Updated the docker images documentation

2ee00075 · Martin Weise · 4decab6d · 2ee00075 · 2ee00075 · 2ee00075
Unverified Commit 2ee00075 authored 2 years ago by Martin Weise
--- a/dockerhub/fda-analyse-service.md
+++ b/dockerhub/fda-analyse-service.md
@@ -8,8 +8,30 @@ $ docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp -p 5000:5
 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
+* `FLASK_APP`, default: `app.py`
-  the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service).
+  The file that represents a flask app in the container.
+* `FLASK_RUN_HOST`, default: `0.0.0.0`
+  The bind address for the flask server.
+* `PORT_APP`, default: `5000`
+  The bind port for the flask server.
+* `FLASK_ENV`, default: `production`
+  The flask environment mode.
+* `HOSTNAME`, default: `analyse-service`
+  The name that is used at the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service) to register the
+  Analyse Service.
+* `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

--- a/dockerhub/fda-authentication-service.md
+++ b/dockerhub/fda-authentication-service.md
@@ -8,79 +8,83 @@ $ docker run -p 9097:9097 -e SPRING_PROFILES_ACTIVE=docker
 Change the default behavior by setting the following environment variables to different values:
-* `METADATA_DB`, default: fda
+* `METADATA_DB`, default: `fda`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
-* `METADATA_USERNAME`, default: postgres
+* `METADATA_USERNAME`, default: `root`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
-* `METADATA_PASSWORD`, default: postgres
+* `METADATA_PASSWORD`, default: `dbrepo`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
-* `BROKER_USERNAME`, default: fda
+* `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
+* `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
+* `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
+* `GATEWAY_ENDPOINT`, default: `http://gateway-service:9095`
  The gateway endpoint.
-* `MAIL_FROM`, default: "Database Repository <noreply@example.com>"
+* `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>"
+* `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
+* `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
+* `JWT_ISSUER`, default: `dbrepo`
  The Java Web Token issuer name.
-* `JWT_SECRET`, default: secret
+* `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
+* `JWT_EXPIRATION`, default: `86400000`
  By default, the Java Web Token expire after 1 day.
-* `SMTP_HOST`, optional.
+* `SMTP_HOST`, optional
  The e-mail server that sends e-mails to the users. Specify the hostname.
-* `SMTP_PORT`, optional.
+* `SMTP_PORT`, optional
  The e-mail server that sends e-mails to the users. Specify the port.
-* `SMTP_USERNAME`, optional.
+* `SMTP_USERNAME`, optional
  The e-mail server that sends e-mails to the users. Specify the username.
-* `SMTP_PASSWORD`, optional.
+* `SMTP_PASSWORD`, optional
  The e-mail server that sends e-mails to the users. Specify the password.
+* `LOG_LEVEL`, default: `debug`
+  The minimum logging level for the service.
 ## Swagger Endpoints
 * **OpenAPI**:

--- a/dockerhub/fda-broker-service.md
+++ b/dockerhub/fda-broker-service.md
@@ -8,11 +8,11 @@ $ docker run -v ./fda-broker-service-data:/var/lib/rabbitmq/ -p 9098:9098 -p 567
 Change the default behavior by setting the following variables in `rabbitmq.conf` to different values:
-* `default_user`, default: fda
+* `default_user`, default: `fda`
  The Broker Service username.
-* `default_pass`, default: fda
+* `default_pass`, default: `fda`
  The Broker Service password.

--- a/dockerhub/fda-container-service.md
+++ b/dockerhub/fda-container-service.md
@@ -8,28 +8,40 @@ $ docker run -p 9091:9091 -v /var/run/docker.sock:/var/run/docker.sock -e SPRING
 Change the default behavior by setting the following environment variables to different values:
-* `METADATA_DB`, default: fda
+* `METADATA_DB`, default: `fda`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
-* `METADATA_USERNAME`, default: postgres
+* `METADATA_USERNAME`, default: `root`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
-* `METADATA_PASSWORD`, default: postgres
+* `METADATA_PASSWORD`, default: `mariadb`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
-* `BROKER_USERNAME`, default: fda
+* `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
+* `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.
+* `SHARED_FILESYSTEM`, default: `/tmp`
+  The folder that has a shared filesystem among services.
+* `USER_NETWORK`, default: `userdb`
+  The Docker network that user-generated databases are connected to when created.
+* `LOG_LEVEL`, default: `debug`
+  The minimum logging level for the service.
 ## Swagger Endpoints
 * **OpenAPI**:

