test --tests doesn't work properly after barclay update

[lbergelson]

Bug Report

Affected tool(s)

running tests manually on the command line

Affected version(s)

• [ x ] Latest public release version [version?]
• [ x ] Latest development/master branch as of [date of test?]

Description

Running

./gradlew tests --tests "*<SomeTestClass>*"

or

./gradlew tests -Dtest.single=<SomeTestClass>

should restrict the tests to only run the test class you explicitly asked for.

Since the barclay introduction it runs all the tests and then the one you asked for. This seems to be because the new gradle test task depends on the barclayTest task. So it first executes that task which runs all the tests and then runs your restricted test set after that.

The workaround is to run ./gradlew legacyTest --tests "*<SomeTestClass>*" which will only run one set of tests.

I would have expected that the --tests and -Dtest.single parameters are propagated to all tasks of type test, so I'm not sure why they're not being respected by barclayTest when run as a prerequisite for test

Seems like we need to dive into the gradle and figure out what's going on. In the meantime, use the barclayTest and legacyTest tasks instead of test when invoking on the command line.

[lbergelson]

@eitanbanks Here's the ticket for what we were talking about yesterday.

[kbergin]

It seems this has been addressed via #984

[cmnbroad]

@kbergin I assume you meant to refer to samtools/htsjdk#984, which is an htsjdk issue that has a similar manifestation but a different cause. AFAIK this issue still exists in Picard, although it is a duplicate of #1211. Finally, note that these issues would be eliminated if we moved forward with #1120.