Merge pull request #55 from kairos-fhir/FNUSA-enhancements

Fnusa enhancements
kairos-fhir · Apr 5, 2024 · b56f53a · b56f53a
2 parents 00ec776 + 447a2d3
commit b56f53a
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Showing 3 changed files with 177 additions and 3 deletions.
diff --git a/pom.xml b/pom.xml
@@ -16,7 +16,7 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <java.compiler.level>1.8</java.compiler.level>
     <maven-compiler-plugin.version>3.11.0</maven-compiler-plugin.version>
-    <kairos-fhir-dsl.version>1.30.0</kairos-fhir-dsl.version>
+    <kairos-fhir-dsl.version>1.31.0-SNAPSHOT</kairos-fhir-dsl.version>
     <junit-jupiter.version>5.8.2</junit-jupiter.version>
     <maven-surefire-plugin.version>3.1.2</maven-surefire-plugin.version>
     <gmavenplus-plugin.version>1.9.1</gmavenplus-plugin.version>

diff --git a/src/main/groovy/projects/patientfinder/procedureWithMapping.groovy b/src/main/groovy/projects/patientfinder/procedureWithMapping.groovy
@@ -0,0 +1,144 @@
+package projects.patientfinder
+
+import ca.uhn.fhir.model.api.TemporalPrecisionEnum
+import de.kairos.fhir.centraxx.metamodel.CrfTemplateField
+import de.kairos.fhir.centraxx.metamodel.Episode
+import de.kairos.fhir.centraxx.metamodel.LaborFinding
+import de.kairos.fhir.centraxx.metamodel.LaborFindingLaborValue
+import de.kairos.fhir.centraxx.metamodel.LaborMapping
+import de.kairos.fhir.centraxx.metamodel.OrganisationUnit
+import de.kairos.fhir.centraxx.metamodel.ValueReference
+import org.hl7.fhir.r4.model.Procedure
+
+import static de.kairos.fhir.centraxx.metamodel.AbstractCode.CODE
+import static de.kairos.fhir.centraxx.metamodel.AbstractIdContainer.PSN
+import static de.kairos.fhir.centraxx.metamodel.MultilingualEntry.LANG
+import static de.kairos.fhir.centraxx.metamodel.MultilingualEntry.VALUE
+import static de.kairos.fhir.centraxx.metamodel.RootEntities.medProcedure
+
+/**
+ * Represented by CXX MedProcedure
+ * Exports extra data that is documented in a measurement profile with code ADDITIONAL_PROCEDURE_DATA
+ * The measurement profile 2 parameters:
+ * 1.  Code: "DEPARTMENT", Type: SingleChoice on MasterDataCatalog of all OrgUnits
+ * 2.  Code: "IS_SURGICAL_PROCEDURE", Type: boolean
+ *
+ */
+procedure {
+  id = "Procedure/" + context.source[medProcedure().id()]
+
+  status = Procedure.ProcedureStatus.UNKNOWN
+  //println(context.source)
+
+  final def mapping = context.source[medProcedure().laborMappings()].find {
+    it[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_METHOD][CODE] == "ADDITIONAL_PROCEDURE_DATA"
+  }
+
+  if (mapping != null) {
+    final def departmentValue = mapping[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_FINDING_LABOR_VALUES].find {
+      it[LaborFindingLaborValue.CRF_TEMPLATE_FIELD][CrfTemplateField.LABOR_VALUE][CODE] == "DEPARTMENT"
+    }
+
+    final def procedureType = mapping[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_FINDING_LABOR_VALUES].find {
+      it[LaborFindingLaborValue.CRF_TEMPLATE_FIELD][CrfTemplateField.LABOR_VALUE][CODE] == "IS_SURGICAL_PROCEDURE"
+    }
+
+    println(departmentValue)
+    println(procedureType)
+
+
+    if (departmentValue != null) {
+      println(departmentValue[LaborFindingLaborValue.MULTI_VALUE_REFERENCES])
+      departmentValue[LaborFindingLaborValue.MULTI_VALUE_REFERENCES].each { final def valRef ->
+        performer {
+          onBehalfOf {
+            reference = "Organization/" + valRef[ValueReference.ORGANIZATION_VALUE][OrganisationUnit.ID]
+          }
+        }
+      }
+    }
+
+    if (procedureType != null && procedureType[LaborFindingLaborValue.BOOLEAN_VALUE] == true) {
+      category {
+        coding {
+          system = "http://hl7.org/fhir/ValueSet/procedure-category"
+          code = "387713003"
+          display = "Surgical procedure (procedure)"
+        }
+      }
+    }
+  }
+
+  code {
+    if (context.source[medProcedure().opsEntry()]) {
+      coding {
+        system = "https://fhir.centraxx.de/system/" + context.source[medProcedure().opsEntry().catalogue().name()]
+        version = context.source[medProcedure().opsEntry().catalogue().catalogueVersion()]
+        code = context.source[medProcedure().opsEntry().code()] as String
+        display = context.source[medProcedure().opsEntry().preferredLong()] as String
+      }
+    }
+
+    if (context.source[medProcedure().userDefinedCatalogEntry()]) {
+      coding {
+        system = "https://fhir.centraxx.de/system/" + context.source[medProcedure().userDefinedCatalogEntry().catalog().code()]
+        version = context.source[medProcedure().userDefinedCatalogEntry().catalog().version()]
+        code = context.source[medProcedure().userDefinedCatalogEntry().code()] as String
+        display = context.source[medProcedure().userDefinedCatalogEntry().nameMultilingualEntries()]?.find { it[LANG] == "en" }?.getAt(VALUE)
+      }
+    }
+
+    if (context.source[medProcedure().procedureCode()]) {
+      coding {
+        code = context.source[medProcedure().procedureCode()] as String
+        display = context.source[medProcedure().procedureText()] as String
+      }
+    }
+  }
+
+  if (context.source[medProcedure().procedureDate().date()]) {
+    performedDateTime {
+      date = normalizeDate(context.source[medProcedure().procedureDate().date()] as String)
+      precision = TemporalPrecisionEnum.DAY.toString()
+    }
+  }
+
+  final String opsNote = context.source[medProcedure().comments()] as String
+  if (opsNote) {
+    note {
+      text = opsNote
+    }
+  }
+
+  subject {
+    reference = "Patient/" + context.source[medProcedure().patientContainer().id()]
+  }
+
+  if (!isFakeEpisode(context.source[medProcedure().episode()])) {
+    encounter {
+      reference = "Encounter/" + context.source[medProcedure().episode().id()]
+    }
+  }
+}
+
+static boolean isFakeEpisode(final def episode) {
+  if (episode == null) {
+    return true
+  }
+
+  if (["SACT", "COSD"].contains(episode[Episode.ENTITY_SOURCE])) {
+    return true
+  }
+
+  final def fakeId = episode[Episode.ID_CONTAINER]?.find { (it[PSN] as String).toUpperCase().startsWith("FAKE") }
+  return fakeId != null
+}
+
+/**
+ * removes milli seconds and time zone.
+ * @param dateTimeString the date time string
+ * @return the result might be something like "1989-01-15T00:00:00"
+ */
+static String normalizeDate(final String dateTimeString) {
+  return dateTimeString != null ? dateTimeString.substring(0, 19) : null
+}
diff --git a/src/main/groovy/projects/patientfinder/specimen.groovy b/src/main/groovy/projects/patientfinder/specimen.groovy
@@ -2,17 +2,27 @@ package projects.patientfinder
 
