Skip to content
Snippets Groups Projects
Unverified Commit 87cd3aee authored by Martin Weise's avatar Martin Weise
Browse files

Updated docs

parent 987d67f7
No related branches found
No related tags found
No related merge requests found
Pipeline #5472 failed
Showing
with 529 additions and 265 deletions
......@@ -6,7 +6,7 @@
* **Where to get help**:
[the official documentation](https://dbrepo-docs.ossdip.at/),
[the official documentation](https://www.ifs.tuwien.ac.at/infrastructures/dbrepo/),
[ICoDSE'22 paper](https://doi.org/10.1109/ICoDSE56892.2022.9971958),
[IJDC'22 paper](https://doi.org/10.2218/ijdc.v17i1.825),
[iPRES'21 paper](https://doi.org/10.17605/OSF.IO/B7NX5)
......@@ -32,6 +32,10 @@
[docs repo's `dockerhub/` directory](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-docs/-/tree/master/dockerhub)
([history](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-docs/-/commits/master/dockerhub))
* **Verify image signature**
[`mweise.pub`](https://www.ifs.tuwien.ac.at/infrastructures/dbrepo/docker/mweise.pub)
# What is DBRepo?
We present a database repository system that allows researchers to ingest data into a central, versioned repository
......
# How to use this image
```console
$ docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp -p 5000:5000
$ docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp -p 5000:5000 dbrepo/analyse-service:1.3
```
## Customization
......@@ -26,13 +26,9 @@ Change the default behavior by setting the following environment variables to di
* `HOSTNAME`, default: `analyse-service`
The name that is used at the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service) to register the
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
* **OpenAPI**:
......
# How to use this image
```console
$ docker run -p 9097:9097 -e SPRING_PROFILES_ACTIVE=docker
$ docker run -p 8443:8443 -p 8080:8080 dbrepo/authentication-service:1.3
```
## 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: `root`
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
* `METADATA_PASSWORD`, default: `dbrepo`
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.
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
* `LOG_LEVEL`, default: `debug`
* `KEYCLOAK_ADMIN`, default: `fda`
The minimum logging level for the service.
The admin user account username. It is **important** to change this value for public deployments.
## Swagger Endpoints
* `KEYCLOAK_ADMIN_PASSWORD`, default: `fda`
* **OpenAPI**:
The admin user account password. It is **important** to change this value for public deployments.
http://localhost:9097/swagger-ui/index.html
* `KEYCLOAK_IMPORT`, default: `/opt/keycloak/data/import/dbrepo-realm.json`
* **OpenAPI `.json`**:
The default realm "dbrepo" that is pre-configured with the roles from the backend services. Only change this value
if you want to not use the pre-configured realm and want to use your own. In this case, set the `KEYCLOAK_IMPORT=`
to empty.
http://localhost:9097/v3/api-docs/
## Keycloak Endpoints
* **OpenAPI `.yaml`**:
* **Admin Console**:
http://localhost:9097/v3/api-docs.yaml
https://localhost:8443/admin/master/console/
# How to use this image
```console
$ docker run -v ./fda-broker-service-data:/var/lib/rabbitmq/ -p 9098:9098 -p 5672:5672 -p 15672:15672
$ docker run -v ./fda-broker-service-data:/var/lib/rabbitmq/ -p 5672:5672 -p 15672:15672 dbrepo/broker-service:1.3
```
## Customization
Change the default behavior by setting the following variables in `rabbitmq.conf` to different values:
Change the default behavior by setting the following environment variables to different values:
* `default_user`, default: `fda`
* `RABBITMQ_DEFAULT_VHOST`, default `dbrepo`
The Broker Service username.
The backend services are configured to listen by default to the `dbrepo` virtual host.
* `default_pass`, default: `fda`
* `JWT_PUBKEY`, default `MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB`
The Broker Service password.
This value needs to be changed to the RS256 public key from the [authentication-service](https://hub.docker.com/r/dbrepo/authentication-service) in the admin console for public deployments under:
## Swagger Endpoints
*dbrepo > Realm settings > Keys > Algorithm > RS256 > Public key*
* **OpenAPI**:
* `JWT_CERT`, default `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`
http://localhost:9098/swagger-ui/index.html
This value needs to be changed to the RS256 certificate from the [authentication-service](https://hub.docker.com/r/dbrepo/authentication-service) in the admin console for public deployments under:
* **OpenAPI `.json`**:
*dbrepo > Realm settings > Keys > Algorithm > RS256 > Certificate*
http://localhost:9098/v3/api-docs/
Also change the values of the `rabbitmq.conf` file:
* **OpenAPI `.yaml`**:
* `default_user`, default: `fda`
http://localhost:9098/v3/api-docs.yaml
The Broker Service username.
