girder-large-image 1.29.3.dev6__tar.gz → 1.29.3.dev22__tar.gz

{girder-large-image-1.29.3.dev6 → girder-large-image-1.29.3.dev22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: girder-large-image
-Version: 1.29.3.dev6
+Version: 1.29.3.dev22
 Summary: A Girder plugin to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -19,9 +19,9 @@ Requires-Python: >=3.8
 License-File: LICENSE
 Requires-Dist: girder>=3.1.18
 Requires-Dist: girder-jobs>=3.0.3
-Requires-Dist: large_image>=1.29.3.dev6
+Requires-Dist: large_image>=1.29.3.dev22
 Provides-Extra: tasks
-Requires-Dist: large-image-tasks[girder]>=1.29.3.dev6; extra == "tasks"
+Requires-Dist: large-image-tasks[girder]>=1.29.3.dev22; extra == "tasks"
 Requires-Dist: girder-worker[girder]>=0.6.0; extra == "tasks"
 
 A Girder plugin to work with large, multiresolution images.

{girder-large-image-1.29.3.dev6 → girder-large-image-1.29.3.dev22}/girder_large_image/__init__.py

@@ -673,6 +673,26 @@ def unbindGirderEventsByHandlerName(handlerName):
         events.unbind(eventName, handlerName)
 
 
+def patchMount():
+    try:
+        import girder.cli.mount
+
+        def _flatItemFile(self, item):
+            return next(File().collection.aggregate([
+                {'$match': {'itemId': item['_id']}},
+            ] + ([
+                {'$addFields': {'matchLI': {'$eq': ['$_id', item['largeImage']['fileId']]}}},
+            ] if 'largeImage' in item and 'expected' not in item['largeImage'] else []) + [
+                {'$addFields': {'matchName': {'$eq': ['$name', item['name']]}}},
+                {'$sort': {'matchLI': -1, 'matchName': -1, '_id': 1}},
+                {'$limit': 1},
+            ]), None)
+
+        girder.cli.mount.ServerFuse._flatItemFile = _flatItemFile
+    except Exception:
+        pass
+
+
 class LargeImagePlugin(GirderPlugin):
     DISPLAY_NAME = 'Large Image'
     CLIENT_SOURCE_PATH = 'web_client'
@@ -727,3 +747,5 @@ class LargeImagePlugin(GirderPlugin):
 
         search._allowedSearchMode.pop('li_metadata', None)
         search.addSearchMode('li_metadata', metadataSearchHandler)
+
+        patchMount()

{girder-large-image-1.29.3.dev6 → girder-large-image-1.29.3.dev22}/girder_large_image/girder_tilesource.py

@@ -1,3 +1,4 @@
+import inspect
 import os
 import re
 
@@ -99,7 +100,10 @@ class GirderTileSource(tilesource.FileTileSource):
                     pass
                 if not largeImagePath:
                     try:
-                        largeImagePath = File().getGirderMountFilePath(largeImageFile)
+                        largeImagePath = File().getGirderMountFilePath(
+                            largeImageFile,
+                            **({'preferFlat': True} if 'preferFlat' in inspect.signature(
+                                File.getGirderMountFilePath).parameters else {}))
                     except FilePathException:
                         pass
             if not largeImagePath:

{girder-large-image-1.29.3.dev6 → girder-large-image-1.29.3.dev22}/girder_large_image/rest/large_image_resource.py

@@ -35,13 +35,14 @@ from girder import logger
 from girder.api import access
 from girder.api.describe import Description, autoDescribeRoute, describeRoute
 from girder.api.rest import Resource
-from girder.constants import SortDir, TokenScope
+from girder.constants import AccessType, SortDir, TokenScope
 from girder.exceptions import RestException
 from girder.models.file import File
+from girder.models.folder import Folder
 from girder.models.item import Item
 from girder.models.setting import Setting
 from large_image import cache_util
-from large_image.exceptions import TileGeneralError
+from large_image.exceptions import TileGeneralError, TileSourceError
 
 from .. import constants, girder_tilesource
 from ..models.image_item import ImageItem
@@ -255,6 +256,7 @@ class LargeImageResource(Resource):
         self.route('GET', ('histograms',), self.countHistograms)
         self.route('DELETE', ('histograms',), self.deleteHistograms)
         self.route('DELETE', ('tiles', 'incomplete'), self.deleteIncompleteTiles)
+        self.route('PUT', ('folder', ':id', 'tiles'), self.createLargeImages)
 
     @describeRoute(
         Description('Clear tile source caches to release resources and file handles.'),
@@ -445,6 +447,70 @@ class LargeImageResource(Resource):
                 removed += 1
         return removed
 
