aclum
aclum
This was causing trouble so we updated the range to allow an input of a biosample or processed sample and then records were updated via changesheets to populate these records....
Is there a way tell linkml-validate to use the value for slot type within an individual record to pick the most relevant error if the Class is Database?
Transferring to nmdc-schema per conversations with Mark. Suggestion was to set min cardinality in the schema. This needs to be coordinated with workflows so code that generates submissions gets updated....
@eecavanna offered to run a check in python to see what slots are populated with empty lists so we can reach out to the folks that write these documents.
@turbomam does this mean we should covert this back to a nmdc-runtime issue? Can the pypi package check this?
From what I've seen this issue is limited to [external identifier slots](https://microbiomedata.github.io/nmdc-schema/external_database_identifiers/) Yes, this should be run against prod.
Unique list of collection, slot collection_name,path_to_empty_list biosample_set,gold_biosample_identifiers data_object_set,alternative_identifiers mags_activity_set,mags_list metabolomics_analysis_activity_set,has_metabolite_quantifications metabolomics_analysis_activity_set,has_metabolite_quantifications[].alternative_identifiers metagenome_annotation_activity_set,gold_analysis_project_identifiers metaproteomics_analysis_activity_set,has_peptide_quantifications[].all_proteins omics_processing_set,gold_sequencing_project_identifiers read_based_taxonomy_analysis_activity_set,part_of study_set,gold_study_identifiers --- ➕ @eecavanna generated the following Markdown table from the above CSV string: |Unique...
Once scripts that generate json ( the referenced issues) for ingest to mongo prod are updated we can make a plan to have runtime API return that records with empty...
processes that submit to mongo continue to do this. The latest ive found this week are ETL code, #373 has been in the backlog and https://github.com/microbiomedata/nmdc_automation/issues/259
I think if populated both the submission schema and nmdc schema should use validate against the same enumeration and we need a process to keep this in sync with what...