adding transform FHIR Bundle to OMOP Bundle (CoreFHIR2OMOP)

Author: davidouagne

input/fml/usages/core/StructureMap-CoreFHIRPatient2OMOP.fml

@@ -6,7 +6,7 @@ map "https://aphp.fr/ig/fhir/dm/StructureMap/CoreFHIRPatient2OMOP" = "CoreFHIRPa
 /// status = 'draft'
 
 uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as source
-uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/LogicalBundle" alias LogicalBundle as target
+//uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/LogicalBundle" alias LogicalBundle as target
 uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/OMOPPerson" alias PersonTable as target
 uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/OMOPLocation" alias LocationTable as target
 uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/OMOPDeath" alias DeathTable as target
@@ -15,22 +15,14 @@ imports "https://aphp.fr/ig/fhir/dm/StructureMap/CoreFHIR2OMOPPerson"
 imports "https://aphp.fr/ig/fhir/dm/StructureMap/CoreFHIR2OMOPLocation"
 imports "https://aphp.fr/ig/fhir/dm/StructureMap/CoreFHIR2OMOPDeath"
 
-group Patient(source src: Patient, target tgtBundle : LogicalBundle) {
-	src -> tgtBundle.id = uuid() "setId";
-	src -> tgtBundle.type = 'transaction' "setType";
-	src -> tgtBundle.entry as newEntry then {
-		src -> newEntry.person = create("PersonTable") as newPerson then {
-			src then Person(src, newPerson) "transformPerson";
-		} "createPerson";
-	} "newEntryPerson";
-	src.address as srcAddress where use = 'home' and period.end.empty() -> tgtBundle.entry as newEntry then {
-		srcAddress -> newEntry.location = create("LocationTable") as newLocation then {
-			srcAddress then Location(srcAddress, newLocation) "transformLocation";
-		} "createLocation";
-	} "newEntryLocation";
-	src where deceased.is(System.DateTime) or deceased.is(System.Boolean) -> tgtBundle.entry as newEntry then {
-		src -> newEntry.death = create("DeathTable") as newDeath then {
-			src then Death(src, newDeath) "transformDeath";
-		} "createDeath";
-	} "newEntryDeath";
-}
+group Patient(source src: Patient, target tgtEntry) <<types>> {
+	src -> tgtEntry.person = create("PersonTable") as newPerson then {
+		src then Person(src, newPerson) "transformPerson";
+	} "createPerson";
+	src.address as srcAddress where use = 'home' and period.end.empty() -> tgtEntry.location = create("LocationTable") as newLocation then {
+		srcAddress then Location(srcAddress, newLocation) "transformLocation";
+	} "createLocation";
+	src where deceased.is(System.DateTime) or deceased.is(System.Boolean) -> tgtEntry.death = create("DeathTable") as newDeath then {
+		src then Death(src, newDeath) "transformDeath";
+	} "createDeath";
+}

input/fml/usages/core/StrucutreMap-CoreFHIR2OMOP.fml

@@ -0,0 +1,23 @@
+map "https://aphp.fr/ig/fhir/dm/StructureMap/CoreFHIR2OMOP" = "CoreFHIR2OMOP"
+
+/// name = 'CoreFHIR2OMOP'
+/// title = 'FHIR resources to Tables CDM OMOP'
+/// description = 'Cette ressource présente les spécifications de l\'alignement entre les ressources FHIR vers les tables correspodantes du CDM OMOP.'
+
+uses "http://hl7.org/fhir/StructureDefinition/Bundle" alias Bundle as source
+uses "http://hl7.org/fhir/StructureDefinition/Patient" alias Patient as source
+uses "https://aphp.fr/ig/fhir/dm/StructureDefinition/LogicalBundle" alias LogicalBundle as target
+
+imports "https://aphp.fr/ig/fhir/dm/StructureMap/CoreFHIRPatient2OMOP"
+
+group Bundle(source src: Bundle, target tgtBundle : LogicalBundle) <<types>> {
+  src -> tgtBundle.id = uuid() "setId";
+	src -> tgtBundle.type = 'transaction' "setType";
+  src.entry as srcEntry where srcEntry.resource.is(FHIR.Patient) then {
+    srcEntry.resource as srcResource -> (%srcResource.as(FHIR.Patient)) as srcPatient, tgtBundle.entry as newEntry then Patient(srcPatient, newEntry) "addPatient";
+  } "entryLoop4Patient";
+}
+
+group PatientTest(source src: Patient, target tgtBundle : LogicalBundle) {
+  src -> tgtBundle.entry as newEntry then Patient(src, newEntry) "addPatient";
+}