Release 2025.11

What's Changed

• Update GHA workflow to deploy main image to GKE-hosted dev Runtime by @eecavanna in #1323
• Create NCBI BioSample <Action> blocks based on insdc_biosample_identifiers assertions by @sujaypatil96 in #1325
• Implement admin API endpoints for managing user allowances by @Copilot in #1327
• Install and configure Sentry SDK for Python/FastAPI by @Copilot in #1315
• Fix broken links in user-facing descriptions of changesheet endpoints by @eecavanna in #1335
• Do not create <Attribute> when soil_horizon slot has a value of "M horizon" by @sujaypatil96 in #1331
• Refrain from pushing container images to Docker Hub (push to GHCR only) by @eecavanna in #1342
• Run materialize_alldocs op hourly and remove it from "upstream" graphs by @eecavanna in #1340
• Document site client credential customization procedures for local development by @hesspnnl in #1343
• Upgrade to nmdc-schema version 11.14.0 by @pkalita-lbl in #1345
• Implement dedicated health check API endpoint at /health by @eecavanna in #1349
• Implement API endpoint admins can use to update site client secrets by @Copilot in #1351

Full Changelog: v2.12.1...v2.13.0

Release 2025.10.1

[hotfix] What's changed

• Hotfix: Run materialize_alldocs op hourly only and remove it from "upstream" graphs by @eecavanna in #1340 (fixes #1338)
• Update GitHub Actions workflow to no longer push container images to Docker Hub (only to GitHub Container Registry)

Full Changelog: v2.12.0...v2.12.1

Release 2025.10

What's Changed

• Fix issue preventing GHA workflow from publishing to PyPI by @eecavanna in #1248
• Refactor Web Component JavaScript to facilitate maintenance by @eecavanna in #1250
• Hotfix: Prevent uv from installing dependencies when running application by @eecavanna in #1259
• Fix bug where cursor-based pagination tried to access nonexistent list item by @eecavanna in #1258
• Short-circuit ID pattern removal function by @pkalita-lbl in #1271
• Upgrade nmdc-schema to version 11.12.1 by @pkalita-lbl in #1269
• Fix bug causing Swagger UI page header to be "null" by @eecavanna in #1274
• Configure GHA workflow to build container image when CSS or JS change by @eecavanna in #1276
• Temporarily disable release step in workflow by @pkalita-lbl in #1278
• Use storage_units annotation in QuantityValue translation by @pkalita-lbl in #1272
• Implement POST /jobs API endpoint that creates a job by @hesspnnl in #1268
• Handle submission images in translation process by @pkalita-lbl in #1281
• Pin Swagger UI CSS and JS versions to 5.29.4 by @eecavanna in #1284
• Replace direct jsonschema use with LinkML validation tools by @pkalita-lbl in #1287
• Add new allowance for wf_file_staging endpoints by @hesspnnl in #1294
• Make errors related to access tokens be more specific and actionable by @eecavanna in #1288
• Create Globus collection-related endpoints by @hesspnnl in #1293
• Create Sample collection related endpoints by @hesspnnl in #1302
• Re-enable Spin workload redeployment via GHA workflow by @eecavanna in #1304
• Tag container images with commit hashes also by @Copilot in #1305
• Update Runtime to use nmdc-schema version 11.13.0 by @eecavanna in #1307
• Implement API endpoints for creating and retrieving JGISequencingProjects by @mflynn-lanl in #1297
• Drop stale _runtime.tmp.linked_instances.* collections by @dwinston in #1245
• Invoke the jgi_samples index function by @hesspnnl in #1311
• Omit unset fields from created jobs (in database and API response) by @eecavanna in #1314
• Fix bugs where response validation would fail when projection was used by @hesspnnl in #1318

New Contributors

• @mflynn-lanl made their first contribution in #1297

Full Changelog: v2.11.1...v2.12.0

Release 2025.9.1

In this hotfix release, we made it so uv does not install the project's dev dependencies when launching the application.

