Merge pull request #9 from SevKohler/fix_missing_day

added exclusion for partial date and updated test
SevKohler · Sep 6, 2024 · c8b1c38 · c8b1c38
2 parents 87bdfdc + cb76cd5
commit c8b1c38
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Showing 9 changed files with 46 additions and 14 deletions.
diff --git a/src/main/java/org/bih/eos/controller/CompositionController.java b/src/main/java/org/bih/eos/controller/CompositionController.java
@@ -36,7 +36,6 @@ public ResponseEntity<Object> addCompositionJson(@RequestBody String json, @Path
         if (ehrToPerson.isPresent()) {
             Composition composition = new CanonicalJson().
                     unmarshal(json, com.nedap.archie.rm.composition.Composition.class);
-            System.out.println(composition);
             return runConversion(composition, ehrToPerson.get().getPerson());
         } else {
             return new ResponseEntity<>("{ \"message\" : \"EHR id has no person, create either one or enter a correct ehr id\" }", HttpStatus.CONFLICT);

diff --git a/src/main/java/org/bih/eos/converter/cdm_field/date/DVToDateConverter.java b/src/main/java/org/bih/eos/converter/cdm_field/date/DVToDateConverter.java
@@ -16,6 +16,7 @@
 import java.time.LocalDate;
 import java.time.OffsetDateTime;
 import java.time.ZoneId;
+import java.time.temporal.ChronoField;
 import java.time.temporal.Temporal;
 import java.time.temporal.TemporalAccessor;
 import java.time.temporal.TemporalAmount;
@@ -106,7 +107,8 @@ private Optional<Date> getIntervalEventStart(IntervalEvent intervalEvent) {
     }
 
     public Optional<Date> parseDvDateTime(TemporalAccessor dvDateTime) {
-        if (dvDateTime == null) {
+        if (dvDateTime == null || !dvDateTime.isSupported(ChronoField.DAY_OF_MONTH)) {
+            LOG.warn("Date was empty, or partial (e.g. Day missing), therefore Date is returned empty.");
             return Optional.empty();
         } else {
             OffsetDateTime dateTime = OffsetDateTime.parse(dvDateTime.toString());

diff --git a/src/main/java/org/bih/eos/converter/cdt/conversion_entities/VisitOccurrenceEntity.java b/src/main/java/org/bih/eos/converter/cdt/conversion_entities/VisitOccurrenceEntity.java
@@ -1,14 +1,18 @@
 package org.bih.eos.converter.cdt.conversion_entities;
 
+import org.bih.eos.converter.cdt.converter.nonconfigurable.VisitOccurrenceConverter;
 import org.bih.eos.exceptions.UnprocessableEntityException;
 import org.bih.eos.jpabase.entity.Concept;
 import org.bih.eos.jpabase.entity.Person;
 import org.bih.eos.jpabase.entity.VisitOccurrence;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.util.Date;
 import java.util.Optional;
 
 public class VisitOccurrenceEntity extends EntityWithStandardConcept<VisitOccurrence> {
+    private static final Logger LOG = LoggerFactory.getLogger(VisitOccurrenceEntity.class);
 
 
     public VisitOccurrenceEntity(VisitOccurrence jpaEntity, Person person, Concept type) {
@@ -39,11 +43,24 @@ public void setEntitySourceValue(Optional<String> entitySourceValue) {
         //ignored field doesnt exist
     }
 
-    public void setEndDate(Optional<Date> date) {
-        populateFieldIfPresent(date, dateTimeValue -> {
-            jpaEntity.setVisitEndDate(dateTimeValue);
-            jpaEntity.setVisitEndDateTime(dateTimeValue);
-        });
+    public void setEndDate(Optional<Date> endDate, Optional<Date> startDate) {
+        if(endDate.isPresent()){
+            populateFieldIfPresent(endDate, dateTimeValue -> {
+                jpaEntity.setVisitEndDate(dateTimeValue);
+                jpaEntity.setVisitEndDateTime(dateTimeValue);
+            });
+        }else if(startDate.isPresent()){ //Set StartDate as EndDate since Enddate is emtpy
+            LOG.warn("EndDate time was empty provided by the composition, startDate is set instead for Visit_occurrence");
+            populateFieldIfPresent(startDate, dateTimeValue -> {
+                jpaEntity.setVisitEndDate(dateTimeValue);
+                jpaEntity.setVisitEndDateTime(dateTimeValue);
+            });
+        }
+    }
+
+    public void setDateStartAndEnd(Optional<Date> startDate, Optional<Date> endDate) {
+        setDateTime(startDate);
+        setEndDate(endDate, startDate);
     }
 
