0.6.2

pom.xml

@@ -8,7 +8,7 @@
 
   <groupId>de.difuture.uds</groupId>
   <artifactId>odm2fhir</artifactId>
-  <version>0.6.1</version>
+  <version>0.6.2</version>
 
   <name>ODM2FHIR</name>
   <description>Mapper for GECCO based study/patient data in CDISC ODM to HL7 FHIR</description>

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/Item.java

@@ -83,6 +83,7 @@
 import static de.difuture.uds.odm2fhir.fhir.util.NUMStructureDefinition.UNCERTAINTY_OF_PRESENCE;
 import static de.difuture.uds.odm2fhir.util.EnvironmentProvider.getEnvironment;
 
+import static org.apache.commons.codec.digest.DigestUtils.sha256Hex;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.split;
 import static org.apache.commons.lang3.StringUtils.splitByWholeSeparator;
@@ -387,14 +388,20 @@ protected final Identifier createIdentifier(ResourceTypes resourceType, ItemData
     var formData = itemGroupData.getFormData();
     var studyEventData = formData.getStudyEventData();
     var subjectData = studyEventData.getSubjectData();
+    var value = format("%s-%s.%s-%s.%s-%s.%s-%s",
+                       subjectData.getSubjectKey(),
+                       studyEventData.getStudyEventOID(), studyEventData.getStudyEventRepeatKey(),
+                       formData.getFormOID(), formData.getFormRepeatKey(),
+                       itemGroupData.getItemGroupOID(), itemGroupData.getItemGroupRepeatKey(),
+                       itemData.getItemOID());
+
+    if (!getEnvironment().containsProperty("debug"))  {
+      value = sha256Hex(value);
+    }
+
     return new Identifier()
         .setSystem(getEnvironment().getProperty("fhir.identifier.system." + resourceType.toCode().toLowerCase()))
-        .setValue(format("%s-%s.%s-%s.%s-%s.%s-%s",
-                         subjectData.getSubjectKey(),
-                         studyEventData.getStudyEventOID(), studyEventData.getStudyEventRepeatKey(),
-                         formData.getFormOID(), formData.getFormRepeatKey(),
-                         itemGroupData.getItemGroupOID(), itemGroupData.getItemGroupRepeatKey(),
-                         itemData.getItemOID()));
+        .setValue(value);
   }
 
   protected final Age createAge(ItemData itemData) {

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/StudyEvent.java

@@ -48,7 +48,7 @@
 
 import static de.difuture.uds.odm2fhir.util.EnvironmentProvider.getEnvironment;
 
-import static org.apache.commons.codec.digest.DigestUtils.md5Hex;
+import static org.apache.commons.codec.digest.DigestUtils.sha256Hex;
 import static org.apache.commons.lang3.StringUtils.containsAny;
 import static org.apache.commons.lang3.StringUtils.equalsAny;
 
@@ -92,17 +92,23 @@ public Stream<DomainResource> map(Subject subject, StudyEventData studyEventData
     var encounter = new Encounter();
 
     if (containsAny(studyEventData.getStudyEventOID(), "GECCOVISIT", "fall")) {
+      var value = format("%s-%s.%s",
+                         studyEventData.getSubjectData().getSubjectKey(),
+                         studyEventData.getStudyEventOID(), studyEventData.getStudyEventRepeatKey());
+
+      if (!getEnvironment().containsProperty("debug")) {
+        value = sha256Hex(value);
+      }
+
       var encounterIdentifier = new Identifier()
           .setSystem(getEnvironment().getProperty("fhir.identifier.system.encounter"))
-          .setValue(format("%s-%s.%s",
-                           studyEventData.getSubjectData().getSubjectKey(),
-                           studyEventData.getStudyEventOID(), studyEventData.getStudyEventRepeatKey()))
+          .setValue(value)
           .setAssigner(subject.getOrganizationReference());
 
       encounter.setStatus(UNKNOWN)
           .setClass_(new Coding(IMP.getSystem(), IMP.toCode(), IMP.getDisplay()))
           .addIdentifier(encounterIdentifier)
-          .setId(md5Hex(encounterIdentifier.getSystem() + encounterIdentifier.getValue()));
+          .setId(sha256Hex(encounterIdentifier.getSystem() + encounterIdentifier.getValue()));
 
       encounterReference = new Reference(format("%s/%s", ENCOUNTER.toCode(), encounter.getId()));
     }

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/Subject.java

@@ -39,7 +39,7 @@
 import static de.difuture.uds.odm2fhir.fhir.util.CommonCodeSystem.IDENTIFIER_TYPE_CODES;
 import static de.difuture.uds.odm2fhir.util.EnvironmentProvider.getEnvironment;
 
