Validate WDL dir contents in tests

[sckott]

So there's some expectations that we have of contents in each WDL dir (what others call unit tests) that are not checked right now in code, but should be:

• validate that the .wdl file in the dir has the same exact name as the dir name
• inputs.json and options.json: we look for these, but at least in 1 case, there was an inputs file that was a different name and so we just silently didn't load it, leading to confusion. probably warn if there's some other files (json or otherwise) so the program doesn't stop but there's a warning at least - or maybe error since a warning could be missed?
• validate that if there's an inputs.json file there's only 1, same for options.json
• anything else?

[tefirman]

Love this idea. And I'm assuming we would want all of the other GitHub actions to "depend" on this one? i.e. they will only run if this check completes successfully first?

Might also want to check for the data subdirectory in case each test needs example data (see arrayOperations)

One other thing we might eventually want to check for is a "cromwell.conf" configuration file, but not now.

[sitapriyamoorthi]

Maybe relevant but from what I know about womtools it only accepts 1 JSON file so if there are workflows that have two input jsons (for example sometime one may write a json that specifes parameters as a separate json) both of those wont be parsed and the validate will fail.

[sckott]

@tefirman

And I'm assuming we would want all of the other GitHub actions to "depend" on this one?

No, I'm not proposing a new gh action file. The logic would be in python code for both the api and java classes https://github.com/FredHutch/wdl-unit-tests/blob/main/tests/cromwellapi/cromwell.py and https://github.com/FredHutch/wdl-unit-tests/blob/main/tests/cromwelljava/utils.py

[sckott]

thanks @sitapriyamoorthi

the way the Womtool class works in https://github.com/FredHutch/wdl-unit-tests/blob/main/tests/cromwelljava/utils.py is it look for a file called inputs.json and only uses that as input in addition to the wdl file, so any additional files would be ignored. this does mean (just as for the CromwellJava class) that we need to check that files names are in the accepted set - which we'll do as discussed here