0.7.4

README.md

@@ -18,6 +18,8 @@ docker run **ENVIRONMENTS** **VOLUMES** ghcr.io/num-codex/odm2fhir **ARGUMENTS**
 
 * `--odm.redcap.mapping` Print current mapping.
 
+* `--odm.incompleteforms.allowed=true` Allow processing of incomplete forms. 
+
 * `--fhir.identifier.system.**TYPE**=**TYPE_IDENTIFIER_SYSTEM**` Add an identifier system with `**TYPE**` of `condition`, `consent`, `diagnosticreport`, `encounter`, `immunization`, `medicationstatement`, `observation`, `patient` or `procedure` (see [here](https://simplifier.net/guide/GermanCoronaConsensusDataSet-ImplementationGuide/TransactionBundle)).
 
 * `--fhir.identifier.assigner=**IDENTIFIER_ASSIGNER**` Add an identifier assigner.

docs/index.md

@@ -18,6 +18,8 @@ docker run **ENVIRONMENTS** **VOLUMES** ghcr.io/num-codex/odm2fhir **ARGUMENTS**
 
 * `--odm.redcap.mapping` Print current mapping.
 
+* `--odm.incompleteforms.allowed=true` Allow processing of incomplete forms. 
+
 * `--fhir.identifier.system.**TYPE**=**TYPE_IDENTIFIER_SYSTEM**` Add an identifier system with `**TYPE**` of `condition`, `consent`, `diagnosticreport`, `encounter`, `immunization`, `medicationstatement`, `observation`, `patient` or `procedure` (see [here](https://simplifier.net/guide/GermanCoronaConsensusDataSet-ImplementationGuide/TransactionBundle)).
 
 * `--fhir.identifier.assigner=**IDENTIFIER_ASSIGNER**` Add an identifier assigner.

pom.xml

@@ -8,15 +8,15 @@
 
   <groupId>de.difuture.uds</groupId>
   <artifactId>odm2fhir</artifactId>
-  <version>0.7.3</version>
+  <version>0.7.4</version>
 
   <name>ODM2FHIR</name>
   <description>Mapper for GECCO based study/patient data in CDISC ODM to HL7 FHIR</description>
 
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>2.6.0</version>
+    <version>2.6.1</version>
   </parent>
 
   <properties>
@@ -25,7 +25,7 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 
-    <hapi-fhir.version>5.6.0</hapi-fhir.version>
+    <hapi-fhir.version>5.6.1</hapi-fhir.version>
     <jackson.version>2.13.0</jackson.version>
     <lombok.version>1.18.22</lombok.version>
     <spring-boot.version>${project.parent.version}</spring-boot.version>

src/main/java/de/difuture/uds/odm2fhir/ODM2FHIRApplication.java

@@ -53,7 +53,7 @@ public class ODM2FHIRApplication implements CommandLineRunner {
   private ODMProcessor odmProcessor;
 
   @Autowired
-  BuildProperties buildProperties;
+  private BuildProperties buildProperties;
 
   @Value("classpath:README.md")
   private Path readme;

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

@@ -31,6 +31,7 @@
 import static de.difuture.uds.odm2fhir.util.EnvironmentProvider.ENVIRONMENT;
 
 import static org.apache.commons.lang3.StringUtils.equalsAny;
+import static org.apache.commons.lang3.StringUtils.removeStart;
 
 import static java.util.function.Predicate.not;
 
@@ -39,7 +40,7 @@ public abstract class Form {
   @Getter
   private StudyEvent studyEvent;
 
-  public abstract String getOID();
+  protected abstract String getOID();
 
   protected abstract List<Item> getItems();
 
