microbiomedata/nmdc-schema issues and pull requests

#2071 - Implement a "no op" migrator from `v10.4.0` to `v10.5.4`

Pull Request - State: closed - Opened by eecavanna 4 months ago - 1 comment

#2070 - Migrations: Implement "no op" migrator from `v10.4.0` to `v10.5.4`

Issue - State: closed - Opened by eecavanna 4 months ago
Labels: X SMALL

#2069 - Publish schema to PyPI via GitHub Release `v10.5.4`

Issue - State: closed - Opened by aclum 4 months ago - 1 comment
Labels: high priority, X SMALL

#2068 - `berkeley-schema-fy24`: Update migrators to account for `WorkflowChain` class being removed

Issue - State: closed - Opened by eecavanna 4 months ago
Labels: X SMALL, berkeley-fy24-refactor

#2067 - Migrations: Make it easier to test migrators against a Mongo database

Issue - State: open - Opened by eecavanna 4 months ago
Labels: documentation, enhancement, X SMALL

#2066 - check if classes associated with `alternative_identifiers` can use ANY `alternative_identifiers`

Issue - State: open - Opened by turbomam 4 months ago - 5 comments

#2065 - Find a home for these comments taken from `src/scripts/report_biosamples_per_study.py`

Issue - State: open - Opened by turbomam 4 months ago

#2064 - `berkeley-schema-fy24`: Implement super migrator that runs all partial migrators in correct order

Issue - State: closed - Opened by eecavanna 4 months ago - 1 comment
Labels: enhancement, X SMALL

#2063 - Delete Class WorkflowChain in Berkeley schema

Issue - State: closed - Opened by aclum 4 months ago - 2 comments
Labels: berkeley-fy24-refactor

#2062 - `berkeley-schema-fy24`: Facilitate access to `nmdc_materialized_patterns` schema via PyPI package

Issue - State: closed - Opened by eecavanna 4 months ago - 2 comments
Labels: X SMALL

#2061 - `has_input`, `has_output`, and `has_process_parts` slots on `ProtocolExecution` need pattern constraints

Issue - State: closed - Opened by kheal 4 months ago

#2060 - Remodel class that aggregates steps of `WorkflowExecution` for easier schema traversal

Issue - State: open - Opened by kheal 4 months ago - 1 comment

#2059 - Add migrator for `nom_analysis_activity` ID

Pull Request - State: closed - Opened by JamesTessmer 4 months ago - 8 comments

#2058 - write a notebook report class.slot paths that take a ControlledTermValue* range

Issue - State: open - Opened by turbomam 4 months ago

#2057 - GitHub workflow to preview documentation changes/builds with example changes

Pull Request - State: closed - Opened by sujaypatil96 4 months ago - 4 comments

#2056 - `berkeley-schema-fy24`: Delete obsolete code, including code obsoleted by Berkeley schema changes

Issue - State: closed - Opened by eecavanna 4 months ago
Labels: X SMALL, cleanup

#2055 - `berkeley-schema-fy24`: Implement migrator that adds `replaces` field to `WorkflowChain` documents

Issue - State: closed - Opened by eecavanna 4 months ago - 1 comment
Labels: X SMALL, decision needed, berkeley-fy24-refactor

#2054 - Workflow execution constraints nmdc schema 2053

Pull Request - State: closed - Opened by turbomam 4 months ago

#2053 - backmerge issue with ID mention pattern constraints on WorkflowExecution

Issue - State: closed - Opened by aclum 4 months ago - 3 comments

#2052 - `berkeley-schema-fy24`: Make migrator that removes `MetagenomeAnnotation.gold_analysis_project_identifiers` field

Issue - State: closed - Opened by eecavanna 4 months ago - 2 comments
Labels: enhancement, X SMALL, berkeley-fy24-refactor

