Version: Next

InterMine Tests

Continuous Integration#

We run all our tests on every commit using the Continuous Integration service Travis. You can do the same for your fork:

  • Log in to Travis-CI with your GitHub account.
  • Enable your fork of intermine for Travis builds.

All the tests will be run on every change you make, and you will be notified of errors by email.

Setting up a Local Test Environment#

After getting the source code for InterMine and ensuring you have all of the required prerequisites, the next step is to try the tests to confirm that everything runs well in your environment.

We also recommend looking at the files that run our continuous integration tests for examples of how this can be automated:

  • config/travis/init.sh
  • config/travis/run.sh

Running the core tests#

Create databases#

Create blank databases required by the tests named: unittest, truncunittest, fulldatatest, flatmodetest, notxmltest. See PostgresBasics and introduction to some Postgres commands.

$ for db in unittest truncunittest fulldatatest flatmodetest notxmltest; do createdb $db; done

Update properties file#

You need to set up a properties file to provide database details to the test code. In your home directory create a file called intermine-test.properties and update the server name, database names, and database username and password. You can use different database names as long as the actual database name used to create the database and the db.xxx.datasource.databaseName value match.

# super user
superuser.account=test
# common properties
os.query.max-time=10000000
os.query.max-limit=100000
os.query.max-offset=10000000
os.queue-len=100
# testing properties
db.notxmlunittest.datasource.serverName=localhost
db.notxmlunittest.datasource.databaseName=notxmltest
db.notxmlunittest.datasource.user=USERNAME
db.notxmlunittest.datasource.password=SECRET_PASSWORD
db.truncunittest.datasource.serverName=localhost
db.truncunittest.datasource.databaseName=truncunittest
db.truncunittest.datasource.user=USERNAME
db.truncunittest.datasource.password=SECRET_PASSWORD
db.flatmodeunittest.datasource.serverName=localhost
db.flatmodeunittest.datasource.databaseName=flatmodetest
db.flatmodeunittest.datasource.user=USERNAME
db.flatmodeunittest.datasource.password=SECRET_PASSWORD
db.fulldatatest.datasource.serverName=localhost
db.fulldatatest.datasource.databaseName=fulldatatest
db.fulldatatest.datasource.user=USERNAME
db.fulldatatest.datasource.password=SECRET_PASSWORD
db.userprofile-test.datasource.serverName=localhost
db.userprofile-test.datasource.databaseName=userprofile-test
db.userprofile-test.datasource.user=USERNAME
db.userprofile-test.datasource.password=SECRET_PASSWORD
db.unittest.datasource.serverName=localhost
db.unittest.datasource.databaseName=unittest
db.unittest.datasource.user=USERNAME
db.unittest.datasource.password=SECRET_PASSWORD

Run the tests#

# in intermine
$ ./gradlew test

View results#

The HTML test report will be created in the build directory, eg. intermine/objectstore/test/build/test/results/index.html

Pull requests are not accepted without passing tests, and we have Travis set up to run tests on every commit. We keep the tests at a 100% pass rate at all times.

Running the bio tests#

InterMine includes a bio project which contains specific code for biological data and parsers for many data formats. To run tests on this code you need to set up another properties file and create some more databases.

Create databases#

Create blank databases called bio-test and bio-fulldata-test(as above you can use different names as long as they match the db.xxx.datasource.databaseName values. For example:

$ createdb bio-test
$ createdb bio-fulldata-test

Update properties file#

Set up a properties file to provide database details to the test code. In .intermine create a file called intermine-bio-test.properties and configure the server name, database names, and database username and password.

os.default=os.production-client
# common properties
os.query.max-time=10000000
os.query.max-limit=100000
os.query.max-offset=10000000
os.queue-len=100
# testing properties
db.bio-fulldata-test.datasource.serverName=localhost
db.bio-fulldata-test.datasource.databaseName=bio-fulldata-test
db.bio-fulldata-test.datasource.user=USERNAME
db.bio-fulldata-test.datasource.password=SECRET_PASSWORD
db.bio-test.datasource.serverName=localhost
db.bio-test.datasource.databaseName=bio-test
db.bio-test.datasource.user=USERNAME
db.bio-test.datasource.password=SECRET_PASSWORD

Build the databases#

Build database tables automatically generated from the bio model by running the following in bio:

$ ./gradlew builddb

Run the tests#

Execute the tests, in bio run:

$ ./gradlew test

Run a single test#

You can also run a test for an individual source by using this syntax:

# in bio
$ ./gradlew bio-model:test

The test results will be located at bio/model/test/build/test/results/index.html. You can also run these as JUnit tests directly from Eclipse or Intellij.

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