     @Override

diff --git a/...in/java/org/bih/eos/converter/cdt/converter/nonconfigurable/VisitOccurrenceConverter.java b/...in/java/org/bih/eos/converter/cdt/converter/nonconfigurable/VisitOccurrenceConverter.java
@@ -31,8 +31,7 @@ public VisitOccurrenceConverter(DefaultConverterServices defaultConverterService
     public Optional<JPABaseEntity> convert(Composition composition, Person person) {
         VisitOccurrenceEntity visitOccurrence = new VisitOccurrenceEntity(new VisitOccurrence(), person, defaultConverterServices.getConceptService().findById(32817L));
         convertStandardAndSourceConcept(visitOccurrence);
-        visitOccurrence.setDateTime(convertStartDate(composition));
-        visitOccurrence.setEndDate(convertEndDate(composition));
+        visitOccurrence.setDateStartAndEnd(convertStartDate(composition), convertEndDate(composition));
         visitOccurrence.setAdmittedFromConcept(defaultConverterServices.getConceptService().findById(0L));
         visitOccurrence.setDischargeToConcept(defaultConverterServices.getConceptService().findById(0L));
         return visitOccurrence.toJpaEntity();

diff --git a/src/main/java/org/bih/eos/converter/composition/CompositionToMDConverter.java b/src/main/java/org/bih/eos/converter/composition/CompositionToMDConverter.java
@@ -19,6 +19,7 @@
 import org.springframework.lang.NonNull;
 
 import java.util.*;
+import java.util.concurrent.atomic.AtomicInteger;
 
 public class CompositionToMDConverter extends CompositionToEntityConverter<CDTConverter, ConvertableComposition> {
     HashMap<String, Integer> archetypeList = new HashMap<String, Integer>();
@@ -44,7 +45,7 @@ private List<JPABaseEntity> runCDTConverters(List<ConversionTrack> conversionTra
         Optional<VisitOccurrence> visitOccurrence = convertVisitOccurrence(convertableComposition.getComposition(), convertableComposition.getPerson());
         CdtExecutionParameterMedData cdtExecutionParameters = new CdtExecutionParameterMedData(convertableComposition.getPerson(), visitOccurrence);
         cdtConverterResults = iterateContent(convertableComposition.getComposition().getContent(), cdtExecutionParameters, conversionTracker, cdtConverterResults);
-        LOG.info("Mapped amount of archetypes: " + archetypeList.values().stream().mapToInt(i -> i.intValue()).sum() + ", including following archetypes: " + archetypeList);
+        LOG.info("Mapped amount of all transformed archetypes: " + archetypeList.values().stream().mapToInt(i -> i.intValue()).sum() + ", including following archetypes: " + archetypeList);
         return cdtConverterResults;
     }
 
@@ -71,7 +72,7 @@ private void increaseArchetypeCounter(String archetypeNodeId) {
         if (archetypeList.containsKey(archetypeNodeId)) {
             archetypeList.put(archetypeNodeId, archetypeList.get(archetypeNodeId) + 1);
         } else {
-            archetypeList.put(archetypeNodeId, 0);
+            archetypeList.put(archetypeNodeId, 1);
         }
     }
 

diff --git a/src/main/java/org/bih/eos/services/ConverterService.java b/src/main/java/org/bih/eos/services/ConverterService.java
@@ -1,8 +1,11 @@
 package org.bih.eos.services;
 
 import com.nedap.archie.rm.composition.Composition;
+import org.bih.eos.converter.cdt.conversion_entities.VisitOccurrenceEntity;
 import org.bih.eos.services.dao.ConvertableComposition;
 import org.bih.eos.jpabase.entity.JPABaseEntity;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.core.convert.ConversionService;
 import org.springframework.core.convert.TypeDescriptor;
 import org.springframework.stereotype.Service;
@@ -14,21 +17,31 @@ public class ConverterService {
     private final ConversionService conversionService;
     private final PersistenceService persistenceService;
 
