Merge pull request #385 from ehrbase/refactoring/sofascore

Refactor SOFA score
ehrbase · Jul 12, 2021 · 805ca8f · 805ca8f
2 parents f9c041c + c453a78
commit 805ca8f
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Showing 15 changed files with 15,410 additions and 14,502 deletions.
diff --git a/src/main/java/org/ehrbase/fhirbridge/ehr/converter/specific/CodeSystem.java b/src/main/java/org/ehrbase/fhirbridge/ehr/converter/specific/CodeSystem.java
@@ -2,6 +2,8 @@
 
 public enum CodeSystem {
 
+    ECRF_PARAMETERS("https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/ecrf-parameter-codes"),
+
     LOINC("http://loinc.org"),
 
     SNOMED("http://snomed.info/sct"),
@@ -15,11 +17,11 @@ public enum CodeSystem {
 
     private final String url;
 
-    CodeSystem(String url){
+    CodeSystem(String url) {
         this.url = url;
     }
 
-    public String getUrl(){
+    public String getUrl() {
         return url;
     }
 

diff --git a/...rg/ehrbase/fhirbridge/ehr/converter/specific/sofascore/SofaScoreCompositionConverter.java b/...rg/ehrbase/fhirbridge/ehr/converter/specific/sofascore/SofaScoreCompositionConverter.java
@@ -1,18 +1,74 @@
+/*
+ * Copyright 2020-2021 the original author or authors.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
 package org.ehrbase.fhirbridge.ehr.converter.specific.sofascore;
 
+import org.ehrbase.fhirbridge.ehr.converter.ConversionException;
 import org.ehrbase.fhirbridge.ehr.converter.generic.ObservationToCompositionConverter;
 import org.ehrbase.fhirbridge.ehr.opt.sofacomposition.SOFAComposition;
+import org.ehrbase.fhirbridge.ehr.opt.sofacomposition.definition.SofaScoreKategorieElement;
+import org.ehrbase.fhirbridge.ehr.opt.sofacomposition.definition.StatusDefiningCode;
+import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Observation;
 import org.springframework.lang.NonNull;
 
+import java.util.List;
+import java.util.stream.Collectors;
+
+@SuppressWarnings("java:S6212")
 public class SofaScoreCompositionConverter extends ObservationToCompositionConverter<SOFAComposition> {
 
     private final SofaScoreObservationConverter sofaScoreObservationConverter = new SofaScoreObservationConverter();
 
