fix nested CWL enum in array and single-value combined + CWL Workflow step output chaining with glob

[fmigneault]

Changes

• Remove attribute WpsProcessInterface.stage_output_id_nested and enforce the behavior of nesting output by ID under corresponding directories for all remote Process execution when resolving CWL Workflow steps. This ensures a more consistent file and directory resolution between steps of different nature (CWL, WPS, OGC based) using multiple combinations of glob patterns and expected media-types.

Fixes

• Fix CWL definitions combining nested enum types as ["null", <enum>, {type: array, items: <enum>] without an explicit name or SchemaDefRequirement causing failing schema_salad resolution under cwltool. A patch is applied for the moment to inject a temporary name to let the CWL engine succeed schema validation (relates to https://github.com/common-workflow-language/cwltool/issues/1908.

References

• Enum isssue relates to:
  • https://github.com/bird-house/finch/issues/301
  • https://github.com/bird-house/finch/issues/302

[fmigneault]

@perronld Assuming https://github.com/bird-house/finch/pull/302 is fixed (which I commented out duplicates in my local XML WPS definition to test), combined with this PR, your ensemble_grid_point_wetdays process should work 🤞

[codecov[bot]]

Codecov Report

Merging #566 (5f8962c) into master (f0abcd1) will increase coverage by 0.07%. The diff coverage is 91.11%.

@@            Coverage Diff             @@
##           master     #566      +/-   ##
==========================================
+ Coverage   84.47%   84.55%   +0.07%     
==========================================
  Files          79       79              
  Lines       17732    17788      +56     
  Branches     2688     2708      +20     
==========================================
+ Hits        14979    15040      +61     
+ Misses       2024     2020       -4     
+ Partials      729      728       -1     

Files Changed	Coverage Δ
weaver/processes/wps1_process.py	75.20% <ø> (+2.25%)	:arrow_up:
weaver/processes/wps_workflow.py	87.36% <83.33%> (-1.14%)	:arrow_down:
weaver/processes/wps_package.py	84.15% <88.88%> (+0.09%)	:arrow_up:
weaver/processes/convert.py	84.60% <93.02%> (+0.40%)	:arrow_up:
weaver/processes/wps_process_base.py	85.20% <100.00%> (+0.68%)	:arrow_up:
weaver/wps_restapi/swagger_definitions.py	99.82% <100.00%> (+<0.01%)	:arrow_up:

... and 1 file with indirect coverage changes