Merge dandi archive updates from december 2023 onwards

.github/workflows/backend-ci.yml

@@ -40,7 +40,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       - name: Install tox

.github/workflows/cli-integration.yml

@@ -29,7 +29,7 @@ jobs:
           docker image save -o dandiarchive-api.tgz dandiarchive/dandiarchive-api
 
       - name: Upload Docker image tarball
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: dandiarchive-api.tgz
           path: dandiarchive-api.tgz
@@ -50,15 +50,15 @@ jobs:
       DANDI_TESTS_PULL_DOCKER_COMPOSE: 0
     steps:
       - name: Download Docker image tarball
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: dandiarchive-api.tgz
 
       - name: Import Docker image
         run: docker image load -i dandiarchive-api.tgz
 
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
 

.github/workflows/frontend-ci.yml

@@ -26,7 +26,7 @@ jobs:
         run: yarn run lint --no-fix
 
       - name: Type-check Vue app
-        run: yarn run type
+        run: yarn run type-check
 
       - name: Build Vue app
         run: yarn run build
@@ -70,9 +70,9 @@ jobs:
       DANDI_ALLOW_LOCALHOST_URLS: 1
 
       # Web client env vars
-      VUE_APP_DANDI_API_ROOT: http://localhost:8000/api/
-      VUE_APP_OAUTH_API_ROOT: http://localhost:8000/oauth/
-      VUE_APP_OAUTH_CLIENT_ID: Dk0zosgt1GAAKfN8LT4STJmLJXwMDPbYWYzfNtAl
+      VITE_APP_DANDI_API_ROOT: http://localhost:8000/api/
+      VITE_APP_OAUTH_API_ROOT: http://localhost:8000/oauth/
+      VITE_APP_OAUTH_CLIENT_ID: Dk0zosgt1GAAKfN8LT4STJmLJXwMDPbYWYzfNtAl
 
       # E2E tests env vars
       CLIENT_URL: http://localhost:8085
@@ -82,7 +82,6 @@ jobs:
 
       - uses: actions/setup-node@v4
         with:
-          node-version: '16'
           cache: 'yarn'
           cache-dependency-path: web/yarn.lock
 
@@ -92,7 +91,7 @@ jobs:
         working-directory: web
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -116,23 +115,23 @@ jobs:
 
       - name: Install E2E tests
         run: yarn install --frozen-lockfile
-        working-directory: web/test
+        working-directory: e2e
 
       - name: Lint E2E tests
         run: yarn run lint --no-fix --max-warnings=0
-        working-directory: web/test
+        working-directory: e2e
 
       - name: Run E2E tests
         run: |
           # start vue dev server and wait for it to start
-          yarn --cwd .. run serve 2> /dev/null &
+          yarn --cwd ../web/ run dev 2> /dev/null &
           while ! nc -z localhost 8085; do
             sleep 3
           done
 
