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UofS-Pulse-Binfo / genotypes_loader

A Drush-based loader for VCF files that follows the genotype storage rules outlined by ND genotypes.
GNU General Public License v2.0
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Could not find germplasm type 'accession' with the vocabulary 'GCP germplasm' #61

Open risharde opened 1 year ago

risharde commented 1 year ago

Attempting to run the genotype_loader results in the following error:

Could not find germplasm type 'accession' with the vocabulary 'GCP germplasm[error] ontology'

Lacey's initial response point to the following code where it should be creating this: https://github.com/tripal/tripal/blob/7.x-3.x/tripal_chado/includes/setup/tripal_chado.setup.inc#L646-L656

laceysanderson commented 1 year ago

Following up on this conversation, the loader expects the accession term to be in the "GCP germplasm" vocabulary but core Tripal would add it in the "CO_010" vocabulary. Also, this term may not always be available in a Tripal 3 site (e.g. if someone upgraded from T2 and did not need to run the prepare).

In our T3 code we would want to check that this term exists in under either of those cv names. That said, we're moving towards T4 right now and the T3 version has moved into bare maitenance mode...

For testing @risharde, you will want to create a cv and cvterm through the UI with these key details:

The rest are not used for lookup but I would suggest either matching them to the tripal 3 core version or using the 'local' database and accession the same as the cvterm name.