girder-large-image 1.32.2.dev10__tar.gz → 1.32.3.dev3__tar.gz

{girder_large_image-1.32.2.dev10 → girder_large_image-1.32.3.dev3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: girder-large-image
-Version: 1.32.2.dev10
+Version: 1.32.3.dev3
 Summary: A Girder plugin to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -21,9 +21,9 @@ Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: girder>=3.1.18
 Requires-Dist: girder-jobs>=3.0.3
-Requires-Dist: large_image>=1.32.2.dev10
+Requires-Dist: large_image>=1.32.3.dev3
 Provides-Extra: tasks
-Requires-Dist: large-image-tasks[girder]>=1.32.2.dev10; extra == "tasks"
+Requires-Dist: large-image-tasks[girder]>=1.32.3.dev3; extra == "tasks"
 Requires-Dist: girder-worker[girder]>=0.6.0; extra == "tasks"
 Dynamic: author
 Dynamic: author-email

{girder_large_image-1.32.2.dev10 → girder_large_image-1.32.3.dev3}/girder_large_image/models/image_item.py

@@ -39,6 +39,9 @@ from .. import constants, girder_tilesource
 
 
 class ImageItem(Item):
+    _cacheSaveDataLock = threading.RLock()
+    _cacheSaveDataThreads = []
+
     # We try these sources in this order.  The first entry is the fallback for
     # items that antedate there being multiple options.
     def initialize(self):
@@ -419,6 +422,58 @@ class ImageItem(Item):
         return self.getAndCacheImageOrDataRun(
             checkAndCreate, imageFunc, item, key, keydict, pickleCache, lockkey, **kwargs)
 
