The specimen table update script stopped executing, and I was able to track the issue to a problem with one study where one of the assay metadata files had been incorrectly annotated as a biospecimen file. During the step where specimenIDs are extracted from the metadata files, the function was erroring when it tried to index a list element that didn't exist (was looking for two biospecimen files when there was only one).
I fixed the erroneous annotation so the update script runs as expected
I added some checks to cause the joining function to error if more than one individual or biospecimen file per study is detected
in the future it would be nice to add something that will tell you which study caused the problem, if any error occurs at this stage
The specimen table update script stopped executing, and I was able to track the issue to a problem with one study where one of the assay metadata files had been incorrectly annotated as a biospecimen file. During the step where specimenIDs are extracted from the metadata files, the function was erroring when it tried to index a list element that didn't exist (was looking for two biospecimen files when there was only one).