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Merge Berkeley schema (berkeley-schema-fy24/main) into Legacy schema (nmdc-schema/main) #2195

Merged
merged 1,438 commits into from
Oct 7, 2024
Merged

Merge Berkeley schema (berkeley-schema-fy24/main) into Legacy schema (nmdc-schema/main) #2195

merged 1,438 commits into from
Oct 7, 2024
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Commits on Jun 26, 2024

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    light -> soft
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  66. Update pull_request_template_berk_schema.yml 

    multiplicity -> multivalued
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  67. Update pull_request_template_berk_schema.yml 

    add review expectations
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  68. Update pull_request_template_berk.md 

    update for .md tempalte
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  69. move to PR temp dir

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Commits on Jun 28, 2024

  1. Rename partial migrators to indicate their final order

    @eecavanna
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  2. Consolidate 16 import statements into a single one

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Commits on Jul 1, 2024

  1. Fix typos, rephrase things, eliminate redundant section

    @eecavanna
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  2. Use consistent terminology

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  3. Merge pull request #218 from microbiomedata/1983-berkeley-schema-fy24… 

    …-finalize-names-of-berkeley-schema-migrators

Finalize names of Berkeley schema migrators
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Commits on Jul 2, 2024

  1. all invalid files have one error, moved problems to problem/invalid

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Commits on Jul 3, 2024

  1. Merge pull request #219 from microbiomedata/eecavanna-patch-1 

    PR Template: Fix typos, rephrase things, eliminate redundant section
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  2. Update pull_request_template_berk.md 

    light -> soft
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  3. Update pull_request_template_berk.md

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  4. Update pull_request_template_berk.md 

    update language around reviewer expectations
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  5. Update pull_request_template_berk.md 

    stupid new lines not showing
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  6. first pass at fixing problem/invalid files

    @bmeluch
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  7. mam pr tempalte suggestions v1

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  8. enum/PV wording

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  9. Merge pull request #221 from microbiomedata/mam-pr-template-suggestions 

    mam pr template suggestions v1
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  10. Update .github/PULL_REQUEST_TEMPLATE/pull_request_template_berk.md 

    Co-authored-by: eecavanna <[email protected]>
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  11. Update .github/PULL_REQUEST_TEMPLATE/pull_request_template_berk.md 

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  12. Update .github/PULL_REQUEST_TEMPLATE/pull_request_template_berk.md 

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  13. Update .github/PULL_REQUEST_TEMPLATE/pull_request_template_berk.md 

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  14. Delete YAML file originally planned to be a PR template

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  15. Merge pull request #217 from microbiomedata/1995-add-pr-template_berk… 

    …_schema

Add PR template specific to the schema soft freeze (`berkeley-schema-fy24`)
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Commits on Jul 9, 2024

  1. no restriction on known_as, delete invalid files

    @bmeluch
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  2. deprecate EnvironmentalMaterialTerm

    @bmeluch
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  3. deprecate FunctionalAnnotationTerm and children

    @bmeluch
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  4. add deprecation date

    @bmeluch
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  5. add deprecation dates

    @bmeluch
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  6. changing some Database invalid examples to Extraction invalid examples

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Commits on Jul 10, 2024

  1. correct deprecation strings

    @bmeluch
    bmeluch committed Jul 10, 2024
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Commits on Jul 16, 2024

  1. Remove extraneous parentheses on ids

    @kheal
    kheal committed Jul 16, 2024
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  2. Shorten typecodes to adhere to standards

    @kheal
    kheal committed Jul 16, 2024
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  3. Add to Modeling Best Practices for id practices

    @kheal
    kheal committed Jul 16, 2024
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  4. Fix typecodes on example data and class-linking slots

    @kheal
    kheal committed Jul 16, 2024
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  5. fix file name

    @mslarae13
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  6. Merge pull request #226 from microbiomedata/fix_pr-template 

    fix file name
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  7. fake

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  8. moving pr template

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  9. Elaborate on CONTRIBUTING guide regarding ids

    @kheal
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  10. leftovers

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  11. Update migrator to treat metatranscriptome_expression_analysis_set … 

    …as child of `workflow_execution_set`
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  12. nmdc.yaml still has conflicts

