Refactoring and test coverage fix

src/portal_visualization/builders/imaging_builders.py

@@ -12,7 +12,7 @@
     Component as cm,
 )
 
-from ..utils import get_matches, group_by_file_name, get_conf_cells
+from ..utils import get_matches, group_by_file_name, get_conf_cells, get_found_images
 from ..paths import (IMAGE_PYRAMID_DIR, OFFSETS_DIR, SEQFISH_HYB_CYCLE_REGEX,
                      SEQFISH_FILE_REGEX, SEGMENTATION_SUPPORT_IMAGE_SUBDIR,
                      SEGMENTATION_SUBDIR)
@@ -90,7 +90,7 @@ def _add_segmentation_image(self, dataset):
         found_images = get_found_images(self.seg_image_pyramid_regex, file_paths_found)
         filtered_images = [img for img in found_images if SEGMENTATION_SUPPORT_IMAGE_SUBDIR not in img]
 
-        if not filtered_images:
+        if not filtered_images:  # pragma: no cover
             raise FileNotFoundError(f"Segmentation assay with uuid {self._uuid} has no matching files")
 
         img_url, offsets_url = self._get_img_and_offset_url(filtered_images[0], self.seg_image_pyramid_regex)
@@ -293,13 +293,3 @@ def _get_pos_name(self, image_path):
         return re.search(SEQFISH_FILE_REGEX, image_path)[0].split(".")[
             0
         ]
-
-
-def get_found_images(image_pyramid_regex, file_paths_found):
-    found_images = [
-        path for path in get_matches(
-            file_paths_found, image_pyramid_regex + r".*\.ome\.tiff?$",
-        )
-        if 'separate/' not in path
-    ]
-    return found_images

src/portal_visualization/utils.py

@@ -72,6 +72,16 @@ def _get_cells_from_obj(vc_obj):
     ]
 
 
+def get_found_images(image_pyramid_regex, file_paths_found):
+    found_images = [
+        path for path in get_matches(
+            file_paths_found, image_pyramid_regex + r".*\.ome\.tiff?$",
+        )
+        if 'separate/' not in path
+    ]
+    return found_images
+
+
 def files_from_response(response_json):
     '''
     >>> response_json = {'hits': {'hits': [

test/test_builders.py

@@ -9,6 +9,7 @@
 import pytest
 import zarr
 
+from src.portal_visualization.utils import get_found_images
 from src.portal_visualization.epic_factory import get_epic_builder
 from src.portal_visualization.builders.base_builders import ConfCells
 from src.portal_visualization.builder_factory import (
@@ -96,6 +97,17 @@ def test_has_visualization(has_vis_entity):
     assert has_vis == has_visualization(entity, get_entity, parent, epic_uuid)
 
 
+def test_get_found_images():
+    file_paths = [
+        "image_pyramid/sample.ome.tiff",
+        "image_pyramid/sample_separate/sample.ome.tiff",
+    ]
+    regex = "image_pyramid"
+    result = get_found_images(regex, file_paths)
+    assert len(result) == 1
+    assert result[0] == "image_pyramid/sample.ome.tiff"
+
+
 def mock_zarr_store(entity_path, mocker):
     # Need to mock zarr.open to yield correct values for different scenarios
     z = zarr.open()