Merge branch 'master' into amend-dicomweb-assetstore

.circleci/config.yml

@@ -197,6 +197,19 @@ jobs:
       - coverage
       - store_artifacts:
           path: build/test/artifacts
+  py312:
+    machine:
+      image: ubuntu-2004:202111-02
+    steps:
+      - checkout
+      - allservices:
+          version: "3.12"
+          node: v14
+      - tox:
+          env: test-py312
+      - coverage
+      - store_artifacts:
+          path: build/test/artifacts
   lint_and_docs:
     executor: toxandnode
     steps:
@@ -318,6 +331,13 @@ workflows:
             branches:
               ignore:
                 - gh-pages
+      - py312:
+          filters:
+            tags:
+              only: /^v.*/
+            branches:
+              ignore:
+                - gh-pages
       - lint_and_docs:
           filters:
             tags:
@@ -333,6 +353,7 @@ workflows:
             - py39
             - py310
             - py311
+            - py312
             - lint_and_docs
           filters:
             tags:
@@ -348,6 +369,7 @@ workflows:
             - py39
             - py310
             - py311
+            - py312
             - lint_and_docs
           filters:
             tags:
@@ -362,6 +384,7 @@ workflows:
             - py39
             - py310
             - py311
+            - py312
             - lint_and_docs
           filters:
             tags:
@@ -386,5 +409,6 @@ workflows:
       - py39
       - py310
       - py311
+      - py312
       - lint_and_docs
       - wheels

.pre-commit-config.yaml

@@ -4,7 +4,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-added-large-files
   - id: check-ast
@@ -44,7 +44,7 @@ repos:
     files: README.rst
     name: rst-linter of README.rst
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.5
+  rev: v2.2.6
   hooks:
   - id: codespell
     args:
@@ -62,15 +62,15 @@ repos:
         - '--options'
         - './girder/girder_large_image/web_client/package.json'
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.10.1
+  rev: v3.15.0
   hooks:
     - id: pyupgrade
       args:
         - --py36-plus
         - --keep-percent-format
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.0.286
+  rev: v0.1.0
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

CHANGELOG.md

@@ -4,10 +4,15 @@
 
 ### Improvements
 - Style can specify a dtype of 'source' to maintain the original dtype even when compositing frames ([#1326](../../pull/1326))
-- Max Merge option in Frame Selector ([#1306](../../pull/1306))
+- Max Merge option in Frame Selector ([#1306](../../pull/1306), [#1330](../../pull/1330), [#1336](../../pull/1336))
+- Improve tifffile associated image detection ([#1333](../../pull/1333))
+- Guard against throwing a javascript warning ([#1337](../../pull/1337))
+- Test on Python 3.12 ([#1335](../../pull/1335))
 
 ### Changes
 - Prohibit bioformats and vips from reading mrxs directly ([#1328](../../pull/1328))
+- Handle Python 3.12 deprecating utcnow ([#1331](../../pull/1331))
+- Turn down logging about annotation ACLs ([#1332](../../pull/1332))
 
 ## 1.25.0
 
@@ -493,7 +498,7 @@
 ## 1.15.1
 
 ### Improvements
-- When scaling heatmap annoations, use an appropriate value ([#878](../../pull/878))
+- When scaling heatmap annotations, use an appropriate value ([#878](../../pull/878))
 - Use the girder client build time for cache control ([#879](../../pull/879))
 
 ## 1.15.0

docs/girder_config_options.rst

@@ -346,7 +346,7 @@ This is used to specify a list of preset defaults, in order of precedence.
 These presets are to be automatically applied to an image in this folder if they are applicable.
 In the case that a preset is not applicable to an image, the next item in this list will be used.
 
