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microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model
https://microbiomedata.github.io/nmdc-schema/
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Re-ID, Ingest to Napa DB, and Verify Napa compliance for "EMP" study: `nmdc:sty-11-547rwq94` #1792

Closed mbthornton-lbl closed 6 months ago

mbthornton-lbl commented 7 months ago

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

mbthornton-lbl commented 7 months ago

nmdc:sty-11-547rwq94_linkml_validate.log

mbthornton-lbl commented 7 months ago

linkml-validate vs nmdc-schema v8.0.0

mbthornton-lbl commented 7 months ago

SPARQL query for Orphan DataObjects returns no results

mbthornton-lbl commented 7 months ago

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 commented 7 months ago

@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 commented 7 months ago

Version 10 schema compatibility issues will be addressed by:

1834

https://github.com/microbiomedata/nmdc_automation/issues/66

ssarrafan commented 7 months ago

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

mbthornton-lbl commented 6 months ago

Referential Integrity Exception: omics_processing_has_output_data_object

<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

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 commented 6 months ago

Applied: delete_omics_processing_has_output_ref_integrity_exceptions Re-ran omics_processing_has_output_data_object which returned 0 results

mbthornton-lbl commented 6 months ago

Resolved with https://github.com/microbiomedata/nmdc-schema/issues/1897