+    def _saveDataFile(self, item, imageMime, dataStored, key, pickleCache, keylock, lockkey):
+        with keylock:
+            # Save the data as a file
+            try:
+                datafile = Upload().uploadFromFile(
+                    io.BytesIO(dataStored), size=len(dataStored),
+                    name='_largeImageThumbnail', parentType='item', parent=item,
+                    user=None, mimeType=imageMime, attachParent=True)
+                if not len(dataStored) and 'received' in datafile:
+                    datafile = Upload().finalizeUpload(
+                        datafile, Assetstore().load(datafile['assetstoreId']))
+                datafile.update({
+                    'isLargeImageThumbnail' if not pickleCache else
+                    'isLargeImageData': True,
+                    'thumbnailKey': key,
+                })
+                # Ideally, we would check that the file is still wanted before
+                # we save it.  This is probably impossible without true
+                # transactions in Mongo.
+                File().save(datafile)
+            except (GirderException, PermissionError, FileNotFoundError):
+                logger.warning('Could not cache data for large image')
+            finally:
+                with self._getAndCacheImageOrDataLock['lock']:
+                    self._getAndCacheImageOrDataLock['keys'].pop(lockkey, None)
+
+    def cacheSaveDataManagement(self, timeout=0.0):
+        """
+        Check any of the threads used for caching data from slow functions and
+        join those that are finished.
+
+        :param timeout: 0 to return without blocking, just harvesting the
+            finished threads.  None to block until all are finished.  Since all
+            threads will be checked, specifying a positive timeout will
+            possibly take that long times the number of threads.
+        :returns: the number of active threads
+        """
+        with self._cacheSaveDataLock:
+            numthreads = len(self._cacheSaveDataThreads)
+        for idx in range(numthreads - 1, -1, -1):
+            with self._cacheSaveDataLock:
+                if idx >= len(self._cacheSaveDataThreads):
+                    continue
+                t = self._cacheSaveDataThreads[idx]
+            t.join(timeout)
+            if not t.is_alive():
+                with self._cacheSaveDataLock:
+                    self._cacheSaveDataThreads.remove(t)
+        with self._cacheSaveDataLock:
+            numthreads = len(self._cacheSaveDataThreads)
+        return numthreads
+
     def getAndCacheImageOrDataRun(
             self, checkAndCreate, imageFunc, item, key, keydict, pickleCache, lockkey, **kwargs):
         """
@@ -428,6 +483,7 @@ class ImageItem(Item):
             if lockkey not in self._getAndCacheImageOrDataLock['keys']:
                 self._getAndCacheImageOrDataLock['keys'][lockkey] = threading.Lock()
             keylock = self._getAndCacheImageOrDataLock['keys'][lockkey]
+        nounlock = False
         with keylock:
             logger.debug('Computing %r', (lockkey, ))
             try:
@@ -452,30 +508,20 @@ class ImageItem(Item):
                         pickleCache or isinstance(imageData, bytes))):
                     dataStored = imageData if not pickleCache else pickle.dumps(
                         imageData, protocol=4)
-                    # Save the data as a file
-                    try:
-                        datafile = Upload().uploadFromFile(
-                            io.BytesIO(dataStored), size=len(dataStored),
-                            name='_largeImageThumbnail', parentType='item', parent=item,
-                            user=None, mimeType=imageMime, attachParent=True)
-                        if not len(dataStored) and 'received' in datafile:
-                            datafile = Upload().finalizeUpload(
-                                datafile, Assetstore().load(datafile['assetstoreId']))
-                        datafile.update({
-                            'isLargeImageThumbnail' if not pickleCache else
-                            'isLargeImageData': True,
-                            'thumbnailKey': key,
-                        })
-                        # Ideally, we would check that the file is still wanted before
-                        # we save it.  This is probably impossible without true
-                        # transactions in Mongo.
-                        File().save(datafile)
-                    except (GirderException, PermissionError):
-                        logger.warning('Could not cache data for large image')
+                    self.cacheSaveDataManagement()
+                    with self._cacheSaveDataLock:
+                        t = threading.Thread(
+                            target=self._saveDataFile,
+                            args=(item, imageMime, dataStored, key, pickleCache, keylock, lockkey),
+                            daemon=True)
+                        t.start()
+                        self._cacheSaveDataThreads.append(t)
+                    nounlock = True
                 return imageData, imageMime
             finally:
-                with self._getAndCacheImageOrDataLock['lock']:
-                    self._getAndCacheImageOrDataLock['keys'].pop(lockkey, None)
+                if not nounlock:
+                    with self._getAndCacheImageOrDataLock['lock']:
+                        self._getAndCacheImageOrDataLock['keys'].pop(lockkey, None)
 
     def removeThumbnailFiles(self, item, keep=0, sort=None, imageKey=None,
                              onlyList=False, **kwargs):

{girder_large_image-1.32.2.dev10 → girder_large_image-1.32.3.dev3}/girder_large_image/rest/large_image_resource.py

@@ -102,7 +102,10 @@ def createThumbnailsJobLog(job, info, prefix='', status=None):
         msg += 'Failed on %d thumbnail file%s (last failure on item %s)\n' % (
             info['failed'],
             's' if info['failed'] != 1 else '', info['lastFailed'])
-    job = Job().updateJob(job, log=msg, status=status)
+    try:
+        job = Job().updateJob(job, log=msg, status=status)
+    except TypeError:
+        pass
     return job, msg
 
 
@@ -115,7 +118,7 @@ def cursorNextOrNone(cursor):
     :returns: the next value or None.
     """
     try:
-        return cursor.next()
+        return cursor.next()  # B305
     except StopIteration:
         return None
 

{girder_large_image-1.32.2.dev10 → girder_large_image-1.32.3.dev3}/girder_large_image/web_client/widgets/CompositeLayers.vue

@@ -504,14 +504,14 @@ module.exports = {
     cursor: pointer;
 }
 .picker{
-    background-color: white;
+    background-color: transparent;
     border: none;
     width: 100%
 }
 .table-header {
     position: sticky;
     top: 0px;
-    background-color: white;
+    background-color: transparent;
     z-index: 2;
     border-bottom: 3px solid !important;
 }

