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updates to the google sheet and the converter #68

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merged 2 commits into from
Aug 21, 2024
Merged

updates to the google sheet and the converter #68

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2f6a85e
updates to the google sheet and the converter
djarecka Aug 20, 2024
9e32587
changing pydantic generator syntax; using old version of schemasheet
djarecka Aug 21, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/generate_other_formats.yaml
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Expand Up @@ -47,7 +47,7 @@ jobs:
# generating jsonld context and removing generation_date field to avoid constant updates
gen-jsonld-context ${file} > ../jsonld-context-autogen/${name}.context.jsonld;
sed -i "/generation_date/d" ../jsonld-context-autogen/${name}.context.jsonld;
gen-pydantic --pydantic-version 2 ${file} > ../models_py-autogen/${name}.py;
gen-pydantic ${file} > ../models_py-autogen/${name}.py;
if [ ${name} = "library_generation" ] || [ ${name} = "genome_annotation" ]; then
echo "Creating and Fixing diagrams for $name";
python ../utils/fix_and_create_erdiagram.py
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1 change: 1 addition & 0 deletions .github/workflows/generate_yaml_model.yaml
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Expand Up @@ -26,6 +26,7 @@ jobs:
run: |
python -m pip install .[test]
pip install git+https://github.com/brain-bican/bkbit.git
pip install git+https://github.com/linkml/schemasheets.git@649af7e1

- name: Other installations
run: |
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2 changes: 1 addition & 1 deletion .github/workflows/test_other_formats.yaml
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Expand Up @@ -39,7 +39,7 @@ jobs:
# generating jsonld context
gen-jsonld-context ${file};
# generating pydantic schema
gen-pydantic --pydantic-version 2 ${file};
gen-pydantic ${file};
if [ ${name} != "library_generation" ] && [ ${name} != "genome_annotation" ]; then
gen-erdiagram ${file};
fi
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6 changes: 5 additions & 1 deletion linkml-schema/source_library_generation/README.md
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Expand Up @@ -2,4 +2,8 @@

- Metadata from [Google Sheet](https://docs.google.com/spreadsheets/d/11OcQz1Vk3ofny3Ql7wN-XlHkZwub-hojt-fO094SxiI/edit?usp=sharing)
- All the sheets will be saved as tsv files in `gsheet_output`
- Current Google Sheet version: `bk_workshop_mit24`
- Current Google Sheet version: `aug20_2024`
- The generated LinkML schema will be saved in `bkbit/models/library_generation_model.yaml`
- Additional information:
- currently using `no-inlined` due to some issues with pydantic generation
- currently using an older version of schemasheets due to issues with newer versions
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