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  13. Elaborate on ID patterning and checks

    @kheal
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  14. problem tests remain

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  15. Merge pull request #227 from microbiomedata/test_pr-tempalte 

    Move PR template file
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  16. all valid examples passing

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  17. require fastjsonschema for dev.dependencies

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Commits on Jul 17, 2024

  1. update poetry lock

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  2. Add note regarding multiple typecodes

    @kheal
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  3. Add note regarding multiple typecodes

    @kheal
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  4. Update CONTRIBUTING.md 

    Co-authored-by: eecavanna <[email protected]>
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  5. Update CONTRIBUTING.md 

    Co-authored-by: eecavanna <[email protected]>
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Commits on Jul 19, 2024

  1. Update range of was_generated_by

    @aclum
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  2. update template

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  3. Merge branch 'main' into backmerge-2024-07-16

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  4. requested changes esp @aclum and @eecavanna

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Commits on Jul 24, 2024

  1. Merge pull request #229 from microbiomedata/backmerge-2024-07-16 

    Backmerge 2024-07-16 (`nmdc-schema/main` -> `berkeley-schema-fy24/main`)
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  2. Merge pull request #231 from microbiomedata/2134-berkeley-fix-range-f… 

    …or-was_generated_by

Update range of `was_generated_by` slot
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  3. Merge pull request #225 from microbiomedata/2122_typecode_fix 

    Typecode fixes on IDs for `ChromatographyConfiguration`, `StorageProcess`, and `MassSpectrometryConfiguration` class ids
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Commits on Jul 25, 2024

  1. typos

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  2. recreating files; no documentation yet

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  3. Update .github/pull_request_template.md 

    Co-authored-by: eecavanna <[email protected]>
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  4. Update .github/pull_request_template.md 

    Co-authored-by: eecavanna <[email protected]>
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  5. add persons role

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  6. Update .github/pull_request_template.md 

    Co-authored-by: eecavanna <[email protected]>
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Commits on Jul 26, 2024

  1. Merge pull request #232 from microbiomedata/add-names-to-PR-template 

    Update PR template
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Commits on Aug 1, 2024

  1. remove deprecation for OrthologyGroup, FunctionalAnnotationTerm

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Commits on Aug 7, 2024

  1. Merge pull request #228 from microbiomedata/upstream-issue-2124-berke… 

    …ley-schema-fy24-update-part_16-migrator-to-include-metatranscriptome_expression_analysis_set-collection

Update migrator to treat `metatranscriptome_expression_analysis_set` as child of `workflow_execution_set`
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  2. Merge pull request #222 from microbiomedata/1881-deprecate-unused-cla… 

    …sses

Deprecate `EnvironmentalMaterialTerm`, `Pathway`
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Commits on Aug 12, 2024

  1. Merge pull request #234 from microbiomedata/2150-berkeley-schema-fy24… 

    …-document-new-location-of-json-schema-and-yaml-schema-files-within-repository

Regenerate accidentally-deleted JSON/YAML files in `nmdc_schema` directory
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Commits on Aug 14, 2024

  1. correct Database problem example files, delete PlaceholderClass

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  2. deleted problem files that were corrected and moved to invalid

    @bmeluch
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  3. clarified error in file name

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Commits on Aug 19, 2024

  1. Update workflow_execution_activity.yaml 

    update MetatranscriptomeExpressionAnalysis
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  2. fix example data for MetatranscriptomeExpressionAnalysis

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  3. Add example invalid data

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Commits on Aug 20, 2024

  1. remove limit on pydantic 1

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  1. remove magically commented lines

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Commits on Aug 22, 2024

  1. Expanding FailureWhereEnum to include all DataGeneration and Workflow… 

    …Execution subclasses
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  2. Merge pull request #238 from microbiomedata/ignore-less-for-releases 

    Restore missing `nmdc.py` file, add a TSV file, and remove several files from `.gitignore`
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  3. add nmdc_schema/nmdc.py; no new content

