diff --git a/dockerhub/fda-analyse-service.md b/dockerhub/fda-analyse-service.md index 9f11cf6f65244ddba1951f202defb20b37dcccac..d6e1551e2b42e9ac8669ac606a5ef21422333521 100644 --- 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 - the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service). +* `FLASK_APP`, default: `app.py` + + 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 diff --git a/dockerhub/fda-authentication-service.md b/dockerhub/fda-authentication-service.md index 8de21c528be3a1b7449c9d9df33774a6d1dbca92..2c7ccb4dcc66c4efb48b785345bfa1bf851277f9 100644 --- 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**: diff --git a/dockerhub/fda-broker-service.md b/dockerhub/fda-broker-service.md index 1f28834e569d135f5333c63fca249e9e96b51108..4a0a79e7cc3237ffc31a8bcf38258b872db56e5a 100644 --- 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. diff --git a/dockerhub/fda-container-service.md b/dockerhub/fda-container-service.md index 9057cba137039a139629fda791fe7862164b5a00..1e1f3ed6ce95487e5baab3a8b412994c9f7f9bc8 100644 --- 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**: diff --git a/dockerhub/fda-database-service.md b/dockerhub/fda-database-service.md index a2c6a91c06b7e9f70b8a8187087a946cb7f12f8f..bd7ed8d8bee3c05ede7754e39dd680757c8dccb2 100644 --- 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**: diff --git a/dockerhub/fda-discovery-service.md b/dockerhub/fda-discovery-service.md index 627ef21ceed1ae16af15e61f4dd9211534ad8eb9..fdc99ce911243a2a9762135dd6dc9f40abd8c9a8 100644 --- 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. \ No newline at end of file + 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 diff --git a/dockerhub/fda-docs.md b/dockerhub/fda-docs.md deleted file mode 100644 index 262f431a6d8fed492ffaa61d69ac5f8a52ea3c56..0000000000000000000000000000000000000000 --- a/dockerhub/fda-docs.md +++ /dev/null @@ -1,9 +0,0 @@ -# How to use this image - -```console -$ docker run -p 80:80 -``` - -## Customization - -No customization. \ No newline at end of file diff --git a/dockerhub/fda-gateway-service.md b/dockerhub/fda-gateway-service.md index 09911f67068ea409261f3952862d93e846982248..df9bf111262bf2ae38fdc9febb2853090e7c5870 100644 --- 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. \ No newline at end of file + The gateway endpoint. + +* `LOG_LEVEL`, default: `debug` + + The minimum logging level for the service. \ No newline at end of file diff --git a/dockerhub/fda-identifier-service.md b/dockerhub/fda-identifier-service.md index 70d65f8dca8073b28080701de28c14cb89a18652..96d413c8557c9516e1c4ae98efd877c2f1d96d09 100644 --- 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**: diff --git a/dockerhub/fda-query-service.md b/dockerhub/fda-query-service.md index 6b12bc5b8595ff1964d613c2befc50341863d260..7fcb9c6ebebd518b5deed77f2e334de79c8c1d0c 100644 --- 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**: diff --git a/dockerhub/fda-search-service.md b/dockerhub/fda-search-service.md deleted file mode 100644 index 7b6a38a492de7d41eaea0b5828f0df5265769515..0000000000000000000000000000000000000000 --- a/dockerhub/fda-search-service.md +++ /dev/null @@ -1,11 +0,0 @@ -# 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 diff --git a/dockerhub/fda-table-service.md b/dockerhub/fda-table-service.md index a6e8653ad2c9eba6b69ecbe55c5f5aaf6b538489..429bddb277d5dcbcb8a932636dc4a87c2f4b0663 100644 --- 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 diff --git a/dockerhub/fda-ui.md b/dockerhub/fda-ui.md index b40cc26125c800965e7222876d4525555461f9b8..b0b01f70075d86a8efbbc2fa4549da9fe6ef65e1 100644 --- 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 - $ sed -E ':a;N;$!ba;s/\r{0,1}\n/\\n/g' /path/to/privkey.pem - ``` +* `SHARED_FILESYSTEM`, default: `/tmp` -* `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 - easily prepared by the command line: +* `VERSION`, default: `1.1` - ```console - $ sed -E ':a;N;$!ba;s/\r{0,1}\n/\\n/g' /path/to/cert.pem - ``` + The version number to display on the left navigation drawer. -* `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 - point in the `docker-compose.yml` file. For example add in the `docker-compose.yml`: + The file that is used to display the logo on the left navigation drawer. Tip: place the file in `/app`. - ```yaml - fda-ui: - ... - volumes: - - /tmp:/tmp - - /path/to/logo.png:/app/static/logo.png:ro # <<< add this line pointing to your local logo.png file - ``` +* `MAIL_VERIFY`, default: `false` - 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 diff --git a/dockerhub/fda-units-service.md b/dockerhub/fda-units-service.md index f36edd7c1e3084e646a2880b825ccf1acdd309a7..150b158558c99a579d573f330e69186588364b79 100644 --- 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 - the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service). +* `FLASK_APP`, default: `app.py` + + 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 @@ -18,5 +60,5 @@ Change the default behavior by setting the following environment variables to di http://localhost:5010/swagger-ui/ * **OpenAPI `.json`**: - + http://localhost:5010/api-analyze.json