VS_1327 ensure sample ids are unique #8818
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…ed input file) are unique.
…sureSampleIdsAreUnique
rsasch
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koncheto-broad
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gbggrant
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* Have GvsAssignIds.wdl validate that input sample names (in the provided input file) are unique.
gbggrant
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* VS_1327 ensure sample ids are unique (#8818) * Have GvsAssignIds.wdl validate that input sample names (in the provided input file) are unique.
RoriCremer
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* Have GvsAssignIds.wdl validate that input sample names (in the provided input file) are unique.
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This PR adds a task to GvsAssignIds to verify that there are no duplicate sample names in the file provided.
Here is an example run of BulkIngest that replicates the original reported problem. No sample set provided, the sample id column is not sample_id and there's a duplicate in THAT column.
Here is an example run where the updated code runs and reports the problem early-ish without creating database tables that need to be cleaned up.
Here is a normal run that passes (same basic idea as the initial problem, except that I removed the duplicate row from the samples table.
Here is a passing integration test.