#2051 - Microbiomedata main

Pull Request - State: closed - Opened by turbomam 4 months ago

#2050 - standardize quotation marks in schema and example data files

Issue - State: open - Opened by turbomam 4 months ago - 2 comments

#2049 - reassess temporal modeling esp. for WorkflowChain

Issue - State: open - Opened by turbomam 4 months ago - 1 comment

#2048 - `Extraction` class lacks a constraint that indicates its expected usage

Issue - State: open - Opened by anastasiyaprymolenna 4 months ago

#2047 - generate reports of all observed MIxS environmental triad slot values, within a given context

Issue - State: open - Opened by turbomam 4 months ago - 2 comments

#2046 - Map 1:1 Database slots to PlannedProcess subclasses with depth of 1

Issue - State: closed - Opened by aclum 4 months ago - 1 comment
Labels: berkeley-fy24-refactor

#2045 - `berkeley-schema-fy24`: Implement migrator that merges some collections

Issue - State: closed - Opened by eecavanna 4 months ago - 5 comments
Labels: enhancement, X SMALL, berkeley-fy24-refactor, needs_details

#2044 - add metagnome input id pattern constraint

Pull Request - State: closed - Opened by turbomam 4 months ago

#2043 - Make `ExtractionTarget` mutlivalued to accommodate MPLEX extractions

Issue - State: closed - Opened by brynnz22 4 months ago - 1 comment

#2042 - `berkeley-schema-fy24`: Update migrators to use optimized adapter methods

Issue - State: closed - Opened by eecavanna 4 months ago
Labels: enhancement, X SMALL, medium priority, berkeley-fy24-refactor

#2041 - Poetry `linkml-runtime` dependency version update

Pull Request - State: closed - Opened by sujaypatil96 4 months ago

#2040 - regenerated poetry.lock

Pull Request - State: closed - Opened by turbomam 4 months ago

#2039 - don't pin pymongo in pyproject.toml

Pull Request - State: closed - Opened by turbomam 4 months ago

#2038 - remove unused Python code

Issue - State: open - Opened by turbomam 4 months ago - 2 comments

#2037 - nmdc-schema needs a more global mechanism for capturing ownership-like credit

Issue - State: closed - Opened by turbomam 4 months ago - 13 comments

#2036 - Restore recent migrators; install linters

Pull Request - State: closed - Opened by turbomam 4 months ago

#2035 - establish technical and social barriers to clever schema workarounds

Issue - State: open - Opened by turbomam 4 months ago - 1 comment

#2034 - restore schema module independence tests

Issue - State: open - Opened by turbomam 4 months ago - 1 comment

#2033 - define "soft schema freeze" along with exceptions framework

Issue - State: open - Opened by turbomam 4 months ago - 8 comments
Labels: ❔ awaiting-info

#2032 - Restore adapter method lost during PR #2009 merge: `do_for_each_document`

Pull Request - State: closed - Opened by eecavanna 4 months ago - 3 comments

#2031 - Migrations: Restore adapter method that was discarded during merge

Issue - State: closed - Opened by eecavanna 4 months ago - 2 comments
Labels: bug, high priority, X SMALL

#2030 - degenerate metagenome sequencing

Pull Request - State: closed - Opened by turbomam 4 months ago

#2029 - tooltips not alt descriptions or display hints

Pull Request - State: closed - Opened by turbomam 4 months ago

#2028 - review id_locus pattern

Issue - State: open - Opened by aclum 4 months ago - 6 comments

#2027 - `berkeley-schema-fy24`: Implement migrator that removes slots from `nmdc:MassSpectrometry` documents

Issue - State: closed - Opened by eecavanna 4 months ago
Labels: bug, X SMALL, berkeley-fy24-refactor

#2026 - remove-keep-keep-paths

Pull Request - State: closed - Opened by turbomam 4 months ago

#2025 - Markdown docs contain broken links

Issue - State: open - Opened by github-actions[bot] 4 months ago
Labels: documentation, broken-link

