Create generateLecternJsonFromCustomLinkml.py #18
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Contributor
edsu7
commented
Jan 22, 2025
edsu7
commented
- generates lectern JSON from full linkML model
- generates lectern JSON from full linkML model
- add missing unique field
- add missing foreign key logic
lindaxiang
requested changes
Feb 4, 2025
| tmp['fields']=[] | ||
| lectern['schemas'].append(tmp) | ||
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| def populateFieldProperties(model,lectern): |
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Do you consider how to handle the mapping of an array defined in LinkML to Lectern isArray?
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LinkML's support for multivalue is not handled as cleanly as lectern
for example data is structured as so according to example:
www.hello.com/testJPEGf.jpeg JPEG pipelineF Bob 1
www.hello.com/3.pdf PDF pipelineF Unknown [1]
www.hello.com/4.pdf PDF pipelineF Bob [1|2|3]
but will complain during validation:
- example run
linkml-validate -s custom/example/example_full.yaml -C Imaging test_data/example/good_data/imaging.tsv
- outcome
[ERROR] [test_data/example/good_data/imaging.tsv/11] 1 is not of type 'array' in /image_number
[ERROR] [test_data/example/good_data/imaging.tsv/12] '[1]' is not of type 'array' in /image_number
[ERROR] [test_data/example/good_data/imaging.tsv/13] '[1|2|3]' is not of type 'array' in /image_number
For the moment this is the implementation:
data-dictionary/scripts/generateLecternJsonFromCustomLinkml.py
Lines 186 to 191 in 989b47e
lindaxiang
approved these changes
Feb 6, 2025
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