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Open Targets Platform API BETA (experimental)

Experimental GraphQL API.

Requirement

SBT (Scala) Java 1.8 or later Play Framework

ES server: 7.2 Eg. localhost:9200 (tunnelling or locally installed)

How to use

Sangria caches

This application uses Sangria as a GraphQL wrapper and uses deferred resolver caches to improve query times. In cases where the data is updated in Elasticsearch it will not be available on the front-end if it has previously been cached.

To reset the cache following a data update use the following request:

curl --location --request GET 'http://localhost:9000/api/v4/rest/cache/clear' \
--header 'apikey: <very secret code>'

Logging

Logging to local use / development can be configured by updating the logback.xml file in the conf directory.

Production deployments use the production.xml file to configure loggging. These should be set conservatively because GCP charges based on the quantity of logs, so we only want to produce what we need for monitoring, basic trouble-shooting.

Testing

Tests annoted with IntegrationTestTag require there to be access to a configured ElasticSearch instance against which to run the queries.

Testing GraphQL queries

The Open Targets Platform front end makes use of pre-written GraphQL queries. Since we want to be aware if changes in the API are likely to break the FE, we have integration tests in place to check if this is going to happen.

Note, make sure you have access to ElasticSearch on a configured port!

gcloud beta compute ssh --zone "europe-west1-d" [some es instance] --tunnel-through-iap -- -L 9200:localhost:9200
  1. Get the files: run sbt updateGqlFiles to retrieve all '*.gql' files from the front-end repository and copy them to the test/resources/gqlQueries directory and prints output regarding which files are new / changed.
  2. Run tests sbt testOnly controllers.GqlTest

Maintaining up to date

Since the FE and BE are developed independently, it's worth checking what has changed since we last tested. Before testing run sbt updateGqlFiles. This will print which files are new or updated.

If there are updated files, run git diff test/resources/gqlQueries to see if any previously configured tests require updating (mainly if the input parameters change. If there are new files new tests will need to be added.

Adding new tests and inputs

If the above step shows that there are more files to add, create a new test for them using an existing one as a template. For example:

"Cancer gene census queries" must {
  "return a valid response" in {
    testQueryAgainstGqlEndpoint(TargetDiseaseSize("CancerGeneCensus_sectionQuery"))
  }
}

Take note of the following:

  • 'CancerGeneCensus_sectionQuery' is the name of the file, this will be used to read in the actual query.
  • TargetDiseaseSize is a case class which extends GqlCase. You choose the relevant case class based on which inputs are required by the file you are adding. Looking at the 'CancerGeneCensus_sectionQuery' query, we see that it takes three parameters, target, disease and size:
query CancerGeneCensusQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
  disease(efoId: $efoId) {
    id
    evidences(
      ensemblIds: [$ensemblId]
  • It just so happens that TargetDiseaseSize will generate inputs that satisfy this requirement. To see what else is available consider other case classes which extend GqlCase.
Adding new inputs
  • The GraphQL test are using generators to create inputs for the queries. The generators themselves are defined in GqlItTestInputs.scala and read from files in /test/resources/gqpInputs.
  • The starting point for the input lists were those used by Checkomatic to identify useful targets and diseases to test against. To add more inputs add them to the resource files.

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.