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Fix Illumina flowcells query to use the entity_type column #233

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merged 1 commit into from
Jan 9, 2024

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kjsanger
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@kjsanger kjsanger commented Jan 4, 2024

The query to find Illumina flowcells in the MLWH by component was
using tag index to try to identify controls. This is not a reliable
method; entity_type should be used instead. The set of valid entity
types is defined in the metadata of the MLWH schema.

Builds on #231 , which should be merged first.

@kjsanger kjsanger added the bug Something isn't working label Jan 4, 2024
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mgcam commented Jan 8, 2024

The position attribute of the component object is not optional, therefore the condition is not required. Also see the type definition for the position (lane) in Perl code

The iseq_product_metrics table does contain rows with NULL position value. However, these rows do not correspond to the components

@mgcam mgcam self-requested a review January 8, 2024 14:56
src/npg_irods/illumina.py Outdated Show resolved Hide resolved
@kjsanger kjsanger force-pushed the fix/find-illumina-flowcells-query branch from 6e11eb5 to 1a4efcf Compare January 9, 2024 12:06
The query to find Illumina flowcells in the MLWH by component was
using tag index to try to identify controls. This is not a reliable
method; entity_type should be used instead. The set of valid entity
types is defined in the metadata of the MLWH schema.
@kjsanger kjsanger force-pushed the fix/find-illumina-flowcells-query branch from 1a4efcf to 3d7336a Compare January 9, 2024 12:13
@kjsanger kjsanger requested a review from mgcam January 9, 2024 13:37
@mgcam mgcam merged commit b5c3180 into wtsi-npg:devel Jan 9, 2024
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@kjsanger kjsanger deleted the fix/find-illumina-flowcells-query branch January 9, 2024 13:56
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2 participants