-import static org.apache.commons.codec.digest.DigestUtils.md5Hex;
+import static org.apache.commons.codec.digest.DigestUtils.sha256Hex;
 import static org.apache.commons.lang3.StringUtils.equalsAny;
 
 import static org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR;
@@ -63,7 +63,7 @@ public class Subject {
 
   public Stream<DomainResource> map(SubjectData subjectData) {
     var organization = new Organization().setName(getEnvironment().getProperty("fhir.identifier.assigner"));
-    organization.setId(md5Hex(organization.getName()));
+    organization.setId(sha256Hex(organization.getName()));
 
     organizationReference = new Reference(format("%s/%s", ORGANIZATION.toCode(), organization.getId()));
 
@@ -75,7 +75,7 @@ public Stream<DomainResource> map(SubjectData subjectData) {
 
     patient = (Patient) new Patient()
         .addIdentifier(patientIdentifier)
-        .setId(md5Hex(patientIdentifier.getSystem() + patientIdentifier.getValue()))
+        .setId(sha256Hex(patientIdentifier.getSystem() + patientIdentifier.getValue()))
         .setMeta(new Meta().addProfile(NUMStructureDefinition.PATIENT.getUrl()));
 
     patientReference = new Reference(format("%s/%s", PATIENT.toCode(), patient.getId()));
@@ -91,7 +91,7 @@ public Stream<DomainResource> map(SubjectData subjectData) {
   private void setId(DomainResource domainResource) {
     var identifier = (Identifier) invokeMethod(
         findMethod(domainResource.getClass(), "getIdentifierFirstRep"), domainResource);
-    domainResource.setId(md5Hex(identifier.getSystem() + identifier.getValue()));
+    domainResource.setId(sha256Hex(identifier.getSystem() + identifier.getValue()));
   }
 
   private void setPatientSubject(DomainResource domainResource) {

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/imaging/item/ImagingProcedures.java

@@ -37,7 +37,7 @@
 import static de.difuture.uds.odm2fhir.fhir.util.NUMStructureDefinition.DIAGNOSTIC_REPORT_RADIOLOGY;
 import static de.difuture.uds.odm2fhir.fhir.util.NUMStructureDefinition.RADIOLOGY_PROCEDURES;
 
-import static org.apache.commons.codec.digest.DigestUtils.md5Hex;
+import static org.apache.commons.codec.digest.DigestUtils.sha256Hex;
 import static org.apache.commons.lang3.StringUtils.contains;
 import static org.apache.commons.lang3.StringUtils.equalsAny;
 
@@ -90,7 +90,7 @@ public DiagnosticReport createDiagnosticReport(ItemData befundCoding) {
         .setCode(createCodeableConcept(createCoding(LOINC, "18748-4", "Diagnostic imaging study")))
         .addConclusionCode(createCodeableConcept(befundCoding))
         .setMeta(createMeta(DIAGNOSTIC_REPORT_RADIOLOGY))
-        .setId(md5Hex(identifier.getSystem() + identifier.getValue()));
+        .setId(sha256Hex(identifier.getSystem() + identifier.getValue()));
   }
 
   private Procedure createProcedure(ItemData techniqueCoding) {

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/laboratory_values/item/SARSCoV2Antibodies.java

@@ -44,7 +44,7 @@
 import static de.difuture.uds.odm2fhir.fhir.util.NUMStructureDefinition.SARS_COV_2_IGM_SER_PL_IA_ACNC;
 import static de.difuture.uds.odm2fhir.fhir.util.NUMStructureDefinition.SARS_COV_2_IGM_SER_PL_QL_IA;
 
-import static org.apache.commons.codec.digest.DigestUtils.md5Hex;
+import static org.apache.commons.codec.digest.DigestUtils.sha256Hex;
 import static org.apache.commons.lang3.StringUtils.substringAfterLast;
 
 import static org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL;
@@ -137,7 +137,7 @@ private Observation createObservation(FormData formData, ItemData labValue) {
         .addCategory(LABORATORY.copy().addCoding(createCoding(LOINC.getUrl(), "26436-6")))
         .setValue(value)
         .setCode(new CodeableConcept().setCoding(usableCodings).setText(labValueName)) // TODO Add parameter name as text!!!
-        .setId(md5Hex(identifier.getSystem() + identifier.getValue())) // This really needs to be and stay here!!!
+        .setId(sha256Hex(identifier.getSystem() + identifier.getValue())) // This really needs to be and stay here!!!
         .setMeta(createMeta(PROFILES.get(labValueName)));
   }