Added parsers for CWL input files #199
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Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #199 +/- ##
==========================================
- Coverage 40.99% 33.26% -7.73%
==========================================
Files 30 30
Lines 23563 31014 +7451
Branches 6406 8997 +2591
==========================================
+ Hits 9659 10316 +657
- Misses 11827 18284 +6457
- Partials 2077 2414 +337 ☔ View full report in Codecov by Sentry. |
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mr-c
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Feb 12, 2023
|
Added tests for the most critical parts:
As usual, complete coverage would require to run conformance tests suite using this parser. |
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mr-c
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Feb 12, 2023
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| if isinstance(doc, str): | ||
| url = loadingOptions.fetcher.urljoin(baseuri, doc) | ||
| if url in loadingOptions.idx: | ||
| return loadingOptions.idx[url] | ||
| doc_url, frg = urldefrag(url) | ||
| text = loadingOptions.fetcher.fetch_text(doc_url) | ||
| textIO = StringIO(text) | ||
| textIO.name = str(doc_url) | ||
| yaml = yaml_no_ts() | ||
| result = yaml.load(textIO) | ||
| add_lc_filename(result, doc_url) | ||
| loadingOptions = cwl.LoadingOptions(copyfrom=loadingOptions, fileuri=doc_url) | ||
| _inputfile_load( | ||
| result, | ||
| doc_url, | ||
| loadingOptions, | ||
| ) | ||
| return loadingOptions.idx[url] |
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Can we get a test for this code branch?
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This commit adds support for parsing CWL input files with autogenerated Schema SALAD parsers, in order to obtain a coherent representation of CWL object between processfile and jobfile.
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This commit adds support for parsing CWL input files with autogenerated Schema SALAD parsers, in order to obtain a coherent representation of CWL object between processfile and jobfile.
This PR depends on common-workflow-language/common-workflow-language#953, common-workflow-language/cwl-v1.1#83, and common-workflow-language/cwl-v1.2#220.