           # start the dandi-api server
-          python ../../manage.py runserver &
+          python ../manage.py runserver &
 
           # run the E2E tests
           yarn run test
-        working-directory: web/test
+        working-directory: e2e

CHANGELOG.md

@@ -1,3 +1,142 @@
+# v0.3.69 (Wed Dec 20 2023)
+
+#### 🐛 Bug Fix
+
+- Approval view: automatically redirect back to page after authentication [#1786](https://github.com/dandi/dandi-archive/pull/1786) ([@mvandenburgh](https://github.com/mvandenburgh))
+- Remove explicit dependency on `pydantic` [#1796](https://github.com/dandi/dandi-archive/pull/1796) ([@mvandenburgh](https://github.com/mvandenburgh))
+
+#### Authors: 1
+
+- Mike VanDenburgh ([@mvandenburgh](https://github.com/mvandenburgh))
+
+---
+
+# v0.3.68 (Wed Dec 20 2023)
+
+#### 🐛 Bug Fix
+
+- Update + Reconfigure Vue Sentry SDK [#1795](https://github.com/dandi/dandi-archive/pull/1795) ([@mvandenburgh](https://github.com/mvandenburgh))
+- Remove old squashed migrations [#1778](https://github.com/dandi/dandi-archive/pull/1778) ([@brianhelba](https://github.com/brianhelba))
+- Fix S101 Use of `assert` detected [#1783](https://github.com/dandi/dandi-archive/pull/1783) ([@brianhelba](https://github.com/brianhelba))
+
+#### Authors: 2
+
+- Brian Helba ([@brianhelba](https://github.com/brianhelba))
+- Mike VanDenburgh ([@mvandenburgh](https://github.com/mvandenburgh))
+
+---
+
+# v0.3.67 (Thu Dec 14 2023)
+
+#### 🐛 Bug Fix
+
+- Convert `rest.ts` to composition API [#1774](https://github.com/dandi/dandi-archive/pull/1774) ([@mvandenburgh](https://github.com/mvandenburgh))
+- Add login redirect to user dashboard [#1781](https://github.com/dandi/dandi-archive/pull/1781) ([@mvandenburgh](https://github.com/mvandenburgh))
+- Add embargo re-design doc [#1772](https://github.com/dandi/dandi-archive/pull/1772) ([@AlmightyYakob](https://github.com/AlmightyYakob))
+- Ensure that creating the default OAuth2 Application works on staging [#1779](https://github.com/dandi/dandi-archive/pull/1779) ([@brianhelba](https://github.com/brianhelba))
+- Squash migrations for "api", "analytics", and "zarr" apps [#1777](https://github.com/dandi/dandi-archive/pull/1777) ([@brianhelba](https://github.com/brianhelba))
+- Fix issues found by Ruff [#1776](https://github.com/dandi/dandi-archive/pull/1776) ([@brianhelba](https://github.com/brianhelba))
+- Switch frontend build process from Webpack to Vite [#1725](https://github.com/dandi/dandi-archive/pull/1725) ([@mvandenburgh](https://github.com/mvandenburgh))
+- Fix FBT001 Boolean-typed positional argument in function definition [#1765](https://github.com/dandi/dandi-archive/pull/1765) ([@brianhelba](https://github.com/brianhelba))
+- Fix RET505 Unnecessary `else` / `elif` after `return` statement [#1752](https://github.com/dandi/dandi-archive/pull/1752) ([@brianhelba](https://github.com/brianhelba))
+- Avoid clobbering version metadata when calculating assets summary [#1557](https://github.com/dandi/dandi-archive/pull/1557) ([@danlamanna](https://github.com/danlamanna))
+- Add upload/asset blob garbage collection design doc [#1733](https://github.com/dandi/dandi-archive/pull/1733) ([@mvandenburgh](https://github.com/mvandenburgh))
+- Fix DJ008 Model does not define `__str__` method [#1767](https://github.com/dandi/dandi-archive/pull/1767) ([@brianhelba](https://github.com/brianhelba))
+- [FIX] serviceUrl replacement [#1770](https://github.com/dandi/dandi-archive/pull/1770) ([@magland](https://github.com/magland))
+
+#### 🏠 Internal
+
+- [gh-actions](deps): Bump actions/setup-python from 4 to 5 [#1780](https://github.com/dandi/dandi-archive/pull/1780) ([@dependabot[bot]](https://github.com/dependabot[bot]))
+- `test_zarr.py`: Import `EMPTY_CHECKSUM` from `zarr_checksum` [#1775](https://github.com/dandi/dandi-archive/pull/1775) ([@jwodder](https://github.com/jwodder))
+
+#### Authors: 7
+
+- [@dependabot[bot]](https://github.com/dependabot[bot])
+- Brian Helba ([@brianhelba](https://github.com/brianhelba))
