remove get_assay, track down sample datasets for each builder

src/portal_visualization/builder_factory.py

@@ -26,51 +26,72 @@
 # {
 #   "assaytype": "image_pyramid",
 #   "description": "Image Pyramid",
-#   "vitessce_hints": [
+#   "vitessce-hints": [
 #     "is_image",
 #     "pyramid"
 #   ]
 # }
 
 
 def get_ancestor_assaytypes(entity, get_assaytype):
-    return [get_assaytype(ancestor.get('uuid')).get('assaytype')
+    return [get_assaytype(ancestor).get('assaytype')
             for ancestor
             in entity.get('immediate_ancestors')]
 
 
+#
+# This function is the main entrypoint for the builder factory.
+# It returns the correct builder for the given entity.
+#
+# The entity is a dict that contains the entity UUID and metadata.
+# `get_assaytype` is a function which takes an entity UUID and returns
+# the assaytype and vitessce-hints for that entity.
 def get_view_config_builder(entity, get_assaytype):
-    assay = get_assaytype(entity.get('uuid'))
+    assay = get_assaytype(entity)
     assay_name = assay.get('assaytype')
     hints = assay.get('vitessce-hints', [])
     dag_provenance_list = entity.get('metadata', {}).get('dag_provenance_list', [])
     dag_names = [dag['name']
                  for dag in dag_provenance_list if 'name' in dag]
     if "is_image" in hints:
         if 'sprm' in hints and 'anndata' in hints:
+            # e.g. CellDIVE [DeepCell + SPRM]
+            # sample entity: c3be5650e93907b68ddbdb22b948db32
             return MultiImageSPRMAnndataViewConfBuilder
         if "codex" in hints:
             if ('sprm-to-anndata.cwl' in dag_names):
+                # e.g. 'CODEX [Cytokit + SPRM]
+                # sample entity: 43213991a54ce196d406707ffe2e86bd
                 return StitchedCytokitSPRMViewConfBuilder
+            # Cannot find an example of this in the wild, every CODEX entity has the
+            # sprm-to-anndata.cwl in its dag_provenance_list
             return TiledSPRMViewConfBuilder
         # Check types of image pyramid ancestors to determine which builder to use
         ancestor_assaytypes = get_ancestor_assaytypes(entity, get_assaytype)
+        # e.g. c6a254b2dc2ed46b002500ade163a7cc
         if SEQFISH in [assaytype for assaytype in ancestor_assaytypes]:
             return SeqFISHViewConfBuilder
+        # e.g. 3bc3ad124014a632d558255626bf38c9
         if MALDI_IMS in [assaytype for assaytype in ancestor_assaytypes]:
             return IMSViewConfBuilder
+        # e.g. 6b93107731199733f266bbd0f3bc9747
         if NANODESI in [assaytype for assaytype in ancestor_assaytypes]:
             return NanoDESIViewConfBuilder
         return ImagePyramidViewConfBuilder
     if "rna" in hints:
         # This is the zarr-backed anndata pipeline.
         if "anndata-to-ui.cwl" in dag_names:
             if assay_name == SALMON_RNASSEQ_SLIDE:
+                # e.g. 2a590db3d7ab1e1512816b165d95cdcf
                 return SpatialRNASeqAnnDataZarrViewConfBuilder
+            # e.g. e65175561b4b17da5352e3837aa0e497
             return RNASeqAnnDataZarrViewConfBuilder
+        # e.g. c019a1cd35aab4d2b4a6ff221e92aaab
         return RNASeqViewConfBuilder
     if "atac" in hints:
+        # e.g. d4493657cde29702c5ed73932da5317c
         return ATACSeqViewConfBuilder
+    # any entity with no hints, e.g. 2c2179ea741d3bbb47772172a316a2bf
     return NullViewConfBuilder
 
 

test/test_builders.py

@@ -10,8 +10,6 @@
 import pytest
 import zarr
 
-from hubmap_commons.type_client import TypeClient
-
 from src.portal_visualization.builder_factory import get_view_config_builder, has_visualization
 
 
@@ -38,18 +36,10 @@ class MockResponse:
 
 defaults = json.load((Path(__file__).parent.parent / 'src/defaults.json').open())
 
-
-def get_assay(name):
-    # This code could also be used in portal-ui.
-    # search-api might skip the REST interface.
-    type_client = TypeClient(defaults['types_url'])
-    return type_client.getAssayType(name)
-
-
+
 def get_assaytype(uuid):
     requests.get(f'{defaults["assaytypes_url"]}/{uuid}').json()
 
-
 @pytest.mark.parametrize(
     "has_vis_entity",
     [
@@ -61,7 +51,7 @@ def get_assaytype(uuid):
     ids=lambda has_vis_entity: f'has_visualization={has_vis_entity[0]}')
 def test_has_visualization(has_vis_entity):
     has_vis, entity = has_vis_entity
-    assert has_vis == has_visualization(entity, get_assay)
+    assert has_vis == has_visualization(entity, get_assaytype)
 
 
 def mock_zarr_store(entity_path, mocker):
@@ -97,7 +87,7 @@ def test_entity_to_vitessce_conf(entity_path, mocker):
         else None)
 
     entity = json.loads(entity_path.read_text())
-    Builder = get_view_config_builder(entity, get_assay)
+    Builder = get_view_config_builder(entity, get_assaytype)
     assert Builder.__name__ == entity_path.parent.name
 
     # Envvars should not be set during normal test runs,
@@ -130,7 +120,7 @@ def test_entity_to_error(entity_path, mocker):
 
     entity = json.loads(entity_path.read_text())
     with pytest.raises(Exception) as error_info:
-        Builder = get_view_config_builder(entity, get_assay)
+        Builder = get_view_config_builder(entity, get_assaytype)
         builder = Builder(entity, 'groups_token', 'https://example.com/')
         builder.get_conf_cells()
     actual_error = f'{error_info.type.__name__}: {error_info.value.args[0]}'
@@ -157,7 +147,7 @@ def clean_cells(cells):
 
     args = parser.parse_args()
     entity = json.loads(args.input.read_text())
-    Builder = get_view_config_builder(entity, get_assay)
+    Builder = get_view_config_builder(entity, get_assaytype)
     builder = Builder(entity, 'groups_token', 'https://example.com/')
     conf, cells = builder.get_conf_cells()