Merge pull request #965 from hubmapconsortium/nickakhmetov/add-is-integrated

NickAkhmetov/Add `is_integrated` to portal index transformations

Author: yuanzhou

src/hubmap_translation/addl_index_transformations/portal/__init__.py

@@ -8,6 +8,7 @@
 from yaml import safe_load as load_yaml
 import jsonschema
 
+from hubmap_translation.addl_index_transformations.portal.add_is_integrated import add_is_integrated
 from hubmap_translation.addl_index_transformations.portal.translate import (
     translate, TranslationException
 )
@@ -76,6 +77,7 @@ def transform(doc, transformation_resources, batch_id='unspecified'):
         return None
     sort_files(doc_copy)
     add_counts(doc_copy)
+    add_is_integrated(doc_copy)
     add_partonomy(doc_copy, organ_map)
     reset_entity_type(doc_copy)
     if len(doc_copy['transformation_errors']) == 0:

src/hubmap_translation/addl_index_transformations/portal/add_is_integrated.py

@@ -0,0 +1,29 @@
+from hubmap_translation.addl_index_transformations.portal.add_assay_details import (
+    CreationAction,
+)
+
+
+# Determines whether to display the raw dataset-focused UI or the processed outline-focused UI
+# Must be run after add_counts transformation, since it relies on ancestor_counts
+def add_is_integrated(doc):
+    # only datasets can be integrated
+    if doc.get("entity_type") != "Dataset":
+        return
+
+    # EPIC datasets are always considered integrated (including segmentation masks):
+    # - they can be derived from multiple datasets
+    # - they are always processed
+    # - they always have visualization support
+    # - they have their own list of contributors that may differ from the base dataset's contributors
+    if doc.get("creation_action") == CreationAction.EPIC:
+        doc["is_integrated"] = True
+        return
+
+    # If a dataset is immediately descended from multiple datasets, it is considered integrated
+    # This covers Snare-Seq2 experiments
+    if doc.get("ancestor_counts"):
+        if doc["ancestor_counts"].get("entity_type", {}).get("Dataset", 0) > 1:
+            doc["is_integrated"] = True
+            return
+
+    doc["is_integrated"] = False