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Commits on Aug 23, 2024

  1. Update migrators to use MetatranscriptomeExpressionAnalysis type/enum

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Commits on Aug 26, 2024

  1. tested with check-invalids-for-single-failure and then repaired

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Commits on Aug 27, 2024

  1. Merge branch 'main' into bjm-example-data-work

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Commits on Aug 28, 2024

  1. changing from Database to ReadQcAnalysis to get expected error messag… 

    …e for Database-ReadQcAnalysisActivity-invalid.yaml
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  2. builds but src/data/problem/valid need collaborative debugging

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  3. mixs.yaml is autogenerated but required in build so must be pushed

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Commits on Aug 29, 2024

  1. fix and move Database-metatranscriptome_workflow.yaml

    @aclum
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  2. Update Database-metatranscriptome_workflow-invalidDatabase.yaml 

    updating so there is only one invalid thing
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  3. Update MagsAnalysisActivity-invalid_ncbi_lineage_tax_ids.yaml 

    Fix class uri
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  4. deletions for @aclum; mv src/data/problem/valid/*yaml to src/data/valid

    @turbomam
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  5. reorganzing location of create_legacy_orphan_deletion_requests.py

    @aclum
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  6. reorganzing location of create_legacy_orphan_deletion_requests.py

    @aclum
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Commits on Sep 3, 2024

  1. correcting comments and file names for clarity

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  2. Rename Database-functional_annotation_agg.yaml to Database-functional… 

    …_annotation_agg-missing_gene_function_id.yaml
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  3. Merge pull request #246 from microbiomedata/mam-stage-for-merging-ups… 

    …tream-into-fork

staging of merging upstream into fork
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Commits on Sep 4, 2024

  1. Merge pull request #220 from microbiomedata/bjm-example-data-work 

    Checking that all invalid example files fail ONLY for the specified reason
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Commits on Sep 10, 2024

  1. Update instrument_set.yaml

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  2. Remove parthood from DataGeneration

    @aclum
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  3. updating invalid data files

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  4. Remove part_of slot_usage on DataGeneration

    @kheal
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  5. fix migrator to map novaseq 6000 specifically

    @brynnz22
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  6. Updates to InstrumentModelEnum 

    Adding aliases and structured aliases.
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  7. More updates to InstrumentModelEnum

    @aclum
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  8. Merge branch 'main' into 2164-backmerge-metatranscriptome-issues

    @aclum
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  9. Removing duplicate slot on MetatranscriptomeExpressionAnalysis 

    Dup added by incorrect merge conflict resolution.
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  10. test uri vs url for alias_contexts

    @aclum
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  11. Add doctest targeting special handling of "NovaSeq" name

    @eecavanna
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  12. Eliminate unnecessary indentation of code block

    @eecavanna
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  13. Fix issue where instance was being used as identifier

    @eecavanna
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  14. Make the if condition be more explicit

    @eecavanna
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  15. Refactor function to clarify logic

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Commits on Sep 11, 2024

  1. Cache the instruments from the YAML file

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  2. Codify example instrument name mappings that were reviewed

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  3. Add draft of protocol_link type migrator

    @kheal
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  4. Add PR number and return to migrator

    @kheal
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  5. Expand collections to search for protocol link

    @kheal
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  6. Add valid and invalid examples for protocol_link type

    @kheal
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  7. Add part 17 to migrators for berkeley database

    @kheal
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  8. reformatting structured_aliases for InstrumentModelEnum

    @aclum
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  9. More syntax fixes for structued_alises on InstrumentModelEnum

    @aclum
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  10. Syntax fixes for StructuredAliases for InstrumentModelEnum

    @aclum
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  11. more fixing structued alias syntax

    @aclum
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  12. Update nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/… 

    …migrator_from_10_2_0_to_11_0_0_part_17.py

Co-authored-by: eecavanna <[email protected]>
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  13. Change slot to field in docstring of migrator part 17 

    Co-authored-by: eecavanna <[email protected]>
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  14. Update LibraryPreparation.yaml

    @kheal
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  15. Updating predicate for InstrumentTypeEnum

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  16. Merge pull request #247 from microbiomedata/modify-inst-migrator-asset 

    Refine the list of `Instrument`s a migrator can map an instrument name to
    @aclum
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  17. Merge pull request #248 from microbiomedata/2179-berkeley-reverse-par… 

    …thood-on-datageneration

Remove parthood from DataGeneration
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  18. Merge pull request #250 from microbiomedata/2180_protocol_type_migrator 

    Add migrator to check and add `type` slot to `Protocol` records
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  19. add type protocol migrator to existing migrator

    @brynnz22
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  20. add metatranscritpome analysis after accidentally removing

    @brynnz22
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  21. add three metatranscriptome sets

    @brynnz22
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  22. Add novaseq x to InstrumentModelEnum.

