We run all our tests on every commit using the Continous Integration service Travis-CI. 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.
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 continous integration tests for examples of how this can be automated:
- config/travis/init.sh
- config/travis/run.sh
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
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
There are separate test projects for the main InterMine libraries: core objectstore code, the integration code and the web code. These are the packages/directories:
Run the tests by changing to the appropriate directory and running ant with no arguments. For example:
# in intermine/objectstore/test/
$ ant
In this initial setup you may see some Java Exceptions, for diagnosis of common errors see: CommonErrors
The HTML test report will be created in the build directory, eg. intermine/objectstore/test/build/test/results/index.html
We aim to keep the tests at a 100% pass rate at all times.
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 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
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 database tables automatically generated from the bio model by running the following in bio/test-all/dbmodel:
$ ant clean build-db
You can also run a test for an individual source by running the ant command with no arguments.
# in bio/sources/uniprot/test
$ ant
The test results will be located at uniprot/test/build/test/results/index.html. You can also run these as JUnit tests directly from Eclipse.
InterMine includes tests for running automated browser based user interface testing using Selenium. In particular the tests are meant to cover the main interface features of the generic web-application.
InterMine’s web applications tests are written in Python using unittest as the main test framework, selenium to interact with the Selenium webdriver and nose as a test runner.
The test suite can be found in the intermine/testmodel/webapp/selenium/ directory.
All tests run against a target which is the base URL of an InterMine instance.
# The base URL of the web application.
# Example: http://localhost:8080/intermine-demo
TESTMODEL_BASE
Credentials for a Gmail account are required to test OpenID authentication in account-login-openid-test.py:
# The username of a Gmail account
TESTMODEL_OPENID_NAME
# The password of a Gmail account
TESTMODEL_OPENID_PASSWORD
The tests are normally run as part of the CI test suite. They can also be run locally which is always a good idea when a new test is added or an existing test is modified.
To the run tests manually:
# in intermine/testmodel/webapp/selenium/
$ virtualenv venv
$ source venv/bin/activate
$ pip install -r requirements.txt
$ nosetests
Selenium offers a Firefox plugin called Selinium IDE that can be used to record a user’s actions in the browser and then generate Selenium code in a variety of languages. While you may need to write code for more complex scenarios, the plugin can be a fast way to generate most of the work.
Python based test scrips should be placed in intermine/testmodel/webapp/selenium/test/ and their filename should end with “[filename]-test.py”. Test scripts in this directory are automatically included when nosetests is executed or when continual integration takes place.