--- a/dockerhub/fda-database-service.md
+++ b/dockerhub/fda-database-service.md
@@ -8,32 +8,40 @@ $ docker run -p 9092:9092 -v /var/run/docker.sock:/var/run/docker.sock -e SPRING
 Change the default behavior by setting the following environment variables to different values:
-* `METADATA_DB`, default: fda
+* `METADATA_DB`, default: `fda`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
-* `METADATA_USERNAME`, default: postgres
+* `METADATA_USERNAME`, default: `root`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
-* `METADATA_PASSWORD`, default: postgres
+* `METADATA_PASSWORD`, default: `mariadb`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
-* `BROKER_USERNAME`, default: fda
+* `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
+* `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.
+* `SEARCH_ENDPOINT`, default `search-service`
+  Container hostname of the Search Service.
 * `GATEWAY_ENDPOINT`, default: http://gateway-service:9095
  The gateway endpoint.
+* `LOG_LEVEL`, default: `debug`
+  The minimum logging level for the service.
 ## Swagger Endpoints
 * **OpenAPI**:

--- a/dockerhub/fda-discovery-service.md
+++ b/dockerhub/fda-discovery-service.md
@@ -8,14 +8,18 @@ $ docker run -p 9090:9090 -e SPRING_PROFILES_ACTIVE=docker
 Change the default behavior by setting the following environment variables to different values:
-* `METADATA_DB`, default: fda
+* `METADATA_DB`, default: `fda`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
-* `METADATA_USERNAME`, default: postgres
+* `METADATA_USERNAME`, default: `root`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
-* `METADATA_PASSWORD`, default: postgres
+* `METADATA_PASSWORD`, default: `dbrepo`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
+* `LOG_LEVEL`, default: `debug`
+  The minimum logging level for the service.
\ No newline at end of file
--- a/dockerhub/fda-docs.md
+++ b/dockerhub/fda-docs.md
-# How to use this image
-```console
-$ docker run -p 80:80
-```
-## Customization
-No customization.
\ No newline at end of file
--- a/dockerhub/fda-gateway-service.md
+++ b/dockerhub/fda-gateway-service.md
@@ -8,18 +8,22 @@ $ docker run -p 9095:9095 -e SPRING_PROFILES_ACTIVE=docker
 Change the default behavior by setting the following environment variables to different values:
-* `METADATA_DB`, default: fda
+* `METADATA_DB`, default: `fda`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
-* `METADATA_USERNAME`, default: postgres
+* `METADATA_USERNAME`, default: `root`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
-* `METADATA_PASSWORD`, default: postgres
+* `METADATA_PASSWORD`, default: `mariadb`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
-* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095
+* `GATEWAY_ENDPOINT`, default: `http://gateway-service:9095`
  The gateway endpoint.
+* `LOG_LEVEL`, default: `debug`
+  The minimum logging level for the service.
\ No newline at end of file
--- a/dockerhub/fda-identifier-service.md
+++ b/dockerhub/fda-identifier-service.md
@@ -8,22 +8,30 @@ $ docker run -p 9096:9096 -e SPRING_PROFILES_ACTIVE=docker
 Change the default behavior by setting the following environment variables to different values:
-* `METADATA_DB`, default: fda
+* `METADATA_DB`, default: `fda`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
-* `METADATA_USERNAME`, default: postgres
+* `METADATA_USERNAME`, default: `root`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
-* `METADATA_PASSWORD`, default: postgres
+* `METADATA_PASSWORD`, default: `dbrepo`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
-* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095
+* `GATEWAY_ENDPOINT`, default: `http://gateway-service:9095`
  The gateway endpoint.
+* `WEBSITE`, default: `http://localhost:3000`
+  The absolute url to the front end for redirecting PID lookups.
+* `LOG_LEVEL`, default: `debug`
+  The minimum logging level for the service.
 ## Swagger Endpoints
 * **OpenAPI**:

--- a/dockerhub/fda-query-service.md
+++ b/dockerhub/fda-query-service.md
@@ -8,32 +8,49 @@ $ docker run -p 9093:9093 -e SPRING_PROFILES_ACTIVE=docker
 Change the default behavior by setting the following environment variables to different values:
-* `METADATA_DB`, default: fda
+* `METADATA_DB`, default: `fda`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
-* `METADATA_USERNAME`, default: postgres
+* `METADATA_USERNAME`, default: `root`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
-* `METADATA_PASSWORD`, default: postgres
+* `METADATA_PASSWORD`, default: `dbrepo`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
-* `BROKER_USERNAME`, default: fda
+* `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
+* `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
+* `GATEWAY_ENDPOINT`, default: `http://gateway-service:9095`
  The gateway endpoint.
+* `SHARED_FILESYSTEM`, default: `/tmp`
+  The folder that has a shared filesystem among services.
+* `BROKER_CONSUMERS`, default: `2`
+  Number of consumers each queue in the [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) should 
+  maintain in the Query Service. Minimum 1.
+* `LOG_LEVEL`, default: `debug`
+  The minimum logging level for the service.
+* `NOT_SUPPORTED_KEYWORDS`, default: `*,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,--`
+  Comma-separated list of (key-)words that are not allowed in any query or view. The case does not matter.
 ## Swagger Endpoints
 * **OpenAPI**:

