: fda
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
+
+* `METADATA_USERNAME`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
+
+* `METADATA_PASSWORD`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
+
+* `BROKER_USERNAME`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags
+  associated to the account.
+
+* `BROKER_PASSWORD`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags
+  associated to the account.
+
+* `WEBSITE`, default: http://example.com
+
+  The public endpoint of the [User Interface](https://hub.docker.com/r/dbrepo/ui). Internally, it is used to redirect
+  when a user verifies the e-mail address.
+
+* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095
+
+  The gateway endpoint.
+
+* `MAIL_FROM`, default: "Database Repository <noreply@example.com>"
+
+  When users verify their e-mail addresses, this is used to declare where the mail is coming from.
+
+* `MAIL_REPLY_TO`, default: "Somebody <somebody@example.com>"
+
+  When users verify their e-mail addresses, this is used to declare where to reply to.
+
+* `MAIL_VERIFY`, default: false
+
+  When set to `1`, the service requires all users to verify their e-mail before they can use the repository system, e.g.
+  they cannot log in without clicking the link in the e-mail.
+
+* `JWT_ISSUER`, default: dbrepo
+
+  The Java Web Token issuer name.
+
+* `JWT_SECRET`, default: secret
+
+  The Java Web Token secret that is used to sign the token generated by the system. This should be treated like with the
+  same caution as a private key.
+
+* `JWT_EXPIRATION`, default: 86400000
+
+  By default, the Java Web Token expire after 1 day.
+
+* `SMTP_HOST`, optional.
+
+  The e-mail server that sends e-mails to the users. Specify the hostname.
+
+* `SMTP_PORT`, optional.
+
+  The e-mail server that sends e-mails to the users. Specify the port.
+
+* `SMTP_USERNAME`, optional.
+
+  The e-mail server that sends e-mails to the users. Specify the username.
+
+* `SMTP_PASSWORD`, optional.
+
+  The e-mail server that sends e-mails to the users. Specify the password.
+
 ## Swagger Endpoints
 
 * **OpenAPI**:

dockerhub/fda-broker-service.md

@@ -4,6 +4,18 @@
 $ docker run -v ./fda-broker-service-data:/var/lib/rabbitmq/ -p 9098:9098 -p 5672:5672 -p 15672:15672
 ```
 
+## Customization
+
+Change the default behavior by setting the following variables in `rabbitmq.conf` to different values:
+
+* `default_user`, default: fda
+
+  The Broker Service username.
+
+* `default_pass`, default: fda
+
+  The Broker Service password.
+
 ## Swagger Endpoints
 
 * **OpenAPI**:

dockerhub/fda-container-service.md

@@ -4,6 +4,32 @@
 $ docker run -p 9091:9091 -v /var/run/docker.sock:/var/run/docker.sock -e SPRING_PROFILES_ACTIVE=docker
 ```
 
+## Customization
+
+Change the default behavior by setting the following environment variables to different values:
+
+* `METADATA_DB`, default: fda
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
+
+* `METADATA_USERNAME`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
+
+* `METADATA_PASSWORD`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
+
+* `BROKER_USERNAME`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags
+  associated to the account.
+
+* `BROKER_PASSWORD`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags
+  associated to the account.
+
 ## Swagger Endpoints
 
 * **OpenAPI**:

dockerhub/fda-database-service.md

@@ -4,6 +4,36 @@
 $ docker run -p 9092:9092 -v /var/run/docker.sock:/var/run/docker.sock -e SPRING_PROFILES_ACTIVE=docker
 ```
 
+## Customization
+
+Change the default behavior by setting the following environment variables to different values:
+
+* `METADATA_DB`, default: fda
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
+
+* `METADATA_USERNAME`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
+
+* `METADATA_PASSWORD`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
+
+* `BROKER_USERNAME`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags
+  associated to the account.
+
+* `BROKER_PASSWORD`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags
+  associated to the account.
+
+* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095
+
+  The gateway endpoint.
+
 ## Swagger Endpoints
 
 * **OpenAPI**:

dockerhub/fda-discovery-service.md

@@ -3,3 +3,19 @@
 ```console
 $ docker run -p 9090:9090 -e SPRING_PROFILES_ACTIVE=docker
 ```
+
+## Customization
+
+Change the default behavior by setting the following environment variables to different values:
+
+* `METADATA_DB`, default: fda
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
+
+* `METADATA_USERNAME`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
+
+* `METADATA_PASSWORD`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
\ No newline at end of file

dockerhub/fda-gateway-service.md

@@ -3,3 +3,23 @@
 ```console
 $ docker run -p 9095:9095 -e SPRING_PROFILES_ACTIVE=docker
 ```
+
+## Customization
+
+Change the default behavior by setting the following environment variables to different values:
+
+* `METADATA_DB`, default: fda
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
+
+* `METADATA_USERNAME`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
+
+* `METADATA_PASSWORD`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
+
+* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095
+
+  The gateway endpoint.
\ No newline at end of file

dockerhub/fda-identifier-service.md

@@ -4,6 +4,26 @@
 $ docker run -p 9096:9096 -e SPRING_PROFILES_ACTIVE=docker
 ```
 
