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add tests
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‎testdata/v1.0/params_inc.yml‎

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type: Any
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outputBinding:
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outputEval: $(inputs)
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outputBinding:
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outputEval: $(inputs.bar)
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outputBinding:
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outputEval: $(inputs['bar'])
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outputBinding:
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outputEval: $(inputs["bar"])
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outputBinding:
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outputEval: $(inputs.bar.baz)
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outputBinding:
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outputEval: $(inputs['bar'].baz)
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outputBinding:
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outputEval: $(inputs['bar']["baz"])
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outputBinding:
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outputEval: $(inputs.bar['baz'])
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outputBinding:
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outputEval: $(inputs.bar['b az'])
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outputBinding:
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outputEval: $(inputs.bar['b\'az'])
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outputBinding:
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outputEval: $(inputs.bar["b'az"])
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type: "null"
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outputBinding:
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outputEval: $(inputs.bar['b"az'])
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outputBinding:
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outputEval: -$(inputs.bar.baz)
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outputBinding:
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outputEval: -$(inputs['bar'].baz)
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outputBinding:
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outputEval: -$(inputs['bar']["baz"])
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outputBinding:
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outputEval: -$(inputs.bar['baz'])
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outputBinding:
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outputEval: $(inputs.bar.baz) $(inputs.bar.baz)
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outputBinding:
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outputEval: $(inputs['bar'].baz) $(inputs['bar'].baz)
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outputBinding:
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outputEval: $(inputs['bar']["baz"]) $(inputs['bar']["baz"])
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type: Any
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outputBinding:
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outputEval: $(inputs.bar['baz']) $(inputs.bar['baz'])
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type: Any
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outputBinding:
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outputEval: $(inputs.bar['b az']) $(inputs.bar['b az'])
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outputBinding:
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outputEval: $(inputs.bar['b\'az']) $(inputs.bar['b\'az'])
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type: Any
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outputBinding:
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outputEval: $(inputs.bar["b'az"]) $(inputs.bar["b'az"])
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outputBinding:
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outputEval: $(inputs.bar['b"az']) $(inputs.bar['b"az'])
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type: Any
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outputBinding:
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outputEval: $(inputs.bar.buz[1])
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outputBinding:
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outputEval: $(inputs.bar.buz[1]) $(inputs.bar.buz[1])
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type: "null"
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outputBinding:
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outputEval: $(null)
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type: int
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outputBinding:
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outputEval: $(inputs.bar.buz.length)

‎testdata/v1.0/subdir/params.cwl‎

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class: CommandLineTool
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cwlVersion: v1.0
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hints:
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ResourceRequirement:
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ramMin: 8
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inputs:
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bar:
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type: Any
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default: {
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"baz": "zab1",
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"b az": 2,
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"b'az": true,
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'b"az': null,
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"buz": ['a', 'b', 'c']
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}
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outputs: {"$import": ../params_inc.yml}
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baseCommand: "true"

‎testdata/v1.1/params_inc.yml‎

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type: Any
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outputBinding:
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outputEval: $(inputs)
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type: Any
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outputBinding:
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outputEval: $(inputs.bar)
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type: Any
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outputBinding:
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outputEval: $(inputs['bar'])
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outputBinding:
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outputEval: $(inputs["bar"])
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outputBinding:
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outputEval: $(inputs.bar.baz)
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outputBinding:
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outputEval: $(inputs['bar'].baz)
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outputBinding:
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outputEval: $(inputs['bar']["baz"])
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outputBinding:
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outputEval: $(inputs.bar['baz'])
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outputBinding:
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outputEval: $(inputs.bar['b az'])
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outputBinding:
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outputEval: $(inputs.bar['b\'az'])
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outputBinding:
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outputEval: $(inputs.bar["b'az"])
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type: "null"
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outputBinding:
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outputEval: $(inputs.bar['b"az'])
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type: Any
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outputBinding:
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outputEval: -$(inputs.bar.baz)
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outputBinding:
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outputEval: -$(inputs['bar'].baz)
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outputBinding:
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outputEval: -$(inputs['bar']["baz"])
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outputBinding:
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outputEval: -$(inputs.bar['baz'])
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outputBinding:
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outputEval: $(inputs.bar.baz) $(inputs.bar.baz)
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outputBinding:
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outputEval: $(inputs['bar'].baz) $(inputs['bar'].baz)
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outputBinding:
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outputEval: $(inputs['bar']["baz"]) $(inputs['bar']["baz"])
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outputBinding:
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outputEval: $(inputs.bar['baz']) $(inputs.bar['baz'])
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outputBinding:
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outputEval: $(inputs.bar['b az']) $(inputs.bar['b az'])
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outputEval: $(inputs.bar['b\'az']) $(inputs.bar['b\'az'])
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outputEval: $(inputs.bar["b'az"]) $(inputs.bar["b'az"])
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outputBinding:
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outputEval: $(inputs.bar['b"az']) $(inputs.bar['b"az'])
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outputEval: $(inputs.bar.buz[1])
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outputEval: $(inputs.bar.buz.length)

‎testdata/v1.1/subdir/params.cwl‎

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.1
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class: CommandLineTool
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requirements:
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NetworkAccess:
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networkAccess: true
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LoadListingRequirement:
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loadListing: deep_listing
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hints:
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ResourceRequirement:
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ramMin: 8
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inputs:
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bar:
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type: Any
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default: {"baz": "zab1", "b az": 2, "b'az": true, 'b"az': null, "buz": ['a', 'b',
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'c']}
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baseCommand: "true"
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outputs: {"$import": ../params_inc.yml}

‎tests/test_import.py‎

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import filecmp
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from pathlib import Path
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from cwlupgrader.main import load_cwl_document, main, upgrade_document
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import pytest
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import logging
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from .util import get_data
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import re
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def test_import_parent_directory(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None:
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"""Confirm that $import to a superior directory still preserves the directory structure."""
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caplog.set_level(logging.WARN)
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out_dir = tmp_path/"out"
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out_dir.mkdir()
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doc = load_cwl_document(get_data("testdata/v1.0/subdir/params.cwl"))
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upgraded = upgrade_document(doc, out_dir, out_dir, "v1.1")
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expected = load_cwl_document(get_data("testdata/v1.1/subdir/params.cwl"))
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assert upgraded == expected
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assert len(caplog.records) == 1
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assert re.search(re.escape(f"Writing file, '{tmp_path}/params_inc.yml', outside of the output directory, '{out_dir}'."), caplog.records[0].getMessage())
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def test_import_parent_directory_safe(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None:
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"""Confirm no warning when $import to a superior directory (but still in the current working directory) still preserves the directory structure."""
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caplog.set_level(logging.WARN)
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out_dir = tmp_path/"out"
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out_dir.mkdir()
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doc = load_cwl_document(get_data("testdata/v1.0/subdir/params.cwl"))
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upgraded = upgrade_document(doc, out_dir, tmp_path, "v1.1")
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expected = load_cwl_document(get_data("testdata/v1.1/subdir/params.cwl"))
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assert upgraded == expected
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assert len(caplog.records) == 0

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