hubmapconsortium / ontology-api

The HuBMAP Ontology Service
MIT License
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Ontology: add basic QA statements related to ontology ingestion #168

Closed AlanSimmons closed 1 year ago

AlanSimmons commented 1 year ago

Long-term enhancement.

Issue

The ontology framework currently ignores ingest data with quality issues.

For example, if ontology A depends on concepts from ontology B and you try to ingest A before ingesting B and the B nodes are not defined explicitly in the nodes metadata, the framework will simply not ingest the concepts from ontology B.

This can make debugging data quality issues difficult: you have to work through the code step-by-step to figure out why something wasn't ingested. This is particularly difficult for scripts that work with large datasets via pandas--you often have to do things like load the script into a Jupyter notebook.

Solution

Log basic QA issues during script execution.

AlanSimmons commented 1 year ago

This will be moved to the new UBKG repo.

AlanSimmons commented 1 year ago

Moved.