#2019 - Conflict resolved backmerge

Pull Request - State: closed - Opened by turbomam 4 months ago

#2018 - Remove `acquisition_category` slot and `AcquisitionCategoryEnum`

Issue - State: closed - Opened by kheal 4 months ago - 3 comments
Labels: berkeley-fy24-refactor

#2017 - DO NOT MERGE: Biosample sparsity analysis

Pull Request - State: open - Opened by turbomam 4 months ago
Labels: do not merge

#2016 - `berkeley-schema-fy24`: `make squeaky-clean all` fails at `gendoc` command

Issue - State: closed - Opened by eecavanna 4 months ago - 6 comments
Labels: bug

#2015 - Migrations: Update `create_migrator.py` to use template file and omit leading/trailing newlines

Pull Request - State: closed - Opened by eecavanna 4 months ago

#2014 - Migrations: Update migrator skeleton creation tool to use template and remove leading/trailing newlines

Issue - State: closed - Opened by eecavanna 4 months ago
Labels: X SMALL

#2013 - Delete queries for orphan functional_annotation_agg records and id non-conformaing Data Objects

Pull Request - State: closed - Opened by mbthornton-lbl 4 months ago - 2 comments

#2012 - Identify redundant EMP500 records and generate queries:run delete commands

Pull Request - State: closed - Opened by aclum 4 months ago

#2011 - Command to generate delete API requests legacy orphan data objects and functional annotation agg records

Issue - State: closed - Opened by mbthornton-lbl 4 months ago - 3 comments

#2010 - Migrator: Write migrator for `NomAnalysisActivity` documents

Issue - State: closed - Opened by aclum 4 months ago - 8 comments

#2009 - Migrations: Implement `set_field_of_each_document` adapter method

Pull Request - State: closed - Opened by eecavanna 4 months ago - 3 comments

#2008 - Migrations: Implement `set_field_of_each_document` Adapter method

Issue - State: closed - Opened by eecavanna 4 months ago
Labels: enhancement, X SMALL

#2007 - Implement PoC of Makefile target documentation pattern

Pull Request - State: open - Opened by eecavanna 4 months ago - 3 comments

#2006 - Migrations: Implement `do_for_each_document` adapter method

Pull Request - State: closed - Opened by eecavanna 4 months ago - 1 comment

#2005 - Migrations: Implement `do_for_each_document` Adapter method

Issue - State: closed - Opened by eecavanna 4 months ago
Labels: enhancement, X SMALL

#2004 - Migrations: Update migrators to raise Exception instead of printing error message

Issue - State: closed - Opened by eecavanna 4 months ago - 3 comments
Labels: enhancement, X SMALL

#1997 - Migrations: Update adapter to support callback for when a new collection is being processed

Issue - State: closed - Opened by eecavanna 4 months ago - 1 comment
Labels: enhancement, X SMALL

#1996 - Update `FailureWhereEnum` to reflect updated class names

Issue - State: closed - Opened by kheal 5 months ago - 8 comments
Labels: berkeley-fy24-refactor, closed_via_berkeley

#1995 - Add PR template

Issue - State: closed - Opened by kheal 5 months ago - 5 comments
Labels: documentation

#1994 - Manual addition of `structured_pattern` constraints on class mentioning slots, plus...

Pull Request - State: closed - Opened by turbomam 5 months ago - 4 comments

#1993 - 1992 add alternative identifiers to WorkflowExeuctionActivity

Pull Request - State: closed - Opened by aclum 5 months ago

#1992 - Add alternative identifiers to WorkflowExeuctionActivity

Issue - State: closed - Opened by aclum 5 months ago

#1991 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#1990 - Report slots, as used by some class, that have another class in their range, when that range class has a strcutred pattern

Pull Request - State: closed - Opened by turbomam 5 months ago - 5 comments

#1971 - `src/data/valid/Database-biosample-exhasutive.yaml` requires MIxS `multivalued` slots with class ranges to be `inlined_as_list`

Issue - State: closed - Opened by turbomam 5 months ago - 2 comments

GitHub / microbiomedata/nmdc-schema issues and pull requests