+- Dan LaManna ([@danlamanna](https://github.com/danlamanna))
+- Jacob Nesbitt ([@AlmightyYakob](https://github.com/AlmightyYakob))
+- Jeremy Magland ([@magland](https://github.com/magland))
+- John T. Wodder II ([@jwodder](https://github.com/jwodder))
+- Mike VanDenburgh ([@mvandenburgh](https://github.com/mvandenburgh))
+
+---
+
+# v0.3.66 (Fri Dec 01 2023)
+
+#### 🐛 Bug Fix
+
+- Fix invalid contributors causing crash [#1771](https://github.com/dandi/dandi-archive/pull/1771) ([@mvandenburgh](https://github.com/mvandenburgh))
+- Remove unnecessary quote escaping [#1766](https://github.com/dandi/dandi-archive/pull/1766) ([@brianhelba](https://github.com/brianhelba))
+- Fix a test failure [#1768](https://github.com/dandi/dandi-archive/pull/1768) ([@brianhelba](https://github.com/brianhelba))
+- Fix issues found by Ruff [#1763](https://github.com/dandi/dandi-archive/pull/1763) ([@brianhelba](https://github.com/brianhelba))
+- WIP: Fix RET503 Missing explicit `return` at the end of function able to return non-`None` value [#1762](https://github.com/dandi/dandi-archive/pull/1762) ([@brianhelba](https://github.com/brianhelba))
+- Fix issues found by Ruff [#1748](https://github.com/dandi/dandi-archive/pull/1748) ([@brianhelba](https://github.com/brianhelba))
+- Fix G004 Logging statement uses f-string [#1750](https://github.com/dandi/dandi-archive/pull/1750) ([@brianhelba](https://github.com/brianhelba))
+- Fix S113 Probable use of requests call without timeout [#1751](https://github.com/dandi/dandi-archive/pull/1751) ([@brianhelba](https://github.com/brianhelba))
+- Upgrade django-s3-file-field [#1735](https://github.com/dandi/dandi-archive/pull/1735) ([@brianhelba](https://github.com/brianhelba))
+- Fix N818 Exception name should be named with an Error suffix [#1749](https://github.com/dandi/dandi-archive/pull/1749) ([@brianhelba](https://github.com/brianhelba))
+
+#### Authors: 2
+
+- Brian Helba ([@brianhelba](https://github.com/brianhelba))
+- Mike VanDenburgh ([@mvandenburgh](https://github.com/mvandenburgh))
+
+---
+
+# v0.3.65 (Wed Nov 22 2023)
+
+#### 🐛 Bug Fix
+
+- Check that path is an asset before proceeding [#1759](https://github.com/dandi/dandi-archive/pull/1759) ([@AlmightyYakob](https://github.com/AlmightyYakob))
+
+#### Authors: 1
+
+- Jacob Nesbitt ([@AlmightyYakob](https://github.com/AlmightyYakob))
+
+---
+
+# v0.3.64 (Wed Nov 22 2023)
+
+#### 🐛 Bug Fix
+
+- adjust neurosift service endpoint URL, passing additional info [#1706](https://github.com/dandi/dandi-archive/pull/1706) ([@magland](https://github.com/magland) [@waxlamp](https://github.com/waxlamp))
+- Optimize dandiset owner PUT endpoint [#1737](https://github.com/dandi/dandi-archive/pull/1737) ([@mvandenburgh](https://github.com/mvandenburgh) [@AlmightyYakob](https://github.com/AlmightyYakob))
+
+#### Authors: 4
+
+- Jacob Nesbitt ([@AlmightyYakob](https://github.com/AlmightyYakob))
+- Jeremy Magland ([@magland](https://github.com/magland))
+- Mike VanDenburgh ([@mvandenburgh](https://github.com/mvandenburgh))
+- Roni Choudhury ([@waxlamp](https://github.com/waxlamp))
+
+---
+
+# v0.3.63 (Tue Nov 21 2023)
+
+#### 🐛 Bug Fix
+
+- Fix race condition in version PUT endpoint [#1757](https://github.com/dandi/dandi-archive/pull/1757) ([@mvandenburgh](https://github.com/mvandenburgh))
+
+#### Authors: 1
+
+- Mike VanDenburgh ([@mvandenburgh](https://github.com/mvandenburgh))
+
+---
+
+# v0.3.62 (Fri Nov 17 2023)
+
+#### 🐛 Bug Fix
+
+- [DATALAD RUNCMD] Replace youtube URL with the one with @dandiarchive [#1754](https://github.com/dandi/dandi-archive/pull/1754) ([@yarikoptic](https://github.com/yarikoptic))
+- Fix style issues found by Ruff [#1741](https://github.com/dandi/dandi-archive/pull/1741) ([@brianhelba](https://github.com/brianhelba))
+
+#### Authors: 2
+
+- Brian Helba ([@brianhelba](https://github.com/brianhelba))
+- Yaroslav Halchenko ([@yarikoptic](https://github.com/yarikoptic))
+
+---
+
 # v0.3.61 (Thu Nov 09 2023)
 
