Merge pull request #519 from ehrbase/bugfix/issues_514_and_516

Bugfix/516 unexpected error
ehrbase · Oct 20, 2021 · 6499227 · 6499227
2 parents 285730a + 6e0bb17
commit 6499227
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -32,120 +32,120 @@ workflows:
                             # - release
 
     # WORKFLOW 2/2 Build, Fully Test & Analyze FHIR-bridge code
-#    QUALITY-GATE-II:
-#        jobs:
-#            - build-test-analyse-fhirbridge:
-#                context: org-global
-#                filters:
-#                    branches:
-#                        ignore: gh-pages
-#
-#            # Execute Robot Integration Tests (Parallel Execution)
-#            - BUNDLE-tests:
-#                context: org-global
-#                requires:
-#                    - build-test-analyse-fhirbridge
-#                filters:
-#                    branches:
-#                        ignore: gh-pages
-#
-#            - CONDITION-tests:
-#                context: org-global
-#                requires:
-#                    - build-test-analyse-fhirbridge
-#                filters:
-#                    branches:
-#                        ignore: gh-pages
-#
-#            - CONSENT-tests:
-#                  context: org-global
-#                  requires:
-#                      - build-test-analyse-fhirbridge
-#                  filters:
-#                      branches:
-#                          ignore: gh-pages
-#
-#            - DIAGNOSTIC-tests:
-#                context: org-global
-#                requires:
-#                    - build-test-analyse-fhirbridge
-#                filters:
-#                    branches:
-#                        ignore: gh-pages
-#
-#            - IMMUNIZATION-tests:
-#                context: org-global
-#                requires:
-#                    - build-test-analyse-fhirbridge
-#                filters:
-#                    branches:
-#                        ignore: gh-pages
-#
-#            - MEDICATIONSTATEMENT-tests:
-#                context: org-global
-#                requires:
-#                    - build-test-analyse-fhirbridge
-#                filters:
-#                    branches:
-#                        ignore: gh-pages
-#
-#            - OBSERVATION-tests:
-#                context: org-global
-#                requires:
-#                    - build-test-analyse-fhirbridge
-#                filters:
-#                    branches:
-#                        ignore: gh-pages
-#
-#            - PROCEDURE-tests:
-#                context: org-global
-#                requires:
-#                    - build-test-analyse-fhirbridge
-#                filters:
-#                    branches:
-#                        ignore: gh-pages
-#
-#            - QUESTIONAIRE-tests:
-#                context: org-global
-#                requires:
-#                    - build-test-analyse-fhirbridge
-#                filters:
-#                    branches:
-#                        ignore: gh-pages
-#
-#            - ROBOT-TEST-REPORT:
-#                context: org-global
-#                requires:
-#                    - BUNDLE-tests
-#                    - CONDITION-tests
-#                    - CONSENT-tests
-#                    - DIAGNOSTIC-tests
-#                    - IMMUNIZATION-tests
-#                    - MEDICATIONSTATEMENT-tests
-#                    - OBSERVATION-tests
-#                    - PROCEDURE-tests
-#                    - QUESTIONAIRE-tests
-#
-#
-#            - tag-version:
-#                context: org-global
-#                requires:
-#                    - build-test-analyse-fhirbridge
-#                filters:
-#                    branches:
-#                        only:
-#                            - /^(release\/v\d+\.\d+\.\d+|hotfix\/v\d+\.\d+\.\d+)$/
-#
-#
-#            - build-and-deploy:
-#                context: org-global
-#                requires:
-#                    - build-test-analyse-fhirbridge
-#                filters:
-#                    branches:
-#                        only:
-#                            - /^(release\/v\d+\.\d+\.\d+|hotfix\/v\d+\.\d+\.\d+|master|develop)$/
-#
+    QUALITY-GATE-II:
+        jobs:
+            - build-test-analyse-fhirbridge:
+                context: org-global
+                filters:
+                    branches:
+                        ignore: gh-pages
+
+            # Execute Robot Integration Tests (Parallel Execution)
+            - BUNDLE-tests:
+                context: org-global
+                requires:
+                    - build-test-analyse-fhirbridge
+                filters:
+                    branches:
+                        ignore: gh-pages
+
+            - CONDITION-tests:
+                context: org-global
+                requires:
+                    - build-test-analyse-fhirbridge
+                filters:
+                    branches:
+                        ignore: gh-pages
+
+            - CONSENT-tests:
+                  context: org-global
+                  requires:
+                      - build-test-analyse-fhirbridge
+                  filters:
+                      branches:
+                          ignore: gh-pages
+
+            - DIAGNOSTIC-tests:
+                context: org-global
+                requires:
+                    - build-test-analyse-fhirbridge
+                filters:
+                    branches:
+                        ignore: gh-pages
+
+            - IMMUNIZATION-tests:
+                context: org-global
+                requires:
+                    - build-test-analyse-fhirbridge
+                filters:
+                    branches:
+                        ignore: gh-pages
+
+            - MEDICATIONSTATEMENT-tests:
+                context: org-global
+                requires:
+                    - build-test-analyse-fhirbridge
+                filters:
+                    branches:
+                        ignore: gh-pages
+
+            - OBSERVATION-tests:
+                context: org-global
+                requires:
+                    - build-test-analyse-fhirbridge
+                filters:
+                    branches:
+                        ignore: gh-pages
+
+            - PROCEDURE-tests:
+                context: org-global
+                requires:
+                    - build-test-analyse-fhirbridge
+                filters:
+                    branches:
+                        ignore: gh-pages
+
+            - QUESTIONAIRE-tests:
+                context: org-global
+                requires:
+                    - build-test-analyse-fhirbridge
+                filters:
+                    branches:
+                        ignore: gh-pages
+
+            - ROBOT-TEST-REPORT:
+                context: org-global
+                requires:
+                    - BUNDLE-tests
+                    - CONDITION-tests
+                    - CONSENT-tests
+                    - DIAGNOSTIC-tests
+                    - IMMUNIZATION-tests
+                    - MEDICATIONSTATEMENT-tests
+                    - OBSERVATION-tests
+                    - PROCEDURE-tests
+                    - QUESTIONAIRE-tests
+
+
+            - tag-version:
+                context: org-global
+                requires:
+                    - build-test-analyse-fhirbridge
+                filters:
+                    branches:
+                        only:
+                            - /^(release\/v\d+\.\d+\.\d+|hotfix\/v\d+\.\d+\.\d+)$/
+
+
+            - build-and-deploy:
+                context: org-global
+                requires:
+                    - build-test-analyse-fhirbridge
+                filters:
+                    branches:
+                        only:
+                            - /^(release\/v\d+\.\d+\.\d+|hotfix\/v\d+\.\d+\.\d+|master|develop)$/
+
 #
 #
 #            - deploy-testdocs-githup-pages:

diff --git a/pom.xml b/pom.xml
@@ -39,6 +39,7 @@
         <maven-jacoco-plugin.version>0.8.5</maven-jacoco-plugin.version>
         <maven-surefire-plugin.version>2.22.2</maven-surefire-plugin.version>
         <minio.version>8.3.1</minio.version>
+        <okhttp.version>4.9.2</okhttp.version>
         <saxon.version>10.5</saxon.version>
         <spring-boot.version>2.5.5</spring-boot.version>
         <woodstox.version>6.2.6</woodstox.version>
@@ -382,16 +383,21 @@
                 <artifactId>guava</artifactId>
                 <version>${guava.version}</version>
             </dependency>
-            <dependency>
-                <groupId>commons-io</groupId>
-                <artifactId>commons-io</artifactId>
-                <version>${commons-io.version}</version>
-            </dependency>
             <dependency>
                 <groupId>com.sun.xml.bind</groupId>
                 <artifactId>jaxb-core</artifactId>
                 <version>${jaxb-core.version}</version>
             </dependency>
+            <dependency>
+                <groupId>com.squareup.okhttp3</groupId>
+                <artifactId>okhttp</artifactId>
+                <version>${okhttp.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>commons-io</groupId>
+                <artifactId>commons-io</artifactId>
+                <version>${commons-io.version}</version>
+            </dependency>
             <dependency>
                 <groupId>io.github.classgraph</groupId>
                 <artifactId>classgraph</artifactId>

diff --git a/src/main/java/org/ehrbase/fhirbridge/camel/processor/PatientReferenceProcessor.java b/src/main/java/org/ehrbase/fhirbridge/camel/processor/PatientReferenceProcessor.java
@@ -70,7 +70,8 @@ public void process(Exchange exchange) throws Exception {
 