@@ -57,7 +58,7 @@ private boolean isComplete(FormData formData) {
     return "demographie".equals(getOID()) ||
            ENVIRONMENT.getProperty("odm.incompleteforms.allowed", Boolean.class, false) ||
            // Check REDCap X_complete and  DIS status field for complete (2), locked (4) or signed (5)
-           Stream.of(formData.getFormOID() + "_complete", "Status")
+           Stream.of(removeStart(formData.getFormOID(), "Form.") + "_complete", "Status")
                  .map(formData::getItemData)
                  .map(ItemData::getValue)
                  .anyMatch(value -> equalsAny(value, "2", "4", "5"));

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

@@ -104,7 +104,8 @@
 @Slf4j
 public abstract class Item {
 
-  @Getter private Form form;
+  @Getter
+  private Form form;
 
   public Stream<DomainResource> map(Form form, FormData formData) {
     this.form = form;

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/CardiovascularDiseases.java

@@ -41,7 +41,7 @@
 
 public class CardiovascularDiseases extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var itemGroupData = formData.getItemGroupData("anamnese_risikofaktoren.herzkreislauferkrankungen_bluthochdruck");
     var generalPresence = formData.getItemData("herzkreislauferkrankungen");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/ChronicKidneyDiseases.java

@@ -37,7 +37,7 @@
 
 public class ChronicKidneyDiseases extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("chronische_nierenerkrankungen");
     var stageCoding = formData.getItemData("chronische_nierenerkrankungen_schweregrad");
     var generalCoding = formData.getItemData("chronische_nierenerkrankungen_code");

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/ChronicLiverDiseases.java

@@ -41,7 +41,7 @@
 
 public class ChronicLiverDiseases extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var itemGroupData = formData.getItemGroupData("anamnese_risikofaktoren.chronische_lebererkrankungen_fettleber");
     var generalPresence = formData.getItemData("chronische_lebererkrankungen");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/ChronicLungDiseases.java

@@ -41,7 +41,7 @@
 
 public class ChronicLungDiseases extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var itemGroupData = formData.getItemGroupData("anamnese_risikofaktoren.chronische_lungenerkrankungen_asthma");
     var generalPresence = formData.getItemData("chronische_lungenerkrankungen");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/ChronicNeurologicalMentalDiseases.java

@@ -40,7 +40,7 @@
 
 public class ChronicNeurologicalMentalDiseases extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var itemGroupData = formData.getItemGroupData("anamnese_risikofaktoren.chronische_neurologische_oder_psychiatrische_erkrankungen_m_parkinson");
     var generalPresence = formData.getItemData("chronische_neurologische_oder_psychiatrische_erkrankungen");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/DNROrder.java

@@ -37,7 +37,7 @@ public class DNROrder extends Item {
 
   private static final String POLICY = "https://www.aerzteblatt.de/archiv/65440/DNR-Anordnungen-Das-fehlende-Bindeglied";
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("dnranordnung");
 
     return answerCoding.isEmpty() ? Stream.empty() : Stream.of(createConsent(answerCoding));

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/GastrointestinalUlcers.java

@@ -34,7 +34,7 @@
 
 public class GastrointestinalUlcers extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("magengeschwure");
     var generalCoding = formData.getItemData("magengeschwure_code");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/HIVInfection.java

@@ -34,7 +34,7 @@
 
 public class HIVInfection extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("bestehende_hivinfektion");
     var generalCoding = formData.getItemData("bestehende_hivinfektion_code");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/HistoryOfTravel.java

@@ -66,7 +66,7 @@ public class HistoryOfTravel extends Item {
     STATES.put("DE-TH", "Thüringen");
   }
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("reiseaktivitat");
     var generalCoding = formData.getItemData("reiseaktivitat_code");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/ImmunizationStatus.java

@@ -43,7 +43,7 @@
 
 public class ImmunizationStatus extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var itemGroupData = formData.getItemGroupData("anamnese_risikofaktoren.impfungen_influenza");
 
     return itemGroupData.isEmpty() ? Stream.empty() :

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/MalignantNeoplasticDiseases.java

