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Open Targets Genetics GraphQL API

This repo contains the application code for the GraphQL of Open Targets Genetics.

It is one component of several and the overarching project is described here, which is also where issues can be raised.

User guide

The API is a GraphQL implementation and can be queried at the following endpoint

The data used by the service is updated regularly; to see which version is currently in use you can use the following query in the browser linked to above:

query metadataQ {
  meta{
    dataVersion {
      major
      minor
      patch
    }
  }
}

The dataVersion can be typically interpreted as the major version being the year, the minor version the month, and the patch number indicating iterative releases. Older data can be found on the Genetics Portal's data mirror.

To set up developer environment

You can use an IDE such as IntelliJ IDEA, which is recommended, but it's also sufficient to have sbt installed.

Testing

Testing relies on external databases and Elasticsearch, if you only want to run the tests which can be run locally use the following sbt command: sbt testOnly * -- -l configuration.IntegrationTestTag . This excludes any test tagged as an integration test.

Connect to development databases

The current development database configuration contains the following nodes:

  • default: runs clickhouse and elasticsearch instances covering most queries

You can forward the needed ports to the remote databases defined in conf/application.conf.

gcloud --project=<gcloud-project> compute ssh <default> -- -L 8123:localhost:8123 -L 9200:localhost:9200

Run the API

Hit build within IntelliJ. Alternatively, start sbt in a terminal and use the run and test commands. If the build was successful, you should be able to view the running API at localhost:9000.

To deploy in production

You have to define production.conf file at the root of the project and it must contain at least these lines

include "application.conf"
# https://www.playframework.com/documentation/latest/Configuration
http.port = 8080
http.port = ${?PLAY_PORT}
play.http.secret.key = "changeme"
play.http.secret.key = ${?PLAY_SECRET}

# Root logger:
logger=ERROR
# Logger used by the framework:
logger.play=ERROR
# Logger provided to your application:
logger.application=INFO

slick.dbs {
  default {
    profile = "clickhouse.ClickHouseProfile$"
    db {
      driver = "ru.yandex.clickhouse.ClickHouseDriver"
      url = "jdbc:clickhouse://machine.internal:8123/ot"
      url = ${?SLICK_CLICKHOUSE_URL}
      numThreads = 4
      queueSize = 128
    }
  }
}

ot.elasticsearch {
  host = "machine.internal:8123"
  host = ${?ELASTICSEARCH_HOST}
  port = 9200
}

Docker

If using Docker set the following variables:

# env vars to pass to docker image or `-D`
# http.port=${?PLAY_PORT}
# play.http.secret.key=${?PLAY_SECRET}
# slick.dbs.default.db.url=${?SLICK_CLICKHOUSE_URL}
# ot.elasticsearch.host=${?ELASTICSEARCH_HOST}
# slick.dbs.default.db.url=${?SLICK_CLICKHOUSE_URL_SS}

Copyright

Copyright 2014-2018 Biogen, Celgene Corporation, EMBL - European Bioinformatics Institute, GlaxoSmithKline, Takeda Pharmaceutical Company and Wellcome Sanger Institute

This software was developed as part of the Open Targets project. For more information please see: http://www.opentargets.org

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.