Releases: microbiomedata/nmdc-server
Releases · microbiomedata/nmdc-server
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
intoberkeley-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 indata_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
andnmdc-submission-schema
from10.7.0
to10.8.0
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
Full Changelog: v0.23.0...v0.24.0
Release 2024.7
What's Changed
- Change router to go to homepage instead of previous history index by @marySalvi in #1293
- Add user info page by @pkalita-lbl in #1294
- Add contact support panel by @marySalvi in #1292
- Add ability to track which client created a submission by @pkalita-lbl in #1300
- Add endpoint for explicitly requesting
SubmissionMetadata
lock by @pkalita-lbl in #1299 - Use more descriptive section name for envo terms by @naglepuff in #1296
- Pass correct string to showColumnsBySectionTitle when showing single section by @pkalita-lbl in #1308
- Bump decode-uri-component from 0.2.0 to 0.2.2 in /web by @dependabot in #809
- Remove unnecesary container by @marySalvi in #1309
- Fix DataHarmonizer help sidebar positioning by @pkalita-lbl in #1310
- Add Data Integration link to header menus by @pkalita-lbl in #1312
- Derive Excel worksheet names from schema annotations by @pkalita-lbl in #1311
- Update ingest and data model to account for Metatranscriptomics by @naglepuff in #1313
- Revalidate form when permission level changes by @naglepuff in #1317
Full Changelog: v0.22.0...v0.23.0
Release 2024.6
What's Changed
- Standardize sample verbage by @marySalvi in #1270
- Use Bearer tokens for authentication by @pkalita-lbl in #1257
- Show save progress by @marySalvi in #1269
- Fix DataHarmonizer scrolling issue by @pkalita-lbl in #1267
- Document current ORCID Redirect URIs by @shreddd in #1273
- Redirect users to submission portal if logging in from submission portal by @naglepuff in #1275
- Add source to gh issue creation by @JamesTessmer in #1278
- Add biosample columns to partial search by @marySalvi in #1276
- Upgrade to latest nmdc-schema and nmdc-submission-schema by @pkalita-lbl in #1284
- Rename
expires
toexpires_in
in TokenResponse by @pkalita-lbl in #1287 - Remove extraneous data update call when changing tabs by @pkalita-lbl in #1288
Full Changelog: v0.21.0...v0.22.0
Release 2024.5
What's Changed
- Fix for bug where studies would not scroll to return to the top of the page when revisited by @JamesTessmer in #1225
- Refrain from reporting "0 results" and "0 samples" while loading data by @eecavanna in #1212
- Update banner to indicate new re-ID-ing date by @eecavanna in #1233
- Only show AppBanner component on submission portal Home page by @pkalita-lbl in #1236
- Add nmdc-server CLI subcommand for loading local database with production data by @pkalita-lbl in #1229
- Bump moment from 2.29.2 to 2.29.4 in /web by @dependabot in #746
- Bump vuetify from 2.6.1 to 2.6.10 in /web by @dependabot in #789
- Bump vuetify and moment by @naglepuff in #1239
- Create github issue when user submits metadata by @JamesTessmer in #1208
- Filter out irrelevant omics_processing results by @naglepuff in #1213
- Remove limit reset for pagination when conditions change. by @marySalvi in #1247
- Make query conditions section sticky and max size to 50vh by @marySalvi in #1248
- Bump terser from 4.8.0 to 4.8.1 in /web by @dependabot in #751
- Bump ip from 1.1.5 to 1.1.9 in /web by @dependabot in #1246
- Add FAQs, Blog, and Media Materials links to header menu by @pkalita-lbl in #1252
- Allow Github issue creation to track all IDs by @JamesTessmer in #1253
- Change "Done" to "Submitted" by @JamesTessmer in #1255
- Upgrade nmdc-schema and nmdc-submission-schema to 10.3.0 by @pkalita-lbl in #1254
- Refrain from rendering any
<AppBanner />
elements by @eecavanna in #1259
Full Changelog: v0.20.3...v0.21.0
Release 2024.4.3
- Only show AppBanner component on submission portal Home page #1236
Full Changelog: v0.20.2...v0.20.3