Merge pull request #1576 from girder/flat-mount

Use flat mount paths where possible.
girder · Jul 15, 2024 · f58e07c · f58e07c
2 parents 9f0fa4a + f049329
commit f58e07c
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Showing 4 changed files with 33 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Improvements
 
 - Improve plottable data endpoint to better fetch adjacent items and annotations ([#1573](../../pull/1573), [#1574](../../pull/1574))), [#1575](../../pull/1575)))
+- Support Girder flat-mount paths ([#1576](../../pull/1576))
 
 ## 1.29.2
 

diff --git a/girder/girder_large_image/__init__.py b/girder/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 @@ def load(self, info):
 
         search._allowedSearchMode.pop('li_metadata', None)
         search.addSearchMode('li_metadata', metadataSearchHandler)
+
+        patchMount()
diff --git a/girder/girder_large_image/girder_tilesource.py b/girder/girder_large_image/girder_tilesource.py
@@ -1,3 +1,4 @@
+import inspect
 import os
 import re
 
@@ -99,7 +100,10 @@ def _getLargeImagePath(self):
                     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:

diff --git a/utilities/tasks/large_image_tasks/tasks.py b/utilities/tasks/large_image_tasks/tasks.py
@@ -1,3 +1,4 @@
+import inspect
 import logging
 import os
 import shutil
@@ -128,7 +129,10 @@ def convert_image_job(job):
         inputPath = None
         if not fileObj.get('imported'):
             try:
-                inputPath = File().getGirderMountFilePath(fileObj)
+                inputPath = File().getGirderMountFilePath(
+                    fileObj,
+                    **({'preferFlat': True} if 'preferFlat' in inspect.signature(
+                        File.getGirderMountFilePath).parameters else {}))
             except Exception:
                 pass
         inputPath = inputPath or File().getLocalFilePath(fileObj)