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linkml / schemasheets

Structure your data in a FAIR way using google sheets or TSVs. These are then converted to LinkML, and from there other formats
https://linkml.io/schemasheets/
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schemasheets doesn't seem to instantiate mixins yet #32

Closed turbomam closed 2 years ago

turbomam commented 2 years ago

Traceback (most recent call last): File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/sheets-and-friends-XU_YBljG-py3.9/bin/sheets2linkml", line 8, in sys.exit(convert()) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/sheets-and-friends-XU_YBljG-py3.9/lib/python3.9/site-packages/click/core.py", line 1128, in call return self.main(args, kwargs) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/sheets-and-friends-XU_YBljG-py3.9/lib/python3.9/site-packages/click/core.py", line 1053, in main rv = self.invoke(ctx) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/sheets-and-friends-XU_YBljG-py3.9/lib/python3.9/site-packages/click/core.py", line 1395, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/sheets-and-friends-XU_YBljG-py3.9/lib/python3.9/site-packages/click/core.py", line 754, in invoke return __callback(args, kwargs) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/sheets-and-friends-XU_YBljG-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 701, in convert schema = sm.create_schema(list(tsv_files)) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/sheets-and-friends-XU_YBljG-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 213, in create_schema self.merge_sheet(f, kwargs) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/sheets-and-friends-XU_YBljG-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 276, in merge_sheet raise SchemaSheetRowException(f'Error in line {line_num}, row={row}') from e schemasheets.schemamaker.SchemaSheetRowException: Error in line 5, row={'class': '', 'slot': '', 'description': 'a test mixin', 'mixin': 'test mixin'}

turbomam commented 2 years ago

@cmungall kindly reminded me that there's no such thing as a mixin element, only an element with the mixin attribute set to true.