--- a/dockerhub/fda-search-service.md
+++ b/dockerhub/fda-search-service.md
-# How to use this image
-```console
-$ docker run -p 9200:9200 -p 9600:9600 -e discovery.type=single-node -e "ES_JAVA_OPTS=-Xms512m -Xmx512m" -e logger.level=WARN
-```
-## ElasticSearch Endpoints
-* **Database Index**:
-  http://localhost:9000/databaseindex
--- a/dockerhub/fda-table-service.md
+++ b/dockerhub/fda-table-service.md
@@ -12,31 +12,35 @@ Change the default behavior by setting the following environment variables to di
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
-* `METADATA_USERNAME`, default: postgres
+* `METADATA_USERNAME`, default: `root`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
-* `METADATA_PASSWORD`, default: postgres
+* `METADATA_PASSWORD`, default: `dbrepo`
  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
-* `BROKER_USERNAME`, default: fda
+* `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
+* `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
+* `GATEWAY_ENDPOINT`, default: `http://gateway-service:9095`
  The gateway endpoint.
-* `multipart.location`, default: /tmp
+* `multipart.location`, default: `/tmp`
-  The shared file-system directory where the temporary files are stored to for the front-end and the .csv import.
+  The folder that has a shared filesystem among services.
+* `LOG_LEVEL`, default: `debug`
+  The minimum logging level for the service.
 ## Swagger Endpoints

--- a/dockerhub/fda-ui.md
+++ b/dockerhub/fda-ui.md
@@ -8,55 +8,45 @@ $ docker run -v /tmp:/tmp -p 3000:3000 -e HOST=0.0.0.0 -e API=http://fda-gateway
 Change the default behavior by setting the following environment variables to different values:
-* `API`, default: http://gateway-service:9095
+* `API`, default: `http://gateway-service:9095`
  The [Gateway Service](https://hub.docker.com/r/dbrepo/gateway-service) endpoint.
-* `BROKER_USERNAME`, default: fda
+* `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
+* `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
+* `SANDBOX`, default: `false`
  When set to `1`, the interface displays a warning not to include production data.
-* `KEY`, optional.
+* `SEARCH`, default: `http://search-service:9200`
-  The private key of an SSL/TLS certificate to be used by the webserver. The key needs to be a single-line string and
+  The endpoint of the Search Service.
-  ```console
+* `SHARED_FILESYSTEM`, default: `/tmp`
-  $ sed -E ':a;N;$!ba;s/\r{0,1}\n/\\n/g' /path/to/privkey.pem
-  ```
-* `CERT`, optional.
+  The folder that has a shared filesystem among services.
-  The SSL/TLS certificate to be used by the webserver. The certificate needs to be a single-line string and can be
+* `VERSION`, default: `1.1`
-  easily prepared by the command line:
-  ```console
+  The version number to display on the left navigation drawer.
-  $ sed -E ':a;N;$!ba;s/\r{0,1}\n/\\n/g' /path/to/cert.pem
-  ```
-* `LOGO`, optional.
+* `LOGO`, default: `/logo.png`
-  Relative path to the graphics that should be displayed as a logo in the left pane. The path is relative to the mount
+  The file that is used to display the logo on the left navigation drawer. Tip: place the file in `/app`.
-  point in the `docker-compose.yml` file. For example add in the `docker-compose.yml`:
-  ```yaml
+* `MAIL_VERIFY`, default: `false`
-  fda-ui:
-    ...
-    volumes:
-      - /tmp:/tmp
-      - /path/to/logo.png:/app/static/logo.png:ro # <<< add this line pointing to your local logo.png file
-  ```
-  And place the logo on the host at `/logos/logo.png`, then set the value of `LOGO` to `/logos/logo.png`
+  If set to `true`, a mail will be sent via
+  the [Authentication Service](https://hub.docker.com/r/dbrepo/authentication-service) endpoint and it will be mandatory
+  to click a link in the e-mail before proceeding to login.
 ## Graphical Endpoints

--- a/dockerhub/fda-units-service.md
+++ b/dockerhub/fda-units-service.md
@@ -8,8 +8,50 @@ $ docker run -p 5010:5010 -e SPRING_PROFILES_ACTIVE=docker
 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
+* `FLASK_APP`, default: `app.py`
-  the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service).
+  The file that represents a flask app in the container.
+* `FLASK_RUN_HOST`, default: `0.0.0.0`
+  The bind address for the flask server.
+* `PORT_APP`, default: `5010`
+  The bind port for the flask server.
+* `FLASK_ENV`, default: `production`
+  The flask environment mode.
+* `HOSTNAME`, default: `units-service`
+  The name that is used at the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service) to register the
+  Units Service.
+* `EUREKA_SERVER`, default: `http://discovery-service:9090/eureka/`
+  Needs to point to the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service).
+* `READY_FILE`, default: `/ready`
+  The full path to the file with filename where to place a file when the service is ready.
+* `LOG_LEVEL`, default: `debug`
+  The minimum logging level for the service.
+* `METADATA_DB`, default: `fda`
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
+* `METADATA_USERNAME`, default: `root`
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
+* `METADATA_PASSWORD`, default: `mariadb`
+  The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
 ## Swagger Endpoints