Implement a subset of the Common Workflow Language.#47

Closed

jmchilton wants to merge 37 commits intodevfrom cwl-1.0

+4,788-197

Commits on Nov 11, 2021

Allow unit testing tool init to specify paths.

jmchilton
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nsoranzo
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[WIP] Implement records - heterogenous dataset collections.

jmchilton
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nsoranzo
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Deal with workflow definitions without position fields.

jmchilton
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nsoranzo
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Add CWL conformance test data to Galaxy for testing.

jmchilton
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nsoranzo
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Implement subset of the Common Workflow Language tool and workflow formats.

committed
Generate Python test cases from CWL conformance tests
nsoranzo
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CWL Testing and Runner Improvements.

jmchilton
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nsoranzo
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Swap default for beta formats (do not include in Galaxy).

jmchilton
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nsoranzo
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More logging messages... REMOVE LATER

jmchilton
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nsoranzo
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WIP: Work toward Galaxy-flavored CWL tools.

jmchilton
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nsoranzo
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[WIP] Implement client UI for field parameter type for CWL.

jmchilton
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nsoranzo
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Revert complex objectstore - for docker tests (needed for CWL).

jmchilton
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nsoranzo
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WORKAROUND TO GET TAR TO DIRECTORY WORKING AGAIN.

jmchilton
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nsoranzo
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Create codeql-analysis.yml

mr-c
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nsoranzo
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Update .github/workflows/codeql-analysis.yml

mr-c
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nsoranzo
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Move CWL unit tests to test/unit/app/tools
nsoranzo
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Generate CWL conformance tests only when needed
nsoranzo
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Code cleanups
nsoranzo
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Fix CwlToolObjectTestCase unit test
nsoranzo
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Ignore fals-y scatter_type

mvdbeek
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nsoranzo
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Add fields parameter to create collection schema

mvdbeek
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nsoranzo
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Fix non_data_connection workflows

mvdbeek
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nsoranzo
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Use staged_addition/add_pending_items

mvdbeek
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nsoranzo
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Use allow_tool_state_corrections when running CWL conformance tests

mvdbeek
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nsoranzo
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Can't used TypedDict in python < 3.8

mvdbeek
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nsoranzo
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Fix inverted worklfow ids and invocation ids

mvdbeek
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nsoranzo
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Fix nested collections getting reduced completely

mvdbeek
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nsoranzo
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Fix handling of uploaded_file_name

mvdbeek
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nsoranzo
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Reenable check_upload_content

mvdbeek
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nsoranzo
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Remove unneeded check_upload_content=True
nsoranzo
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Undo persisting ephemeral collections

mvdbeek
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nsoranzo
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Fix directory location tests

mvdbeek
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nsoranzo
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Consider a history not new once there are any items in it

mvdbeek
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nsoranzo
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Move num_hdas to else branch

mvdbeek
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nsoranzo
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Fix test_command_factory unit test

mvdbeek
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nsoranzo
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Make structure argument optional in subworkflow_progress

mvdbeek
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nsoranzo
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Fix typing issue
nsoranzo
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