Release 2024.12.1

Hotfix for study page bugs:

• Improper use of length with a Set
• Improper handling of null values for a study's funding_sources

Fix #1493

Release 2024.12

What's Changed

• 767 add email field by @marySalvi in #1442
• Post message to Slack when ingest completes successfully by @eecavanna in #1466
• Implement API endpoint that returns TSV report about submissions that are pending review by @cristina-stonepedraza in #1443
• Add nmdc_edge as a permissible source_client value by @pkalita-lbl in #1471
• Enable gene function search on GO terms by @naglepuff in #1465
• Add ability to store Field Notes-related metadata on submissions by @pkalita-lbl in #1473
• Add additional data proxies by @naglepuff in #1472
• Model KEGG/GO mappings by @naglepuff in #1477
• Upgrade to nmdc-schema v11.2.1 by @pkalita-lbl in #1488
• Add delete submission button and overflow menu by @JamesTessmer in #1446
• Synchronize portal's navigation menu with upstream website's navigation menu by @eecavanna in #1490
• 1367 multiple env select by @marySalvi in #1372
• Allow users to submit without an email stored for their account by @marySalvi in #1487
• Allow creating a submission with string or list of strings for packageName by @pkalita-lbl in #1491
• Fix GO search bugs by @naglepuff in #1492
• Support Lipidome Results by @naglepuff in #1481

New Contributors

• @cristina-stonepedraza made their first contribution in #1443

Full Changelog: v1.1.0...v1.2.0

2024.11.1

Full Changelog: v1.1.0...v1.1.1

Hotfix to properly ingest metap gene function annotations.

Fixes #1479

Release 2024.11

What's Changed

• Update dependencies and enable sentry tracing by @naglepuff in #1420
• Update DOI award box for new use cases by @JamesTessmer in #1380
• Set profiles_sample_rate for sentry by @naglepuff in #1427
• Fix ingest post dependency upgrade by @naglepuff in #1428
• Hide banner about Berkeley Schema Roll Out downtime, and reset its content by @eecavanna in #1426
• Skip BRITE terms by @naglepuff in #1409
• Make submission portal login prompt be more prominent by @eecavanna in #1188
• Remove Berkeley update banner from data and submission portals by @naglepuff in #1421
• Add COG and PFAM facets to Data Portal by @naglepuff in #1436
• nginx payload size config and sample metadata loading indicator by @pkalita-lbl in #1445
• Use correct slot when querying gene aggregations by @naglepuff in #1433
• Bump nmdc-schema and nmdc-submission-schema to 11.1.0 by @eecavanna in #1448
• Change base url and order of string parsing by @marySalvi in #1455
• Remove has_calibration column from metab table by @naglepuff in #1454
• Properly ingest ko terms and COG pathways by @naglepuff in #1459
• Change base urls for kegg by @marySalvi in #1460
• Update base url for cog by @marySalvi in #1461

Full Changelog: v1.0.1...v1.1.0

Release 2024.10.1

Hotfix to remove site banner about Berkeley rollout downtime.

Fixes: #1424

Full Changelog: v1.0.0...v1.0.1

Release 2024.10

Summary

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

What's Changed

• Merge main into berkeley-schema-migration by @eecavanna in #1349
• Replace Omics with Data Generation by @naglepuff in #1336
• Update to berkeley schema by @naglepuff in #1368
• Upgrade to nmdc-submission-schema v11.0.0rc1 by @pkalita-lbl in #1374
• Fix Berkeley schema element usage in frontend code by @pkalita-lbl in #1375
• Guard against request errors for PI images by @marySalvi in #1262
• Bump express from 4.19.2 to 4.21.0 in /web by @dependabot in #1396
• Bump dompurify from 2.4.7 to 2.5.7 in /web by @dependabot in #1398
• Update submission report to include "Source Client" and "Status" by @eecavanna in #1401
• Replace stale list of Redirect URIs with link to latest list by @eecavanna in #1402
• Initial implementation of metadata suggestion endpoint by @pkalita-lbl in #1403
• Rename omics_processing endpoints to data_generation by @naglepuff in #1404
• Use correct slot for study protocols for Berkeley schema by @naglepuff in #1407
• Berkeley Merge Cleanup by @naglepuff in #1408
• Update Data and Submission Portals to work with/use NMDC Schema version v11.0.1 (Berkeley schema) by @naglepuff in #1321
• Create index on download/data object association by @naglepuff in #1411
• Add banner announcing upcoming maintenance events (October 15-16) by @eecavanna in #1413
• Migrate workflow_type values in data_object table by @pkalita-lbl in #1416