@@ -34,7 +34,7 @@
 
 public class MalignantNeoplasticDiseases extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("aktive_tumorkrebserkrankungen");
     var generalCoding = formData.getItemData("aktive_tumorkrebserkrankungen_code");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/OrganRecipient.java

@@ -41,7 +41,7 @@
 
 public class OrganRecipient extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var itemGroupData = formData.getItemGroupData("anamnese_risikofaktoren.organtransplantiert_herz");
     var generalPresence = formData.getItemData("organtransplantiert");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/RespiratoryTherapies.java

@@ -40,7 +40,7 @@
 
 public class RespiratoryTherapies extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("bestehende_sauerstoff_oder_beatmungstherapie");
     var generalCoding = formData.getItemData("bestehende_sauerstoff_oder_beatmungstherapie_code");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/RheumatologicalImmunologicalDiseases.java

@@ -41,7 +41,7 @@
 
 public class RheumatologicalImmunologicalDiseases extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var itemGroupData = formData.getItemGroupData("anamnese_risikofaktoren.rheumatologischeimmunologische_erkrankungen_chronisch_entzuendl_darmerkrankung");
     var generalPresence = formData.getItemData("rheumatologischeimmunologische_erkrankungen");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/anamnesis/item/SmokingStatus.java

@@ -34,7 +34,7 @@
 
 public class SmokingStatus extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("raucherstatus");
     var generalCoding = formData.getItemData("raucherstatus_code");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/complications/item/ComplicationConditions.java

@@ -41,7 +41,7 @@ public class ComplicationConditions extends Item {
                                                             "lungenarterienembolie", "stroke", "myokardinfarkt",
                                                             "andere", "pulmonale_co_infektionen", "blutstrominfektionen");
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var generalComplicationCoding = formData.getItemData("komplikation_code");
 
     return !"1".equals(formData.getItemData("komplikation").getValue()) ? Stream.empty() :

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/consent/item/BroadConsent.java

@@ -35,9 +35,6 @@
 import static de.difuture.uds.odm2fhir.fhir.util.CommonCodeSystem.LOINC;
 import static de.difuture.uds.odm2fhir.fhir.util.CommonStructureDefinition.GERMAN_CONSENT;
 
-import static java.util.function.Predicate.not;
-import static java.util.stream.Collectors.toList;
-
 import static org.apache.commons.lang3.StringUtils.removeStart;
 import static org.apache.commons.lang3.time.DateUtils.addYears;
 
@@ -48,6 +45,9 @@
 import static org.hl7.fhir.r4.model.Consent.ConsentState.REJECTED;
 import static org.hl7.fhir.r4.model.codesystems.ResourceTypes.CONSENT;
 
+import static java.util.function.Predicate.not;
+import static java.util.stream.Collectors.toList;
+
 public class BroadConsent extends Item {
 
   private static final List<String> ELEMENTS = List.of("erhebung_verarbeitung", "krankenkassendaten_retro",
@@ -103,7 +103,7 @@ public class BroadConsent extends Item {
     OIDS.put("projekt_codex_zusatz_4", 38);
   }
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var consentPresented = formData.getItemData("miibc_vorlage"); //1=Yes, 2=No, 3=Unknown
 
     return !"1".equals(consentPresented.getValue()) ? Stream.empty() : Stream.of(createConsent(formData));

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/demographics/item/Age.java

@@ -33,7 +33,7 @@
 
 public class Age extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("alter");
 
     // TODO Age should not be attached to a patient but rather to an encounter...

