Update get_view_config_builder to use get_assaytype instead of `g…

…et_assay`

src/portal_visualization/assays.py

@@ -11,3 +11,4 @@
 SCATAC_SEQ_SCI = "sc_atac_seq_sci"
 SCATAC_SEQ_SNARE = "sc_atac_seq_snare"
 SCATAC_SEQ_SN = "sn_atac_seq"
+SALMON_RNASSEQ_SLIDE = "salmon_rnaseq_slideseq"

src/portal_visualization/builder_factory.py

@@ -18,18 +18,33 @@
 from .assays import (
  SEQFISH,
  MALDI_IMS,
- NANODESI
+ NANODESI,
+ SALMON_RNASSEQ_SLIDE
 )
 
+# get_assaytype response example:
+# {
+# "assaytype": "image_pyramid",
+# "description": "Image Pyramid",
+# "vitessce_hints": [
+# "is_image",
+# "pyramid"
+# ]
+# }
 
-def get_view_config_builder(entity, get_assay):
- data_types = entity["data_types"]
- assay_objs = [get_assay(dt) for dt in data_types]
- assay_names = [assay.name for assay in assay_objs]
- hints = [hint for assay in assay_objs for hint in assay.vitessce_hints]
+
+def get_ancestor_assaytypes(entity, get_assaytype):
+ return [get_assaytype(ancestor.get('uuid')).get('assaytype') for ancestor in entity['immediate_ancestors']]
+
+
+def get_view_config_builder(entity, get_assaytype):
+ assay = get_assaytype(entity.get('uuid'))
+ 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]
+ print(entity.get('uuid'), assay_name)
  if "is_image" in hints:
  if 'sprm' in hints and 'anndata' in hints:
  return MultiImageSPRMAnndataViewConfBuilder
@@ -40,17 +55,17 @@ def get_view_config_builder(entity, get_assay):
  # Both SeqFISH and IMS were submitted very early on, before the
  # special image pyramid datasets existed. Their assay names should be in
  # the `entity["data_types"]` while newer ones, like NanoDESI, are in the parents
- if SEQFISH in assay_names:
+ if assay_name == SEQFISH:
  return SeqFISHViewConfBuilder
- if MALDI_IMS in assay_names:
+ if assay_name == MALDI_IMS:
  return IMSViewConfBuilder
- if NANODESI in [dt for e in entity["immediate_ancestors"] for dt in e["data_types"]]:
+ if NANODESI in [assaytype for assaytype in get_ancestor_assaytypes(entity, get_assaytype)]:
  return NanoDESIViewConfBuilder
  return ImagePyramidViewConfBuilder
  if "rna" in hints:
  # This is the zarr-backed anndata pipeline.
  if "anndata-to-ui.cwl" in dag_names:
- if "salmon_rnaseq_slideseq" in data_types:
+ if assay_name == SALMON_RNASSEQ_SLIDE:
  return SpatialRNASeqAnnDataZarrViewConfBuilder
  return RNASeqAnnDataZarrViewConfBuilder
  return RNASeqViewConfBuilder
@@ -59,6 +74,6 @@ def get_view_config_builder(entity, get_assay):
  return NullViewConfBuilder
 
 
-def has_visualization(entity, get_assay):
- builder = get_view_config_builder(entity, get_assay)
+def has_visualization(entity, get_assaytype):
+ builder = get_view_config_builder(entity, get_assaytype)
  return builder != NullViewConfBuilder