microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model
https://microbiomedata.github.io/nmdc-schema/
Creative Commons Zero v1.0 Universal
26 stars 8 forks source link

Handle emsl:output does not match nmdc:dobj failures vs. v10.1 schema #1833

Closed mbthornton-lbl closed 3 months ago

mbthornton-lbl commented 3 months ago
[ERROR] [./local/nmdc:sty-11-aygzgv51.yaml/0] 'emsl:output_500091' does not match '^nmdc:dobj-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$' in /omics_processing_set/256/has_output/0
aclum commented 3 months ago

@picowatt this is a proteomics data object. can you make sure all the proteomics data objects are deleted?

mbthornton-lbl commented 3 months ago

@picowatt Is there any other data apart from the emsl:output_ ID pattern that I need to know about when I go deleting?

mbthornton-lbl commented 3 months ago

Re-extracted the Stegen study and re-ran validtion:

 % linkml-validate -s ../../local/nmdc-schema-v10.1.1.yaml ../../local/nmdc:sty-11-aygzgv51.yaml

INFO:root:Using SchemaView with im=None
[ERROR] [../../local/nmdc:sty-11-aygzgv51.yaml/0] Additional properties are not allowed ('award_dois', 'publication_dois' were unexpected) in /study_set/0
[ERROR] [../../local/nmdc:sty-11-aygzgv51.yaml/0] 'study_category' is a required property in /study_set/0

study_category, award_dois, and publication_dois errors are expected here, and will be addressed by the v10 data migration process

mbthornton-lbl commented 3 months ago

@aclum @picowatt Based on the results of linkml-validate above, this ticket can be closed. There were not code changes so noPR