GBA Bridgehead

The Bridgehead consists of two main components, the Store and the Connector running in Tomcat 8. In addition to that, both need a Postgres 9.6 database.

Steps:

• Install and run Bridgehead (Docker-Compose which is recommended, or manual with WINDOWS OR LINUX)
• Create xml and import into Store (Import-Readme)
• Connect to central Searchbroker

Docker-Compose

This Docker Compose project includes both, the Store and the Connector, both Postgres databases and to showcase monitoring, a Prometheus instance together with Grafana.

1. Install Docker And test Docker in any command line with:

    docker run hello-world
   

2. After checking for free ports, bring all up with:

    git clone https://github.com/martinbreu/gba-bridgehead-compose
    cd gba-bridgehead-compose
    docker-compose up
   

Docker compose will start all containers and print the logs to the console.

If you see database connection errors from the store or the connector, open a second terminal and run docker-compose stop followed by docker-compose start. Database connection problems should only occur at the first start because the store and the connector doesn't wait for the databases to be ready. Both try to connect at startup which might be to early.

If one needs only one of them, on can bring up only the specific one with:

docker-compose up store
docker-compose up connector

Environment (Optional)

The Docker containers and docker-compose.yml accept certain environment variables:

Ports outside container

• PORT_STORE - defaults to 8081
• PORT_CONNECTOR - defaults to 8082
• PORT_STORE_METRICS - defaults to 9101
• PORT_CONNECTOR_METRICS - defaults to 9102
• PORT_STORE_POSTGRES - defaults to 5433
• PORT_CONNECTOR_POSTGRES - defaults to 5434
• PORT_PROMETHEUS - defaults to 9090
• PORT_GRAFANA - defaults to 3000

You can either stop all services occupying those ports or change and save your personal environments

Store specific (Optional)

• STORE_MDR_NAMESPACE - current namespace which changes after every change depending data-elements, defaults to mdr16
• STORE_MDR_MAP - mapping of mdr elements and db, defaults to <dataElementGroup name="biobank">urn:mdr16:dataelementgroup:1:1</dataElementGroup><dataElementGroup name="collection">urn:mdr16:dataelementgroup:2:1</dataElementGroup><dataElementGroup name="sample">urn:mdr16:dataelementgroup:3:1</dataElementGroup><dataElementGroup name="sampleContext">urn:mdr16:dataelementgroup:4:1</dataElementGroup><dataElementGroup name="donor">urn:mdr16:dataelementgroup:5:1</dataElementGroup><dataElementGroup name="event">urn:mdr16:dataelementgroup:6:1</dataElementGroup>
• STORE_MDR_VALIDATION - validation against mdr during store import, defaults to true
• STORE_POSTGRES_HOST - the host name of the Postgres DB, defaults to store-db. Change only if built-in-databse is not used
• STORE_POSTGRES_PORT - the port of the Postgres DB, defaults to 5432. Change only if built-in-databse is not used
• STORE_POSTGRES_DB - the database name, defaults to samply.store
• STORE_POSTGRES_USER - the database username, defaults to samply
• STORE_POSTGRES_PASS - the database password, defaults to samply
• STORE_CATALINA_OPTS - JVM options for Tomcat, defaults to -Xmx1g

Connector specific (Optional)

• CONNECTOR_POSTGRES_HOST - the host name of the Postgres DB, defaults to connector-db. Change only if built-in-databse is not used
• CONNECTOR_POSTGRES_PORT - the port of the Postgres DB, defaults to 5432. Change only if built-in-databse is not used
• CONNECTOR_POSTGRES_DB - the database name, defaults to samply.connector. Change only if built-in-databse is not used
• CONNECTOR_POSTGRES_USER - the database username, defaults to samply
• CONNECTOR_POSTGRES_PASS - the database password, defaults to samply
• CONNECTOR_STORE_URL - the URL of the store to connect to, defaults to http://store:8080. Change only if built-in-store is not used
• CONNECTOR_CATALINA_OPTS - JVM options, defaults to -Xmx1g
• CONNECTOR_OPERATOR_FIRST_NAME - the IT staff which runs the connector
• CONNECTOR_OPERATOR_LAST_NAME - the IT staff which runs the connector
• CONNECTOR_OPERATOR_EMAIL - the IT staff which runs the connector
• CONNECTOR_OPERATOR_PHONE - the IT staff which runs the connector
• CONNECTOR_MAIL_HOST - mail host which is able to send mails, defaults to ``
• CONNECTOR_MAIL_PORT - port to mail host, defaults to ``
• CONNECTOR_MAIL_PROTOCOL - protocol for mail, defaults to ``
• CONNECTOR_MAIL_FROM_ADDRESS - mail address from which mails are sent, defaults to ``
• CONNECTOR_MAIL_FROM_NAME - subject of mails, defaults to ``

Common (Optional)

• MDR_URL - api-url of mdr host, defaults to http://mdr.germanbiobanknode.de/v3/api/mdr
• PROXY_URL - the URL of the HTTP proxy to use for outgoing connections, "url:port"; enables proxy usage if set
• PROXY_USER - the user of the proxy account (optional)
• PROXY_PASS - the password of the proxy account (optional)

Save your environments (Optional)

In the repo directory, create a file called .env, here you can save your environments if default values changed. Docker-Compose will find this file at startup.

.env example:

MDR_NAMESPACE=mdr17
MDR_URL=https://mdr.germanbiobanknode.de/v3/api/mdr

WINDOWS

Under construction!!! (Follow config.yml and Dockerfile)

• Install Tomcat 8.5

• Install Postgresql 9.6

  • Create databases: samply.store and samply.connector with user and password = samply

• Copy and edit configuration files (DOWNLOADLINK MISSING) to 'C:%username%.config\samply'

• Download and move WAR files to '%tomcat-dir%\webapps
  https://maven.samply.de/nexus/service/local/repositories/oss-releases/content/de/samply/store-rest/4.2.6/store-rest-4.2.6.war https://maven.samply.de/nexus/service/local/repositories/oss-releases/content/de/samply/share-client/3.0.7/share-client-3.0.7.war

LINUX

Under construction!!! (Follow config.yml and Dockerfile)

Description of running components

Store

You can access the Store under http://localhost:8081. A simple test is fetching the import XSD under: http://localhost:8081/importXSD.

Most work is to import patient/sample data into the store. You have to create a xml file which will be tested against our Metadata Repository. The current namespace where all data-elements are defined and all GBA-Components work with can be found under http://mdr.germanbiobanknode.de/view.xhtml?namespace=mdr16

Instructions for import can be found here

Connector

You can access the Connector under http://localhost:8082 and login to it under http://localhost:8082/login.xhtml The login credentials are admin, adminpass.

Add a Searchbroker to get and answer queries at http://localhost:8082/admin/broker_list.xhtml

• Broker Adresse = https://search.germanbiobanknode.de/broker/
• Ihre Email Adresse = your email address to get the API-Key for registration
• Automatisch antworten = Nur Anzahl (default, so you answer automatically with number of samples)

You will receive an email with API-Key from Searchbroker Backend, paste these eight numbers and press "ok". Call an ITC to validate your request.

Create a new user at http://localhost:8082/admin/user_list.xhtml

Logout and login as normal user to see all handled queries.

Grafana (Optional)

You can access Grafana under http://localhost:3000. The login credentials are admin, admin.

There are two dashboards available. One for the Store and one for the Connector. Currently, they only show JVM metrics.

• Store dashboard: http://localhost:3000/d/wEuwMIpmz
• Connector dashboard: http://localhost:3000/d/wEuwMIpmy