* `default_pass`, default: `fda`
The Broker Service password.
## RabbitMQ Endpoints
* **Management**:
* **Management Plugin**:
http://localhost:15672/
# How to use this image
```console
$ docker run -p 9091:9091 -v /var/run/docker.sock:/var/run/docker.sock -e SPRING_PROFILES_ACTIVE=docker
$ docker run -p 9091:9091 -v /var/run/docker.sock:/var/run/docker.sock dbrepo/container-service:1.3
```
## Customization
......@@ -42,6 +42,41 @@ Change the default behavior by setting the following environment variables to di
The minimum logging level for the service.
* `CLIENT_ID`, default: `dbrepo-client`
The client id of the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service).
* `DBREPO_CLIENT_SECRET`, default: `MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG`
The client secret of the client with the above client id. This value needs to be changed by regenerating the client
secret in the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service):
*Realm dbrepo > Clients > dbrepo-client > Credentials > Client Secret > Regenerate*
* `JWT_ISSUER`, default: `http://localhost/realms/dbrepo`
The address in the `iss` (issuer) field of the JWT token must match this value.
* `JWT_PUBKEY`, default: `MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB`
This value needs to be changed to the RS256 public key from the [authentication-service](https://hub.docker.com/r/dbrepo/authentication-service) in the admin console for public deployments under:
*dbrepo > Realm settings > Keys > Algorithm > RS256 > Public key*
## Actuator Endpoints
* **Info Actuator**:
http://localhost:9091/actuator/info
* **Health Actuator**:
http://localhost:9091/actuator/health
* **Prometheus Actuator**:
http://localhost:9091/actuator/prometheus
## Swagger Endpoints
* **OpenAPI**:
......
# How to use this image
```console
$ docker run -p 9092:9092 -v /var/run/docker.sock:/var/run/docker.sock -e SPRING_PROFILES_ACTIVE=docker
$ docker run -p 9092:9092 -v /var/run/docker.sock:/var/run/docker.sock dbrepo/database-service:1.3
```
## Customization
......@@ -10,31 +10,35 @@ Change the default behavior by setting the following environment variables to di
* `METADATA_DB`, default: `fda`
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
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.
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.
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
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
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`
* `ELASTIC_USERNAME`, default `elastic`
Container hostname of the Search Service.
The username of the user that can create the search indexes and update them in the search database.
* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095
* `ELASTIC_PASSWORD`, default `elastic`
The password of the user that can create the search indexes and update them in the search database.
* `GATEWAY_ENDPOINT`, default: http://gateway-service
The gateway endpoint.
......@@ -42,6 +46,41 @@ Change the default behavior by setting the following environment variables to di
The minimum logging level for the service.
* `CLIENT_ID`, default: `dbrepo-client`
The client id of the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service).
* `DBREPO_CLIENT_SECRET`, default: `MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG`
The client secret of the client with the above client id. This value needs to be changed by regenerating the client
secret in the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service):
*Realm dbrepo > Clients > dbrepo-client > Credentials > Client Secret > Regenerate*
* `JWT_ISSUER`, default: `http://localhost/realms/dbrepo`
The address in the `iss` (issuer) field of the JWT token must match this value.
* `JWT_PUBKEY`, default: `MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB`
This value needs to be changed to the RS256 public key from the [authentication-service](https://hub.docker.com/r/dbrepo/authentication-service) in the admin console for public deployments under:
*dbrepo > Realm settings > Keys > Algorithm > RS256 > Public key*
## Actuator Endpoints
* **Info Actuator**:
http://localhost:9092/actuator/info
* **Health Actuator**:
http://localhost:9092/actuator/health
* **Prometheus Actuator**:
http://localhost:9092/actuator/prometheus
## Swagger Endpoints
* **OpenAPI**:
......
# How to use this image
```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: `root`
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
* `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
# How to use this image
```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: `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.
* `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
# How to use this image
```console
$ docker run -p 9096:9096 -e SPRING_PROFILES_ACTIVE=docker
$ docker run -p 9096:9096 -v /tmp:/tmp dbrepo/database-service:1.3
```
## Customization
......@@ -10,21 +10,21 @@ Change the default behavior by setting the following environment variables to di
* `METADATA_DB`, default: `fda`
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
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.
