aclum
aclum
linked issues - https://github.com/microbiomedata/issues/issues/430 - [Re-ID NOM and Metabolomics OmicsProcessing, DataObjects, AnalysisActivies#524](https://github.com/microbiomedata/issues/issues/524)
This is Yuri's code for re-iding. Review should focus on nmdc_schema/metab_id_refactor.py as other files python files were not used, instead Michael refactored them into code in nmdc_automation repo.
Just a noting that in nmdc-schema has_calibration has a range of a string and is currently populated with either a data object identifier, "False", or "false". In the berkeley schema...
There is code from https://github.com/microbiomedata/nmdc-schema/blob/28823618de2c17189934cdae0ca291d14fda0c08/nmdc_schema/connect_napa_mongo.py#L454 , lines 454 to 490, which based on a list of gold projects deletes workflow execution activities and data objects. These won't have a study...
After re-iding is complete we can remove the extra logic to support from nmdc_schema_accepting_legacy_ids.py Depends on: https://github.com/microbiomedata/issues/issues/532 Target release 2024.4
@sujaypatil96 suggested at the metadata meeting last week that we add slot `type` to the new PlanndedProcess classes and ProcessedSample -Pooling -Extraction -LibraryPreparation -ProcessedSample This will make the classes more...
**Describe the bug** The hyperlink for the ['GitHub repository'](https://github.com/GenomicsStandardsConsortium/mixs/tree/main/release) in the first paragraph of https://www.gensc.org//news/2022/04/01/MIxSv6.0-release.html has a 404 response code. **To Reproduce** Steps to reproduce the behavior: 1. Go to...
**Describe the bug** The error message describes an issue with the incorrect slot. **To reproduce** Steps to reproduce the behavior: poetry run linkml-validate -s ../../../project/nmdc_materialized_patterns.yaml Database-Extraction-extraction_method-slot-retired.yaml where the materialized pattern...
**Is your feature request related to a problem? Please describe.** The default nmdc.schema.json doesn't contain the materialized patterns we've been working on. This has caused some issues and confusion within...