-** Important: the presets named in this list must have corresponding entries in the `imageFramePresets` configuration, else this configuration will have no effect. **
+** Important: the presets named in this list must have corresponding entries in the ``imageFramePresets`` configuration, else this configuration will have no effect. **
 
 ::
 
@@ -362,7 +362,7 @@ In the case that a preset is not applicable to an image, the next item in this l
 ::
 
     ---
-    # This example would be used with the example for `imageFramePresets` shown above.
+    # This example would be used with the example for ``imageFramePresets`` shown above.
     # Images with 7 or more channels would use "Auto Ranged Channels"
     # Images with fewer than 7 but at least 4 channels would use "Channels with Min and Max"
     # Images with 3 channels would use "3 channels"

girder/girder_large_image/__init__.py

@@ -156,7 +156,8 @@ def _updateJob(event):
                 'status': status,
             },
             user={'_id': job.get('userId')},
-            expires=datetime.datetime.utcnow() + datetime.timedelta(seconds=30))
+            expires=(datetime.datetime.now(datetime.timezone.utc) +
+                     datetime.timedelta(seconds=30)))
 
 
 def checkForLargeImageFiles(event):

girder/girder_large_image/rest/large_image_resource.py

@@ -255,7 +255,11 @@ def cacheClear(self, params):
             time.sleep(0.1)
             after = cache_util.cachesInfo()
         gc.collect()
-        return {'cacheCleared': datetime.datetime.utcnow(), 'before': before, 'after': after}
+        return {
+            'cacheCleared': datetime.datetime.now(datetime.timezone.utc),
+            'before': before,
+            'after': after,
+        }
 
     @describeRoute(
         Description('Get information on caches.'),
@@ -671,5 +675,5 @@ def run(self):
             restart = Restart(cherrypy.engine)
             restart.subscribe()
             restart.start()
-            return {'restarted': datetime.datetime.utcnow()}
-        return {'status': 'updated', 'time': datetime.datetime.utcnow()}
+            return {'restarted': datetime.datetime.now(datetime.timezone.utc)}
+        return {'status': 'updated', 'time': datetime.datetime.now(datetime.timezone.utc)}

girder/girder_large_image/web_client/vue/components/DualInput.vue

@@ -38,7 +38,7 @@ export default {
         :disabled="merge"
       >
     </td>
-    <td style="width: 100%">
+    <td class="slider-control-cell">
       <input
         v-model="value"
         type="range"
@@ -64,13 +64,13 @@ export default {
     </td>
     <td
       v-show="merge !== undefined"
-      style="min-width: 150px; text-align: right;"
+      class="max-merge-cell"
+      :title="'Max Merge ' + label"
     >
       <input
         :id="'maxMerge'+label"
         v-model="merge"
         type="checkbox"
-        style="margin: 0px 5px 0px 10px"
       >
       <label :for="'maxMerge'+label">Max Merge</label>
     </td>
@@ -110,4 +110,14 @@ export default {
   top: -1px;
   left: 50%;
 }
+.slider-control-cell {
+  width: 100%;
+}
+.max-merge-cell {
+  min-width: 125px;
+  text-align: right;
+}
+.max-merge-cell input[type="checkbox"] {
+  margin: 0px 2px 0px 0px;
+}
 </style>

girder/girder_large_image/web_client/vue/components/FrameSelector.vue

@@ -70,7 +70,7 @@ export default Vue.extend({
             this.histogramParamStyles = {};
             Array.from([2, 3]).forEach((modeID) => {
                 const mergedStyle = this.maxMergeStyle();
-                if (mergedStyle.bands.length) {
+                if (mergedStyle && mergedStyle.bands && mergedStyle.bands.length) {
                     const simpleMergedStyleString = JSON.stringify({
                         dtype: 'source',
                         bands: mergedStyle.bands.map((b) => ({
@@ -173,7 +173,7 @@ export default Vue.extend({
                 // no max merge permutations to apply, keep old bandsArray
                 newBandsArray = bandsArray;
             }
-            return {bands: newBandsArray};
+            return newBandsArray.length ? {bands: newBandsArray} : style;
         },
         fillMetadata() {
             if (!this.metadata.frames) {