             IIdType patientId;
             if (subject.hasReference()) {
-                patientId = subject.getReferenceElement();
+                Patient patient = patientDao.read(subject.getReferenceElement());
+                patientId = patient.getIdElement();
             } else if (hasIdentifier(subject)) {
                 patientId = handleSubjectIdentifier(subject, requestDetails);
             } else {

diff --git a/src/main/java/org/ehrbase/fhirbridge/ehr/converter/parser/DvCodedTextParser.java b/src/main/java/org/ehrbase/fhirbridge/ehr/converter/parser/DvCodedTextParser.java
@@ -20,39 +20,11 @@ public static DvCodedText parseDefiningCode(EnumValueSet enumValueSet) {
         return new DvCodedText(enumValueSet.getValue(), new CodePhrase(new TerminologyId(enumValueSet.getTerminologyId(), ""), enumValueSet.getCode()));
     }
 
-    /**
-     * @deprecated Use {@link org.ehrbase.fhirbridge.ehr.converter.DvCodedTextParser#parseFHIRCoding(Coding)}
-     */
-    @Deprecated(since = "1.4", forRemoval = true)
-    public static Optional<DvCodedText> parseFHIRCodingOld(Coding coding) {
-        if (coding.hasDisplay() && coding.hasSystem() && coding.hasCode() && coding.getSystem().equals(CodeSystem.SNOMED.getUrl())) {
-            return Optional.of(new DvCodedText(coding.getDisplay(), new CodePhrase(new TerminologyId("SNOMED Clinical Terms", ""), coding.getCode())));
-        } else if (coding.hasCode() && coding.getSystem().equals(CodeSystem.SNOMED.getUrl())) {
-            return Optional.of(new DvCodedText("", new CodePhrase(new TerminologyId("SNOMED Clinical Terms", ""), coding.getCode())));
-        } else {
-            return Optional.empty();
-        }
-    }
-
-    /**
-     * @deprecated Use {@link org.ehrbase.fhirbridge.ehr.converter.DvCodedTextParser#parseFHIRCoding(Coding)}
-     */
-    @Deprecated(since = "1.4", forRemoval = true)
-    public static Optional<DvCodedText> parseFHIRCoding(Coding coding) {
-        if (coding.hasDisplay() && coding.hasSystem() && coding.hasCode()) {
-            return Optional.of(new DvCodedText(coding.getDisplay(), new CodePhrase(new TerminologyId(coding.getSystem(), ""), coding.getCode())));
-        } else {
-            return Optional.empty();
-        }
-    }
-
     public static DvCodedText parseBirthInteger(IntegerType multipleBirthIntegerType) {
         return new DvCodedText("amount of multiple births", new CodePhrase(new TerminologyId("", ""), multipleBirthIntegerType.toString()));
     }
 
     public static DvCodedText parseBirthBoolean(BooleanType multipleBirthBoolean) {
         return new DvCodedText("multiple births present", new CodePhrase(new TerminologyId("", ""), multipleBirthBoolean.toString()));
     }
-
-
 }
diff --git a/...erter/specific/bloodgas/laboratoryanalyteconverter/KohlendioxidpartialdruckConverter.java b/...erter/specific/bloodgas/laboratoryanalyteconverter/KohlendioxidpartialdruckConverter.java
@@ -2,7 +2,7 @@
 
 import org.ehrbase.client.classgenerator.interfaces.LocatableEntity;
 import org.ehrbase.client.classgenerator.shareddefinition.NullFlavour;
-import org.ehrbase.fhirbridge.ehr.converter.parser.DvCodedTextParser;
+import org.ehrbase.fhirbridge.ehr.converter.DvCodedTextParser;
 import org.ehrbase.fhirbridge.ehr.opt.befundderblutgasanalysecomposition.definition.KohlendioxidpartialdruckCluster;
 import org.ehrbase.fhirbridge.ehr.opt.befundderblutgasanalysecomposition.definition.KohlendioxidpartialdruckErgebnisStatusElement;
 import org.hl7.fhir.r4.model.Observation;
@@ -18,17 +18,19 @@ public KohlendioxidpartialdruckConverter(Observation fhirObservation) {
     public KohlendioxidpartialdruckCluster map() {
         KohlendioxidpartialdruckCluster kohlendioxidpartialdruckCluster = new KohlendioxidpartialdruckCluster();
         kohlendioxidpartialdruckCluster.setErgebnisStatus(mapKohlendioxidErgebnisStatus());
-        DvCodedTextParser.parseFHIRCoding(fhirObservation.getCode().getCoding().get(0)).ifPresent(kohlendioxidpartialdruckCluster::setBezeichnungDesAnalyts);
+        DvCodedTextParser.getInstance()
+                .parseFHIRCoding(fhirObservation.getCode().getCoding().get(0))
+                .ifPresent(kohlendioxidpartialdruckCluster::setBezeichnungDesAnalyts);
         convertAnalytErgebnis(kohlendioxidpartialdruckCluster);
         return kohlendioxidpartialdruckCluster;
     }
 