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
* `METADATA_PASSWORD`, default: `dbrepo`
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
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`
The gateway endpoint.
* `WEBSITE`, default: `http://localhost:3000`
* `WEBSITE`, default: `http://localhost`
The absolute url to the front end for redirecting PID lookups.
......@@ -32,6 +32,41 @@ Change the default behavior by setting the following environment variables to di
The minimum logging level for the service.
* `CLIENT_ID`, default: `dbrepo-client`
The client id of the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service).
* `DBREPO_CLIENT_SECRET`, default: `MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG`
The client secret of the client with the above client id. This value needs to be changed by regenerating the client
secret in the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service):
*Realm dbrepo > Clients > dbrepo-client > Credentials > Client Secret > Regenerate*
* `JWT_ISSUER`, default: `http://localhost/realms/dbrepo`
The address in the `iss` (issuer) field of the JWT token must match this value.
* `JWT_PUBKEY`, default: `MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB`
This value needs to be changed to the RS256 public key from the [authentication-service](https://hub.docker.com/r/dbrepo/authentication-service) in the admin console for public deployments under:
*dbrepo > Realm settings > Keys > Algorithm > RS256 > Public key*
## Actuator Endpoints
* **Info Actuator**:
http://localhost:9096/actuator/info
* **Health Actuator**:
http://localhost:9096/actuator/health
* **Prometheus Actuator**:
http://localhost:9096/actuator/prometheus
## Swagger Endpoints
* **OpenAPI**:
......
# How to use this image
```console
$ docker run -v ./data:/var/lib/postgresql/data -p 5432:5432 -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=postgres -e POSTGRES_DB=fda
$ docker run -v ./metadata-db-data:/var/lib/mysql -p 3306:3306 dbrepo/metadata-db:1.3
```
## Customization
......@@ -10,12 +10,24 @@ Change the default behavior by setting the following environment variables to di
* `METADATA_DB`, default: fda
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
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.
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
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
## Actuator Endpoints
* **Prometheus Actuator**:
http://localhost:9100/actuator/prometheus
## Other Endpoints
* **JDBC Endpoint**:
`jdbc:mariadb://localhost:3306/fda`
# How to use this image
```console
$ docker run -p 9099:9099 -e SPRING_PROFILES_ACTIVE=docker
$ docker run -p 9099:9099 dbrepo/metadata-service:1.3
```
## Customization
......@@ -10,15 +10,47 @@ Change the default behavior by setting the following environment variables to di
* `METADATA_DB`, default: `fda`
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
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.
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.
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
* `GATEWAY_ENDPOINT`, default: `http://gateway-service`
The gateway endpoint.
* `PID_BASE`, default: `http://localhost/pid/`
The base redirect endpoint for persistent identifiers in the OAI-PMH protocol.
* `REPOSITORY_NAME`, default: `Example Repository`
The name of the repository for the OAI-PMH protocol.
* `BASE_URL`, default: `http://localhost`
The base url of the repository for the OAI-PMH protocol.
* `ADMIN_EMAIL`, default: `noreply@localhost`
The administrator contact e-mail for the OAI-PMH protocol.
* `EARLIEST_DATESTAMP`, default: `2022-09-17T18:23:00Z`
The first date and time where the repository was providing information to the public.
* `DELETED_RECORD`, default: `persistent`
Information for the OAI-PMH protocol on the deletion policy of records.
* `GRANULARITY`, default: `YYYY-MM-DDThh:mm:ssZ`
Denomination of the record granularity for the OAI-PMH protocol.
* `LOG_LEVEL`, default: `debug`
......
# How to use this image
```console
$ docker run -p 9093:9093 -e SPRING_PROFILES_ACTIVE=docker
$ docker run -p 9093:9093 -v /tmp:/tmp dbrepo/query-service:1.3
```
## Customization
......@@ -10,27 +10,27 @@ Change the default behavior by setting the following environment variables to di
* `METADATA_DB`, default: `fda`
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
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.
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
* `METADATA_PASSWORD`, default: `dbrepo`
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
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
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
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`
The gateway endpoint.
......@@ -40,17 +40,52 @@ Change the default behavior by setting the following environment variables to di
* `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.
Number of consumers each queue in the [broker service](https://hub.docker.com/r/dbrepo/broker-service) should
maintain. Minimum 1.
* `LOG_LEVEL`, default: `debug`
The minimum logging level for the service.
* `CLIENT_ID`, default: `dbrepo-client`
The client id of the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service).
