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kubernetes job owner name #2872

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merged 5 commits into from
Dec 6, 2019
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jeffrey856
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Added env var TOIL_KUBERNETES_OWNER to help identify different users kube jobs.

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@adamnovak adamnovak left a comment

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This is pretty much exactly what I want.

We're relying on the user not to give us a too-long/uppercase/otherwise prohibited TOIL_KUBERNETES_OWNER, but I think that's fine.

I'm going to slightly tweak the documentation, though.

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The Python 2 integration tests are failing with this:

_____ AWSJobStoreTest.test_testImportSharedFile__otherCls_filejobstoretest _____
Traceback (most recent call last):
  File "/builds/databiosphere/toil/src/toil/test/jobStores/jobStoreTest.py", line 124, in setUp
    self.jobstore_initialized.initialize(self.config)
  File "/builds/databiosphere/toil/src/toil/jobStores/aws/jobStore.py", line 148, in initialize
    super(AWSJobStore, self).initialize(config)
  File "/builds/databiosphere/toil/src/toil/jobStores/abstractJobStore.py", line 146, in initialize
    self.writeConfig()
  File "/builds/databiosphere/toil/src/toil/jobStores/abstractJobStore.py", line 154, in writeConfig
    pickle.dump(self.__config, fileHandle, pickle.HIGHEST_PROTOCOL)
  File "/usr/lib/python2.7/contextlib.py", line 24, in __exit__
    self.gen.next()
  File "/builds/databiosphere/toil/src/toil/jobStores/aws/jobStore.py", line 552, in writeSharedFileStream
    yield writable
  File "/usr/lib/python2.7/contextlib.py", line 24, in __exit__
    self.gen.next()
  File "/builds/databiosphere/toil/src/toil/jobStores/aws/jobStore.py", line 1122, in uploadStream
    assert bool(self.version) == (self.content is None)
AssertionError

This is the same problem as observed in #2869; I think there's a problem with that test now. Maybe Amazon changed something? I'll open an issue.

@adamnovak adamnovak force-pushed the issues/2865-kubernetes-owner-name branch from ac915b2 to 7b825d8 Compare December 5, 2019 23:55
@adamnovak adamnovak merged commit 5145330 into master Dec 6, 2019
DailyDreaming pushed a commit that referenced this pull request Feb 12, 2020
* brought provider scope to module level

* Added env var to name kube job

* Revert "brought provider scope to module level"

This reverts commit 5dd0d24.

* added is not

* Revise variable description.
DailyDreaming pushed a commit that referenced this pull request Feb 13, 2020
* brought provider scope to module level

* Added env var to name kube job

* Revert "brought provider scope to module level"

This reverts commit 5dd0d24.

* added is not

* Revise variable description.
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3 participants