Adjusted arguments and minor fixes

hubmapconsortium · Sep 13, 2024 · 52293d3 · 52293d3
1 parent e25f2f0
commit 52293d3
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Showing 3 changed files with 44 additions and 45 deletions.
diff --git a/README.md b/README.md
@@ -40,6 +40,7 @@ optional arguments:
   --marker MARKER       Marker to highlight in visualization; Only used in
                         some visualizations.
   --to_json             Output viewconf, rather than open in browser.
+  --epic_uuid           uuid for EPIC dataset, if available.
   ```
 
   ```

diff --git a/src/portal_visualization/builders/epic_builders.py b/src/portal_visualization/builders/epic_builders.py
@@ -60,11 +60,11 @@ class SegmentationMaskBuilder(EPICConfBuilder):
     def _apply(self, conf):
         zarr_url = self.zarr_store_url()
         datasets = conf.get_datasets()
-        # TODO: add the correct path to the segmentation mask ome-tiff
+        # TODO: add the correct path to the segmentation mask ome-tiff (image-pyramid)?
         seg_path = f'{self.segmentations_url}/'
         seg_path = 'https://assets.hubmapconsortium.org/c9d9ab5c9ee9642b60dd351024968627/ometiff-pyramids/VAN0042-RK-3-18-registered-PAS-to-postAF-registered.ome_mask.ome.tif?token=AgzQXm7nvOW32vWw0EPpKonwbOqjNBzNvvW1p15855NoYglJxyfkC8rlJJWy8V6E8MeyXOwlpKdNBnHb5qnv7f8oeeG',
         mask_names = self.read_metadata_from_url()
-        mask_names = ['mask1', 'mask2']
+        mask_names = ['mask1', 'mask2'] #for testing purposes
         if(mask_names is not None):
             segmentation_objects = create_segmentation_objects(zarr_url, mask_names)
             segmentations = ObsSegmentationsOmeTiffWrapper (
@@ -75,50 +75,46 @@ def _apply(self, conf):
                 }
                 )
 
-            for dataset in datasets:
+            for dataset in datasets: 
                 dataset.add_object(segmentations)
                 for obj in segmentation_objects:
                     dataset.add_object(obj)
 
-        # TODO: what happens if these views already exist , and if there are other views, how to place these?
-        spatial_view = conf.add_view("spatialBeta", dataset=dataset, w=8, h=12)
-        lc_view = conf.add_view("layerControllerBeta", dataset=dataset, w=4, h=12, x=8, y=0)
+                # TODO: what happens if these views already exist , and if there are other views, how to place these?
+                spatial_view = conf.add_view("spatialBeta", dataset=dataset, w=8, h=12)
+                lc_view = conf.add_view("layerControllerBeta", dataset=dataset, w=4, h=12, x=8, y=0)
+                # without add_view can't access the metaCoordincatinSpace 
+                # (e.g. get_coordination_scope() https://python-docs.vitessce.io/api_config.html?highlight=coordination#vitessce.config.VitessceChainableConfig.get_coordination_scope)
+                conf.link_views_by_dict([spatial_view, lc_view], {
+                    "segmentationLayer":CL([
+                        {
+                            "fileUid": "segmentation-mask",
+                            "spatialLayerVisible": True,
+                            "spatialLayerOpacity": 1,
+                        }
+                    ])
 
-        conf.link_views_by_dict([spatial_view, lc_view], {
-            "segmentationLayer":CL([
-                {
-                    "fileUid": "segmentation-mask",
-                    "spatialLayerVisible": True,
-                    "spatialLayerOpacity": 1,
-                }
-            ])
-
-        }, meta=True, scope_prefix=get_initial_coordination_scope_prefix("A", "obsSegmentations"))
+                }, meta=True, scope_prefix=get_initial_coordination_scope_prefix("A", "obsSegmentations"))
 
 
     def read_metadata_from_url(self):
         url = f'{self.zarr_store_url()}/metadata.json'
-        print(url)
-        url ='https://portal.hubmapconsortium.org/browse/dataset/004d4f157df4ba07356cd805131dfc04.json'
+        print(f"metadata.json URL: {url}")
+        # url ='https://portal.hubmapconsortium.org/browse/dataset/004d4f157df4ba07356cd805131dfc04.json'
         request_init = self._get_request_init() or {}
-        print("req", request_init)
-        try:
-            response = get(url, **request_init)
-            if response.status_code == 200:
-                data = response.json()
-                if isinstance(data, dict) and "mask_name" in data:
-                    mask_name = data["mask_name"]
-                    print(f"Mask name found: {mask_name}")
-                    return mask_name
-                else:
-                    print("'mask_name' key not found in the response.")
-                    return None
+        response = get(url, **request_init)
+        if response.status_code == 200:
+            data = response.json()
+            if isinstance(data, dict) and "mask_name" in data:
+                mask_name = data["mask_name"]
+                print(f"Mask name found: {mask_name}")
+                return mask_name
             else:
-                # Handle errors (e.g., URL not found, server issues)
-                raise Exception(f"Failed to retrieve data: {response.status_code} - {response.reason}")
-            
-        except Exception as e:
-                raise Exception(f"Failed to connect to the url: {url} - {str(e)}")
+                print("'mask_name' key not found in the response.")
+                return None
+        else:
+            # raise Exception(f"Failed to retrieve data: {response.status_code} - {response.reason}")
+            pass # for testing purposes 
 
 
 def create_segmentation_objects(base_url, mask_names):

diff --git a/src/vis-preview.py b/src/vis-preview.py
@@ -42,26 +42,27 @@ def main():  # pragma: no cover
     parser.add_argument(
         '--to_json', action='store_true',
         help='Output viewconf, rather than open in browser.')
-    parser.add_argument(
-        '--parent_uuid', action='store_true',
-        help='Parent uuid for the dataset',
-        default=None)
 
+    # parser.add_argument(
+    #     '--parent_uuid', action='store_true',
+    #     help='Parent uuid for the dataset',
+    #     default=None)
     parser.add_argument(
         '--epic_uuid', metavar='URL',
         help='Epic dataset"s uuid',
         default=None)
 
-    parser.add_argument(
-        '--epic_builder',  action='store_true',
-        help='Whether to use the epic_builder or not',
-        default=None)
+    # 
+    # parser.add_argument(
+    #     '--epic_builder',  action='store_true',
+    #     help='Whether to use the epic_builder or not',
+    #     default=None)
 
     args = parser.parse_args()
     marker = args.marker
-    epic_builder = args.epic_builder
+    # epic_builder = args.epic_builder
     epic_uuid = args.epic_uuid
-    parent_uuid = args.parent_uuid # this may not be needed, as the --url provides the parent dataset json?
+    # parent_uuid = args.parent_uuid # this may not be needed, as the --url provides the parent dataset json?
 
     if args.url:
         response = requests.get(args.url)
@@ -111,6 +112,7 @@ def get_assaytype(uuid):
     if args.to_json:
         print(conf_as_json)
 
+    ## For testing
     # with open ('epic.json','w') as file:
     #     if isinstance(conf_cells.conf, list):
     #         json.dump( conf_cells.conf[0], file, indent=4, separators=(',', ': '))