Add withdrawn and is_control columns [VS-70] [VS-213] #7736
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RoriCremer
reviewed
Mar 29, 2022
RoriCremer
reviewed
Mar 29, 2022
| echo "SELECT i.sample_name FROM \`${INFO_SCHEMA_TABLE}\` p JOIN items i ON (p.partition_id = CAST(i.sample_id AS STRING)) WHERE p.total_logical_bytes > 0 AND (table_name like 'ref_ranges_%' OR table_name like 'vet_%' OR table_name like 'pet_%')" >> query.sql | ||
| echo "UNION DISTINCT " >> query.sql | ||
| echo "SELECT i.sample_name FROM items i WHERE i.is_loaded = True " >> query.sql | ||
| echo "SELECT i.sample_name FROM items i WHERE i.is_loaded = True AND i.withdrawn IS NULL " >> query.sql |
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since we are doing this---is the benefit to clustering the samples table by the withdrawn col too negligible?
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I don't believe this adds clustering, it is checking for samples that should have data loaded in ref_ranges or vet tables.
RoriCremer
approved these changes
Mar 29, 2022
This was referenced Mar 17, 2023
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From https://docs.google.com/document/d/1YxYddVhQ-ZHEjRY9_XRTLCufDAUtq-MDZYpoO1ex0wA
withdrawnfield (type: TIMESTAMP, nullable) tosample_infotableis_controlfield (type: BOOLEAN, required) tosample_infotablesamples_are_controlsboolean parameter to GvsAssignIds (false by default) which will populate that field for ingestwithdrawn IS NULLcontrol_samplesboolean parameter to GvsPrepareRangesCallset.wdl (false by default)__SAMPLES tableifwithdrawn IS NULLcontrol_samplesboolean parameter to GvsExtractCallset.wdl (false by default)Closes