 import de.kairos.centraxx.fhir.r4.utils.FhirUrls
 import de.kairos.fhir.centraxx.metamodel.AbstractSample
+import de.kairos.fhir.centraxx.metamodel.CrfTemplateField
+import de.kairos.fhir.centraxx.metamodel.LaborFinding
+import de.kairos.fhir.centraxx.metamodel.LaborFindingLaborValue
+import de.kairos.fhir.centraxx.metamodel.LaborMapping
 
 import static de.kairos.fhir.centraxx.metamodel.AbstractCode.CODE
 import static de.kairos.fhir.centraxx.metamodel.AbstractIdContainer.ID_CONTAINER_TYPE
 import static de.kairos.fhir.centraxx.metamodel.AbstractIdContainer.PSN
 import static de.kairos.fhir.centraxx.metamodel.IdContainerType.DECISIVE
 import static de.kairos.fhir.centraxx.metamodel.RootEntities.sample
 
+/**
+ * Export additional data via a SAMPLETYPELABORMAPPING that links to a finding
+ * with LABORMETHOD code "ADDITIONAL_SAMPLE_DATA". If that finding
+ * contains a value for a parameter with code "COLLECTION_METHOD", the value
+ * is exported to collection.method.coding.code
+ */
 specimen {
 
   id = "Specimen/" + context.source[sample().id()]
-
+  println(context.source)
   context.source[sample().idContainer()].each { final idContainer ->
     final boolean isDecisive = idContainer[ID_CONTAINER_TYPE]?.getAt(DECISIVE)
     if (isDecisive) {
@@ -28,6 +38,7 @@ specimen {
     }
   }
 
+
   type {
     coding {
       system = FhirUrls.System.Sample.SampleKind.BASE_URL
@@ -41,12 +52,17 @@ specimen {
 
   final def parentSample = context.source[sample().parent()]
 
-  if (parentSample != null){
+  if (parentSample != null) {
     parent {
       reference = "Specimen/" + parentSample[AbstractSample.ID]
     }
   }
 
+  final def finding = context.source[sample().laborMappings()].find {
+    it[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_METHOD][CODE] == "ADDITIONAL_SAMPLE_DATA"
+  }
+
+
   collection {
     collectedDateTime {
       date = context.source[sample().samplingDate().date()]
@@ -55,5 +71,19 @@ specimen {
         unit = context.source[sample().initialAmount().unit()]
       }
     }
+
+    if (finding != null) {
+      final def collectionMethod = finding[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_FINDING_LABOR_VALUES].find {
+        it[LaborFindingLaborValue.CRF_TEMPLATE_FIELD][CrfTemplateField.LABOR_VALUE][CODE] == "COLLECTION_METHOD"
+      }
+
+      if (collectionMethod != null) {
+        method {
+          coding {
+            code = collectionMethod[LaborFindingLaborValue.STRING_VALUE]
+          }
+        }
+      }
+    }
   }
 }