Resource requirement min max validation

[Stellatsuu]

Related to : common-workflow-language/cwltool#2163

• Added a minmax check in save() function of ResourceRequirement
• Added tests related to save() function of ResourceRequirement
• Added a minmax check in fromDoc() function of ResourceRequirement. I couldn't understand how to test the fromDoc() function though so tests are missing for this one. Any explanations or tips would be appreciated on that so I can add some.

[mr-c]

Thank you for prototyping the validation. This file is autogenerated, so any changes here would get overwritten.

https://github.com/common-workflow-language/cwl-utils/blob/4a8390d897913c3776a0d2b2a01e1e6134b968bc/cwl_utils/parser/cwl_v1_2.py#L2

cwl-utils/Makefile

Lines 191 to 209 in 4a8390d

	cwl_utils/parser/cwl_v1_0.py: FORCE
	schema-salad-tool --codegen python \
	--codegen-parser-info "org.w3id.cwl.v1_0" \
	https://github.com/common-workflow-language/common-workflow-language/raw/codegen/v1.0/extensions.yml \
	> $@
	cwl_utils/parser/cwl_v1_1.py: FORCE
	schema-salad-tool --codegen python \
	--codegen-parser-info "org.w3id.cwl.v1_1" \
	https://github.com/common-workflow-language/cwl-v1.1/raw/codegen/extensions.yml \
	> $@
	cwl_utils/parser/cwl_v1_2.py: FORCE
	schema-salad-tool --codegen python \
	--codegen-parser-info "org.w3id.cwl.v1_2" \
	https://github.com/common-workflow-language/cwl-v1.2/raw/codegen/extensions.yml \
	> $@
	regen_parsers: cwl_utils/parser/cwl_v1_*.py

Additional validation logic should be added elsewhere, perhaps cwl_utils/parser/utils.py

[Stellatsuu]

Oh, my bad on that! I didn't see it was autogenerated, those comments were hidden on my IDE.
I will look to add this validation in cwltool only then, since you mentioned that there isn't much validation code to add in cwl-utils 🙂

[aldbr]

Is there any documentation to onboard developers?
I am also trying to understand the workflow to see where we should add that piece of logic. From what I understand:

• You define the CWL specifications in these repos: cwl 1.3, cwl 1.2, ...
• You are using schema_salad to convert the CWL specifications into python code in cwl-utils
• So cwl-utils is the repository we should use to manipulate CWL workflows in Python
• And then on top of that there is cwltool, used for the execution of CWL workflows

IIUC, checks should generally be included in the CWL specifications in JSON/YAML; But the structure would not enable the comparison of 2 attributes like minCores and maxCores for instance.
So this would need to be added in the cwl_utils/parser/utils.py module.

From here - and if my understanding has been correct so far - I am a bit confused. I don't see where these functions are used. They don't seem to appear in the generated parser files, and in cwltool I see functions with the same names but they are redefined. Example:

• cwl-utils/cwl_utils/parser/utils.py

  Line 35 in 4a8390d

  def convert_stdstreams_to_files(process: Process) -> None:

• cwl-utils/cwl_utils/parser/cwl_v1_2_utils.py

  Line 358 in 4a8390d

  def convert_stdstreams_to_files(clt: cwl.CommandLineTool) -> None:

• https://github.com/common-workflow-language/cwltool/blob/135a0c67afd67383c44e89fba136ccd9ce6afb1f/cwltool/load_tool.py#L144

Ideally I think we would love to have this min-max validation when we call load_document.

Thank you very much for you guidance

[codecov]

Codecov Report

❌ Patch coverage is 43.75000% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 34.70%. Comparing base (4a8390d) to head (18635e6).

Files with missing lines	Patch %	Lines
cwl_utils/parser/cwl_v1_2.py	43.75%	4 Missing and 5 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #384      +/-   ##
==========================================
+ Coverage   34.63%   34.70%   +0.07%     
==========================================
  Files          30       30              
  Lines       35396    35412      +16     
  Branches     9538     9546       +8     
==========================================
+ Hits        12259    12290      +31     
+ Misses      20257    20234      -23     
- Partials     2880     2888       +8     

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