fix: Support unquoted int exit code

[adamnovak]

Issue #, if available: #314

Description of Changes

This adds some custom unmarshalling logic to the Log object that should let it support both quoted and unquoted integral exit codes in JSON input.

Description of how you validated changes

I haven't validated my changes yet.

Checklist

• If this change would make any existing documentation invalid, I have included those updates within this PR
• I have added unit tests that prove my fix is effective or that my feature works
• I have linted my code before raising the PR
• Title of this Pull Request follows Conventional Commits standard: https://www.conventionalcommits.org/en/v1.0.0/

---

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache-2.0 license

[adamnovak]

@nbraid, I'm going to fix #314 so I can use unmodified Toil with AGC.

Do you have any idea what's breaking the linter here? It seems like it can't even run.

[nbraid]

It looks like there's a difference in the go.mod file? I'm not sure what could be causing that if you haven't modified the go.mod file.

Run git diff --exit-code
diff --git a/packages/cli/go.mod b/packages/cli/go.mod
index bf3f117..99df139 100644
--- a/packages/cli/go.mod
+++ b/packages/cli/go.mod
@@ -35,7 +35,7 @@ require (
 	github.com/stretchr/testify v1.7.0
 	github.com/xeipuuv/gojsonschema v1.2.0
 	golang.org/x/net v0.0.0-20211015210444-4f30a5c0130f
-	golang.org/x/tools v0.1.9 // indirect
+	golang.org/x/tools v0.1.10 // indirect
 	gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 // indirect
 	gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b
 )

[nbraid]

Sounds like this is because we run go mod vendor in the check, which will update to the latest version. You might need to run go mod vendor from the package/cli directory so your commit matches what our built version will download.

[adamnovak]

When I check this out and run go mod vendor in packages/cli, it makes no changes to go.mod in that directory. Running make doesn't make any changes either.

I manually bumped the tools version; maybe that will help?

[adamnovak]

I've pulled the Makefile down into the included WES client module, and given its test and formatting steps (which is why I'm reformatting all its files).

And I added some unit tests for deserializing example log objects of the different shapes we want to support.

So I think this is now ready for review! Hopefully CI likes it.

[adamnovak]

@nbraid This now has tests and passes CI.

[elliot-smith]

Hi Adam,
We currently have a PR that is about to be raised that reverts the exit code back to an integer (including updating the relevant AGC code) which I believe will suit your use case better. Are you okay if we merge that change in over this change? It should be raised within the next couple of days.

[adamnovak]

@elliot-smith That should be fine for us; Toil always sends an integer.

[elliot-smith]

Closing this PR in favor of this one (as discussed above): #380