{girder_large_image-1.32.2.dev10 → girder_large_image-1.32.3.dev3}/girder_large_image/web_client/widgets/components.py

@@ -6,13 +6,14 @@ import ipyvue
 import traitlets
 
 parent = Path(__file__).parent
-colors_file = parent / 'colors.json'
-with open(colors_file) as f:
+with open(parent / 'colors.json') as f:
     colors_data = json.load(f)
-
-ipyvue.register_component_from_file(None, 'dual-input', parent / 'DualInput.vue')
-ipyvue.register_component_from_file(None, 'composite-layers', parent / 'CompositeLayers.vue')
-ipyvue.register_component_from_file(None, 'histogram-editor', parent / 'HistogramEditor.vue')
+with open(parent / 'DualInput.vue') as f:
+    dual_input = f.read()
+with open(parent / 'CompositeLayers.vue') as f:
+    composite_layers = f.read()
+with open(parent / 'HistogramEditor.vue') as f:
+    histogram_editor = f.read()
 
 
 class FrameSelector(ipyvue.VueTemplate):  # type: ignore
@@ -27,6 +28,14 @@ class FrameSelector(ipyvue.VueTemplate):  # type: ignore
     updateFrameCallback: Union[Callable, None] = None
     getFrameHistogram: Union[Callable, None] = None
 
+    # register_component_from_file function does not work in Google Colab;
+    # register child components from strings instead
+    components = traitlets.Dict({
+        'dual-input': dual_input,
+        'composite-layers': composite_layers,
+        'histogram-editor': histogram_editor,
+    }).tag(sync=True)
+
     def vue_frameUpdate(self, data=None):
         frame = int(data.get('frame', 0))
         style = data.get('style', {})

{girder_large_image-1.32.2.dev10 → girder_large_image-1.32.3.dev3}/girder_large_image.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: girder-large-image
-Version: 1.32.2.dev10
+Version: 1.32.3.dev3
 Summary: A Girder plugin to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -21,9 +21,9 @@ Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: girder>=3.1.18
 Requires-Dist: girder-jobs>=3.0.3
-Requires-Dist: large_image>=1.32.2.dev10
+Requires-Dist: large_image>=1.32.3.dev3
 Provides-Extra: tasks
-Requires-Dist: large-image-tasks[girder]>=1.32.2.dev10; extra == "tasks"
+Requires-Dist: large-image-tasks[girder]>=1.32.3.dev3; extra == "tasks"
 Requires-Dist: girder-worker[girder]>=0.6.0; extra == "tasks"
 Dynamic: author
 Dynamic: author-email

{girder_large_image-1.32.2.dev10 → girder_large_image-1.32.3.dev3}/girder_large_image.egg-info/requires.txt

@@ -1,7 +1,7 @@
 girder>=3.1.18
 girder-jobs>=3.0.3
-large_image>=1.32.2.dev10
+large_image>=1.32.3.dev3
 
 [tasks]
-large-image-tasks[girder]>=1.32.2.dev10
+large-image-tasks[girder]>=1.32.3.dev3
 girder-worker[girder]>=0.6.0

{girder_large_image-1.32.2.dev10 → girder_large_image-1.32.3.dev3}/test_girder/test_large_image.py

@@ -350,6 +350,7 @@ def testAssociateImageCaching(server, admin, user, fsAssetstore):
     # Test GET associated_images
     resp = server.request(path='/large_image/associated_images', user=user)
     assert utilities.respStatus(resp) == 403
+    ImageItem().cacheSaveDataManagement(None)
     resp = server.request(path='/large_image/associated_images', user=admin)
     assert utilities.respStatus(resp) == 200
     assert resp.json == 1
@@ -423,6 +424,7 @@ def testHistogramCaching(server, admin, user, fsAssetstore):
     # Test GET histograms
     resp = server.request(path='/large_image/histograms', user=user)
     assert utilities.respStatus(resp) == 403
+    ImageItem().cacheSaveDataManagement(None)
     resp = server.request(path='/large_image/histograms', user=admin)
     assert utilities.respStatus(resp) == 200
     assert resp.json == 1
@@ -461,7 +463,8 @@ def testHistogramConcurrentCaching(server, admin, user, fsAssetstore):
     t2.start()
     t1.join()
     t2.join()
-    assert ImageItem().getAndCacheImageOrDataRun.call_count == lastCount + 1
+    ImageItem().cacheSaveDataManagement(None)
+    assert ImageItem().getAndCacheImageOrDataRun.call_count >= lastCount + 1
     ImageItem().getAndCacheImageOrDataRun = orig
 
 

{girder_large_image-1.32.2.dev10 → girder_large_image-1.32.3.dev3}/test_girder/test_tiles_rest.py

@@ -719,6 +719,7 @@ def testContentDisposition(server, admin, fsAssetstore):
     assert (
         resp.headers.get('Content-Disposition') is None or
         'largeImageThumbnail' in resp.headers['Content-Disposition'])
+    ImageItem().cacheSaveDataManagement(None)
 
 
 @pytest.mark.usefixtures('unbindLargeImage')
@@ -736,6 +737,7 @@ def testContentDispositionFilename(server, admin, fsAssetstore):
     assert utilities.respStatus(resp) == 200
     assert resp.headers['Content-Disposition'].startswith('attachment')
     assert resp.headers['Content-Disposition'].endswith('.jpg')
+    ImageItem().cacheSaveDataManagement(None)
 
 
 @pytest.mark.usefixtures('unbindLargeImage')
@@ -1169,6 +1171,7 @@ def testTilesAssociatedImages(server, admin, fsAssetstore):
     assert utilities.respStatus(resp) == 200
     image = utilities.getBody(resp, text=False)
     assert image == b''
+    ImageItem().cacheSaveDataManagement(None)
 
 
 @pytest.mark.usefixtures('unbindLargeImage')
@@ -1234,6 +1237,7 @@ def testTilesHistogram(server, admin, fsAssetstore):
                 'roundRange': True, 'bins': 512})
     assert len(resp.json) == 3
     assert len(resp.json[0]['hist']) == 256
+    ImageItem().cacheSaveDataManagement(None)
 
 
 @pytest.mark.usefixtures('unbindLargeImage')
@@ -1507,6 +1511,7 @@ def testThumbnailMaintenance(server, admin, fsAssetstore):
     resp = server.request(path='/item/%s/tiles/thumbnail' % itemId,
                           user=admin, isJson=False)
     assert utilities.respStatus(resp) == 200
+    ImageItem().cacheSaveDataManagement(None)
 
     # Check that we list a thumbnail
     resp = server.request(path='/item/%s/tiles/thumbnails' % itemId, user=admin)
@@ -1533,6 +1538,7 @@ def testThumbnailMaintenance(server, admin, fsAssetstore):
     resp = server.request(path='/item/%s/tiles/thumbnail' % itemId,
                           user=admin, isJson=False)
     assert utilities.respStatus(resp) == 200
+    ImageItem().cacheSaveDataManagement(None)
     thumb = utilities.getBody(resp, text=False)
     resp = server.request(path='/item/%s/tiles/thumbnails' % itemId, user=admin)
     assert utilities.respStatus(resp) == 200
@@ -1552,6 +1558,7 @@ def testThumbnailMaintenance(server, admin, fsAssetstore):
         path='/item/%s/tiles/thumbnails' % itemId, method='POST', user=admin,
         params={'key': key}, body=thumb, type='application/octet-stream')
 
+    ImageItem().cacheSaveDataManagement(None)
     resp = server.request(path='/item/%s/tiles/thumbnails' % itemId, user=admin)
     assert utilities.respStatus(resp) == 200
     assert len(resp.json) == 1