Release 2025.2

What's Changed

• Remove reference to non-existent MongoDB collection (metap_gene_function_aggregation) by @eecavanna in #893
• Write how-to guide about minting IDs via the NMDC Runtime API Swagger UI by @eecavanna in #896
• Create notebook that migrates database from nmdc-schema v11.3.0 to v11.4.0 by @eecavanna in #894
• Account for multiple sequencing runs in NEON surface water translator code by @sujaypatil96 in #898
• Bump nmdc-schema from 11.3.0 to 11.4.0 by @eecavanna in #901
• Enable measuring and reporting of Python test coverage by @shreddd in #908
• Update name/description of alldocs-powered endpoint to include caveats by @eecavanna in #912
• Replace the use of alldocs with respective collections for record retrieval in NCBI exporter by @sujaypatil96 in #907
• Update link to point directly to workflow documentation (skipping redirect) by @ssarrafan in #916
• Update migration notebook to only dump/restore relevant collections by @eecavanna in #918

New Contributors

• @ssarrafan made their first contribution in #916

Full Changelog: v2.3.0...v2.4.0

Release 2025.1

What's Changed

• Configure GHA to run tests when example changesheets change by @eecavanna in #845
• Remove whitespace character that was making example changesheet invalid by @eecavanna in #846
• Fix project documentation links by @dwinston in #847
• Register dagster scheduled job to re-materialize alldocs daily by @PeopleMakeCulture in #810
• Account for change in alldocs field name from type to _type_and_ancestors by @sujaypatil96 in #851
• Add tests targeting core functionality of /data_objects/study/{study_id} endpoint by @eecavanna in #849
• Filter GOLD sequencing projects and biosamples based on projectStatus by @sujaypatil96 in #853
• Add multivalued string example to changesheets documentation by @aclum in #848
• Add class with helper methods to fill in missing records in database by @sujaypatil96 in #856
• Implement refscan-based real-time referential integrity checking on /metadata/json:validate by @eecavanna in #835
• Fix bug where validate_json referential integrity check ignored documents in database by @eecavanna in #861
• Update GHA workflows to deploy redirects instead of MkDocs site by @eecavanna in #865
• Create Python notebook demonstrating general usage of Runtime API by @eecavanna in #863
• Fix typos in Python notebook (in docs/nb directory) by @eecavanna in #869
• Clarify example sentence in PR template by @eecavanna in #871
• Clarify explanation of access_token property in Python notebook (in docs/nb) by @eecavanna in #872
• Bump nmdc-schema from 11.2.1 to 11.3.0 and sync transitive deps by @eecavanna in #874
• Dagster job to populate missing biosample records for a study from GOLD by @sujaypatil96 in #859
• Use nmdc-schema-provided function to get typecode from slot pattern by @eecavanna in #878
• Apply projectStatus filter only if sequencingCenter is JGI in GOLD translator by @sujaypatil96 in #881

Full Changelog: v2.2.0...v2.3.0

Release 2024.12.1

This hotfix release addresses the following issues:

• #850 - the /data_objects/study/{study_id} endpoint was still looking for class hierarchy information in the type field, whereas the code that generates the alldocs collection had been modified to store that information in a different field
• #725 - core functionality of that endpoint was not being tested

