C2M2 change for Sample Prep Method

karlcz commented 1 year ago

An updated C2M2 model replaces biosample.assay_type with biosample.sample_prep_method referring to a new sample_prep_method vocabulary.

We want to allow submission of data with this new field while also allowing a release to be built using current submissions, in case a DCC chooses not to resubmit.

Add the sample_prep_method vocab and datapackage associations to the registry to allow tracking of term usage
Add the sample_prep_method vocab table to submission and portal models
Tolerate the deprecated biosample.assay_type field for backward-compatibility
Adjust text search indexing to ingore biosample.assay_type as a source of keyword material
Adjust the core_fact.assay_types dimension to only observe the file.assay_type field (basis for Assay Type facets in UI)
Add new core_fact.sample_prep_methods dimension and Sample Prep Method facets in the UI

karlcz commented 1 year ago

Added this issue belatedly for current in-progress work...

karlcz commented 1 year ago

This is merged and deployed in the app-dev environment were devs have successfully done end-to-end test submissions with both versions of C2M2.

nih-cfde / cfde-deriva

C2M2 change for Sample Prep Method #376