[WX-1468] Implement `returnCodes` runtime attribute #7389

rsaperst · 2024-03-18T16:27:40Z

Implemented the returnCodes runtime attribute, which is new in WDL 1.1.

backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala

jgainerdewar · 2024-03-18T20:44:32Z

This is fantastic work! Which makes me feel terrible saying: I hadn't realized until reviewing the spec just now that the new returnCodes actually means exactly the same thing as the existing continueOnReturnCode, with the addition of *. Would it be possible to modify the existing continueOnReturnCode handling to include the runtime attribute returnCodes rather than creating a parallel method for controlling the same thing?

…nd more testing

rsaperst · 2024-03-21T13:53:17Z

This is fantastic work! Which makes me feel terrible saying: I hadn't realized until reviewing the spec just now that the new returnCodes actually means exactly the same thing as the existing continueOnReturnCode, with the addition of *. Would it be possible to modify the existing continueOnReturnCode handling to include the runtime attribute returnCodes rather than creating a parallel method for controlling the same thing?

I abstracted out the duplicated code between returnCodes and continueOnReturnCode to a new trait ReturnCode (which is very creatively named :) ). I think this is the best solution to avoid code duplication while also supporting both returnCodes and continueOnReturnCode`, but let me know if there is anything else I should modify to decrease parallelism.

jgainerdewar

This is a big improvement, but I think we can go even farther in collapsing these two concepts.

jgainerdewar · 2024-03-22T17:50:07Z

backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala

+   * `continueOnReturnCode` will be used.
+   */
+  lazy val returnCode: ReturnCode =
+    if (returnCodes.isInstanceOf[ReturnCodeSet] && returnCodes.equals(ReturnCodeSet(Set(0)))) continueOnReturnCode


It looks like this is checking whether we have the default value for returnCodes and falling back to continueOnReturnCode if we do. What if someone included the default value in their WDL? Can we insert the default after we choose which attribute to use?

If not, we could build the default check into ReturnCode, so we can call something like returnCodes.isDefault?

Also, just for fun, a more idiomatic Scala way to write this is:

returnCodes match { case ReturnCodeSet(Set(0)) => continueOnReturnCode case _ => returnCodes }

jgainerdewar · 2024-03-22T17:52:59Z

backend/src/main/scala/cromwell/backend/validation/ReturnCode.scala

+   * @param returnCode Return code from the process / script.
+   * @return True if the call is a success.
+   */
+  override def continueFor(returnCode: Int): Boolean = super.continueFor(returnCode)


This method looks like a no-op, since it overrides the super method and then calls it.

jgainerdewar · 2024-03-22T18:31:33Z

backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCodeValidation.scala

    instance.withDefault(configDefaultWdlValue(runtimeConfig) getOrElse WomInteger(0))
  def configDefaultWdlValue(runtimeConfig: Option[Config]): Option[WomValue] =
    instance.configDefaultWomValue(runtimeConfig)
 }

-class ContinueOnReturnCodeValidation extends RuntimeAttributesValidation[ContinueOnReturnCode] {
+class ContinueOnReturnCodeValidation extends ReturnCodeValidation {


I would love to see if we can collapse all the return code stuff into this validation, and have this be the last thing in the code path that's aware of the two different attributes. We could even continue calling it ContinueOnReturnCode to minimize the diff. This validation can look at both keys and make a decision about what ContinueOnReturnCode object to build. We can turn the * into a ContinueOnReturnCodeFlag(true), which seems to have the same meaning.

rsaperst · 2024-03-29T20:23:55Z

This is a big improvement, but I think we can go even farther in collapsing these two concepts.

I believe that all of the comments here should be addressed in my most recent refactor which groups continueOnReturnCode and returnCodes together as much as I think they can be, let me know if there's any better way that I can refactor or improve the PR!

jgainerdewar

Love that this is mostly test changes at this point! Very nice!

jgainerdewar · 2024-04-01T13:26:53Z

.github/workflows/integration_tests.yml

@@ -96,6 +96,14 @@ jobs:
    - uses: ./.github/set_up_cromwell_action #This github action will set up git-secrets, caching, java, and sbt.
      with:
        cromwell_repo_token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
+    # If a build step fails, activate SSH and idle for 30 minutes.
+    - name: Setup tmate session


Should we take this out before merging, or is it meant to be permanent?

