v8.1.2

What's Changed

• for release v8.1.1 by @turbomam in #1260
• v8.1.2: forgot to include new version in pyproject.toml nmdc.yaml by @turbomam in #1261

Full Changelog: v8.1.1...v8.1.2

v8.1.1

What's Changed

• Deprecated emsl_proect_dois and removed from Study class usage by @brynnz22 in #1161
• Require study_category by @brynnz22 in #1162
• remove publications slot, update example data by @brynnz22 in #1136
• prep for migration action: workflow_dispatch by @turbomam in #1176
• prep for migration action: deploy java by @turbomam in #1177
• prep for migration action: get java version by @turbomam in #1178
• download robot by @turbomam in #1179
• prep for migration action: download robot shell script by @turbomam in #1180
• prep for migration action: get robot version by @turbomam in #1181
• prep for migration action: simplify action by @turbomam in #1182
• prep for migration action: robot test convert by @turbomam in #1183
• prep for migration action: add jena by @turbomam in #1184
• prep for migration action: load tdb by @turbomam in #1185
• prep for migration action: query tdb by @turbomam in #1186
• prep for migration action: build before loading or querying by @turbomam in #1187
• prep for migration action: poetry setup before build by @turbomam in #1188
• prep for migration action: query schema and data by @turbomam in #1189
• prep for migration action: blank local/.env ok? by @turbomam in #1190
• Add backticks around file path to format it as code by @eecavanna in #1202
• Extract transformation functions into migration-specific classes by @eecavanna in #1155
• sparql extraction of Gs0114663 and Biosamples by @turbomam in #1206
• id mentions pattern checking including updated example data by @turbomam in #1209
• differentiate cookiecutter-help from help by @turbomam in #1210
• Acknowledge two makefiles in README by @turbomam in #1213
• restored make-rdf stuff and now supporting nmdc:sty-11-hdd4bf83 by @turbomam in #1225
• Finalize name of class that migrates data from 8.0.0 to 8.1.0 by @eecavanna in #1227
• validation of OmicsProcessing outputs by @turbomam in #1218
• Update nmdc-schema-style-and-collaboration-guide.md by @turbomam in #1203
• nmdc-schema style and collaboration guidelines by @turbomam in #1201
• don't check OmicsProcessing has_input id pattern on legacy data by @turbomam in #1231
• Bump urllib3 from 2.0.5 to 2.0.7 by @dependabot in #1232
• polymorphic planned process by @turbomam in #1238
• first steps in migration notes by @turbomam in #1061
• removing old, inflexible doi reporting by @turbomam in #1240
• notebook for reporting classes that can't be aggregated in a Database instance by @turbomam in #1106
• Merge in SubSamplingProcess and supporting changes by @turbomam in #1199

New Contributors

• @dependabot made their first contribution in #1232

Full Changelog: v8.1.0...v8.1.1

v8.1.0

What's Changed

• Move internal lat_lon comment from description to todos by @pkalita-lbl in #1140
• no pydantic 2 yet by @turbomam in #1143
• limit linkml to < 1.6 by @turbomam in #1146
• comment out non-CURIe see_alsos by @turbomam in #1152
• v7.8.0 to v8.0.0 migration not req by @turbomam in #1158
• remove Instrument range on used in MetaproteomicsAnalysisActivity by @turbomam in #1157
• Report the ranges of slot used by @turbomam in #1137
• local/mongo_as_unvalidated_nmdc_database.yaml target needs pure dev input and pure prod input modes by @turbomam in #1150
• Release 8.1.0 artifacts by @pkalita-lbl in #1159

Full Changelog: v8.0.0...v8.1.0

v8.0.0

Curated release notes

Overhaul of the definition and usage of CURIe prefixes.

