✨ D3B-725 add has_match_normal and external_collection_id

kids-first · Aug 28, 2024 · 0170555 · 0170555
1 parent 4e28f86
commit 0170555
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diff --git a/kf_lib_data_ingest/common/concept_schema.py b/kf_lib_data_ingest/common/concept_schema.py
@@ -182,6 +182,7 @@ class VOLUME(QuantityMixin):
         VOLUME_UL = None
         SAMPLE_PROCUREMENT = None
         PRESERVATION_METHOD = None
+        HAS_MATCHED_NORMAL_SAMPLE = None
 
     class BIOSPECIMEN(SAMPLE):
         class QUANTITY(QuantityMixin):

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
@@ -488,6 +488,14 @@ def build_entity(cls, record, get_target_id_from_record):
                 record.get(CONCEPT.SAMPLE.TISSUE_TYPE)
                 or record.get(CONCEPT.BIOSPECIMEN.TISSUE_TYPE)
             ),
+            "has_matched_normal_sample": (
+                record.get(CONCEPT.SAMPLE.HAS_MATCHED_NORMAL_SAMPLE)
+                or record.get(CONCEPT.BIOSPECIMEN.HAS_MATCHED_NORMAL_SAMPLE)
+            ),
+            "external_collection_id": (
+                record.get(CONCEPT.SAMPLE.EXTERNAL_COLLECTION_ID)
+                or record.get(CONCEPT.BIOSPECIMEN.EXTERNAL_COLLECTION_ID)
+            ),
             "visible": record.get(CONCEPT.SAMPLE.VISIBLE),
             "visibility_comment": record.get(CONCEPT.SAMPLE.VISIBILITY_COMMENT),
             "visibility_reason": record.get(CONCEPT.SAMPLE.VISIBILTIY_REASON),
@@ -673,6 +681,10 @@ def build_entity(cls, record, get_target_id_from_record):
             "concentration_mg_per_ml": record.get(
                 CONCEPT.BIOSPECIMEN.CONCENTRATION_MG_PER_ML
             ),
+            "has_matched_normal_sample": (
+                record.get(CONCEPT.SAMPLE.HAS_MATCHED_NORMAL_SAMPLE)
+                or record.get(CONCEPT.BIOSPECIMEN.HAS_MATCHED_NORMAL_SAMPLE)
+            ),
             "volume_ul": (
                 record.get(CONCEPT.SAMPLE.VOLUME_UL)
                 or record.get(CONCEPT.BIOSPECIMEN.VOLUME_UL)