* `DBREPO_CLIENT_SECRET`, default: `MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG`
The client secret of the client with the above client id. This value needs to be changed by regenerating the client
secret in the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service):
*Realm dbrepo > Clients > dbrepo-client > Credentials > Client Secret > Regenerate*
* `JWT_ISSUER`, default: `http://localhost/realms/dbrepo`
The address in the `iss` (issuer) field of the JWT token must match this value.
* `JWT_PUBKEY`, default: `MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB`
This value needs to be changed to the RS256 public key from the [authentication-service](https://hub.docker.com/r/dbrepo/authentication-service) in the admin console for public deployments under:
*dbrepo > Realm settings > Keys > Algorithm > RS256 > Public key*
* `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.
## Actuator Endpoints
* **Info Actuator**:
http://localhost:9093/actuator/info
* **Health Actuator**:
http://localhost:9093/actuator/health
* **Prometheus Actuator**:
http://localhost:9093/actuator/prometheus
## Swagger Endpoints
* **OpenAPI**:
......
# How to use this image
```console
$ docker run -p 9200:9200 dbrepo/search-service:latest
```
## Customization
Change the default behavior by setting the following environment variables to different values:
* `ELASTIC_PASSWORD`, default: `elastic`
The password for the username `elastic`. By default the credentials are `elastic:elastic`.
## Elastic Search Endpoints
* **Index**:
http://localhost:9200/
# How to use this image
```console
$ docker run -p 5010:5010 -e SPRING_PROFILES_ACTIVE=docker
$ docker run -p 9097:9097 -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp dbrepo/semantics-service:1.3
```
## Customization
Change the default behavior by setting the following environment variables to different values:
* `FLASK_APP`, default: `app.py`
* `METADATA_DB`, default: `fda`
The file that represents a flask app in the container.
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
* `FLASK_RUN_HOST`, default: `0.0.0.0`
* `METADATA_USERNAME`, default: `root`
The bind address for the flask server.
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
* `PORT_APP`, default: `5010`
* `METADATA_PASSWORD`, default: `dbrepo`
The bind port for the flask server.
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
* `FLASK_ENV`, default: `production`
* `LOG_LEVEL`, default: `debug`
The flask environment mode.
The minimum logging level for the service.
* `HOSTNAME`, default: `units-service`
* `JWT_ISSUER`, default: `http://localhost/realms/dbrepo`
The name that is used at the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service) to register the
Units Service.
The address in the `iss` (issuer) field of the JWT token must match this value.
* `EUREKA_SERVER`, default: `http://discovery-service:9090/eureka/`
* `JWT_PUBKEY`, default: `MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB`
Needs to point to the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service).
This value needs to be changed to the RS256 public key from the [authentication-service](https://hub.docker.com/r/dbrepo/authentication-service) in the admin console for public deployments under:
* `READY_FILE`, default: `/ready`
*dbrepo > Realm settings > Keys > Algorithm > RS256 > Public key*
The full path to the file with filename where to place a file when the service is ready.
## Actuator Endpoints
* `LOG_LEVEL`, default: `debug`
* **Info Actuator**:
The minimum logging level for the service.
http://localhost:9097/actuator/info
* `METADATA_DB`, default: `fda`
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
* `METADATA_USERNAME`, default: `root`
* **Health Actuator**:
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
http://localhost:9097/actuator/health
* `METADATA_PASSWORD`, default: `mariadb`
* **Prometheus Actuator**:
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
http://localhost:9097/actuator/prometheus
## Swagger Endpoints
* **OpenAPI**:
http://localhost:5010/swagger-ui/
http://localhost:9097/swagger-ui/index.html
* **OpenAPI `.json`**:
http://localhost:5010/api-analyze.json
http://localhost:9097/v3/api-docs/
* **OpenAPI `.yaml`**:
http://localhost:9097/v3/api-docs.yaml
# How to use this image
```console
$ docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp -p 9094:9094 -e SPRING_PROFILES_ACTIVE=docker
$ docker run -p 9094:9094 -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp dbrepo/table-service:1.3
```
## Customization
......@@ -10,38 +10,73 @@ Change the default behavior by setting the following environment variables to di
* `METADATA_DB`, default: fda
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name.
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.
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
* `METADATA_PASSWORD`, default: `dbrepo`
The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
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
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
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`
* `SHARED_FILESYSTEM`, default: `/tmp`
The gateway endpoint.
The folder that has a shared filesystem among services.