Full Changelog: v2.2.0...v2.2.1

Release 2024.12

What's Changed

• Delete unused tests2 directory by @shreddd in #784
• Replace deprecated utcnow() calls with now(timezone.utc) by @shreddd in #788
• Add "Translators" subsystem as option in PR template by @eecavanna in #793
• Remove reference to nonexistent tests2 directory by @eecavanna in #794
• Update bulk_validation_referential_integrity_check notebook to concur with refscan (no false positives) by @dwinston in #796
• Simplify local mongorestore of remote mongodump by @dwinston in #801
• Add was_generated_by index to functional_annotation_agg collection by @dwinston in #802
• Update /nmdcschema/{collection_name} API endpoint description to include performance-related guidance by @eecavanna in #803
• Post berkeley schema NCBI export pipeline updates by @sujaypatil96 in #807
• Document query parameters directly instead of via freeform text blurbs by @eecavanna in #804
• Implement notebook that migrates database from schema v11.1.0 to v11.2.0 by @eecavanna in #813
• Implement an API endpoint an admin can use to update a user's password by @eecavanna in #779
• Add mapping for multiple environments by @marySalvi in #741
• Display copy/pasteable HTTP Authorization header with Bearer token on Swagger UI for ORCiD-Authenticated user by @dwinston in #812
• Delete comment that impacted subsequent code once newlines were replaced by @eecavanna in #819
• Update Python packages to patch security issues reported by Dependabot by @eecavanna in #815
• Upgrade to nmdc-schema v11.2.1 by @pkalita-lbl in #825
• Update migration notebook's destination nmdc-schema version to 11.2.1 by @eecavanna in #827
• Filter biosamples/projects/analysis projects based on sequencingStrategy by @sujaypatil96 in #816
• Address documentation/docstring TODOs by @dwinston in #840
• Add option to GOLD translator to ignore field research sites by @sujaypatil96 in #833
• 696 update dagster op for materialize alldocs by @mkshah605 in #817
• Remove obsolete guidance from development guide by @shreddd in #842
• Update changesheets examples by @aclum in #841

New Contributors

• @marySalvi made their first contribution in #741
• @mkshah605 made their first contribution in #817

Full Changelog: v2.1.1...v2.2.0

Release 2024.11.1

Summary

Hotfix to allow workflow client access tokens to access the /queries:run endpoint, if the client has the right permissions (similar to a user)

What's Changed

• Ensure basic validation occurs for updates via POST /queries:run by @dwinston in #782
• Workflow queries:run access for site_clients by @shreddd in #783

Full Changelog: v2.1.0...v2.1.0-hotfix-776

Release 2024.11

What's Changed

• Add documentation pages about translators and exporters by @sujaypatil96 in #729
• Web docs index page missing translators/exporter tutorials by @sujaypatil96 in #731
• Bumped up nmdc-schema to v11.0.3 by @shreddd in #733
• Update queries:run examples by @aclum in #735
• Make default expiry 24 hours by @shreddd in #739
• /data_objects/study/{study_id} should take into account was_informed_by relationships by @sujaypatil96 in #738
• Migrations: Update notebook to omit Mongo credentials from commands when authentication is disabled by @eecavanna in #745
• Migrations: Update notebook to perform LinkML validation and allow database name configuration by @eecavanna in #750
• Document the /nmdcschema/typecodes API endpoint (reverse engineered) by @eecavanna in #748
• fix: check for LinkML base type "Decimal" on loading changesheet by @dwinston in #752
• Migrations: Fix bug in "progress bar" logic and work around upstream memory leak by @eecavanna in #757
• cleanup: remove obselete version attribute by @dwinston in #763
• fix: update .env load guidance by @dwinston in #764
• Update PR template to produce PR descriptions that are easier to read by @eecavanna in #759
• Implement the 11.0.3-to-11.1.0 migration notebook by @eecavanna in #761
• Bump nmdc-schema from 11.0.3 to 11.1.0 and sync transitive dependencies by @eecavanna in #770
• Fix handling of GOLD and JGI IDs in submission data translator by @pkalita-lbl in #773

Full Changelog: v2.0.1...v2.1.0

Release 2024.10.1

Summary

Hotfix release for nmdc-schema update to v11.0.3

What's Changed

• nmdc-schema update to v11.0.3 - Fixes #732

Full Changelog: v2.0.0...v2.0.1

Release 2024.10

Summary

In this release, we switched from using the legacy schema to using the Berkeley schema.

