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@turbomam turbomam released this 30 Aug 19:00
· 3016 commits to main since this release
13acf18

Curated v7.7.2 -> v7.8.0 release notes

  • More aggressive .gitignore for cleaner merges
    • for releases: git add -f examples nmdc_schema project src
  • Refactored Makefile and project.Makefile
    • doesn't regenerate src/schema/mixs.yaml by default on every make all
    • routine: make squeaky-clean all only-test
    • for regenerating src/schema/mixs.yaml: make squeaky-clean mixs-yaml-clean all only-test
  • New OmicsProcessing-all meta target for illustrating the automatic generation and execution of SPARQL queries for a
    specified class
  • New assets/sparql folder for SPARQL that were generated with the class-sparql CLI and which could be edited and
    resubmitted to class-sparql for in --query-file mode
  • New make-rdf meta target dumps MongoDB in the shape of an NMDC Database instance, makes migrations (including doi
    migration and CURIe coercion), linkml-validation, conversion to RDF/TTL and casting anyURI-typed strings to real
    CURIes
    • skips functional_annotation_agg and metaproteomics_analysis_activity_set by default
    • dois migrations can be performed in one Study
      with nmdc_schema.migration_recursion:migrate_studies_7_7_2_to_7_8_0
  • New accepting-legacy-ids-all meta target for validating MongoDB data that includes legacy ids
  • Commented out old exploratory NEON targets in project.Makefile
  • Commented out old assets/MIxS_6_term_updates_MIxS6* targets in project.Makefile
  • project/prefixmap/nmdc.json is generated as a YAML file. We're renaming it in Makefile's gen-project target
  • Created some new redundancy in terms of supplements to the prefixes defined in the merged NMDC schema
    • assets/misc/extra_prefix_expansions.yaml
    • project/jsonld/nmdc.context.jsonld
    • project/prefixmap/nmdc.json
    • hardcoded prefix expansions in nmdc_schema/class_sparql.py
  • makefiles:
    • added squeaky-clean target
    • harmonization of PROJECT_FOLDERS and the includes/excludes for gen-project and test-schema
    • standardize naming of cleanup targets
    • use hyphens in target names, not underscores
  • Potential sources of breakage for downstream users of the nmdc-schema package:
    • Moved several legacy Python scripts from nmdc_schema/ to assets/old_python
    • removed several pyproject.toml dependencies, or relocated to tool.poetry.group.dev.dependencies
    • removed several legacy tool.poetry.scripts CLI definitions
  • Structural schema changes:
    • addition of class FunctionalAnnotationAggMember, Database slot functional_annotation_agg
      and FunctionalAnnotationAggMember
      slots metagenome_annotation_id, WorkflowExecutionActivity, gene_function_id and count.
      • count sure is a vague slot name
      • example data:
        • src/data/valid/FunctionalAnnotationAggMember-minimal.yaml
        • src/data/valid/Database-functional_annotation_agg.yaml
    • removal of doi slot, along with its assignment to class Study. Requires migration. Also switching from scalar
      to multivalued and from TextValue.has_raw_value to uriorcurie ranges
      • valid example data like src/data/valid/Study-exhaustive.yaml changed to match the schema changes
    • addition of award_dois, dataset_dois publication_dois
      • example data: src/data/valid/Database-study-set-with-dois.yaml
    • removed transient 200-character limit on funding_sources slot
    • moved emsl_project_dois from external_identifiers.yaml to nmdc.yaml and re-rooted in dois including new
      pattern
    • abstract slot has been moved from class Study
  • Schema annotation changes
    • updated examples, comments and description for jgi_portal_study_identifiers (
      in src/schema/external_identifiers.yaml)
    • the description for class Study clarifies that the description of Study instances should not include
      hyperlinks
    • the comments on slot elev in class Biosample have been updated

Autogenerated release notes

  • doi remodeling and migration, mixed with CURIes coercion, RDF generation, and class-specific SPARQL generation by @turbomam in #1074
  • retire doi, created dois and subproperties by @brynnz22 in #1039
  • artifacts for nmdc-schema v7.8.0 by @turbomam in #1094

Full Changelog: v7.7.6...v7.8.0