The Centaur repository is now under the Cromwell repository. Click here for Centaur within Cromwell.
For information about how to use Centaur, see the Cromwell documentation.
Centaur is an integration testing suite for the Cromwell execution server. It's purpose is to exercise the functionality of a specific deployment of Cromwell, to ensure that it is functioning properly 'in the wild'.
Centaur expects to find a Cromwell server properly configured and running in server mode, listening on port 8000. This can be configured by modifying the cromwellUrl parameter in application.conf.
There are two ways to invoke the intergration tests:
sbt test- compiles and run via sbt directly, simple but also has the problem of running 2*cores tests in parallel which can overwhelm your Cromwell server if running in a development environmentrun_tests_parallel.sh [THREADS]- runs the same tests with an enforced parallelism limit. Defaults to3if not specified
All tests are tagged with their name and their TESTFORMAT, and also any custom tags specified in the .test file.
Tag names are all lower case, so a test named "tagFoo" has a tag "tagfoo".
To run only those tests which have been tagged with a specified tag tagFoo:
sbt "testOnly * -- -n tagfoo"
Or to instead exclude all tests which have been tagged with a specified tag tagFoo:
sbt "testOnly * -- -l tagfoo"
You can add your own tests to the test suite by adding -Dcentaur.optionalTestPath=DIR on your sbt invocation,
e.g. sbt -Dcentaur.optionalTestPath=/some/path/to/tests test. The value of DIR is expected to be a directory
which contains one or more test case files.
The same result can be achieved more permanently by adding the custom directory into the application.conf file directly:
centaur {
optionalTestPath = "/some/path/to/tests"
}
Each test case file is a HOCON file with the following structure:
name: NAME // Required: Name of the test
testFormat: TESTFORMAT // Required: One of WorkflowSuccessTest, WorkflowFailureTest
backends: [BACKENDNAME1, BACKENDNAME2, ...] // Optional list of backends. If supplied, this test will be ignored if these backends are not supported by the Cromwell server
basePath: /an/optional/field // Optional, location for the files {} entries to be found relative to
tags: [ "any", "custom", "tags" ] // Optional, a set of custom tags to apply to this test
ignore: false // Optional, whether centaur will ignore this test when running
files {
wdl: path/to/wdl // Required: path to the WDL file to submit
inputs: optional/path/to/inputs // Optional, a path to an inputs JSON to include in the submission
options: optional/path/to/options // Optional, a path to an options JSON to include in the submission
}
// Optional, some metadata to verify on workflow completion:
metadata {
fully.qualified.key.name1: VALUE1
fully.qualified.key.name2: VALUE2
}
The tags are optional. If supplied they will allow people to turn on or off this test case by including or excluding tags when running (see above).
The basePath field is optional, but if supplied all paths will be resolved from that directory. If it is not supplied, all paths will be resolved from the directory the test case file is in.
The testFormat field can be one of the following, case insensitive:
workflowsuccess: The workflow being supplied is expected to successfully completeworkflowfailure: The workflow being supplied is expected to fail
The metadata is optional. If supplied, Centaur will retrieve the metadata from the successfully completed workflow and compare the values retrieved to those supplied. At the moment the only fields supported are strings, numbers and booleans.
For any metadata values which require workflow ID (i.e, file paths), use <<UUID>> as a placeholder instead. For example:
- "calls.hello.hello.stdout": "gs://google-project/jes/root/wdl/<<UUID>>/call-task/task-stdout.log"
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