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DataBiosphere / azul

Metadata indexer and query service used for AnVIL, HCA, LungMAP, and CGP
Apache License 2.0
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FIXMEs reference closed external issues #6596

Open nadove-ucsc opened 4 days ago

nadove-ucsc commented 4 days ago

https://github.com/DataBiosphere/azul/blob/33796d4de83ff10fab3081ec28b3b0e2a2a2f18e/src/azul/plugins/metadata/hca/indexer/transform.py#L1392

The linked issue has been closed. This may manifest as a bug where zarr files are missing from replicas' lists of hub IDs and from the inner entity arrays of cell suspensions and samples.

dsotirho-ucsc commented 4 days ago

Spike to investigate.

nadove-ucsc commented 2 days ago

There is a related FIXME that references another closed ticket: https://github.com/DataBiosphere/azul/blob/319995f1e509e9bf47fec5f1368b51556be51eef/src/azul/plugins/metadata/hca/indexer/transform.py#L1440

nadove-ucsc commented 2 days ago

I couldn't find any evidence of what the symptoms might be because I couldn't find any zarray files in the index.

nadove-ucsc commented 2 days ago

@hannes-ucsc: "The solution is to remove the FIXMEs. While the blocking issue was resolved, there are no more zarrays in DCP2 and I don't want to touch the code that supports them."