 #### 🐛 Bug Fix

dandiapi/analytics/migrations/0001_initial.py → dandiapi/analytics/migrations/0001_initial_v2.py

@@ -1,5 +1,3 @@
-# Generated by Django 4.1.4 on 2023-04-10 21:09
-
 import django.core.validators
 from django.db import migrations, models
 
@@ -33,7 +31,13 @@ class Migration(migrations.Migration):
                 ('embargoed', models.BooleanField()),
             ],
             options={
-                'unique_together': {('name', 'embargoed')},
+                'unique_together': set(),
             },
         ),
+        migrations.AddConstraint(
+            model_name='processeds3log',
+            constraint=models.UniqueConstraint(
+                fields=('name', 'embargoed'), name='analytics_processeds3log_unique_name_embargoed'
+            ),
+        ),
     ]

dandiapi/analytics/models.py

@@ -3,14 +3,6 @@
 
 
 class ProcessedS3Log(models.Model):
-    class Meta:
-        constraints = [
-            models.UniqueConstraint(
-                fields=['name', 'embargoed'],
-                name='%(app_label)s_%(class)s_unique_name_embargoed',
-            )
-        ]
-
     name = models.CharField(
         max_length=36,
         validators=[
@@ -20,3 +12,14 @@ class Meta:
     )
     # This is necessary to determine which bucket the logfile corresponds to
     embargoed = models.BooleanField()
+
+    class Meta:
+        constraints = [
+            models.UniqueConstraint(
+                fields=['name', 'embargoed'],
+                name='%(app_label)s_%(class)s_unique_name_embargoed',
+            )
+        ]
+
+    def __str__(self) -> str:
+        return self.name

dandiapi/analytics/tasks/__init__.py

@@ -22,10 +22,11 @@
 
 
 def _bucket_objects_after(bucket: str, after: str | None) -> Generator[dict, None, None]:
-    assert bucket in [
+    if bucket not in {
         settings.DANDI_DANDISETS_LOG_BUCKET_NAME,
         settings.DANDI_DANDISETS_EMBARGO_LOG_BUCKET_NAME,
-    ]
+    }:
+        raise ValueError(f'Non-log bucket: {bucket}')
     embargoed = bucket == settings.DANDI_DANDISETS_EMBARGO_LOG_BUCKET_NAME
     s3 = get_boto_client(get_storage() if not embargoed else get_embargo_storage())
     kwargs = {}
@@ -40,10 +41,11 @@ def _bucket_objects_after(bucket: str, after: str | None) -> Generator[dict, Non
 @shared_task(queue='s3-log-processing', soft_time_limit=60, time_limit=80)
 def collect_s3_log_records_task(bucket: LogBucket) -> None:
     """Dispatch a task per S3 log file to process for download counts."""
-    assert bucket in [
+    if bucket not in {
         settings.DANDI_DANDISETS_LOG_BUCKET_NAME,
         settings.DANDI_DANDISETS_EMBARGO_LOG_BUCKET_NAME,
-    ]
+    }:
+        raise RuntimeError
     embargoed = bucket == settings.DANDI_DANDISETS_EMBARGO_LOG_BUCKET_NAME
     after = ProcessedS3Log.objects.filter(embargoed=embargoed).aggregate(last_log=Max('name'))[
         'last_log'
@@ -62,10 +64,11 @@ def process_s3_log_file_task(bucket: LogBucket, s3_log_key: str) -> None:
     asset blobs. Prevents duplicate processing with a unique constraint on the ProcessedS3Log name
     and embargoed fields.
     """
-    assert bucket in [
+    if bucket not in {
         settings.DANDI_DANDISETS_LOG_BUCKET_NAME,
         settings.DANDI_DANDISETS_EMBARGO_LOG_BUCKET_NAME,
-    ]
+    }:
+        raise RuntimeError
     embargoed = bucket == settings.DANDI_DANDISETS_EMBARGO_LOG_BUCKET_NAME
 
     # short circuit if the log file has already been processed. note that this doesn't guarantee
@@ -93,7 +96,7 @@ def process_s3_log_file_task(bucket: LogBucket, s3_log_key: str) -> None:
             log.save()
         except IntegrityError as e:
             if 'unique_name_embargoed' in str(e):
-                logger.info(f'Already processed log file {s3_log_key}, embargo: {embargoed}')
+                logger.info('Already processed log file %s, embargo: %s', s3_log_key, embargoed)
             return
 
         # note this task is run serially per log file. this is to avoid the contention between

dandiapi/api/admin.py

@@ -59,7 +59,7 @@ def get_queryset(self, request):
             )
         )
 
-    @admin.action(description="Export selected users\' emails")
+    @admin.action(description="Export selected users' emails")
     def export_emails_to_plaintext(self, request, queryset):
         response = HttpResponse(content_type='text/plain')
         writer = csv.writer(response)
@@ -142,6 +142,7 @@ def queryset(self, request, queryset):
         status = self.value()
         if status:
             return queryset.filter(status=status)
+        return None
 
 
 @admin.register(Version)