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bug: linkml version 1.8.3 causes build-ingest-config to fail #274

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Bento007 opened this issue Sep 17, 2024 · 0 comments
Open

bug: linkml version 1.8.3 causes build-ingest-config to fail #274

Bento007 opened this issue Sep 17, 2024 · 0 comments
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@Bento007
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Bento007 commented Sep 17, 2024

first discovered on the branch: 23b714c

Error

$ make build-ingestion-config                                                          git:(tsmith/linkml|●1✚4-2…1 
rm -f core/v1.1.0/codegen/metadata_materialized.yaml
rm -f core/v1.1.0/codegen/metadata_models.py
rm -f ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml
rm -f ingestion_config/v1.0.0/codegen/ingestion_config_models.py
rm -f ingestion_config/v1.0.0/codegen/ingestion_config_models.schema.json
python3 schema.py materialize core/v1.1.0/metadata.yaml core/v1.1.0/common.yaml core/v1.1.0/codegen/metadata_materialized.yaml
python3 schema.py materialize ingestion_config/v1.0.0/ingestion_config_models.yaml core/v1.1.0/common.yaml ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml
linkml generate pydantic --black core/v1.1.0/codegen/metadata_materialized.yaml > core/v1.1.0/codegen/metadata_models.py
ValueError: The ifabsent value `float(1)` of the `aligned_tiltseries_binning` slot could not be processed
make: *** [build-ingestion-config] Error 1

Steps to reproduce

  1. check out main
  2. run make build-ingest-config -C ./schema

Work around

Pin the linkml version to 1.8.2.

Note:

I suspect it's related to this recent change linkml/linkml#2175

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