Full Changelog: v2.11.0...v2.11.1

Release 2025.9

What's Changed

• Delete some obsolete modules/dependencies and add TODO comments by @eecavanna in #1168
• Delete additional obsolete modules/dependencies and add TODO comments by @eecavanna in #1173
• Change response format of /nmdcschema/linked_instances by @dwinston in #1176
• Avoid invoking bulk_write with no operations by @eecavanna in #1175
• Simplify Swagger authentication field headers ("User login", "Site client login") by @Copilot in #1064
• Add pagination support to /nmdcschema/linked_instances by @dwinston in #1179
• Add optional study ID input to tie submissions to one study by @JamesTessmer in #1167
• Update Swagger UI authorization modal to focus on "Username" field when opened by @eecavanna in #1182
• Migrate from pip-tools to uv by @eecavanna in #1185
• Fix issue preventing MkDocs from rendering notebook as HTML by @eecavanna in #1195
• Make FastAPI application start up 10x faster by @eecavanna in #1192
• Fix bug where analytics middleware would access attribute of None by @eecavanna in #1199
• Configure Swagger UI to persist auth status and simplify login form by @eecavanna in #1183
• Delete unimplemented API endpoints from Swagger UI and codebase by @eecavanna in #1201
• Delete "Search" web page and all references to it by @hesspnnl in #1203
• Delete Jinja2 configuration statement that requires templates/ directory to exist by @eecavanna in #1205
• Update endpoint group description to not imply connection to Data Portal by @eecavanna in #1207
• Un-skip tests that were being skipped by @eecavanna in #1197
• Provide hydrate query param for /nmdcschema/linked_instances by @eecavanna in #1209
• Prevent Swagger UI from automatically logging logged-out ORCID users back in by @eecavanna in #1210
• Handle conversion of unicode to ASCII characters for geo_loc_name Attribute by @sujaypatil96 in #1193
• Document that page number-based pagination only provides access to first 10,000 resources by @eecavanna in #1218
• Guide user in api response to move from page number-based pagination to cursor-based pagination by @dwinston in #1222
• Make it so fastapi console output is in color in local environment by @eecavanna in #1219
• Update GHA workflow that runs tests to dump fastapi container logs by @eecavanna in #1226
• Switch build backend to hatch and enable dynamic versioning by @eecavanna in #1220
• Fix regression (change of hard-coded mongorestore port) in Makefile by @dwinston in #1224
• Update NCBI Submission XML export pipeline to work for pooled samples by @sujaypatil96 in #1137
• Add message to Swagger UI, inviting users to contact us about their use cases by @eecavanna in #1216
• Create ProcessedSample and MaterialProcessing instances based on parsing sample_link by @pkalita-lbl in #1229
• Bump nmdc-schema version to v11.11.0 and update Runtime code by @eecavanna in #1227
• Implement Python notebook that migrates Mongo database from schema 11.10.0 to 11.11.1 by @eecavanna in #1231
• Add /queries:run example demonstrating a join across two collections by @eecavanna in #1233
• Write how-to guide on converting API response from JSON to CSV/TSV by @eecavanna in #1202
• Organize docs-related dependencies and clarify some TODO comments by @eecavanna in #1242
• Add <ExternalLink> in NCBI Submission XML for individual biosamples by @sujaypatil96 in #1239
• Refactor /data_objects/study/{id} API endpoint to invoke get_linked_instances function under the hood by @eecavanna in #1232
• Document generate_ids function and delete obsolete ids.py module by @eecavanna in #1244
• Make Swagger UI page easier to use by @eecavanna in #1191

