✨ Convert family relations to P1+P2+rel

kids-first · Dec 14, 2020 · 860f61e · 860f61e
1 parent d201dfa
commit 860f61e
Showing 1 changed file with 41 additions and 2 deletions.
diff --git a/kf_lib_data_ingest/target_api_plugins/kids_first_dataservice.py b/kf_lib_data_ingest/target_api_plugins/kids_first_dataservice.py
@@ -9,6 +9,7 @@
 requirements for format and content.
 """
 from d3b_utils.requests_retry import Session
+from pandas import DataFrame
 from kf_lib_data_ingest.common import constants
 from kf_lib_data_ingest.common.concept_schema import CONCEPT
 from kf_lib_data_ingest.common.misc import (
@@ -549,6 +550,44 @@ class FamilyRelationship:
     target_id_concept = CONCEPT.FAMILY_RELATIONSHIP.TARGET_SERVICE_ID
     service_id_fields = {"kf_id", "participant1_id", "participant2_id"}
 
+    @classmethod
+    def transform_records_list(cls, records_list):
+        """Convert PID+REL_TO_PROBAND into P1+REL_1_TO_2+P2"""
+        rdf = DataFrame(records_list)
+        if (
+            (CONCEPT.FAMILY_RELATIONSHIP.PERSON1.ID not in rdf)
+            and (CONCEPT.FAMILY_RELATIONSHIP.PERSON2.ID not in rdf)
+            and (CONCEPT.FAMILY_RELATIONSHIP.RELATION_FROM_1_TO_2 not in rdf)
+            and (CONCEPT.PARTICIPANT.RELATIONSHIP_TO_PROBAND in rdf)
+        ):
+            relations = rdf.get(
+                [
+                    CONCEPT.FAMILY.ID,
+                    CONCEPT.PARTICIPANT.ID,
+                    CONCEPT.PARTICIPANT.RELATIONSHIP_TO_PROBAND,
+                    CONCEPT.FAMILY_RELATIONSHIP.VISIBLE,
+                ]
+            ).drop_duplicates()
+
+            side1 = relations[
+                relations[CONCEPT.PARTICIPANT.RELATIONSHIP_TO_PROBAND]
+                != constants.RELATIONSHIP.PROBAND
+            ].rename(
+                columns={
+                    CONCEPT.PARTICIPANT.ID: CONCEPT.FAMILY_RELATIONSHIP.PERSON1.ID,
+                    CONCEPT.PARTICIPANT.RELATIONSHIP_TO_PROBAND: CONCEPT.FAMILY_RELATIONSHIP.RELATION_FROM_1_TO_2,
+                }
+            )
+            side2 = relations[
+                relations[CONCEPT.PARTICIPANT.RELATIONSHIP_TO_PROBAND]
+                == "Proband"
+            ][[CONCEPT.FAMILY.ID, CONCEPT.PARTICIPANT.ID]].rename(
+                columns={
+                    CONCEPT.PARTICIPANT.ID: CONCEPT.FAMILY_RELATIONSHIP.PERSON2.ID,
+                }
+            )
+            return side1.merge(side2).to_dict("records")
+
     @classmethod
     def get_key_components(cls, record, get_target_id_from_record):
         return {
@@ -557,7 +596,7 @@ def get_key_components(cls, record, get_target_id_from_record):
                     Participant,
                     {
                         CONCEPT.PARTICIPANT.ID: record[
-                            CONCEPT.FAMILY_RELATIONSHIP.PERSON1
+                            CONCEPT.FAMILY_RELATIONSHIP.PERSON1.ID
                         ],
                     },
                 )
@@ -567,7 +606,7 @@ def get_key_components(cls, record, get_target_id_from_record):
                     Participant,
                     {
                         CONCEPT.PARTICIPANT.ID: record[
-                            CONCEPT.FAMILY_RELATIONSHIP.PERSON2
+                            CONCEPT.FAMILY_RELATIONSHIP.PERSON2.ID
                         ],
                     },
                 )