Merging latest changes into master#618
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proccaserra merged 26 commits intomasterfrom Mar 23, 2026
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…e others, fixing json2jsonld.py code to resolve to schemas hosted on master branch, reviewing and fixing 4 key jupyter notebooks relying on BII-S-3 roundtrips and conversion
…ng associated tests, tweaks to json-ld context files
Fixed json2jsonld, commented on failing test.
…ng from alterations to isatools/model and isatools/database
sanitizing json2jsonld serialization and fixing failing tests resulti…
partial fix to isa conversion to ld
knirirr
approved these changes
Mar 20, 2026
added 5 commits
March 23, 2026 08:59
knirirr
reviewed
Mar 23, 2026
| :return: None | ||
| """ | ||
| if doi_str != "": | ||
| print("DOI string:", doi_str) |
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Could this be removed? Apologies, can't make an actionable comment for some unknown reason.
knirirr
reviewed
Mar 23, 2026
| """ | ||
| if pubmed_id_str != "": | ||
| if (_RX_PMID.match(pubmed_id_str) is None) and (_RX_PMCID.match(pubmed_id_str) is None): | ||
| if (_RX_PMID.match(pubmed_id_str) is None): # and (_RX_PMCID.match(pubmed_id_str) is None) |
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Another possible removal comment.
knirirr
reviewed
Mar 23, 2026
isatools/isatab/defaults.py
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| _RX_PMID = compile(r"[0-9]{8}") | ||
| _RX_PMCID = compile(r"PMC[0-9]{8}") | ||
| _RX_DOI = compile(r"^(https://doi.org/)?(10\.\d{4,9}/[-._;()/:a-z0-9A-Z]+)$") # | ||
| #_RX_DOI = compile(r"10\.\d{4,9}/[-._;()/:a-z0-9A-Z]+") # |
knirirr
reviewed
Mar 23, 2026
tests/isatab/test_isatab.py
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| with open(os.path.join(self._tab_data_dir, "issue587", "i_Investigation.txt")) as fp: | ||
| ISA = isatab.load(fp) | ||
| self.assertEqual(ISA.ontology_source_references[0].name, "1") | ||
| # self.assertEqual(ISA.ontology_source_references[0].comments[0].value, "onto_stuff") |
knirirr
reviewed
Mar 23, 2026
tests/model/test_assay.py
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| ) | ||
|
|
||
| print("ID:", assay.id) | ||
| # print("ID:", assay.id) |
proccaserra
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Mar 23, 2026
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great, will speed things up and avoid failure
added 2 commits
March 23, 2026 15:20
git add isatools/__init__.py
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