Full Changelog: v2.10.0...v2.11.0

Release 2025.8

What's Changed

• Delete metadata-translation directory and update references by @eecavanna in #1088
• Update filter in ad hoc Mongo migration script to exclude irrelevant documents by @eecavanna in #1104
• Delete unused imports by @dwinston in #1103
• Remove outdated example notebook and test data by @aclum in #1070
• Update schema references to point to nmdc_materialized_patterns variant by @eecavanna in #887
• Delete metadata-translation contents (accidentally restored via merge) by @eecavanna in #1105
• Remove toplevel components directory/module by @dwinston in #1109
• Configure standard test process to include running doctests by @eecavanna in #1108
• Add docstrings and type hints to site and user functions by @eecavanna in #1116
• Fix Dagit failed code locations by removing non-existent translation repositories by @Copilot in #1117
• Refactor GET /nmdcschema/related_ids by @dwinston in #1062
• Add query-param metadata and docstring to /nmdcschema/linked_instances by @dwinston in #1121
• Fix miscellaneous issues about which pytest displays warnings by @eecavanna in #1112
• Replace copied refscan code with invocations of import-ed functions by @eecavanna in #1125
• Clarify user-facing documentation for /jobs/{job_id}:release endpoint by @eecavanna in #1113
• Upgrade to nmdc-schema version 11.10.0rc4 by @pkalita-lbl in #1127
• Document database migration process by @eecavanna in #306
• Upgrade nmdc-schema to version 11.10.0 by @pkalita-lbl in #1143
• Document process of using Locust for load testing the Runtime API by @eecavanna in #1140
• Install and document usage of Pyinstrument for performance profiling by @eecavanna in #1147
• Fix inefficient count_documents() usage in generate_ids function by @Copilot in #1149
• Add documentation about performance profiling non-GET requests by @eecavanna in #1156
• Fix /favicon.ico access and hide / and /favicon.ico endpoints from Swagger UI by @eecavanna in #1154
• Update healthcheck function to not overload MongoDB _id field by @eecavanna in #1159
• Refine performance profiling instructions by @eecavanna in #1162
• Replace slow MongoDB query with faster alternative (in generate_ids function) by @eecavanna in #1163
• Speed up list_resources function for large collections by @eecavanna in #1166

New Contributors

• @Copilot made their first contribution in #1117

Full Changelog: v2.9.0...v2.10.0

Release 2025.7

What's Changed

• Re-enable /nmdcschema/related_ids API endpoint by @eecavanna in #1033
• Remove personal (and unused) dev environment file by @dwinston in #1037
• Remove unused obsolete test file by @dwinston in #1038
• Delete ensure_data_object_type and its test by @dwinston in #1039
• Include trailing dash (-) in w3id pattern match by @dwinston in #1036
• Make it easier to maintain Swagger/OpenAPI tags by @eecavanna in #1034
• pass fully saturated mongo client to ontology-loader package by @sierra-moxon in #1014
• Unpin Swagger UI version so the Runtime always uses the latest version by @eecavanna in #1041
• Source the feature flag value from an environment variable by @eecavanna in #1046
• Serve Scalar API docs at /scalar (according to feature flag) by @eecavanna in #1003
• Update /data_objects/study/{study_id} to accommodate new format of _type_and_ancestors list by @sujaypatil96 in #1060
• Fix bug where /data_objects/study/{study_id} does not return all related data objects by @eecavanna in #1052
• Add depth units when translating submission records by @pkalita-lbl in #1053
• Update /queries:run API endpoint to return more specific errors by @dwinston in #541
• Add referential integrity check to POST /queries:run API endpoint (for update command) by @eecavanna in #1008
• Bump refscan version from 0.3.0 to 0.3.2 by @eecavanna in #1074
• Implement API endpoint that performs cascading deletes from a WorkflowExecution by @shreddd in #1065
• Get data objects that are results (has_output) of workflow execution processes by @sujaypatil96 in #1061
• Add DOI processing to Submission Portal translator by @JamesTessmer in #1079
• Bump nmdc-schema version from 11.8.0 to 11.9.1 by @eecavanna in #1081
• Add mongosh script to migrate config.was_informed_by in jobs collection by @aclum in #1085
• Use MongoDB Compass syntax instead of Studio 3T syntax by @eecavanna in #1086
• Update ensure_default_api_perms function to include aggregation permission by @hesspnnl in #1091
• Add option to enable/disable filtering on biosamples in GOLD translator by @sujaypatil96 in #1090
• Index type field to speed up Mongo queries involving it by @eecavanna in #1097
• Update WorkflowExecution cascading deletion endpoint to also delete related jobs documents by @shreddd in #1096
• Update related_resources endpoint to account for multiple DataGenerations informing a WorkflowExecution by @eecavanna in #1092
• Update log message in run_script_to_update_insdc_biosample_identifiers() Dagster @op by @sujaypatil96 in #1099
• Fix output type of run_script_to_update_insdc_biosample_identifiers() by @sujaypatil96 in #1100
• Update boot code to ensure jobs collection has index on config.activity_id field by @eecavanna in #1102