girder/girder_large_image/web_client/vue/components/PresetsMenu.vue

@@ -102,7 +102,7 @@ export default {
                 if (presets) {
                     this.itemPresets = presets;
                 }
-                if (this.liConfig.imageFramePresets) {
+                if (this.liConfig && this.liConfig.imageFramePresets) {
                     this.folderPresets = this.liConfig.imageFramePresets.filter(this.presetApplicable);
                     if (this.liConfig.imageFramePresetDefaults) {
                         this.liConfig.imageFramePresetDefaults.every(({name}) => {

girder/setup.py

@@ -51,6 +51,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
     ],
     install_requires=[
         'girder>=3.1.18',

girder_annotation/girder_large_image_annotation/models/annotation.py

@@ -759,21 +759,21 @@ def _migrateACL(self, annotation):
 
         item = Item().load(annotation['itemId'], force=True)
         if item is None:
-            logger.warning(
+            logger.debug(
                 'Could not generate annotation ACL due to missing item %s', annotation['_id'])
             return annotation
 
         folder = Folder().load(item['folderId'], force=True)
         if folder is None:
-            logger.warning(
+            logger.debug(
                 'Could not generate annotation ACL due to missing folder %s', annotation['_id'])
             return annotation
 
         user = None
         if annotation.get('creatorId'):
             user = User().load(annotation['creatorId'], force=True)
         if user is None:
-            logger.warning(
+            logger.debug(
                 'Could not generate annotation ACL due to missing user %s', annotation['_id'])
             return annotation
 
@@ -787,7 +787,7 @@ def _migrateACL(self, annotation):
         return annotation
 
     def createAnnotation(self, item, creator, annotation, public=None):
-        now = datetime.datetime.utcnow()
+        now = datetime.datetime.now(datetime.timezone.utc)
         doc = {
             'itemId': item['_id'],
             'creatorId': creator['_id'],
@@ -815,7 +815,7 @@ def createAnnotation(self, item, creator, annotation, public=None):
             type='large_image_annotation.create',
             data={'_id': doc['_id'], 'itemId': doc['itemId']},
             user=creator,
-            expires=datetime.datetime.utcnow() + datetime.timedelta(seconds=1))
+            expires=datetime.datetime.now(datetime.timezone.utc) + datetime.timedelta(seconds=1))
         return doc
 
     def load(self, id, region=None, getElements=True, *args, **kwargs):
@@ -888,7 +888,7 @@ def deleteElements(query, *args, **kwargs):
             type='large_image_annotation.remove',
             data={'_id': annotation['_id'], 'itemId': annotation['itemId']},
             user=User().load(annotation['creatorId'], force=True),
-            expires=datetime.datetime.utcnow() + datetime.timedelta(seconds=1))
+            expires=datetime.datetime.now(datetime.timezone.utc) + datetime.timedelta(seconds=1))
         return result
 
     def save(self, annotation, *args, **kwargs):
@@ -987,14 +987,14 @@ def updateAnnotation(self, annotation, updateUser=None):
         :param updateUser: the user who is creating the update.
         :returns: the annotation document that was updated.
         """
-        annotation['updated'] = datetime.datetime.utcnow()
+        annotation['updated'] = datetime.datetime.now(datetime.timezone.utc)
         annotation['updatedId'] = updateUser['_id'] if updateUser else None
         annotation = self.save(annotation)
         Notification().createNotification(
             type='large_image_annotation.update',
             data={'_id': annotation['_id'], 'itemId': annotation['itemId']},
             user=User().load(annotation['creatorId'], force=True),
-            expires=datetime.datetime.utcnow() + datetime.timedelta(seconds=1))
+            expires=datetime.datetime.now(datetime.timezone.utc) + datetime.timedelta(seconds=1))
         return annotation
 
