test case for python api subworkflow support

workflows/bbbc_sub.py

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+from pathlib import Path
+
+from wic import plugins
+from wic.api import pythonapi
+from wic.api.pythonapi import Step, Workflow
+
+def workflow() -> Workflow:
+    bbbcdownload = Step(clt_path='cwl_adapters/bbbcdownload.cwl')
+    # NOTE: object fields monkey patched at runtime from *.cwl file
+    bbbcdownload.name = 'BBBC001'
+    bbbcdownload.outDir = Path('bbbcdownload.outDir')
+
+    subdirectory = Step(clt_path='../workflow-inference-compiler/cwl_adapters/subdirectory.cwl')
+    subdirectory.directory = bbbcdownload.outDir
+    subdirectory.glob_pattern = 'bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/'
+    subdirectory.subdirectory = Path('subdirectory.subdirectory')
+
+    filerenaming = Step(clt_path='cwl_adapters/file-renaming.cwl')
+    # NOTE: FilePattern {} syntax shadows python f-string {} syntax
+    filerenaming.filePattern = '.*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif'
+    filerenaming.inpDir = subdirectory.subdirectory
+    filerenaming.outDir = Path('file-renaming.outDir')
+    filerenaming.outFilePattern = 'x{row:dd}_y{col:dd}_p{f:dd}_c{channel:d}.tif'
+
+    # Trivially wrap the subdirectory step in a subworkflow.
+    # But notice that we are still linking the individual Steps above,
+    # which defeats the whole purpose of having reusable black boxes.
+    steps = [bbbcdownload,
+             Workflow([subdirectory], 'bbbc_sub_sub_py'),
+             filerenaming]
+    filename = 'bbbc_sub_py'  # .yml
+    return Workflow(steps, filename)
+
+
+def workflow2() -> Workflow:
+    bbbcdownload = Step(clt_path='cwl_adapters/bbbcdownload.cwl')
+    # NOTE: object fields monkey patched at runtime from *.cwl file
+    bbbcdownload.name = 'BBBC001'
+    bbbcdownload.outDir = Path('bbbcdownload.outDir')
+
+    subdirectory = Step(clt_path='../workflow-inference-compiler/cwl_adapters/subdirectory.cwl')
+    subworkflow = Workflow([subdirectory], 'bbbc_sub_sub_py')  # fails validation, due to
+    # https://workflow-inference-compiler.readthedocs.io/en/latest/dev/algorithms.html#deferred-satisfaction
+
+    # First link all inputs within the subworkflow to the explicit inputs: tag.
+    # i.e. This is the API for the subworkflow.
+    subworkflow.steps[0].directory = subworkflow.directory
+    subworkflow.steps[0].glob_pattern = subworkflow.glob_pattern
+    subworkflow.steps[0].subdirectory = Path('subdirectory.subdirectory')
+
+    # Then apply arguments at the call site.
+    # Notice how the caller does not need to know about the internal details of the subworkflow
+    # (For example, that the subdirectory step is index 0)
+    subworkflow.directory = bbbcdownload.outDir
+    subworkflow.glob_pattern = 'bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/'
+
+    filerenaming = Step(clt_path='cwl_adapters/file-renaming.cwl')
+    # NOTE: FilePattern {} syntax shadows python f-string {} syntax
+    filerenaming.filePattern = '.*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif'
+    filerenaming.inpDir = subworkflow.steps[0].subdirectory  # TODO: workflow outputs: tag
+    filerenaming.outDir = Path('file-renaming.outDir')
+    filerenaming.outFilePattern = 'x{row:dd}_y{col:dd}_p{f:dd}_c{channel:d}.tif'
+
+    steps = [bbbcdownload,
+             subworkflow,
+             filerenaming]
+    filename = 'bbbc_sub_py'  # .yml
+    return Workflow(steps, filename)
+
+
+# viz = workflow()
+# viz.compile() # Do NOT .run() here
+
+if __name__ == '__main__':
+    pythonapi.global_config = plugins.get_tools_cwl(str(Path().home()))  # Use path fallback
+
+    viz = workflow2()
+    viz.run()  # .run() here, inside main