Closed enoriega closed 3 years ago
Let me know if you need to have bioresources republished with an updated version number.
@kwalcock, Please do update the version number to 1.1.37 and republish it. Thanks!
Do the kb/ner files need to be regenerated because of this PR?
No, I already regenerated them and pushed them along the latest commit this morning
With the current bioresources master branch and testing with either master or issue722 from reach, there seem to be errors:
[info] TestNERLabeling:
[info] apoptosis, autophagic cell death, quiescence, hematopoiesis, or complex assembly cause cancer.
[info] - should have BioProcess label (56 milliseconds)
[info] MPanc-96, mast, Hyssop, CEM/TART, and ZR75-1 cause cancer.
[info] - should have CellLine label (52 milliseconds)
[info] apud cell, AV nodal myocyte, An1 B Cell, xanthoblast, and zygote cause cancer
[info] - should have CellType label *** FAILED *** (99 milliseconds)
[info] Vector(org.clulab.reach.mentions.CorefTextBoundMention@23b5ee8e, org.clulab.reach.mentions.CorefTextBoundMention@6fedde8e, org.clulab.reach.mentions.CorefTextBoundMention@c710390, org.clulab.reach.mentions.CorefTextBoundMention@ffd18082) had size 4 instead of expected size 5 (TestNERLabeling.scala:56)
[info] apud cells, AV nodal myocytes, An1 B Cells, xanthoblasts, and zygotes cause cancer
[info] - should have CellType label *** FAILED *** (62 milliseconds)
[info] Vector(org.clulab.reach.mentions.CorefTextBoundMention@87cd63e6, org.clulab.reach.mentions.CorefTextBoundMention@567186bc, org.clulab.reach.mentions.CorefTextBoundMention@fad155e, org.clulab.reach.mentions.CorefTextBoundMention@36751ec) had size 4 instead of expected size 5 (TestNERLabeling.scala:64)
[info] TestReachContextKBLister:
[info] Context KBs list
[info] - should have at least 1000 entries (0 milliseconds)
[info] Context KBs list
[info] - should have cell line entries (28 milliseconds)
[info] Context KBs list
[info] - should have cell type entries *** FAILED *** (12 milliseconds)
[info] 26 was not equal to 22 (TestReachContextKBLister.scala:38)
[info] TestNERStopList:
[info] org.clulab.reach.TestNERStopList *** ABORTED *** (0 milliseconds)
[info] Duplicate test name: fig should not have a mention (TestNERStopList.scala:18)
[info] *** 1 SUITE ABORTED ***
[info] *** 3 TESTS FAILED ***
[error] Failed tests:
[error] org.clulab.reach.TestNERLabeling
[error] org.clulab.reach.TestReachContextKBLister
[error] Error during tests:
[error] org.clulab.reach.TestNERStopList
[error] (main / Test / test) sbt.TestsFailedException: Tests unsuccessful
[error] Total time: 349 s (05:49), completed Jan 18, 2021 11:44:10 AM
The 'main/test' suite failed!
The errors might be related to the resource file updates in https://github.com/clulab/bioresources/pull/54, I can look into it this afternoon.
At least one error was introduced accidentally by me. I fixed bioresources and the TestNERStopList
suite shouldn't crash anymore
I examined TestReachContextKBLister
which is a set of tests looking at the content of resource files directly. The counts should be updated as follows to be consistent with https://github.com/clulab/bioresources/pull/54:
(ctypes.count(cg => hasText(cg, "granulocyte"))) should be (26)
(ctypes.count(cg => hasId(cg, "CL:0000557"))) should be (14)
(ctypes.count(cg => hasText(cg, "hair"))) should be (54)
Hope I didn't miscount! I'll look at TestNERLabeling
next.
I looked into
[info] apud cell, AV nodal myocyte, An1 B Cell, xanthoblast, and zygote cause cancer
[info] - should have CellType label *** FAILED *** (99 milliseconds)
[info] Vector(org.clulab.reach.mentions.CorefTextBoundMention@23b5ee8e, org.clulab.reach.mentions.CorefTextBoundMention@6fedde8e, org.clulab.reach.mentions.CorefTextBoundMention@c710390, org.clulab.reach.mentions.CorefTextBoundMention@ffd18082) had size 4 instead of expected size 5 (TestNERLabeling.scala:56)
[info] apud cells, AV nodal myocytes, An1 B Cells, xanthoblasts, and zygotes cause cancer
[info] - should have CellType label *** FAILED *** (62 milliseconds)
[info] Vector(org.clulab.reach.mentions.CorefTextBoundMention@87cd63e6, org.clulab.reach.mentions.CorefTextBoundMention@567186bc, org.clulab.reach.mentions.CorefTextBoundMention@fad155e, org.clulab.reach.mentions.CorefTextBoundMention@36751ec) had size 4 instead of expected size 5 (TestNERLabeling.scala:64)
These happen because zygote
was removed from the Cell Ontology, so I updated to test to use zygospore
instead. I pushed both changes to the PR branch.
Thanks! I'll be looking carefully tomorrow.
Thank you @bgyori !
After @bgyori's changes, all tests pass in this branch.
Thanks, @enoriega. I'll verify and then it sounds like it will help to publish bioresources so that a localPublish of that is not necessary for reach. Then the dependency in reach can be updated and merged with master. Is that right?
That's correct, @kwalcock. Thanks!
Thanks @kwalcock
Before moving approving, what should we do about the bioresources version number?