* `multipart.location`, default: `/tmp`
* `USER_NETWORK`, default: `userdb`
The folder that has a shared filesystem among services.
The Docker network that user-generated databases are connected to when created.
* `LOG_LEVEL`, default: `debug`
The minimum logging level for the service.
* `CLIENT_ID`, default: `dbrepo-client`
The client id of the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service).
* `DBREPO_CLIENT_SECRET`, default: `MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG`
The client secret of the client with the above client id. This value needs to be changed by regenerating the client
secret in the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service):
*Realm dbrepo > Clients > dbrepo-client > Credentials > Client Secret > Regenerate*
* `JWT_ISSUER`, default: `http://localhost/realms/dbrepo`
The address in the `iss` (issuer) field of the JWT token must match this value.
* `JWT_PUBKEY`, default: `MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB`
This value needs to be changed to the RS256 public key from the [authentication-service](https://hub.docker.com/r/dbrepo/authentication-service) in the admin console for public deployments under:
*dbrepo > Realm settings > Keys > Algorithm > RS256 > Public key*
## Actuator Endpoints
* **Info Actuator**:
http://localhost:9094/actuator/info
* **Health Actuator**:
http://localhost:9094/actuator/health
* **Prometheus Actuator**:
http://localhost:9094/actuator/prometheus
## Swagger Endpoints
* **OpenAPI**:
......
# How to use this image
```console
$ docker run -v /tmp:/tmp -p 3000:3000 -e HOST=0.0.0.0 -e API=http://fda-gateway-service:9095
$ docker run -v /tmp:/tmp -p 3000:3000 dbrepo/ui:1.3
```
## Customization
Change the default behavior by setting the following environment variables to different values:
* `API`, default: `http://gateway-service:9095`
* `NODE_ENV`, default: `production`
The [Gateway Service](https://hub.docker.com/r/dbrepo/gateway-service) endpoint.
The environment for node.js.
* `HOST`, default: `0.0.0.0`
The interface the frontend should bind to and be available at.
* `API`, default: `http://:80`
The default API endpoint.
* `BASE_URL`, default: `http://:80`
The base URL for the frontend.
* `BROKER_USERNAME`, default: `fda`
The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags
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
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.
* `SEARCH`, default: `http://search-service:9200`
The endpoint of the Search Service.
......@@ -34,19 +42,46 @@ Change the default behavior by setting the following environment variables to di
The folder that has a shared filesystem among services.
* `VERSION`, default: `1.1`
* `LOGO`, default: `/logo.png`
The file that is used to display the logo on the left navigation drawer. Change this to your organization's logo by
mounting it with the `-v` flag, e.g. `docker run -v /path/to/your_logo.png:/logo.png ...`.
* `ELASTIC_USERNAME`, default `elastic`
The username of the user that can create the search indexes and update them in the search database.
* `ELASTIC_PASSWORD`, default `elastic`
The password of the user that can create the search indexes and update them in the search database.
* `VERSION`, default: `latest`
The version number to display on the left navigation drawer.
* `LOGO`, default: `/logo.png`
* `TITLE`, default: `Database Repository`
The title of the repository.
* `ICON`, default: `/favicon.ico`
Path to the logo displayed on the left navigation drawer. Change this to your organization's logo by mounting it
with the `-v` flag, e.g. `docker run -v /path/to/your_logo.ico:/favicon.ico ...`.
* `CLIENT_ID`, default: `dbrepo-client`
The client id of the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service).
* `DBREPO_CLIENT_SECRET`, default: `MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG`
The client secret of the client with the above client id. This value needs to be changed by regenerating the client
secret in the [authentication service](https://hub.docker.com/r/dbrepo/authentication-service):
The file that is used to display the logo on the left navigation drawer. Tip: place the file in `/app`.
*Realm dbrepo > Clients > dbrepo-client > Credentials > Client Secret > Regenerate*
* `MAIL_VERIFY`, default: `false`
* `GIT_HASH`, default: `deadbeef`
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.
The automatically inserted git hash of the latest commit.
## Graphical Endpoints
......
# How to use this image
```console
$ docker run -p 9098:9098 dbrepo/user-service:1.3
```
## 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: `root`
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database username.
* `METADATA_PASSWORD`, default: `dbrepo`
The [metadata database](https://hub.docker.com/r/dbrepo/metadata-db) database password.
* `GATEWAY_ENDPOINT`, default: `http://gateway-service`
The gateway endpoint.
