microbiomedata nmdc-schema issues

microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

https://microbiomedata.github.io/nmdc-schema/

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issues

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remove logic to repair curies

#2093 aclum opened 1 hour ago
0
extra leading carrot in structured_patterns

#2092 aclum opened 1 hour ago
0
Allow `nmdc_data.py` consumer to specify which variant of schema they want to access

#2091 eecavanna opened 3 days ago
1
Docker Compose shows warning saying `version` (specifier) is obsolete

#2090 eecavanna opened 3 days ago
0
Update migrator to keep `DataObject.was_generated_by` in sync with updated `id`

#2088 eecavanna closed 5 days ago
2
Render `Mappings` section generally on all element documentation pages

#2087 sujaypatil96 opened 6 days ago
2
Migrator: Update `migrator_from_10_3_0_to_10_4_0.py` so it also updates `was_generated_by` values

#2086 eecavanna closed 5 days ago
1
2084 tighter pattern constraint on was_generated_by

#2085 aclum closed 1 week ago
1
tighter pattern constraint on was_generated_by

#2084 aclum closed 1 week ago
0
Use `--include-range-class-descendants` flag in JSON Schema generator calls

#2083 pkalita-lbl closed 1 week ago
1
Remove `activity_set` slot from `Database` class

#2082 aclum closed 1 week ago
4
Remove WorkflowExeuctionActivity as a range for Database slot activity_set

#2081 aclum closed 1 week ago
0
produce a nmdc-schema YAML artifact with deprecated elements included

#2080 sierra-moxon opened 1 week ago
1
Facilitate access to `nmdc_materialized_patterns` schema variant via PyPI package

#2079 eecavanna opened 1 week ago
2
2024-06-18 `id` pattern validation summaries and SPARQL-based referential integrity checks on MongoDB contents with and without migration

#2078 turbomam opened 1 week ago
6
Rename branches to eliminate Berkeley commits from `main`

#2077 eecavanna closed 1 week ago
6
v11.0.0-rc.16

#2076 turbomam closed 1 week ago
0
Bump urllib3 from 2.2.1 to 2.2.2

#2075 dependabot[bot] closed 1 week ago
1
Revert "Merge branch 'main' into main"

#2074 eecavanna closed 1 week ago
1
mismatched-alternative-ids

#2073 turbomam opened 1 week ago
1
`berkeley-schema-fy24`: Some migrators use incorrect collection name (instead of `mags_set`)

#2072 eecavanna closed 1 week ago
0
Implement a "no op" migrator from `v10.4.0` to `v10.5.4`

#2071 eecavanna closed 1 week ago
1
Migrations: Implement "no op" migrator from `v10.4.0` to `v10.5.4`

#2070 eecavanna closed 1 week ago
0
Publish schema to PyPI via GitHub Release `v10.5.4`

#2069 aclum closed 1 week ago
1
`berkeley-schema-fy24`: Update migrators to account for `WorkflowChain` class being removed

#2068 eecavanna closed 2 weeks ago
0
Migrations: Make it easier to test migrators against a Mongo database

#2067 eecavanna opened 2 weeks ago
0
check if classes associated with `alternative_identifiers` can use ANY `alternative_identifiers`

#2066 turbomam opened 2 weeks ago
5
Find a home for these comments taken from `src/scripts/report_biosamples_per_study.py`

#2065 turbomam opened 2 weeks ago
0
`berkeley-schema-fy24`: Implement super migrator that runs all partial migrators in correct order

#2064 eecavanna closed 2 weeks ago
1
Delete Class WorkflowChain in Berkeley schema

#2063 aclum closed 2 weeks ago
2
`berkeley-schema-fy24`: Facilitate access to `nmdc_materialized_patterns` schema via PyPI package

#2062 eecavanna closed 2 weeks ago
2
`has_input`, `has_output`, and `has_process_parts` slots on `ProtocolExecution` need pattern constraints

#2061 kheal closed 2 weeks ago
0
Remodel class that aggregates steps of `WorkflowExecution` for easier schema traversal

#2060 kheal opened 2 weeks ago
1
Add migrator for `nom_analysis_activity` ID

#2059 JamesTessmer closed 2 weeks ago
8
write a notebook report class.slot paths that take a ControlledTermValue* range

#2058 turbomam opened 2 weeks ago
0
GitHub workflow to preview documentation changes/builds with example changes

#2057 sujaypatil96 closed 2 weeks ago
4
`berkeley-schema-fy24`: Delete obsolete code, including code obsoleted by Berkeley schema changes

#2056 eecavanna closed 2 weeks ago
0
`berkeley-schema-fy24`: Implement migrator that adds `replaces` field to `WorkflowChain` documents

#2055 eecavanna closed 2 weeks ago
1
Workflow execution constraints nmdc schema 2053

#2054 turbomam closed 3 weeks ago
0
backmerge issue with ID mention pattern constraints on WorkflowExecution

#2053 aclum closed 3 weeks ago
3
`berkeley-schema-fy24`: Make migrator that removes `MetagenomeAnnotation.gold_analysis_project_identifiers` field

#2052 eecavanna closed 3 weeks ago
2
Microbiomedata main

#2051 turbomam closed 3 weeks ago
0
standardize quotation marks in schema and example data files

#2050 turbomam opened 3 weeks ago
2
reassess temporal modeling esp. for WorkflowChain

#2049 turbomam opened 3 weeks ago
1
`Extraction` class lacks a constraint that indicates its expected usage

#2048 anastasiyaprymolenna opened 3 weeks ago
0
generate reports of all observed MIxS environmental triad slot values, within a given context

#2047 turbomam opened 3 weeks ago
1
Map 1:1 Database slots to PlannedProcess subclasses with depth of 1

#2046 aclum closed 2 weeks ago
1
`berkeley-schema-fy24`: Implement migrator that merges some collections

#2045 eecavanna closed 3 weeks ago
5
add metagnome input id pattern constraint

#2044 turbomam closed 3 weeks ago
0
Make `ExtractionTarget` mutlivalued to accommodate MPLEX extractions

#2043 brynnz22 closed 3 weeks ago
1