Re-ID, Ingest to Napa DB, and Verify Napa compliance for "EMP" study: nmdc:sty-11-547rwq94

[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 "EMP" Study -
id: nmdc:sty-11-547rwq94
legacy id: gold:Gs0154244

• 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 via linkml-validate
• Validate vs. schema v10.1.0
• Transform to RDF datastore
• SPARQL query for referential integrity checks
• Resolve referential integrity exceptions for nmdc:sty-11-547rwq94 Metagenome Omics Processing records #1897
• Pass Referential Integrity query suite
• Handle nmdc:nnn does not match nmdc:dobj errors #1834

[mbthornton-lbl]

nmdc:sty-11-547rwq94_linkml_validate.log

[mbthornton-lbl]

linkml-validate vs nmdc-schema v8.0.0

[mbthornton-lbl]

SPARQL query for Orphan DataObjects returns no results

[mbthornton-lbl]

linkml-validate vs. 10.1.0 schema

[ERROR] [./local/nmdc:sty-11-547rwq94.yaml/0] 'nmdc:8a9d164e1310e5b838d6ceb492f64a61' 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_\\.-]+)?$' in /omics_processing_set/55/has_output/0
[ERROR] [./local/nmdc:sty-11-547rwq94.yaml/0] 'nmdc:9bd3cf378610c02776b54cc797d8c07a' does not match '^nmdc:dobj-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$' in /omics_processing_set/55/has_output/1
[ERROR] [./local/nmdc:sty-11-547rwq94.yaml/0] 'nmdc:9d5f99fba241d6bdd933ccbf405bf872' 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/55/has_output/2
[ERROR] [./local/nmdc:sty-11-547rwq94.yaml/0] Additional properties are not allowed ('publication_dois' was unexpected) in /study_set/0
[ERROR] [./local/nmdc:sty-11-547rwq94.yaml/0] 'study_category' is a required property in /study_set/0

[ssarrafan]

@mbthornton-lbl will this need to go into the next sprint for the last checkbox? I'm assuming you're waiting on the newest version of the schema 10.0.1?

[mbthornton-lbl]

Version 10 schema compatibility issues will be addressed by:
#1834
microbiomedata/nmdc_automation#66

[ssarrafan]

Should this go to the next sprint under in review or pending release? @mbthornton-lbl

[mbthornton-lbl]

Referential Integrity Exception: omics_processing_has_output_data_object

<style> </style>

649b009773e824995934a1d3	nmdc:omprc-11-tdt0js09	Volcanic soil microbial communities from Hawaii, Kilauea Volcano, USA - King27.Edge.1.3.0.2		nmdc:bsm-11-bzj1ca10	nmdc:8a9d164e1310e5b838d6ceb492f64a61	nmdc:sty-11-547rwq94	Metagenome	nmdc:OmicsProcessing
649b009773e824995934a1d3	nmdc:omprc-11-tdt0js09	Volcanic soil microbial communities from Hawaii, Kilauea Volcano, USA - King27.Edge.1.3.0.2		nmdc:bsm-11-bzj1ca10	nmdc:9bd3cf378610c02776b54cc797d8c07a	nmdc:sty-11-547rwq94	Metagenome	nmdc:OmicsProcessing
649b009773e824995934a1d3	nmdc:omprc-11-tdt0js09	Volcanic soil microbial communities from Hawaii, Kilauea Volcano, USA - King27.Edge.1.3.0.2		nmdc:bsm-11-bzj1ca10	nmdc:9d5f99fba241d6bdd933ccbf405bf872	nmdc:sty-11-547rwq94	Metagenome	nmdc:OmicsProcessing

[mbthornton-lbl]

Applied: delete_omics_processing_has_output_ref_integrity_exceptions
Re-ran omics_processing_has_output_data_object which returned 0 results

[mbthornton-lbl]

Resolved with #1897