Great `bq_scripts` refactor

cellarium-ai / cellarium-cloud

Cellarium Cloud Core Library

BSD 3-Clause "New" or "Revised" License

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Great `bq_scripts` refactor #94

Open fedorgrab opened 1 year ago

fedorgrab commented 1 year ago

[ ] Type annotations for all of the code
[ ] All missing Docstrings
[ ] Factor out all BigQuery Schemas
[x] Factor out all SQL queries
[ ] Factor out NumpyEncoder from dump_ingest_info
[ ] Clean up commented code
[ ] Implement pre-ingest curation script
- [ ] Infer the number of cells from the AnnData file
- [ ] Optionally, perform basic QC (# of genes per cell, # of counts per cell) and emit warnings

fedorgrab commented 1 year ago

During PR #101 the following comment is highlighted: "Unrelated to this PR, but we should never simply catch a broad exception, print the error message, and move on. Let's fix this during the great big refactor"

fedorgrab commented 1 year ago

Another comment: make sure to get rid of print statements and establish an appropriate logger.