What's Changed

• Switch to "Berkeley schema" and eliminate broken references preventing application startup by @eecavanna in #579
• berkeley: Merge main into berkeley (to trigger GHA workflow) by @eecavanna in #584
• berkeley: Merge main into berkeley (July 17) by @eecavanna in #599
• berkeley: Update test_endpoints.py to fix some failing tests by @aclum in #596
• berkeley: Update minter to use first typecode when pattern contains multiple typecodes by @eecavanna in #597
• Merge main into berkeley (routine; merged August 9, 2024) by @eecavanna in #625
• Document expectations regarding merging main into berkeley over time by @eecavanna in #634
• Get ORCID base URL (production vs. sandbox) from environment variable by @eecavanna in #637
• Use ORCID environment-specific JWKS values and clean up existing comments by @eecavanna in #639
• Fix Failing Tests in Berkeley Branch by @aclum in #621
• 593 update workflow endpoints by @PeopleMakeCulture in #624
• Merge main into berkeley (routine, August 23, 2024) by @eecavanna in #648
• berkeley: Update nmdc-schema to 11.0.0rc20 and sync transitive dependencies by @eecavanna in #650
• berkeley: Complete conversion of SubmissionPortalTranslator by @pkalita-lbl in #657
• Merge main into berkeley (routine, August 29, 2024) by @aclum in #661
• Update API endpoints to search PlannedProcess-containing collections by @dwinston in #666
• Migration of submission portal translator to be conformant with berkeley schema by @sujaypatil96 in #662
• Update GOLD translator to work with Berkeley schema by @sujaypatil96 in #656
• Fix 3 failing tests, skip others, and bump nmdc-schema to v11.0.0rc22 by @aclum in #676
• Fix bugs in Berkeley migration notebook and update its nmdc-schema version by @eecavanna in #680
• Update Swagger tag descriptions to match Berkeley API GUI how-to guide by @eecavanna in #682
• Restore hyperlinks to "Metadata" section and modernize Runtime description by @eecavanna in #686
• berkeley: Unskip test_submit_workflow_activities test and make it work with Berkeley schema by @aclum in #684
• berkeley: Restore tests that were being skipped by mistake (oops) by @eecavanna in #688
• Quick fixes for GOLD API client tests in tests/test_ops/test_gold_api_ops.py by @sujaypatil96 in #692
• Merge main into berkeley (routine, September 19, 2024) by @eecavanna in #693
• 576 berkeley updates ref integrity notebook by @PeopleMakeCulture in #695
• berkeley: Determine class ancestry per-type value (within collection) instead of per-collection (when generating alldocs) by @eecavanna in #694
• Update field name to be consistent with Berkeley schema by @eecavanna in #697
• Configure pytest GHA workflow so developers can trigger it manually by @eecavanna in #705
• Merge main into berkeley (routine, September 27, 2024) by @eecavanna in #706
• Fix bug where one document in each collection is omitted from alldocs by @eecavanna in #709
• Migrate NEON translators to be conformant with berkeley schema by @sujaypatil96 in #701
• berkeley: Test function that generates alldocs collection by @eecavanna in #715
• Unskip and fix 3 tests that were being skipped in test_metadata.py by @aclum in #716
• Update Runtime to work with Berkeley schema (i.e. nmdc-schema version v11.0.0) by @eecavanna in #718
• Update nmdc-schema package to 11.0.1 and synchronize transitive dependencies by @eecavanna in #722
• NCBI XML Export pipeline migration by @sujaypatil96 in #724
• Remove part_of still being asserted on NucleotideSequencing by @sujaypatil96 in #728

Full Changelog: v1.10.0...v2.0.0

Release 2024.9

What's Changed

• Implement notebook that migrates Mongo database from "legacy" to "Berkeley" schema by @eecavanna in #553
• Missing attribute "qualitycontrolreport" causing multiple NEON tests to fail by @aclum in #660
• Remove test code's dependence on a static Mongo dump by @eecavanna in #664
• Add indexes to alldocs collection for has_input and has_output keys/slots by @sujaypatil96 in #674

Full Changelog: v1.9.0...v1.10.0

Release 2024.8

What's Changed

• feat: refactor notebook and supporting code by @dwinston in #609
• fix: changesheet can update bytes-ranged slot by @dwinston in #614
• Add broker name to NCBI XML, and also pull in protocol_link.name from LibraryPreparation objects by @sujaypatil96 in #612
• be more conservative with builtins by @dwinston in #619
• Make <DataType> in NCBI XML SRA <Action> block more specific by @sujaypatil96 in #618
• not all schema collections suffix with _sets by @dwinston in #620
• hotfix: op fails due to invalid helper method invocation by @dwinston in #633
• feat: test coverage for apply_metadata_in job by @dwinston in #635
• reimplement /data_objects/study/{study_id} using alldocs by @sujaypatil96 in #608
• Update nmdc-schema to v10.8.0 by @aclum in #645
• Add funding source to SubmissionPortalTranslator by @JamesTessmer in #627

New Contributors

• @JamesTessmer made their first contribution in #627

Full Changelog: v1.8.0...v1.9.0