* `JWT_ISSUER`, default: `http://localhost/realms/dbrepo`
The address in the `iss` (issuer) field of the JWT token must match this value.
* `JWT_PUBKEY`, default: `MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB`
This value needs to be changed to the RS256 public key from the [authentication-service](https://hub.docker.com/r/dbrepo/authentication-service) in the admin console for public deployments under:
*dbrepo > Realm settings > Keys > Algorithm > RS256 > Public key*
* `LOG_LEVEL`, default: `debug`
The minimum logging level for the service.
* `DEFAULT_ROLE`, default: `default-researcher-roles`
The default (composite) role of newly created users.
* `ELASTIC_PASSWORD`, default `elastic`
The password of the user that can create the search indexes and update them in the search database.
## Actuator Endpoints
* **Info Actuator**:
http://localhost:9094/actuator/info
* **Health Actuator**:
http://localhost:9094/actuator/health
* **Prometheus Actuator**:
http://localhost:9094/actuator/prometheus
## Swagger Endpoints
* **OpenAPI**:
http://localhost:9094/swagger-ui/index.html
* **OpenAPI `.json`**:
http://localhost:9094/v3/api-docs/
* **OpenAPI `.yaml`**:
http://localhost:9094/v3/api-docs.yaml
-----BEGIN PUBLIC KEY-----
role: mweise
MFkwEwYHKoZIzj0CAQYIKoZIzj0DAQcDQgAEiF4l7rlcaope9LGiodp6yHRtsUek
WjYX8mVi3AAcuoXvKtnbRZTwX78FOID2zZiQSsHWIcuMDOKJfubNzWrtMw==
-----END PUBLIC KEY-----
#!/bin/bash
TAG=latest
DOCKER_CONTENT_TRUST=1
DOCKER_CONTENT_TRUST_ROOT_PASSPHRASE=
DOCKER_CONTENT_TRUST_REPOSITORY_PASSPHRASE=
# generate key
#docker trust key generate mweise
# trust
docker trust signer add --key mweise.pub mweise dbrepo/analyse-service
docker trust signer add --key mweise.pub mweise dbrepo/broker-service
docker trust signer add --key mweise.pub mweise dbrepo/container-service
docker trust signer add --key mweise.pub mweise dbrepo/database-service
docker trust signer add --key mweise.pub mweise dbrepo/identifier-service
docker trust signer add --key mweise.pub mweise dbrepo/metadata-db
docker trust signer add --key mweise.pub mweise dbrepo/metadata-service
docker trust signer add --key mweise.pub mweise dbrepo/query-service
docker trust signer add --key mweise.pub mweise dbrepo/semantics-service
docker trust signer add --key mweise.pub mweise dbrepo/table-service
docker trust signer add --key mweise.pub mweise dbrepo/ui
docker trust signer add --key mweise.pub mweise dbrepo/user-service
# sign
docker trust sign dbrepo/analyse-service:${TAG}
docker trust sign dbrepo/broker-service:${TAG}
docker trust sign dbrepo/container-service:${TAG}
docker trust sign dbrepo/database-service:${TAG}
docker trust sign dbrepo/identifier-service:${TAG}
docker trust sign dbrepo/metadata-db:${TAG}
docker trust sign dbrepo/metadata-service:${TAG}
docker trust sign dbrepo/query-service:${TAG}
docker trust sign dbrepo/semantics-service:${TAG}
docker trust sign dbrepo/table-service:${TAG}
docker trust sign dbrepo/ui:${TAG}
docker trust sign dbrepo/user-service:${TAG}
# push
docker push dbrepo/analyse-service:${TAG}
docker push dbrepo/broker-service:${TAG}
docker push dbrepo/container-service:${TAG}
docker push dbrepo/database-service:${TAG}
docker push dbrepo/identifier-service:${TAG}
docker push dbrepo/metadata-db:${TAG}
docker push dbrepo/metadata-service:${TAG}
docker push dbrepo/query-service:${TAG}
docker push dbrepo/semantics-service:${TAG}
docker push dbrepo/table-service:${TAG}
docker push dbrepo/ui:${TAG}
docker push dbrepo/user-service:${TAG}
-----BEGIN PUBLIC KEY-----
role: mweise
MFkwEwYHKoZIzj0CAQYIKoZIzj0DAQcDQgAEiF4l7rlcaope9LGiodp6yHRtsUek
WjYX8mVi3AAcuoXvKtnbRZTwX78FOID2zZiQSsHWIcuMDOKJfubNzWrtMw==
-----END PUBLIC KEY-----
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment