Re-ID, Ingest to Napa DB, and Verify Napa compliance for "Luqillo" study nmdc:sty-11-076c9980

[mbthornton-lbl]

Note: Scope of this work is the Napa Database Instance. The same steps will need to be repeated in a prod-ready environment

For the "Luqillo" Study -
id: nmdc:sty-11-076c9980
legacy id: gold:Gs0128850

• Extract records
• Process records: generate re-ID'ed records and changesheet for OmicsProcessing records
• Ingest records
• Delete old and failed records
• Add command to re_id_tools.py to delete binning DataObject records nmdc_automation#68
• Apply OmicsProcessing changesheet
• Extract study to YAML
• Validate vs schema v8.0.0
• Validate vs schema 10.1.0
• Convert to RDF datastore
• SPARQL query for referential integrity checks
• Pass Referential Integrity query suite

[mbthornton-lbl]

linkml-validate vs. 8.0.0 schema: No issues found

Imported to GraphDB

PREFIX nmdc: <https://w3id.org/nmdc/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
select * where { 
	?s nmdc:has_output ?o .
    minus {?o rdf:type ?oo}
} limit 100 

No objects that are not Typed Subjects

[mbthornton-lbl]

Validation vs. the 10.1.0 schema has 2 errors:

(nmdc-schema-py3.9) (base) MBThornton@MBThornton-M92 nmdc-schema % linkml-validate -s ./local/nmdc-schema-v10.1.0.yaml ./local/nmdc:sty-11-076c9980.yaml 

INFO:root:Using SchemaView with im=None
[ERROR] [./local/nmdc:sty-11-076c9980.yaml/0] Additional properties are not allowed ('award_dois' was unexpected) in /study_set/0
[ERROR] [./local/nmdc:sty-11-076c9980.yaml/0] 'study_category' is a required property in /study_set/0
(nmdc-schema-py3.9) (base) MBThornton@MBThornton-M92 nmdc-schema % 

[mbthornton-lbl]

Version 10.1 issues will be handled by
microbiomedata/nmdc_automation#66