• Most notably, the default_curi_maps assertions have been
  removed from all schema source file, like src/schema/nmdc.yaml. All prefixes that will be used in the schema
  (slot_uris, mappings, id_prefixes, etc.) must be defined in either nmdc.yaml or another source field that it
  imports. There is now a single, auto-generated file that contains all prefix definitions across the merged schema:
  project/jsonld/nmdc.context.jsonld. Note that it uses two patterns for expanding prefixes. Both are accessed from the
  @context outer key.
  • direct: "EFO": "http://www.ebi.ac.uk/efo/"
  • via an @id inner key: "ENVO": { "@id": "http://purl.obolibrary.org/obo/ENVO_"}.
    Other keys in these dictionaries can usually be ignored.
• The GOLD prefix is no longer allowed in the schema or any schema compliant data. Only gold is allowed now.
• A discussion of prefixes, CURIes, identifiers and mappings has been added: src/docs/prefixes_curies_ids_mappings_etc.md
• https://bioregistry.io is now consistently preferred over http://identifiers.org as a CURIe resolving service.
  The version is this release is a draft, and community members are welcome to ask questions or make suggestions.

New data migration code:

• Extractions must replace usages of the sample_mass slot with input_mass
• replacement of GOLD prefixes with gold prefixes in three classes
• updates to src/data files: /valid shows the post migration state.

Other

• SPARQL queries have been added or updated in assets/sparql
  • see also nmdc_schema/class_sparql.py
• example python QC code, using LinkML SchemaView, has been added
  • nmdc_schema/list_id_prefixes_and_patterns.py
  • nmdc_schema/list_slot_usages.py
  • nmdc_schema/list_structured_patterns.py
• many definitional attributes of slots have been moved out of per-class slot_usage blocks.
  Especially in src/schema/workflow_execution_activity.yaml. Likewise, all class should not assert their slots with a
  slots list, not implicitly via the slot_usage blocks. required: true, customized ranges and customized descriptions
  can still be found in slot_usage blocks. Not that some of these are non-monotonic and need further attention.
  An example would be when the global definition of a slot uses an enumeration range but a slot_usage uses a string range.

Auto-generated (but equally important) release notes

• Remove invalid water content examples by @aclum in #1084
• Issue1031 input sample mass by @brynnz22 in #1109
• Issue 24 omics processing move by @brynnz22 in #1118
• Issue1097 study consortia by @brynnz22 in #1098
• update nucleicAcidQuantMethod mapping by @brynnz22 in #1036
• Prefixes standardization (no default curi maps) and making some slot_usage attributes global by @turbomam in #1116

Full Changelog: v7.8.0...v8.0.0

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

v7.7.6

What's Changed

• with regenerated files for elev comments in v7.7.5 by @turbomam in #1081

Full Changelog: v7.7.5...v7.7.6

v7.7.5

What's Changed

• increase character limit of funding_sources to 200 by @brynnz22 in #1079
• new version for longer funding sources by @turbomam in #1080

Full Changelog: v7.7.4...v7.7.5

v7.7.4

What's Changed

• bumped to v7.7.4 by @turbomam in #1077
• see also https://github.com/microbiomedata/nmdc-schema/releases/tag/v7.7.3

Full Changelog: v7.7.3...v7.7.4

v7.7.3

What's Changed

• clarify Study description to not include links by @brynnz22 in #1050
• update funding_sources to be more specific by @brynnz22 in #1058
• update elev comments for Biosample slot usage by @brynnz22 in #1072
• remove abstract slot globally from schema by @brynnz22 in #1055

Full Changelog: v7.7.2...v7.7.3

v7.7.2

What's Changed

• add benthic mappings and minor edits by @brynnz22 in #1012
• edit neon mapping tsv units and add nmdc unit column by @brynnz22 in #1022
• update nucleicAcidConcentration and purity mappings by @brynnz22 in #1023
• repaired the fully-repaired file paths by @turbomam in #1025
• update neon raw data file mappings tsv by @sujaypatil96 in #1038
• Update nmdc.yaml by @aclum in #1044
• added jgi_portal_study_identifiers slot and example data by @turbomam in #1043

---

• delete old mapping neon_nmdc_term_mappings.tsv file by @brynnz22 in #1020
• remove rawDataFiles table for soil, benthic, and surfacewater mappings by @brynnz22 in #1024

Full Changelog: v7.7.1...v7.7.2