Merge pull request #226 from RENCI/224_show_whole_volume_on_top

224 show whole volume on top
RENCI · Jan 6, 2023 · 6eefc6c · 6eefc6c
2 parents 65e4bf9 + 97f8657
commit 6eefc6c
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/girder/plugins/ninjato_api/girder_ninjato_api/endpoint_utils.py b/girder/plugins/ninjato_api/girder_ninjato_api/endpoint_utils.py
@@ -12,7 +12,7 @@
     merge_region_to_active_assignment, set_assignment_meta, get_history_info, \
     assign_region_to_user, add_meta_to_history, check_subvolume_done, \
     reject_assignment, update_assignment_in_whole_item, get_assignment_status, \
-    add_user_active_assignment_metadata, save_content_data, save_added_and_removed_regions, \
+    WHOLE_ITEM_NAME, save_content_data, save_added_and_removed_regions, \
     update_all_assignment_masks_async
 
 
@@ -304,7 +304,7 @@ def get_subvolume_item_ids(training):
             })
             for folder in folders:
                 whole_item = Item().findOne({'folderId': ObjectId(folder['_id']),
-                                             'name': 'whole'})
+                                             'name': WHOLE_ITEM_NAME})
                 ret_data.append({
                     'id': whole_item['_id'],
                     'parent_id': folder['_id']
@@ -469,7 +469,7 @@ def save_user_annotation_as_item(user, item_id, done, reject, comment, color, cu
     uname = user['login']
     item = Item().findOne({'_id': ObjectId(item_id)})
     whole_item = Item().findOne({'folderId': ObjectId(item['folderId']),
-                                 'name': 'whole'})
+                                 'name': WHOLE_ITEM_NAME})
     if reject:
         # reject the annotation
         reject_assignment(user, item, whole_item, True, comment)
@@ -533,7 +533,7 @@ def save_user_review_result_as_item(user, item_id, done, reject, comment, approv
     uname = user['login']
     item = Item().findOne({'_id': ObjectId(item_id)})
     whole_item = Item().findOne({'folderId': ObjectId(item['folderId']),
-                                 'name': 'whole'})
+                                 'name': WHOLE_ITEM_NAME})
     if reject:
         # reject the review assignment
         reject_assignment(user, item, whole_item, False, comment, task='review')

diff --git a/girder/plugins/ninjato_api/girder_ninjato_api/utils.py b/girder/plugins/ninjato_api/girder_ninjato_api/utils.py
@@ -17,6 +17,7 @@
 
 COLLECTION_NAME = 'nuclei_image_collection'
 TRAINING_COLLECTION_NAME = 'nuclei_image_training_collection'
+WHOLE_ITEM_NAME = '_whole'
 BUFFER_FACTOR = 3
 DATA_PATH = '/girder/data'
 ANNOT_ASSIGN_KEY = 'annotation_assigned_to'
@@ -280,7 +281,7 @@ def find_region_item_from_label(whole_item, region_label):
 
 def get_region_extent(item, region_id, user_extent=True):
     is_whole_item = False
-    if item['name'] == 'whole':
+    if item['name'] == WHOLE_ITEM_NAME:
         is_whole_item = True
     item_files = File().find({'itemId': item['_id']})
     if user_extent:

diff --git a/girder/test_data.gz b/girder/test_data.gz