+    private static final Logger LOG = LoggerFactory.getLogger(ConverterService.class);
+
     public ConverterService(ConversionService conversionService, PersistenceService persistenceService) {
         this.conversionService = conversionService;
         this.persistenceService = persistenceService;
     }
 
     @SuppressWarnings({"Unchecked", "ConstantConditions"})
     public List<JPABaseEntity> convert(ConvertableComposition convertableComposition) {
+        logComposition(convertableComposition.getComposition());
         persistenceService.clearPersistedEntities();
         TypeDescriptor sourceType = TypeDescriptor.valueOf(ConvertableComposition.class);
         TypeDescriptor targetType = TypeDescriptor.collection(List.class, TypeDescriptor.valueOf(JPABaseEntity.class));
         persistenceService.create((List<JPABaseEntity>) conversionService.convert(convertableComposition, sourceType, targetType));
         return persistenceService.getPersistedEntities();
     }
 
+    private void logComposition(Composition composition) {
+        if(composition.getUid() != null){
+            LOG.info("Converting Composition with id: " + composition.getUid().getValue());
+        }
+    }
+
     public List<JPABaseEntity> convertBatch(ConvertableComposition convertableComposition) {
+        logComposition(convertableComposition.getComposition());
         persistenceService.clearPersistedEntities();
         TypeDescriptor sourceType = TypeDescriptor.valueOf(ConvertableComposition.class);
         TypeDescriptor targetType = TypeDescriptor.collection(List.class, TypeDescriptor.valueOf(JPABaseEntity.class));
@@ -42,6 +55,7 @@ public List<JPABaseEntity> convertLastBatch() {
         return persistenceService.getPersistedEntities();
     }
     public List<JPABaseEntity> convert(Composition composition) {
+        logComposition(composition);
         persistenceService.clearPersistedEntities();
         TypeDescriptor sourceType = TypeDescriptor.valueOf(Composition.class);
         TypeDescriptor targetType = TypeDescriptor.collection(List.class, TypeDescriptor.valueOf(JPABaseEntity.class));

diff --git a/...a/json/output/medical_data/observation/laboratory_test_result_v1/virological_finding.json b/...a/json/output/medical_data/observation/laboratory_test_result_v1/virological_finding.json
@@ -72,7 +72,7 @@
     "person": "##ignore",
     "measurementConcept": {
       "id": "##ignore",
-      "conceptName": "SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay",
+      "conceptName": "SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory system specimen by Rapid immunoassay",
       "domainId": "Measurement",
       "vocabularyId": "LOINC",
       "conceptClassId": "Lab Test",

diff --git a/...medical_data/observation/laboratory_test_result_v1/virological_finding_with_quantity.json b/...medical_data/observation/laboratory_test_result_v1/virological_finding_with_quantity.json
@@ -72,7 +72,7 @@
     "person": "##ignore",
     "measurementConcept": {
       "id": "##ignore",
-      "conceptName": "SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay",
+      "conceptName": "SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory system specimen by Rapid immunoassay",
       "domainId": "Measurement",
       "vocabularyId": "LOINC",
       "conceptClassId": "Lab Test",

diff --git a/src/test/java/karate-config.js b/src/test/java/karate-config.js
@@ -2,7 +2,7 @@ function fn() {
 
     var config = {
         baseUrl: 'http://localhost:8081',
-        ehrId: '266ee149-95f7-4b0d-8cbe-9790f91c40f6',
+        ehrId: 'bddb4332-090e-40ea-88d1-6e69f69d17eb',
         action_composition_path: 'classpath:json/compositions/medical_data/action/',
         evaluation_composition_path: 'classpath:json/compositions/medical_data/evaluation/',
         instruction_composition_path: 'classpath:json/compositions/medical_data/instruction/',