Full Changelog: v2.8.0...v2.9.0

Release 2025.6

What's Changed

• Add job that pulls insdc_biosample_identifiers and insdc_bioproject_identifiers onto biosamples by @sujaypatil96 in #980
• Enable certain graph-traversal queries (via alldocs) by @dwinston in #972
  • Subsequently disabled via #1032 👇
• Customize host port mapping via .env file by @dwinston in #999
• Introduce Ontology loader by @sierra-moxon in #923
• Update /queries:run API endpoint so only users having specific allowance can run aggregation command by @hesspnnl in #998
• Add referential integrity check to "delete" command of POST /queries:run API endpoint by @eecavanna in #1001
  • Subsequently disabled via #1022 👇
• Configure Dagster run materialize_alldocs op only after its dependent ops have finished by @eecavanna in #1010
• NCBI XML export pipeline should restrict processing to only non-JGI samples by @sujaypatil96 in #997
• Format QuantityValue slot value appropriately when it is an interval in NCBI XML export logic by @sujaypatil96 in #1013
• Fix incorrect /queries:run "update" command example (Swagger UI) by @eecavanna in #1019
• Create Python notebook that runs schema 11.7.0-to-11.8.0 migrator by @eecavanna in #1017
• Update /queries:run to allow deletions that leave behind broken references by @eecavanna in #1022
• Update related_resources API response to include subject workflow_execution_set document by @eecavanna in #1020
• Bump nmdc-schema version from 11.7.0 to 11.8.0 by @eecavanna in #1023
• Update Faker methods to validate documents before returning them by @eecavanna in #1027
• Implement "on/off" switch for /nmdcschema/related_ids endpoint (and turn it "off") by @eecavanna in #1032

New Contributors

• @sierra-moxon made their first contribution in #923
• @hesspnnl made their first contribution in #998

Full Changelog: v2.7.0...v2.8.0

Release 2025.5

What's Changed

• Create indexes on has_input/has_output in workflow_execution_set by @eecavanna in #973
• Move endpoint definition and add guard clause; improve exception detail readability; add utility endpoint by @dwinston in #976
• Remove obsolete ssh tunnel mapping by @dwinston in #977
• Refactor to avoid separate build step for test service container by @dwinston in #979
• Create Python notebook that runs nmdc-schema 11.6.1-to-11.7.0 migrator by @eecavanna in #984
• Add test showing referential integrity check during pending transaction by @eecavanna in #983
• Bump nmdc-schema to version 11.7.0 and synchronize transitive dependencies by @eecavanna in #986
• Organize MkDocs configuration/content files and use NMDC branding by @eecavanna in #991
• Fix issue preventing "Edit on GitHub" links from working by @eecavanna in #993
• Fix mermaid diagram syntax error by @dwinston in #994

Full Changelog: v2.6.0...v2.7.0

Release 2025.4

What's Changed

• Clean up root directory and fix GitHub Actions issue by @eecavanna in #942
• Swap light/dark mode toggler icons to reflect turning on light (docs) by @eecavanna in #948
• Enable referential integrity checking for /metadata/json:submit API endpoint by @eecavanna in #955
• Fix nersc-sshproxy Make target body by @dwinston in #957
• Add --no-perms flag to rsync invocation in make mongorestore-nmdc-db by @dwinston in #959
• Implement notebook for migrating database from schema version 11.5.1 to 11.6.0 by @eecavanna in #953
• Create "release jobs" endpoint by @dwinston in #962
• Implement translation of external sequencing data from submissions by @pkalita-lbl in #944
• Add referential integrity check to POST /workflows/workflow_executions API endpoint by @eecavanna in #961
• Assert insdc_bioproject_identifiers on DataGeneration records by @sujaypatil96 in #965

Full Changelog: v2.5.0...v2.6.0