     def _similarElementStructure(self, a, b, parentKey=None):  # noqa
@@ -1324,7 +1324,7 @@ def removeOldAnnotations(self, remove=False, minAgeInDays=30, keepInactiveVersio
         if (remove and minAgeInDays < 7) or minAgeInDays < 0:
             msg = 'minAgeInDays must be >= 7'
             raise ValidationException(msg)
-        age = datetime.datetime.utcnow() + datetime.timedelta(-minAgeInDays)
+        age = datetime.datetime.now(datetime.timezone.utc) + datetime.timedelta(-minAgeInDays)
         if keepInactiveVersions < 0:
             msg = 'keepInactiveVersions mist be non-negative'
             raise ValidationException(msg)
@@ -1425,7 +1425,7 @@ def setMetadata(self, annotation, metadata, allowNull=False):
 
         self.validateKeys(annotation['annotation']['attributes'])
 
-        annotation['updated'] = datetime.datetime.utcnow()
+        annotation['updated'] = datetime.datetime.now(datetime.timezone.utc)
 
         # Validate and save the annotation
         return super().save(annotation)
@@ -1451,6 +1451,6 @@ def deleteMetadata(self, annotation, fields):
         for field in fields:
             annotation['annotation']['attributes'].pop(field, None)
 
-        annotation['updated'] = datetime.datetime.utcnow()
+        annotation['updated'] = datetime.datetime.now(datetime.timezone.utc)
 
         return super().save(annotation)

girder_annotation/girder_large_image_annotation/models/annotationelement.py

@@ -600,7 +600,7 @@ def updateElements(self, annotation):
         elements = annotation['annotation'].get('elements', [])
         if not len(elements):
             return
-        now = datetime.datetime.utcnow()
+        now = datetime.datetime.now(datetime.timezone.utc)
         threads = multiprocessing.cpu_count()
         chunkSize = int(max(100000 // threads, 10000))
         with concurrent.futures.ThreadPoolExecutor(max_workers=threads) as pool:

girder_annotation/setup.py

@@ -51,6 +51,7 @@ def prerelease_local_scheme(version):
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
     ],
     install_requires=[
         'jsonschema>=2.5.1',

girder_annotation/test_annotation/test_annotations.py

@@ -691,7 +691,7 @@ def testMigrateAnnotationAccessControlNoItemError(self, user, admin):
         Annotation().save(annot)
         with mock.patch('girder_large_image_annotation.models.annotation.logger') as logger:
             Annotation()._migrateDatabase()
-            logger.warning.assert_called_once()
+            logger.debug.assert_called_once()
         annot = Annotation().load(annot['_id'], force=True)
         assert 'access' not in annot
 
@@ -711,7 +711,7 @@ def testMigrateAnnotationAccessControlNoFolderError(self, user, admin):
         Item().save(item)
         with mock.patch('girder_large_image_annotation.models.annotation.logger') as logger:
             Annotation()._migrateDatabase()
-            logger.warning.assert_called_once()
+            logger.debug.assert_called_once()
         annot = Annotation().load(annot['_id'], force=True)
         assert 'access' not in annot
 
@@ -728,7 +728,7 @@ def testMigrateAnnotationAccessControlNoUserError(self, user, admin):
         Annotation().save(annot)
         with mock.patch('girder_large_image_annotation.models.annotation.logger') as logger:
             Annotation()._migrateDatabase()
-            logger.warning.assert_called_once()
+            logger.debug.assert_called_once()
         annot = Annotation().load(annot['_id'], force=True)
         assert 'access' not in annot
 
@@ -745,6 +745,6 @@ def testMigrateAnnotationAccessControlNullUserError(self, user, admin):
         Annotation().save(annot)
         with mock.patch('girder_large_image_annotation.models.annotation.logger') as logger:
             Annotation()._migrateDatabase()
-            logger.warning.assert_called_once()
+            logger.debug.assert_called_once()
         annot = Annotation().load(annot['_id'], force=True)
         assert 'access' not in annot