    @aclum
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  23. Adding tsv to map GOLD seqMethod to NMDC instrument_set instance

    @aclum
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Commits on Sep 12, 2024

  1. Add doctests targeting recently-implemented functionality

    @eecavanna
    eecavanna committed Sep 12, 2024
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  2. Fix typos in comments (oops)

    @eecavanna
    eecavanna committed Sep 12, 2024
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  3. Merge pull request #237 from microbiomedata/2164-backmerge-metatransc… 

    …riptome-issues

2164 Fix Metatranscriptome Expression class name
    @aclum
    aclum authored Sep 12, 2024
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  4. Update nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/… 

    …migrator_from_10_2_0_to_11_0_0_part_10.py

Co-authored-by: eecavanna <[email protected]>
    @brynnz22 @eecavanna
    brynnz22 and eecavanna authored Sep 12, 2024
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  5. Update nmdc_schema/migrators/partials/migrator_from_10_2_0_to_11_0_0/… 

    …migrator_from_10_2_0_to_11_0_0_part_10.py

Co-authored-by: eecavanna <[email protected]>
    @brynnz22 @eecavanna
    brynnz22 and eecavanna authored Sep 12, 2024
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  6. Merge branch 'main' into update-type-slot-migrator

    @brynnz22
    brynnz22 authored Sep 12, 2024
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  7. Update gold_seqMethod_to_nmdc_instrument_set.tsv

    @aclum
    aclum authored Sep 12, 2024
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  8. Merge pull request #249 from microbiomedata/2174-add-aliases-mappings… 

    …-annotations-for-gold-platform-model-cv

Updates to InstrumentModelEnum
    @aclum
    aclum authored Sep 12, 2024
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Commits on Sep 16, 2024

  1. Merge pull request #251 from microbiomedata/update-type-slot-migrator 

    Update migrator to populate `type` field on inline `Protocol` instances
    @eecavanna
    eecavanna authored Sep 16, 2024
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  2. Generate derivative files for release

    @eecavanna
    eecavanna committed Sep 16, 2024
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Commits on Sep 17, 2024

  1. Merge pull request #253 from microbiomedata/prepare-to-release-v11.0.… 

    …0rc22

Generate derivative files for release `v11.0.0rc22`
    @eecavanna
    eecavanna authored Sep 17, 2024
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Commits on Sep 18, 2024

  1. remove locus from id to match pattern restriction

    @bmeluch
    bmeluch authored Sep 18, 2024
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Commits on Sep 20, 2024

  1. Merge pull request #254 from microbiomedata/2175-fix-functional-annot… 

    …ation-agg-example

Fix ID in `functional_annotation_agg` invalid example
    @bmeluch
    bmeluch authored Sep 20, 2024
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Commits on Sep 23, 2024

  1. add schema changes

    @brynnz22
    brynnz22 committed Sep 23, 2024
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  2. Add Reference Calibration File permissible value to FileTypeEnum

    @brynnz22
    brynnz22 committed Sep 23, 2024
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Commits on Sep 24, 2024

  1. Update basic_slots.yaml 

    Comment about generalizability of term
    @brynnz22
    brynnz22 authored Sep 24, 2024
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  2. Update basic_slots.yaml 

    make description more specific
    @brynnz22
    brynnz22 authored Sep 24, 2024
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  3. Update basic_slots.yaml 

    remove comment
    @brynnz22
    brynnz22 authored Sep 24, 2024
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  4. add NEON NMDC instrument name/id mapping file

    @sujaypatil96
    sujaypatil96 committed Sep 24, 2024
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  5. Merge pull request #257 from microbiomedata/issue-2185-neon-nmdc-inst… 

    …rument-mapping-file

add NEON/NMDC instrument name/id mapping file
    @sujaypatil96
    sujaypatil96 authored Sep 24, 2024
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Commits on Sep 26, 2024