+    @access.user(scope=TokenScope.DATA_WRITE)
+    @autoDescribeRoute(
+        Description('Create new large images for all items within a folder.')
+        .notes('Does not work for items with multiple files and skips over items with '
+               'existing or unfinished large images.')
+        .modelParam('id', 'The ID of the folder.', model=Folder, level=AccessType.WRITE,
+                    required=True)
+        .param('force', 'Whether creation job(s) should be forced for each large image.',
+               required=False, default=False, dataType='boolean')
+        .param('localJobs', 'Whether the job(s) created should be local.', required=False,
+               default=False, dataType='boolean')
+        .param('recurse', 'Whether child folders should be recursed.', required=False,
+               default=False, dataType='boolean')
+        .errorResponse('ID was invalid.')
+        .errorResponse('Write access was denied for the folder.', 403),
+    )
+    def createLargeImages(self, folder, params):
+        user = self.getCurrentUser()
+        createJobs = 'always' if self.boolParam('force', params, default=False) else True
+        return self.createImagesRecurseOption(folder=folder, createJobs=createJobs, user=user,
+                                              recurse=params.get('recurse'),
+                                              localJobs=params.get('localJobs'))
+
+    def createImagesRecurseOption(self, folder, createJobs, user, recurse, localJobs):
+        result = {'childFoldersRecursed': 0,
+                  'itemsSkipped': 0,
+                  'largeImagesCreated': 0,
+                  'largeImagesRemovedAndRecreated': 0,
+                  'totalItems': 0}
+        if recurse:
+            for childFolder in Folder().childFolders(parent=folder, parentType='folder'):
+                result['childFoldersRecursed'] += 1
+                childResult = self.createImagesRecurseOption(folder=childFolder,
+                                                             createJobs=createJobs, user=user,
+                                                             recurse=recurse, localJobs=localJobs)
+                for key in childResult:
+                    result[key] += childResult[key]
+        for item in Folder().childItems(folder=folder):
+            result['totalItems'] += 1
+            if item.get('largeImage'):
+                if item['largeImage'].get('expected'):
+                    result['itemsSkipped'] += 1
+                else:
+                    try:
+                        ImageItem().getMetadata(item)
+                        result['itemsSkipped'] += 1
+                        continue
+                    except (TileSourceError, KeyError):
+                        previousFileId = item['largeImage'].get('originalId',
+                                                                item['largeImage']['fileId'])
+                        ImageItem().delete(item)
+                        ImageItem().createImageItem(item, File().load(user=user, id=previousFileId),
+                                                    createJob=createJobs, localJob=localJobs)
+                        result['largeImagesRemovedAndRecreated'] += 1
+            else:
+                files = list(Item().childFiles(item=item, limit=2))
+                if len(files) == 1:
+                    ImageItem().createImageItem(item, files[0], createJob=createJobs,
+                                                localJob=localJobs)
+                    result['largeImagesCreated'] += 1
+                else:
+                    result['itemsSkipped'] += 1
+        return result
+
     @describeRoute(
         Description('Remove large images from items where the large image job '
                     'incomplete.')

{girder-large-image-1.29.3.dev6 → girder-large-image-1.29.3.dev22}/girder_large_image.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: girder-large-image
-Version: 1.29.3.dev6
+Version: 1.29.3.dev22
 Summary: A Girder plugin to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -19,9 +19,9 @@ Requires-Python: >=3.8
 License-File: LICENSE
 Requires-Dist: girder>=3.1.18
 Requires-Dist: girder-jobs>=3.0.3
-Requires-Dist: large_image>=1.29.3.dev6
+Requires-Dist: large_image>=1.29.3.dev22
 Provides-Extra: tasks
-Requires-Dist: large-image-tasks[girder]>=1.29.3.dev6; extra == "tasks"
+Requires-Dist: large-image-tasks[girder]>=1.29.3.dev22; extra == "tasks"
 Requires-Dist: girder-worker[girder]>=0.6.0; extra == "tasks"
 
 A Girder plugin to work with large, multiresolution images.

{girder-large-image-1.29.3.dev6 → girder-large-image-1.29.3.dev22}/girder_large_image.egg-info/requires.txt

@@ -1,7 +1,7 @@
 girder>=3.1.18
 girder-jobs>=3.0.3
-large_image>=1.29.3.dev6
+large_image>=1.29.3.dev22
 
 [tasks]
-large-image-tasks[girder]>=1.29.3.dev6
+large-image-tasks[girder]>=1.29.3.dev22
 girder-worker[girder]>=0.6.0

{girder-large-image-1.29.3.dev6 → girder-large-image-1.29.3.dev22}/test_girder/test_large_image.py

@@ -237,6 +237,37 @@ def testThumbnailFileJob(server, admin, user, fsAssetstore):
     Setting().set(constants.PluginSettings.LARGE_IMAGE_MAX_THUMBNAIL_FILES, 0)
 
 
+@pytest.mark.usefixtures('unbindLargeImage')
+@pytest.mark.plugin('large_image')
+def testFolderCreateImages(server, admin, user, fsAssetstore):
+    file = utilities.uploadExternalFile('sample_image.ptif', admin, fsAssetstore)
+    itemId = file['itemId']
+    item = Item().load(itemId, user=admin)
+    folderId = str(item['folderId'])
+    # Remove the large image from this item
+    ImageItem().delete(item)
+    # Ask to make all items in this folder large images
+    resp = server.request(
+        method='PUT', path=f'/large_image/folder/{folderId}/tiles', user=admin)
+    assert utilities.respStatus(resp) == 200
+    assert resp.json['largeImagesCreated'] == 1
+    item = Item().load(itemId, user=admin)
+    # Check that this item became a large image again
+    assert 'largeImage' in item
+    # Hitting the endpoint again should skip the item
+    resp = server.request(
+        method='PUT', path=f'/large_image/folder/{folderId}/tiles', user=admin)
+    assert utilities.respStatus(resp) == 200
+    assert resp.json['itemsSkipped'] == 1
+    # If the item's source isn't working, it should be recreated.
+    item['largeImage']['sourceName'] = 'unknown'
+    Item().updateItem(item)
+    resp = server.request(
+        method='PUT', path=f'/large_image/folder/{folderId}/tiles', user=admin)
+    assert utilities.respStatus(resp) == 200
+    assert resp.json['largeImagesRemovedAndRecreated'] == 1
+
+
 @pytest.mark.singular()
 @pytest.mark.usefixtures('unbindLargeImage')
 @pytest.mark.plugin('large_image')