Yes, this will be removed before merging (its still in for debugging right now)

backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala

backend/src/main/scala/cromwell/backend/validation/TwoKeyRuntimeAttributesValidation.scala

backend/src/main/scala/cromwell/backend/validation/ValidatedRuntimeAttributesBuilder.scala

backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala

centaur/src/main/resources/standardTestCases/failing_return_code.test

backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCodeValidation.scala

...eturn_codes_and_continue_on_return_code/invalid_return_codes_and_continue_on_return_code.wdl

aednichols

I really like the new direction. Always worth it to put in extra effort to get less code.

I do have one comment about reducing duplication (ironic, I know, in light of the biscayne vs. cascades thing...) but this looks good and very close!

wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala

jgainerdewar

This is shaping up really well! I think getFinalRuntimeAttributes could use a pass of Scala-ification, I left a few comments but probably a good topic for mob time tomorrow.

wom/src/main/scala/wom/RuntimeAttributes.scala

wdl/transforms/biscayne/src/main/scala/wdl/transforms/biscayne/wdlom2wom/package.scala

Ryan Saperstein and others added 6 commits March 18, 2024 12:21

Implement returnCodes runtime attribute

6e8399b

scalafmt

a183b05

Renamed returnCodes directory to return_codes

d106db0

Fixed failing unit test

f3f9972

Merge branch 'develop' into wx1468

5f0e393

Fixed failing unit test

4f1cadb

jgainerdewar reviewed Mar 18, 2024

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backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala Outdated Show resolved Hide resolved

Ryan Saperstein and others added 2 commits March 21, 2024 09:47

Abstracted duplicated code for returnCodes and continueOnReturnCode a…

d830f48

…nd more testing

Merge branch 'develop' into wx1468

5427d6c

rsaperst marked this pull request as ready for review March 21, 2024 13:48

rsaperst requested a review from a team as a code owner March 21, 2024 13:48

Ryan Saperstein and others added 4 commits March 21, 2024 09:57

scalafmt

2c4d8b3

Added comment

8e1f888

Added step to SSH into VM running integration tests

f2b548c

Comment change to re-run tests

b731aec

jgainerdewar reviewed Mar 22, 2024

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Ryan Saperstein and others added 2 commits March 29, 2024 16:21

Refactored to reduce code duplication

23c6c07

Merge branch 'develop' into wx1468

113b0d4

jgainerdewar reviewed Apr 1, 2024

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Ryan Saperstein added 6 commits April 1, 2024 14:54

Fixed failing tests + more refactoring

1e689fe

Hopefully fixed failing tests

4ca9ca5

Refactor

3f96f9d

Cleanup

021a42e

scalafmt

dba7c9e

Fixed failing tests

461525c

jgainerdewar reviewed Apr 8, 2024

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backend/src/main/scala/cromwell/backend/validation/ContinueOnReturnCodeValidation.scala Outdated Show resolved Hide resolved

...eturn_codes_and_continue_on_return_code/invalid_return_codes_and_continue_on_return_code.wdl Outdated Show resolved Hide resolved

Refactor and fix failing tests

30a1262

Ryan Saperstein and others added 2 commits April 8, 2024 13:42

Optimize imports

58eb36d

Merge branch 'develop' into wx1468

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aednichols reviewed Apr 9, 2024

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wdl/transforms/cascades/src/main/scala/wdl/transforms/cascades/wdlom2wom/package.scala Show resolved Hide resolved

Refactored to reduce code duplication

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jgainerdewar reviewed Apr 10, 2024

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Ryan Saperstein and others added 3 commits April 10, 2024 16:33

Added comments and 'scala-ified' code

27079d7

Fixed failing tests

1091067

Merge branch 'develop' into wx1468

5f16cf1

jgainerdewar approved these changes Apr 11, 2024

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aednichols approved these changes Apr 11, 2024

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Added additional tests

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rsaperst merged commit 3cf06bf into develop Apr 11, 2024
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rsaperst deleted the wx1468 branch April 11, 2024 15:34

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[WX-1468] Implement `returnCodes` runtime attribute #7389

[WX-1468] Implement `returnCodes` runtime attribute #7389

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[WX-1468] Implement returnCodes runtime attribute #7389

[WX-1468] Implement returnCodes runtime attribute #7389

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[WX-1468] Implement `returnCodes` runtime attribute #7389

[WX-1468] Implement `returnCodes` runtime attribute #7389