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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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unintuitively, non-string values require protection by a leading `'` in sheets2linkml gsheet-id mode #67

Closed turbomam closed 1 year ago

turbomam commented 1 year ago

This works

sheets2linkml \
        --output $@ \
        --gsheet-id 1zsxvjvifDcmkt72v9m1_VKa2m73_THDJapJYK6dqidw core

In that sheet, I protected numerical values and Booleans in the examples column by preceding them with '. I think the same thing is required for dates, and the affirmative boolean value must be represented as 'true, not the magic value of TRUE.

But switch term MIXS:0000001's example to 555, and you get 

sheets2linkml \
        --output $@ \
        --gsheet-id 1zsxvjvifDcmkt72v9m1_VKa2m73_THDJapJYK6dqidw core_example_555_num

Traceback (most recent call last): File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 105, in merge_sheet self.add_row(row, schemasheet.table_config) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 111, in add_row for element in self.row_focal_element(row, table_config): File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 233, in row_focal_element raise ValueError(f'No table_config.column_by_element_type') ValueError: No table_config.column_by_element_type

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/bin/sheets2linkml", line 8, in sys.exit(convert()) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/click/core.py", line 1130, in call return self.main(args, kwargs) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(args, kwargs) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 578, in convert schema = sm.create_schema(list(tsv_files)) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 61, in create_schema self.merge_sheet(f, kwargs) File "/Users/MAM/Library/Caches/pypoetry/virtualenvs/mixs-linkml-GchukLmP-py3.9/lib/python3.9/site-packages/schemasheets/schemamaker.py", line 108, in merge_sheet raise SchemaSheetRowException(f'Error in line {line_num}, row={row}') from e schemasheets.schemamaker.SchemaSheetRowException: Error in line 1, row={'Structured comment name > slot > >': 'samp_size', 'Item (rdfs:label) title ': 'amount or size of sample collected', 'Definition description ': 'The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.', 'Expected value annotations inner_key: expected_value': 'measurement value', 'Value syntax structured_pattern ': '{float} {unit}', 'Example examples internal_separator: "|"': '555', 'Section slot_group ': 'nucleic acid sequence source', 'migs_eu annotations applies_to_class: migs_eu inner_key: cardinality': 'X', 'migs_ba annotations applies_to_class: migs_ba inner_key: cardinality': 'X', 'migs_pl annotations applies_to_class: migs_pl inner_key: cardinality': 'X', 'migs_vi annotations applies_to_class: migs_vi inner_key: cardinality': 'X', 'migs_org annotations applies_to_class: migs_org inner_key: cardinality': 'X', 'mims annotations applies_to_class: mims inner_key: cardinality': 'C', 'mimarks_s annotations applies_to_class: mimarks_s inner_key: cardinality': 'C', 'mimarks_c annotations applies_to_class: mimarks_c inner_key: cardinality': 'X', 'misag annotations applies_to_class: misag inner_key: cardinality': 'C', 'mimag annotations applies_to_class: mimag inner_key: cardinality': 'C', 'miuvig annotations applies_to_class: miuvig inner_key: cardinality': 'C', 'Preferred unit annotations inner_key: preferred_unit': 'millliter, gram, milligram, liter', 'Occurrence multivalued vmap: {s: false, m: true}': 's', 'MIXS ID slot_uri ': 'MIXS:0000001', 'MIGS ID (mapping to GOLD) annotations inner_key: gold_migs_id': ''} make: *** [generated/MIxS6_from_gsheet_templates_bad.yaml] Error 1

cmungall commented 1 year ago

This should be fixed by #79