  1. temporary-ncbi-expansion-3

    @turbomam
    turbomam committed Sep 26, 2024
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  2. do-not-use-napa-api

    @turbomam
    turbomam committed Sep 26, 2024
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  3. update-selected-collections

    @turbomam
    turbomam committed Sep 26, 2024
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  4. remove-jena-tdb-fuseki-gold-study-ids

    @turbomam
    turbomam committed Sep 26, 2024
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Commits on Sep 30, 2024

  1. Merge pull request #255 from microbiomedata/fix-calib-target-enum 

    Change `mass` permissible value of `calibration_target` to `mass_charge_ratio`
    @brynnz22
    brynnz22 authored Sep 30, 2024
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  2. Merge pull request #256 from microbiomedata/add-file-type-enum 

    Add `Reference Calibration File` permissible value to `FileTypeEnum`
    @brynnz22
    brynnz22 authored Sep 30, 2024
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  3. force-docs

    @turbomam
    turbomam committed Sep 30, 2024
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  4. Delete deleteme

    @turbomam
    turbomam authored Sep 30, 2024
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Commits on Oct 2, 2024

  1. inlined-as-list-updates

    @turbomam
    turbomam committed Oct 2, 2024
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  2. add updated project.Makefile

    @turbomam
    turbomam committed Oct 2, 2024
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  3. Update project.Makefile 

    more hyphens for pure-export --output option
    @turbomam
    turbomam authored Oct 2, 2024
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  4. Merge pull request #269 from microbiomedata/inlined-as-list-updates 

    inlined-as-list-updates
    @turbomam
    turbomam authored Oct 2, 2024
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  5. Merge pull request #261 from microbiomedata/do-not-use-napa-api 

    Use Berkeley API instead of Napa API
    @turbomam
    turbomam authored Oct 2, 2024
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  6. Merge pull request #262 from microbiomedata/update-selected-collections 

    Update `--selected-collections` options to be consistent with Berkeley schema
    @turbomam
    turbomam authored Oct 2, 2024
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  7. Merge pull request #260 from microbiomedata/temporary-ncbi-expansion-3 

    Add a temporary NCBI prefix expansion
    @turbomam
    turbomam authored Oct 2, 2024
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  8. Merge branch 'main' into exclude-metaproteomicsanalysis

    @turbomam
    turbomam committed Oct 2, 2024
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  9. got rid of fuseki stragglers

    @turbomam
    turbomam committed Oct 2, 2024
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  10. Merge pull request #263 from microbiomedata/remove-jena-tdb-fuseki-go… 

    …ld-study-ids

remove-jena-tdb-fuseki-gold-study-ids
    @turbomam
    turbomam authored Oct 2, 2024
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  11. make-rdf-completes-but

    @turbomam
    turbomam committed Oct 2, 2024
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  12. Merge pull request #271 from microbiomedata/make-rdf-completes-but 

    Make rdf completes but only due to skipping workflows and calibrations
    @turbomam
    turbomam authored Oct 2, 2024
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  13. Merge branch 'main' into exclude-metaproteomicsanalysis

    @turbomam
    turbomam committed Oct 2, 2024
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  14. skip peptide_quantifications, not entire proteomics workflows

    @turbomam
    turbomam committed Oct 2, 2024
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  15. skip peptide_quantifications, not entire proteomics workflows

    @turbomam
    turbomam committed Oct 2, 2024
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  16. Merge pull request #270 from microbiomedata/exclude-metaproteomicsana… 

    …lysis

skip RDF conversion of metaproteomics analyses
    @turbomam
    turbomam authored Oct 2, 2024
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  17. reason for skipping calibration_set

    @turbomam
    turbomam committed Oct 2, 2024
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  18. Merge pull request #272 from microbiomedata/reason-for-skipping-calib… 

    …ration-set

reason for skipping calibration_set
    @turbomam
    turbomam authored Oct 2, 2024
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Commits on Oct 7, 2024

  1. v11.0.0rc24

    @turbomam
    turbomam committed Oct 7, 2024
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  2. Merge branch 'main' into resolve-merge-conflict-in-nmdc.py

    @turbomam
    turbomam authored Oct 7, 2024
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