+## Customization
+
+Change the default behavior by setting the following environment variables to different values:
+
+* `METADATA_DB`, default: fda
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
+
+* `METADATA_USERNAME`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
+
+* `METADATA_PASSWORD`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
+
+* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095
+
+  The gateway endpoint.
+
 ## Swagger Endpoints
 
 * **OpenAPI**:

dockerhub/fda-metadata-db.md

@@ -4,9 +4,18 @@
 $ docker run -v ./data:/var/lib/postgresql/data -p 5432:5432 -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=postgres -e POSTGRES_DB=fda
 ```
 
-The environment variables come from the official [PostgreSQL](https://hub.docker.com/_/postgres) image. They are briefly
-explained here:
+## Customization
 
-* `POSTGRES_USER` is used in conjunction with password to set a user and its password.
-* `POSTGRES_PASSWORD` must not be empty or undefined.
-* `POSTGRES_DB` is used to create a database with this name.
+Change the default behavior by setting the following environment variables to different values:
+
+* `METADATA_DB`, default: fda
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
+
+* `METADATA_USERNAME`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
+
+* `METADATA_PASSWORD`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
\ No newline at end of file

dockerhub/fda-query-service.md

@@ -4,6 +4,36 @@
 $ docker run -p 9093:9093 -e SPRING_PROFILES_ACTIVE=docker
 ```
 
+## Customization
+
+Change the default behavior by setting the following environment variables to different values:
+
+* `METADATA_DB`, default: fda
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
+
+* `METADATA_USERNAME`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
+
+* `METADATA_PASSWORD`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
+
+* `BROKER_USERNAME`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags
+  associated to the account.
+
+* `BROKER_PASSWORD`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags
+  associated to the account.
+
+* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095
+
+  The gateway endpoint.
+
 ## Swagger Endpoints
 
 * **OpenAPI**:

dockerhub/fda-table-service.md

@@ -4,6 +4,40 @@
 $ docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp -p 9094:9094 -e SPRING_PROFILES_ACTIVE=docker
 ```
 
+## Customization
+
+Change the default behavior by setting the following environment variables to different values:
+
+* `METADATA_DB`, default: fda
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
+
+* `METADATA_USERNAME`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
+
+* `METADATA_PASSWORD`, default: postgres
+
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
+
+* `BROKER_USERNAME`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags
+  associated to the account.
+
+* `BROKER_PASSWORD`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags
+  associated to the account.
+
+* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095
+
+  The gateway endpoint.
+
+* `multipart.location`, default: /tmp
+
+  The shared file-system directory where the temporary files are stored to for the front-end and the .csv import.
+
 ## Swagger Endpoints
 
 * **OpenAPI**:

dockerhub/fda-ui.md

@@ -4,6 +4,46 @@
 $ docker run -v /tmp:/tmp -p 3000:3000 -e HOST=0.0.0.0 -e API=http://fda-gateway-service:9095
 ```
 
+## Customization
+
+Change the default behavior by setting the following environment variables to different values:
+
+* `API`, default: http://gateway-service:9095
+
+  The [Gateway Service](https://hub.docker.com/r/dbrepo/gateway-service) endpoint.
+
+* `BROKER_USERNAME`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags
+  associated to the account.
+
+* `BROKER_PASSWORD`, default: fda
+
+  The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags
+  associated to the account.
+
+* `SANDBOX`, default: false
+
+  When set to `1`, the interface displays a warning not to include production data.
+
+* `KEY`, optional.
+
+  The private key of an SSL/TLS certificate to be used by the webserver. The key needs to be a single-line string and
+  can be easily prepared by the command line:
+
+  ```console
+  $ sed -E ':a;N;$!ba;s/\r{0,1}\n/\\n/g' /path/to/privkey.pem
+  ```
+
+* `CERT`, optional.
+
+  The SSL/TLS certificate to be used by the webserver. The certificate needs to be a single-line string and can be
+  easily prepared by the command line:
+
+  ```console
+  $ sed -E ':a;N;$!ba;s/\r{0,1}\n/\\n/g' /path/to/cert.pem
+  ```
+
 ## Graphical Endpoints
 
 * **FAIR Portal**:

dockerhub/fda-units-service.md

@@ -4,6 +4,13 @@
 $ docker run -p 5010:5010 -e SPRING_PROFILES_ACTIVE=docker
 ```
 
+## Customization
+
+Change the default behavior by setting the following environment variables to different values:
+
+* `EUREKA_SERVER` default: http://discovery-service:9090/eureka/, needs to point to
+  the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service).
+
 ## Swagger Endpoints
 
 * **OpenAPI**: