Merge pull request #327 from DigitalSlideArchive/dive-repo

Update repo used by Dive

devops/dsa/utils/cli_test.py

@@ -125,7 +125,7 @@ def get_memory_use(client):
     return info['virtualMemory']['used']
 
 
-def test_cli(client, folder, opts):
+def test_cli(client, folder, opts):  # noqa
     """
     Run the CLI on an image and make sure we get an annotation out of it.
 
@@ -200,6 +200,15 @@ def test_cli(client, folder, opts):
     if len(annot['annotation']['elements']) < 100:
         raise Exception('Got less than 100 annotation elements (%d) from annotation %s' % (
             len(annot['annotation']['elements']), anList[0]['_id']))
+    anList = client.get('annotation', parameters=dict(
+        sort='_id', sortdir=-1, itemId=testItem['_id']))
+    keep = 3
+    for annot in anList:
+        if annot['annotation']['name'] == 'cli_test-nuclei-bbox':
+            if keep:
+                keep -= 1
+            else:
+                client.delete(f'annotation/{annot["_id"]}')
 
 
 def test_tiles(client, folder, opts):

devops/with-dive-volview/provision.divevolview.yaml

@@ -2,7 +2,7 @@
 pip:
   - git+https://github.com/DigitalSlideArchive/girder_volview
   - git+https://github.com/girder/girder-volview-dicomrt
-  - git+https://github.com/BryonLewis/dive-dsa.git#subdirectory=server
+  - git+https://github.com/DigitalSlideArchive/dive-dsa.git#subdirectory=server
   - git+https://github.com/DigitalSlideArchive/girder-clamav
 # both girder-dicom-viewer and girder-xtk-demo can be used to view radiology
 # data, but volview does a better job.  girder-archive-access extends
@@ -21,6 +21,6 @@ slicer-cli-image:
   - ghcr.io/girder/girder-volview-dicomrt/worker-volview-dicomrt:latest
 worker:
   pip:
-    - git+https://github.com/BryonLewis/dive-dsa.git#subdirectory=server
+    - git+https://github.com/DigitalSlideArchive/dive-dsa.git#subdirectory=server
   shell:
     - wget -O ffmpeg.tar.xz https://johnvansickle.com/ffmpeg/releases/ffmpeg-release-amd64-static.tar.xz && mkdir /tmp/ffextracted && tar -xvf ffmpeg.tar.xz -C /tmp/ffextracted --strip-components 1 && cp /tmp/ffextracted/ffmpeg /opt/venv/bin && cp /tmp/ffextracted/ffprobe /opt/venv/bin && rm -rf /tmp/ffextracted