Fixed tests for epic builder

src/portal_visualization/builder_factory.py

@@ -34,7 +34,6 @@ def process_hints(hints):
     is_json = "json_based" in hints
     is_spatial = "spatial" in hints
     is_support = "is_support" in hints
-    is_segmentation_base = "segmentation_base" in hints
 
     return (
         is_image,
@@ -139,6 +138,6 @@ def get_view_config_builder(entity, get_assaytype, parent=None, epic_uuid=None):
     return NullViewConfBuilder
 
 
-def has_visualization(entity, get_assaytype, parent=None):
-    builder = get_view_config_builder(entity, get_assaytype, parent, epic_uuid=None)
+def has_visualization(entity, get_assaytype, parent=None, epic_uuid=None):
+    builder = get_view_config_builder(entity, get_assaytype, parent, epic_uuid)
     return builder != NullViewConfBuilder

src/portal_visualization/builders/base_builders.py

@@ -121,7 +121,6 @@ def _get_file_paths(self):
         return [file["rel_path"] for file in self._entity["files"]]
 
 
-
 class _DocTestBuilder(ViewConfBuilder):  # pragma: no cover
     # The doctests on the methods in this file need a concrete class to instantiate:
     # We need a concrete definition for this method, even if it's never used.

src/portal_visualization/builders/epic_builders.py

@@ -7,8 +7,8 @@
 from requests import get
 import re
 import random
-from ..paths import OFFSETS_DIR, IMAGE_PYRAMID_DIR, SEGMENTATION_SUBDIR, SEGMENTATION_ZARR_STORES, SEGMENTATION_DIR
-
+from ..paths import OFFSETS_DIR, IMAGE_PYRAMID_DIR, SEGMENTATION_SUBDIR, SEGMENTATION_ZARR_STORES, \
+    SEGMENTATION_DIR, SEGMENTATION_SUPPORT_IMAGE_SUBDIR
 
 transformations_filename = 'transformations.json'
 zarr_path = f'{SEGMENTATION_SUBDIR}/{SEGMENTATION_ZARR_STORES}'
@@ -84,20 +84,21 @@ def _apply(self, conf):
         zarr_url = self.zarr_store_url()
         datasets = conf.get_datasets()
         file_paths_found = [file["rel_path"] for file in self._entity["files"]]
-
         found_images = [
             path for path in get_matches(
                 file_paths_found, IMAGE_PYRAMID_DIR + r".*\.ome\.tiff?$",
             )
         ]
-        found_images = sorted(found_images)
-        if len(found_images) == 0:  # pragma: no cover
+        # Remove the base-image pyramids from the found_images
+        filtered_strings = [img_path for img_path in found_images if SEGMENTATION_SUPPORT_IMAGE_SUBDIR not in img_path]
+        if len(filtered_strings) == 0:  # pragma: no cover
+            img_url, offsets_url = None, None
             message = f"Image pyramid assay with uuid {self._uuid} has no matching files"
             raise FileNotFoundError(message)
 
-        elif len(found_images) >= 1:
+        elif len(filtered_strings) >= 1:
             img_url, offsets_url = self.segmentations_ome_offset_url(
-                found_images[0]
+                filtered_strings[0]
             )
 
         segmentation_scale = self.read_segmentation_scale()
@@ -193,7 +194,7 @@ def create_segmentation_objects(base_url, mask_names):  # pragma: no cover
         else:
             channelIndex = index
         seg_CL = {
-            "spatialTargetC": channelIndex ,
+            "spatialTargetC": channelIndex,
             "obsType": mask_name,
             "spatialChannelOpacity": 1,
             "spatialChannelColor": color_channel,

src/vis-preview.py

@@ -79,11 +79,11 @@ def get_assaytype(uuid):
     print(f'Using: {builder.__class__.__name__}', file=stderr)
     conf_cells = builder.get_conf_cells(marker=marker)
 
-    # if (epic_uuid is not None and conf_cells is not None):  # pragma: no cover
-    #     EpicBuilder = get_epic_builder(epic_uuid)
-    #     epic_builder = EpicBuilder(epic_uuid, conf_cells, entity, args.token, args.assets_url)
-    #     print(f'Using: {epic_builder.__class__.__name__}', file=stderr)
-    #     conf_cells = epic_builder.get_conf_cells()
+    if (epic_uuid is not None and conf_cells is not None):  # pragma: no cover
+        EpicBuilder = get_epic_builder(epic_uuid)
+        epic_builder = EpicBuilder(epic_uuid, conf_cells, entity, args.token, args.assets_url)
+        print(f'Using: {epic_builder.__class__.__name__}', file=stderr)
+        conf_cells = epic_builder.get_conf_cells()
 
     if isinstance(conf_cells.conf, list):
         conf_as_json = json.dumps(conf_cells.conf[0])
@@ -94,11 +94,11 @@ def get_assaytype(uuid):
         print(conf_as_json)
 
     # For testing
-    with open('conf.json', 'w') as file:
-        if isinstance(conf_cells.conf, list):
-            json.dump(conf_cells.conf[0], file, indent=4, separators=(',', ': '))
-        else:
-            json.dump(conf_cells.conf, file, indent=4, separators=(',', ': '))
+    # with open('conf.json', 'w') as file:
+    #     if isinstance(conf_cells.conf, list):
+    #         json.dump(conf_cells.conf[0], file, indent=4, separators=(',', ': '))
+    #     else:
+    #         json.dump(conf_cells.conf, file, indent=4, separators=(',', ': '))
 
     data_url = f'data:,{quote_plus(conf_as_json)}'
     vitessce_url = f'http://vitessce.io/#?url={data_url}'