phc-ingestion 0.10.5__py3-none-any.whl → 0.10.6__py3-none-any.whl

ingestion/nebula/manifest_assembler.py

@@ -9,6 +9,7 @@ from ingestion.nebula.constants import (
     NEBULA_BODY_SITE,
     NEBULA_INDICATION,
 )
+import re
 
 
 class HumanName(TypedDict):
@@ -99,7 +100,7 @@ class ManifestAssembler:
         return identifiers[0].get("value", "") if identifiers else ""
 
     def __extract_id_from_reference(self, reference: Reference) -> str:
-        if not reference or not reference.get("reference"):
+        if not reference:
             return ""
 
         ref_string = reference.get("reference")
@@ -109,12 +110,39 @@ class ManifestAssembler:
         parts = ref_string.split("/")
         return parts[1] if len(parts) > 1 else parts[0]
 
+    def __extract_elation_mrn(self, patient: Patient) -> str:
+        if not patient:
+            return ""
+
+        identifier = next(
+            (
+                x
+                for x in patient.get("identifier", [])
+                # if matches LRN format for Elation
+                if re.search(
+                    f"lrn:lo:(dev|us):{self.account_id}:ehr:{self.account_id}:{self.project_id}/Patient",
+                    x.get("system", ""),
+                )
+            ),
+            None,
+        )
+
+        if not identifier:
+            return ""
+
+        return identifier.get("value", "")
+
     def __parse_human_name(self, human_name: list[HumanName] | None):
-        if not human_name or len(human_name) == 0:
+        if not human_name:
+            return None
+
+        human_name = next((x for x in human_name if x.get("use") == "official"), None)
+
+        if not human_name:
             return None
 
-        last_name = human_name[0].get("family", "")
-        first_name = human_name[0].get("given", [])[0]
+        last_name = human_name.get("family", "")
+        first_name = human_name.get("given", [])[0]
 
         return {
             "lastName": last_name,
@@ -149,7 +177,7 @@ class ManifestAssembler:
             "indexedDate": datetime.now().strftime("%Y-%m-%d"),
             "reference": "GRCh38",
             "patientId": patient.get("id"),
-            "mrn": patient.get("id"),
+            "mrn": self.__extract_elation_mrn(patient),
             "bodySite": NEBULA_BODY_SITE,
             "bodySiteDisplay": NEBULA_BODY_SITE,
             "bodySiteSystem": BODY_SITE_SYSTEM,

{phc_ingestion-0.10.5.dist-info → phc_ingestion-0.10.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.5
+Version: 0.10.6
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc_ingestion-0.10.5.dist-info → phc_ingestion-0.10.6.dist-info}/RECORD

@@ -28,7 +28,7 @@ ingestion/generic/process.py,sha256=ZaVnZ_gx9faDUsuresI1A0oCegTa-dPQT7DBFMeZGyY,
 ingestion/generic/utils.py,sha256=1MEIru7uq38IjUdL8lcHqDH0oTki9uWrz1f2e-pmRoU,2814
 ingestion/nebula/__init__.py,sha256=VauK-rup_N8ZXVohx3HYqHX_PE_WoPyMUhdv2R7al4o,45
 ingestion/nebula/constants.py,sha256=thKqSwemdaAwAmKvF4FEVI9l1Ph5ergsnMlx6nWte7E,357
-ingestion/nebula/manifest_assembler.py,sha256=sGZdeMpMT4osOBXlxY9CPZKUJSQXaShT77JJVB30I1s,5704
+ingestion/nebula/manifest_assembler.py,sha256=OPUnuvzL1Bti_1-4N3fDP22wHtaK__4Bwh5K21Mg-C4,6416
 ingestion/nebula/process.py,sha256=D2ct9tF60ZIP_jZdjvgjfTkhEAkNNEhxaSqa04CtNR8,2237
 ingestion/nextgen/__init__.py,sha256=7LQ-h_Bvc5P1QcHMdzsqi1Qm4fTJn04-ozar2ty9wSc,59
 ingestion/nextgen/process.py,sha256=5Z0RfclwTAYZruGDiLPutjPCYFh1DJpoWY9dnttghT4,3993
@@ -59,6 +59,6 @@ ingestion/vcf_standardization/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQe
 ingestion/vcf_standardization/util/af_helpers.py,sha256=dpTzoeIQVeBRt0ETF3a9rp5ojZqznHg4x_hCZ8OPcOg,1061
 ingestion/vcf_standardization/util/dp_helpers.py,sha256=Nq8oLOLObu4_pv16qwwgpALRlUoJVCULrd9cFOD-eoI,823
 ingestion/vcf_standardization/util/read_write.py,sha256=x3Pf6Dq8tmolblbCS5CrNmrcHS3FGfqBSFpFgvFGC4g,2526
-phc_ingestion-0.10.5.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
-phc_ingestion-0.10.5.dist-info/METADATA,sha256=qf_dLgOkjhiTmAL2LjoyPJWs-38ggs82qXsc8wc66eg,677
-phc_ingestion-0.10.5.dist-info/RECORD,,
+phc_ingestion-0.10.6.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
+phc_ingestion-0.10.6.dist-info/METADATA,sha256=IhIQUPLXKsepjBwgwe4ARhaZ2fKrmvsJhsgey1Yui7o,677
+phc_ingestion-0.10.6.dist-info/RECORD,,