Michael Thornton

icon company Lawrence Berkeley Laboratory icon location San Francisco Bay Area

Results 7 issues of Michael Thornton

Global definition of was_informed_by contradicts the class slot_usage. Remove slot_usage and fix the global definition

Resolve referential integrity exceptions for `nmdc:sty-11-547rwq94` Metagenome Omics Processing records

2 comment

## Referential Integrity Exception: `omics_processing_has_output_data_object` 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 |...

Automate `data_qc` scripts

Provide a facility to: - run a series of mongodb shell commands found in `assets/mongodb_queries/data_qc` - provide an alert if errors are found - produce a report detailing data QC...

Referential Integrity errors in 2 imported JGI studies

nmdc:sty-11-5tgfr349 nmdc:sty-11-r2h77870

Automate MongoDB Referential Integrity Queries

Take the queries developed for #1865 and refactor them into a script for automatic execution and report generation

Add commands to `nmdc_database_tools.py` to find, handle, and report on missing / orphan data objects and functional_annotation

Add command(s) to find and report on: - Missing `has_output` Data objects for OmicsProcessing - Missing `has_input` or `has_output` for WrokflowExecutions - Orphan Data Objects with option to delete orphans...

Update nmdc_database_tools `extract-study` command to extract multiple studies

Update the `extract-study` tool: - rename to extract-studies and update docs - support multiple study ID's as input - Pull data for multiple studies, output to a single `nmdc_schema.Database` compliant...