v7.8.0

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
  • see linkml/linkml#1598
• 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