     @Override
     void convertAnalytErgebnis(LocatableEntity locatableEntity) {
-        if(fhirObservation.hasValue()){
+        if (fhirObservation.hasValue()) {
             ((KohlendioxidpartialdruckCluster) locatableEntity).setAnalytErgebnisUnits("mmHg");
             ((KohlendioxidpartialdruckCluster) locatableEntity).setAnalytErgebnisMagnitude(mapValue());
-        }else{
+        } else {
             ((KohlendioxidpartialdruckCluster) locatableEntity).setAnalytErgebnisNullFlavourDefiningCode(NullFlavour.UNKNOWN);
         }
     }

diff --git a/...hirbridge/ehr/converter/specific/bloodgas/laboratoryanalyteconverter/PhWertConverter.java b/...hirbridge/ehr/converter/specific/bloodgas/laboratoryanalyteconverter/PhWertConverter.java
@@ -2,7 +2,7 @@
 
 import org.ehrbase.client.classgenerator.interfaces.LocatableEntity;
 import org.ehrbase.client.classgenerator.shareddefinition.NullFlavour;
-import org.ehrbase.fhirbridge.ehr.converter.parser.DvCodedTextParser;
+import org.ehrbase.fhirbridge.ehr.converter.DvCodedTextParser;
 import org.ehrbase.fhirbridge.ehr.opt.befundderblutgasanalysecomposition.definition.PhWertCluster;
 import org.ehrbase.fhirbridge.ehr.opt.befundderblutgasanalysecomposition.definition.SauerstoffpartialdruckErgebnisStatusElement;
 import org.hl7.fhir.r4.model.Observation;
@@ -18,24 +18,26 @@ public PhWertConverter(Observation fhirObservation) {
     public PhWertCluster map() {
         PhWertCluster phWertCluster = new PhWertCluster();
         phWertCluster.setErgebnisStatus(mapPhClusterErgebnisStatus());
-        DvCodedTextParser.parseFHIRCoding(fhirObservation.getCode().getCoding().get(0)).ifPresent(phWertCluster::setBezeichnungDesAnalyts);
+        DvCodedTextParser.getInstance()
+                .parseFHIRCoding(fhirObservation.getCode().getCoding().get(0))
+                .ifPresent(phWertCluster::setBezeichnungDesAnalyts);
         convertAnalytErgebnis(phWertCluster);
         convertAnalytErgebnis(phWertCluster);
         return phWertCluster;
     }
 
     private List<SauerstoffpartialdruckErgebnisStatusElement> mapPhClusterErgebnisStatus() {
         SauerstoffpartialdruckErgebnisStatusElement sauerstoffpartialdruckErgebnisStatusElement = new SauerstoffpartialdruckErgebnisStatusElement();
-         sauerstoffpartialdruckErgebnisStatusElement.setValue(mapErgebnisStatus());
-         return List.of(sauerstoffpartialdruckErgebnisStatusElement);
+        sauerstoffpartialdruckErgebnisStatusElement.setValue(mapErgebnisStatus());
+        return List.of(sauerstoffpartialdruckErgebnisStatusElement);
     }
 
     @Override
     void convertAnalytErgebnis(LocatableEntity locatableEntity) {
-        if(fhirObservation.hasValue()){
+        if (fhirObservation.hasValue()) {
             ((PhWertCluster) locatableEntity).setAnalytErgebnisUnits("pH");
             ((PhWertCluster) locatableEntity).setAnalytErgebnisMagnitude(mapValue());
-        }else{
+        } else {
             ((PhWertCluster) locatableEntity).setAnalytErgebnisNullFlavourDefiningCode(NullFlavour.UNKNOWN);
         }
     }