     @Override
-    public SOFAComposition convertInternal(@NonNull Observation resource) {
-        SOFAComposition composition = new SOFAComposition();
-        composition.setSofaScore(sofaScoreObservationConverter.convert(resource));
-        return composition;
+    public SOFAComposition convertInternal(@NonNull Observation observation) {
+        SOFAComposition result = new SOFAComposition();
+        result.setStatusDefiningCode(convertStatus(observation));
+        result.setKategorie(convertCategory(observation));
+        result.setSofaScore(sofaScoreObservationConverter.convert(observation));
+        return result;
+    }
+
+    public StatusDefiningCode convertStatus(Observation observation) {
+        Observation.ObservationStatus status = observation.getStatus();
+        switch (status) {
+            case PRELIMINARY:
+                return StatusDefiningCode.VORLAEUFIG;
+            case FINAL:
+                return StatusDefiningCode.FINAL;
+            case REGISTERED:
+                return StatusDefiningCode.REGISTRIERT;
+            case AMENDED:
+                return StatusDefiningCode.GEAENDERT;
+            default:
+                throw new ConversionException("Invalid Code " + status + "" + " for mapping of 'status', valid codes are: registered, final, amended and preliminary");
+        }
+    }
+
+    public List<SofaScoreKategorieElement> convertCategory(Observation observation) {
+        return observation.getCategory()
+                .stream()
+                .flatMap(concept -> concept.getCoding().stream())
+                .filter(Coding::hasCode)
+                .map(coding -> {
+                    SofaScoreKategorieElement element = new SofaScoreKategorieElement();
+                    element.setValue(coding.getCode());
+                    return element;
+                })
+                .collect(Collectors.toList());
     }
 }
diff --git a/...rg/ehrbase/fhirbridge/ehr/converter/specific/sofascore/SofaScoreObservationConverter.java b/...rg/ehrbase/fhirbridge/ehr/converter/specific/sofascore/SofaScoreObservationConverter.java
diff --git a/src/main/resources/profiles/SOFA.xml b/src/main/resources/profiles/SOFA.xml
diff --git a/src/test/java/org/ehrbase/fhirbridge/fhir/observation/SofaScoreIT.java b/src/test/java/org/ehrbase/fhirbridge/fhir/observation/SofaScoreIT.java
@@ -0,0 +1,70 @@
+package org.ehrbase.fhirbridge.fhir.observation;
+
+import org.ehrbase.fhirbridge.comparators.CustomTemporalAcessorComparator;
+import org.ehrbase.fhirbridge.ehr.converter.ConversionException;
+import org.ehrbase.fhirbridge.ehr.converter.specific.sofascore.SofaScoreCompositionConverter;
+import org.ehrbase.fhirbridge.ehr.opt.sofacomposition.SOFAComposition;
+import org.ehrbase.fhirbridge.ehr.opt.sofacomposition.definition.SofaScoreKategorieElement;
+import org.ehrbase.fhirbridge.ehr.opt.sofacomposition.definition.SofaScoreObservation;
+import org.ehrbase.fhirbridge.fhir.AbstractMappingTestSetupIT;
+import org.hl7.fhir.r4.model.Observation;
+import org.javers.core.Javers;
+import org.javers.core.JaversBuilder;
+import org.javers.core.diff.Diff;
+import org.javers.core.metamodel.clazz.ValueObjectDefinition;
+import org.junit.jupiter.api.Test;
+
+import java.io.IOException;
+import java.time.temporal.TemporalAccessor;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+class SofaScoreIT extends AbstractMappingTestSetupIT {
+
+    public SofaScoreIT() {
+        super("Observation/SofaScore/", Observation.class);
+    }
+
+    @Test
+    void createSofaScore() throws IOException {
+        create("create-sofa-score.json");
+    }
+
+    @Test
+    void createSofaScoreMapping() throws IOException {
+        testMapping("create-sofa-score.json", "paragon-create-sofa-score.json");
+    }
+
+    @Test
+    void createSofaScoreGesamtergebnisMapping() throws IOException {
+        testMapping("create-sofa-score_gesamtergebnis.json", "paragon-create-sofa-score_gesamtergebnis.json");
+    }
+
+    @Override
+    public Javers getJavers() {
+        return JaversBuilder.javers()
+                .registerValue(TemporalAccessor.class, new CustomTemporalAcessorComparator())
+                .registerValueObject(new ValueObjectDefinition(SOFAComposition.class, List.of("location", "feederAudit")))
+                .registerValueObject(SofaScoreObservation.class)
+                .registerValueObject(SofaScoreKategorieElement.class)
+                .build();
+    }
+
+    @Override
+    public Exception executeMappingException(String resource) throws IOException {
+        Observation observation = (Observation) testFileLoader.loadResource(resource);
+        SofaScoreCompositionConverter converter = new SofaScoreCompositionConverter();
+        return assertThrows(ConversionException.class, () -> converter.convert(observation));
+    }
+
+    @Override
+    public void testMapping(String resourcePath, String paragonPath) throws IOException {
+        Observation observation = (Observation) super.testFileLoader.loadResource(resourcePath);
+        SofaScoreCompositionConverter converter = new SofaScoreCompositionConverter();
+        SOFAComposition composition = converter.convert(observation);
+        Diff diff = compareCompositions(getJavers(), paragonPath, composition);
+        assertEquals(0, diff.getChanges().size());
+    }
+}
diff --git a/src/test/resources/Observation/SofaScore/create-sofa-score.json b/src/test/resources/Observation/SofaScore/create-sofa-score.json
@@ -0,0 +1,176 @@
+{
+  "resourceType": "Observation",
+  "status": "final",
+  "meta": {
+    "profile": [
+      "https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sofa-score"
+    ]
+  },
+  "category": [
+    {
+      "coding": [
+        {
+          "system": "http://terminology.hl7.org/CodeSystem/observation-category",
+          "code": "survey"
+        }
+      ]
+    }
+  ],
+  "code": {
+    "coding": [
+      {
+        "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/aaaaaa",
+        "code": "aaa",
+        "display": "SOFA-Scorea"
+      },
+      {
+        "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/ecrf-parameter-codes",
+        "code": "06",
+        "display": "SOFA-Score"
+      }
+    ],
+    "text": "Sepsis-related organ failure assessment score"
+  },
+  "subject": {
+    "identifier": {
+      "system": "urn:ietf:rfc:4122",
+      "value": "{{patientId}}"
+    }
+  },
+  "effectiveDateTime": "2020-09-16",
+  "component": [
+    {
+      "code": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "resp",
+            "display": "Respiratory system"
+          }
+        ],
+        "text": "SOFA Respiratory system scoring category"
+      },
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "resp3",
+            "display": "Respiratory system SOFA score 3"
+          }
+        ],
+        "text": "PaO2/FiO2 [mmHg (kPa)] < 200 (26.7) and mechanically ventilated"
+      }
+    },
+    {
+      "code": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "ns",
+            "display": "Nervous system"
+          }
+        ],
+        "text": "SOFA Nervous system scoring category"
+      },
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "ns4",
+            "display": "Nervous system SOFA score 4"
+          }
+        ],
+        "text": "Glasgow Coma Scale (GCS) < 6"
+      }
+    },
+    {
+      "code": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "cvs",
+            "display": "Cardiovascular system"
+          }
+        ],
+        "text": "SOFA Cardiovascular system scoring category"
+      },
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "cvs0",
+            "display": "Cardiovascular system SOFA score 0"
+          }
+        ],
+        "text": "Mean arterial pressure (MAP) ≥ 70 mmHg"
+      }
+    },
+    {
+      "code": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "liv",
+            "display": "Liver"
+          }
+        ],
+        "text": "SOFA Liver scoring category"
+      },
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "liv1",
+            "display": "Liver SOFA score 1"
+          }
+        ],
+        "text": "Bilirubin (mg/dl) [umol/L] 1.2-1.9 [20-32]"
+      }
+    },
+    {
+      "code": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "coa",
+            "display": "Coagulation"
+          }
+        ],
+        "text": "SOFA Coagulation scoring category"
+      },
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "coa2",
+            "display": "Coagulation SOFA score 2"
+          }
+        ],
+        "text": "Platelets×10^3/ul < 100"
+      }
+    },
+    {
+      "code": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "kid",
+            "display": "Kidneys"
+          }
+        ],
+        "text": "SOFA Kidneys scoring category"
+      },
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/sofa-score",
+            "code": "kid4",
+            "display": "Kidneys SOFA score 4"
+          }
+        ],
+        "text": "Creatinine (mg/dl) [umol/L] (or urine output) > 5.0 [> 440] (or < 200 ml/d)"
+      }
+    }
+  ],
+  "valueInteger": 15
+}