Full Changelog: v0.25.0...v1.0.0

Release 2024.9.1

Hotfix to add site banner about Berkeley rollout downtime.

Full Changelog: v0.25.0...v0.25.1

Release 2024.9

What's Changed

• Bump ipython from 7.31.1 to 8.10.0 by @dependabot in #856
• Bump authlib from 1.3.0 to 1.3.1 by @dependabot in #1274
• Bump elliptic from 6.5.4 to 6.5.7 in /web by @dependabot in #1356
• Bump requests from 2.28.1 to 2.32.2 by @dependabot in #1272
• Bump pydantic from 1.10.2 to 1.10.13 by @dependabot in #1244
• Bump axios from 0.24.0 to 0.28.0 in /web by @dependabot in #1245
• Add click functionality to numbers by @marySalvi in #1366
• Hotfix issue 1377 by @marySalvi in #1379
• Ingest COG terms, pathways and functions by @naglepuff in #1359
• Change down_revision of COG table migration by @naglepuff in #1387
• Ensure template props are synced on PATCH by @naglepuff in #1395
• Ingest PFAM entries and clans by @naglepuff in #1376

Full Changelog: v0.24.1...v0.24.2

Release 2024.8.1

• Hotfix for #1377

Full Changelog: v0.24.0...v0.24.1

Release 2024.8

What's Changed

• Update documentation and redirect by @JamesTessmer in #1319
• Replace types-pkg-resources with types-setuptools by @pkalita-lbl in #1325
• Bump minimatch from 3.0.4 to 3.1.2 in /web by @dependabot in #811
• Update httpx to 0.23.0 by @naglepuff in #1329
• Add funding source box to study form by @JamesTessmer in #1323
• Bump dnspython from 2.3.0 to 2.6.1 by @dependabot in #1240
• Bump tar from 6.1.11 to 6.2.1 in /web by @dependabot in #1241
• Bump ws from 6.2.2 to 6.2.3 in /web by @dependabot in #1282
• Bump follow-redirects from 1.14.8 to 1.15.6 in /web by @dependabot in #1242
• Bump express from 4.17.1 to 4.19.2 in /web by @dependabot in #1243
• Close code block by @marySalvi in #1339
• 884 sortable submissions list by @marySalvi in #1322
• Make ORCID Base URL configurable via environment variable by @eecavanna in #1348
• Replace double quotes with single quotes (to appease linter) by @eecavanna in #1351
• Update funding source entry text box and description by @JamesTessmer in #1345
• Bump nmdc-schema and nmdc-submission-schema from 10.7.0 to 10.8.0 by @aclum in #1355
• Implement endpoint that returns TSV file of submission summaries by @eecavanna in #1290
• 1303 add gold tooltip by @marySalvi in #1346
• Add schema version identifiers to /api/version response by @pkalita-lbl in #1358
• Add study id to partial search by @marySalvi in #1360
• Add "Data API" link to navbar ("Products" menu) by @eecavanna in #1364
• Show per-workflow and per-filetype sizes in bulk download by @naglepuff in #1352
• Support pathway search with multiple prefixes by @naglepuff in #1353

New Contributors

• @aclum made their first contribution in #1355

Full Changelog: v0.23.0...v0.24.0