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abstract CWL test: recusively validate #93

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abstract CWL test: recusively validate #93

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ea26057
abstract CWL test: recusively validate
mr-c Nov 4, 2023
33c7572
partial fix for valid CWL abstract export
mr-c Apr 16, 2024
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4 changes: 2 additions & 2 deletions dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# Optional dependencies
schema-salad[pycodegen]
# Needs to validate v1.2
cwltool>=3.0.20200807132242
# Needs to validate v1.2, recursive_resolve_and_validate_document
cwltool>=3.0.20201117141248


mypy
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8 changes: 6 additions & 2 deletions gxformat2/abstract.py
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Expand Up @@ -82,14 +82,18 @@ def _format2_step_to_abstract(format2_step, requirements):
step_run = {
"class": "Operation",
"doc": format2_step.get("doc", ""),
"inputs": {}, # TODO
"outputs": {}, # TODO
"inputs": _format2_wfstep_inputs_to_abstract(format2_step),
"outputs": { out: "Any" for out in format2_step["out"] }
}
abstract_step["run"] = step_run
abstract_step["in"] = _format2_in_to_abstract(format2_step.get("in", []))
abstract_step["out"] = _format2_out_to_abstract(format2_step)
return abstract_step

def _format2_wfstep_inputs_to_abstract(format2_step):
if "in" in format2_step:
return { name: "Any" for name in format2_step["in"].keys() }
return {}

def _format2_in_to_abstract(in_dict):
"""Convert Format2 'in' dict for step into CWL abstract 'in' dict."""
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6 changes: 6 additions & 0 deletions tests/example_wfs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,8 @@
doc: cat doc
in:
input1: the_input
out:
out_file1: {}
"""

WORKFLOW_WITH_REPEAT = """
Expand Down Expand Up @@ -100,6 +102,8 @@
mapping:
- type: list_identifiers
columns: [0, 1]
out:
output: {}
random_lines:
tool_id: random_lines1
state:
Expand All @@ -109,6 +113,8 @@
seed_source:
seed_source_selector: set_seed
seed: asdf
out:
out_file1: {}
"""

RUNTIME_INPUTS = """
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4 changes: 2 additions & 2 deletions tests/test_export_abstract.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,10 @@
getdefault,
LoadingContext,
)
from cwltool.load_tool import recursive_resolve_and_validate_document
from cwltool.main import (
default_loader,
fetch_document,
resolve_and_validate_document,
tool_resolver,
)

Expand Down Expand Up @@ -140,7 +140,7 @@ def _run_example(as_dict, out=None):
)
loadingContext.resolver = getdefault(loadingContext.resolver, tool_resolver)
loadingContext, workflowobj, uri = fetch_document(out, loadingContext)
loadingContext, uri = resolve_and_validate_document(
loadingContext, uri, process = recursive_resolve_and_validate_document(
loadingContext,
workflowobj,
uri,
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