From 2f6a85ef8e5aea14472da60cfe8fe0d0332fdedd Mon Sep 17 00:00:00 2001 From: Dorota Jarecka Date: Tue, 20 Aug 2024 19:53:03 -0400 Subject: [PATCH 1/2] updates to the google sheet and the converter --- linkml-schema/source_library_generation/README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/linkml-schema/source_library_generation/README.md b/linkml-schema/source_library_generation/README.md index d38901a0..08655762 100644 --- a/linkml-schema/source_library_generation/README.md +++ b/linkml-schema/source_library_generation/README.md @@ -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` \ No newline at end of file +- 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 \ No newline at end of file From 9e32587c8590c624713deffe37fa1c19d34f0c28 Mon Sep 17 00:00:00 2001 From: Dorota Jarecka Date: Tue, 20 Aug 2024 20:04:09 -0400 Subject: [PATCH 2/2] changing pydantic generator syntax; using old version of schemasheet --- .github/workflows/generate_other_formats.yaml | 2 +- .github/workflows/generate_yaml_model.yaml | 1 + .github/workflows/test_other_formats.yaml | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/generate_other_formats.yaml b/.github/workflows/generate_other_formats.yaml index d1c345f2..8e068444 100644 --- a/.github/workflows/generate_other_formats.yaml +++ b/.github/workflows/generate_other_formats.yaml @@ -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 diff --git a/.github/workflows/generate_yaml_model.yaml b/.github/workflows/generate_yaml_model.yaml index 87b03604..5ac09909 100644 --- a/.github/workflows/generate_yaml_model.yaml +++ b/.github/workflows/generate_yaml_model.yaml @@ -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: | diff --git a/.github/workflows/test_other_formats.yaml b/.github/workflows/test_other_formats.yaml index 679e0de7..e909aeb3 100644 --- a/.github/workflows/test_other_formats.yaml +++ b/.github/workflows/test_other_formats.yaml @@ -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