Merge pull request #46 from FZJ-INM1-BDA/pr_fixNewSiibraPythonRegion

Fix new siibra-python issues

Author: marcenko

.github/workflows/github-actions.yml

@@ -13,7 +13,7 @@ jobs:
       EBRAINS_IAM_CLIENT_ID: ${{ secrets.EBRAINS_IAM_CLIENT_ID }}
       EBRAINS_IAM_CLIENT_SECRET: ${{ secrets.EBRAINS_IAM_CLIENT_SECRET }}
       EBRAINS_IAM_REFRESH_TOKEN: ${{ secrets.EBRAINS_IAM_REFRESH_TOKEN }}
-      # SIIBRA_CONFIG_GITLAB_PROJECT_TAG: develop
+      SIIBRA_CONFIG_GITLAB_PROJECT_TAG: master
     steps:
       - name: Check out repository code
         uses: actions/checkout@v2

Dockerfile

@@ -16,8 +16,8 @@ ARG DEV_FLAG
 ENV DEPLOY_ENVIRONMENT=${DEV_FLAG:+develop}
 # if DEPLOY_ENVIRONMENT is not yet set, set it to production
 ENV DEPLOY_ENVIRONMENT=${DEPLOY_ENVIRONMENT:-production}
-# if DEV_FLAG flag is set, set SIIBRA_CONFIG_GITLAB_PROJECT_TAG=develop
-#ENV SIIBRA_CONFIG_GITLAB_PROJECT_TAG=${DEV_FLAG:+develop}
+# if DEV_FLAG flag is set, set SIIBRA_CONFIG_GITLAB_PROJECT_TAG=master
+ENV SIIBRA_CONFIG_GITLAB_PROJECT_TAG=${DEV_FLAG:+master}
 
 RUN if [ "$DEPLOY_ENVIRONMENT" = "production" ]; \
   then python -m pip install -r requirements/prod.txt; \

app/core/parcellation_api.py

@@ -30,6 +30,16 @@
 
 preheat_flag = False
 
+parcellation_json_encoder = {
+    siibra.core.Parcellation: lambda parcellation: {
+        'id': split_id(parcellation.id),
+        'name': parcellation.name,
+        'availableSpaces': get_spaces_for_parcellation(parcellation),
+        'modality': parcellation.modality,
+        'version': parcellation.version,
+        '_dataset_specs': parcellation._dataset_specs,
+    }
+}
 
 def get_preheat_status():
     global preheat_flag
@@ -86,9 +96,6 @@ def __parcellation_result_info(parcellation, atlas_id=None, request=None):
     Create the response for a parcellation object
     """
     result_info = {
-        'id': split_id(parcellation.id),
-        'name': parcellation.name,
-        'availableSpaces': get_spaces_for_parcellation(parcellation),
         'links': {
             'self': {
                 'href': '{}atlases/{}/parcellations/{}'.format(get_base_url_from_request(request),
@@ -109,35 +116,13 @@ def __parcellation_result_info(parcellation, atlas_id=None, request=None):
                 atlas_id.replace('/', '%2F'),
                 parcellation.id.replace('/', '%2F')
             )
-        }
+        },
+        **jsonable_encoder(parcellation, custom_encoder={
+            **siibra_custom_json_encoder,
+            **parcellation_json_encoder
+        })
     }
 
-    if hasattr(parcellation, 'modality') and parcellation.modality:
-        result_info['modality'] = parcellation.modality
-
-    if hasattr(parcellation, 'version') and parcellation.version:
-        result_info['version'] = parcellation.version
-
-    if hasattr(parcellation, 'volume_src') and parcellation.volume_src:
-        volumeSrc = {
-            key.id: value for key, value in parcellation.volume_src.items()
-        }
-        result_info['volumeSrc'] = jsonable_encoder(
-            volumeSrc, custom_encoder=siibra_custom_json_encoder)
-    if hasattr(parcellation, 'origin_datainfos'):
-        original_infos = []
-        for datainfo in parcellation.origin_datainfos:
-            try:
-                original_info = origin_data_decoder(datainfo)
-                original_infos.append(original_info)
-            except RuntimeError:
-                continue
-
-        result_info['originDatainfos'] = original_infos
-
-    if hasattr(parcellation, 'deprecated'):
-        result_info['deprecated'] = parcellation.deprecated
-
     return result_info
 
 

app/service/request_utils.py

@@ -48,14 +48,13 @@ def _add_children_to_region(region_json, region, space_id=None, atlas=None):
 
 def _create_region_json_object(region, space_id=None, atlas=None, detail=False):
     region_json = {'name': region.name, 'children': []}
-    if hasattr(region, 'rgb'):
-        region_json['rgb'] = region.rgb
     if hasattr(region, 'fullId'):
         region_json['id'] = region.fullId
-    if hasattr(region, 'labelIndex'):
-        region_json['labelIndex'] = region.labelIndex
+    if len(region.labels) == 1:
+        region_json['labelIndex'] = list(region.labels)[0]
     if hasattr(region, 'attrs'):
-        region_json['volumeSrc'] = region.attrs.get('volumeSrc', {})
+        region_json['rgb'] = region.attrs.get('rgb')
+        region_json['id'] = region.attrs.get('fullId')
     if detail and hasattr(region, 'origin_datainfos'):
         region_json['originDatainfos'] = [origin_data_decoder(datainfo) for datainfo in region.origin_datainfos]
     region_json['availableIn'] = get_available_spaces_for_region(region)

test/core/test_atlas_api.py

@@ -13,7 +13,7 @@ def test_get_all_atlases():
     response = client.get('/v1_0/atlases')
     assert response.status_code == 200
     result_content = json.loads(response.content)
-    assert len(result_content) == 3
+    assert len(result_content) == 4
 
 
 def test_get_singe_atlas():