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/demographics/item/BiologicalSex.java

@@ -34,7 +34,7 @@
 
 public class BiologicalSex extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("biologisches_geschlecht");
     var generalCoding = formData.getItemData("biologisches_geschlecht_code");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/demographics/item/BodyHeight.java

@@ -34,7 +34,7 @@
 
 public class BodyHeight extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("korpergrose");
     var generalCoding = formData.getItemData("korpergrose_code");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/demographics/item/BodyWeight.java

@@ -34,7 +34,7 @@
 
 public class BodyWeight extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("gewicht");
     var generalCoding = formData.getItemData("gewicht_code");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/demographics/item/DateOfBirth.java

@@ -27,7 +27,7 @@
 
 public class DateOfBirth extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     getPatient().setBirthDateElement(createDateType(formData.getItemData("geburtsdatum")));
 
     return Stream.empty();

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/demographics/item/EthnicGroup.java

@@ -31,7 +31,7 @@
 
 public class EthnicGroup extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("ethnische_zugehorigkeit");
 
     var coding = createCoding(answerCoding);

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/demographics/item/FrailtyScore.java

@@ -35,7 +35,7 @@
 
 public class FrailtyScore extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("frailtyscore");
     var generalCoding = formData.getItemData("frailtyscore_code");
 

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/demographics/item/PregnancyStatus.java

@@ -34,7 +34,7 @@
 
 public class PregnancyStatus extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("schwangerschaft");
     var generalCoding = formData.getItemData("schwangerschaft_code");
 

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

@@ -53,7 +53,7 @@
 
 public class ImagingProcedures extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var techniqueGroup = formData.getItemGroupData("bildgebung.bildgebende_verfahren_ct");
     var befundGroup = formData.getItemGroupData("bildgebung.befund_bildgebender_verfahren_ct");
     var generalCoding = formData.getItemData("bildgebende_verfahren");

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

@@ -47,7 +47,7 @@ public class LaboratoryValue extends Item {
                                                          "ptt", "thrombozyten_absolut", "inr", "serumalbumin", "antithrombin_iii",
                                                          "pct_procalcitonin", "il6_interleukin_6", "ntprobnp", "fibrinogen");
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     return PARAMETERS.stream()
         .map(formData::getItemData)
         .filter(not(ItemData::isEmpty))

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

@@ -71,7 +71,7 @@ public class SARSCoV2Antibodies extends Item {
                                                                              "ig_m_ia_ql", SARS_COV_2_IGM_SER_PL_QL_IA,
                                                                              "ig_m_ia_qn", SARS_COV_2_IGM_SER_PL_IA_ACNC);
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     // Extremely ugly and hacky workaround for non-existent panel parameter in form... :-/
     return PARAMETERS.stream()
         .map(key -> "sarsco_v2_covid19_" + key)

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/laboratory_values/item/SARSCoV2RTPCR.java

@@ -36,7 +36,7 @@
 
 public class SARSCoV2RTPCR extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var dateCoding = formData.getItemData("labor_datum");
     var generalCoding = formData.getItemData("sarsco_v2rtpcr_code");
     var answerCoding = formData.getItemData("sarsco_v2rtpcr");

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/medication/item/ACEInhibitors.java

@@ -35,7 +35,7 @@
 
 public class ACEInhibitors extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var answerCoding = formData.getItemData("acehemmer");
     var generalCoding = formData.getItemData("acehemmer_code");
     var dateCoding = formData.getItemData("medikation_datum");

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/medication/item/Anticoagulation.java

@@ -41,7 +41,7 @@
 
 public class Anticoagulation extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var itemGroupData = formData.getItemGroupData("medikation.antikoagulation_absicht");
     var generalPresence = formData.getItemData("antikoagulation");
     var generalCoding = formData.getItemData("antikoagulation_code");

src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/medication/item/COVID19Therapy.java

@@ -41,7 +41,7 @@
 
 public class COVID19Therapy extends Item {
 
-  public Stream<DomainResource> map(FormData formData) {
+  protected Stream<DomainResource> map(FormData formData) {
     var itemGroupData = formData.getItemGroupData("medikation.covid19therapie_antipyretika");
     var generalPresence = formData.getItemData("covid19therapie");
     var dateCoding = formData.getItemData("medikation_datum");