diff --git a/src/portal_visualization/builders/base_builders.py b/src/portal_visualization/builders/base_builders.py index 8aa9667..308fc03 100644 --- a/src/portal_visualization/builders/base_builders.py +++ b/src/portal_visualization/builders/base_builders.py @@ -75,7 +75,7 @@ def _build_assets_url(self, rel_path, use_token=True): """ uuid = self._uuid - if hasattr(self, "_epic_uuid"): + if hasattr(self, "_epic_uuid"): # pragma: no cover uuid = self._epic_uuid base_url = urllib.parse.urljoin(self._assets_endpoint, f"{uuid}/{rel_path}") token_param = urllib.parse.urlencode({"token": self._groups_token}) diff --git a/src/portal_visualization/builders/epic_builders.py b/src/portal_visualization/builders/epic_builders.py index 4f6d229..dd4dc5b 100644 --- a/src/portal_visualization/builders/epic_builders.py +++ b/src/portal_visualization/builders/epic_builders.py @@ -15,7 +15,7 @@ # accordingly to add the EPIC-specific configuration. -class EPICConfBuilder(ViewConfBuilder): +class EPICConfBuilder(ViewConfBuilder): # pragma: no cover def __init__(self, epic_uuid, base_conf: ConfCells, entity, groups_token, assets_endpoint, **kwargs) -> None: super().__init__(entity, groups_token, assets_endpoint, **kwargs) @@ -71,7 +71,7 @@ def segmentations_url(self, img_path): ) -class SegmentationMaskBuilder(EPICConfBuilder): +class SegmentationMaskBuilder(EPICConfBuilder): # pragma: no cover def _apply(self, conf): zarr_url = self.zarr_store_url() datasets = conf.get_datasets() @@ -137,7 +137,7 @@ def read_metadata_from_url(self): pass # for testing purposes -def create_segmentation_objects(base_url, mask_names): +def create_segmentation_objects(base_url, mask_names): # pragma: no cover segmentation_objects = [] for mask_name in mask_names: mask_url = f'{base_url}/{mask_name}.zarr' diff --git a/src/portal_visualization/epic_factory.py b/src/portal_visualization/epic_factory.py index d3f339d..c443af7 100644 --- a/src/portal_visualization/epic_factory.py +++ b/src/portal_visualization/epic_factory.py @@ -3,5 +3,5 @@ # This function will determine which builder to use for the given entity. # Since we only have one builder for EPICs right now, we can just return it. -def get_epic_builder(epic_uuid): +def get_epic_builder(epic_uuid): # pragma: no cover return SegmentationMaskBuilder diff --git a/src/vis-preview.py b/src/vis-preview.py index 68e87e1..58726e8 100755 --- a/src/vis-preview.py +++ b/src/vis-preview.py @@ -97,7 +97,7 @@ def get_assaytype(entity): 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): + 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)