fixes for https://github.com/who-icatx/icatx-project/issues/142

pom.xml

@@ -100,6 +100,21 @@
                 <groupId>org.springframework.boot</groupId>
                 <artifactId>spring-boot-maven-plugin</artifactId>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>3.0.0</version>
+                <configuration>
+                    <systemPropertyVariables>
+                        <spring.profiles.active>test</spring.profiles.active>
+                    </systemPropertyVariables>
+                    <includes>
+                        <include>**/*TestCase.java</include>
+                        <include>**/*Test.java</include>
+                        <include>**/*IT.java</include>
+                    </includes>
+                </configuration>
+            </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>exec-maven-plugin</artifactId>

src/main/java/edu/stanford/protege/gateway/dto/EntityChange.java

@@ -1,10 +1,11 @@
 package edu.stanford.protege.gateway.dto;
 
+import com.fasterxml.jackson.annotation.JsonProperty;
 import edu.stanford.protege.webprotege.common.UserId;
 
 import java.time.LocalDateTime;
 
 public record EntityChange(String changeSummary,
                            UserId userId,
-                           LocalDateTime dateTime) {
+                           @JsonProperty("timestamp") LocalDateTime timestamp) {
 }

src/main/java/edu/stanford/protege/gateway/dto/OWLEntityDto.java

@@ -1,12 +1,11 @@
 package edu.stanford.protege.gateway.dto;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.*;
 
 import java.time.LocalDateTime;
-import java.util.Date;
 import java.util.List;
 
-public record OWLEntityDto(String entityIRI,
+public record OWLEntityDto(@JsonProperty("entityUri") String entityIRI,
 
                            EntityLanguageTerms languageTerms,
                            EntityLinearizationWrapperDto entityLinearizations,

src/main/java/edu/stanford/protege/gateway/history/EntityHistoryService.java

@@ -63,8 +63,8 @@ public CompletableFuture<LocalDateTime> getEntityLatestChangeTime(String project
         return entityHistorySummaryExecutor.execute(new GetEntityHistorySummaryRequest(projectId, entityIri), executionContext)
                 .thenApply(response -> {
                     if (response.entityHistorySummary() != null && response.entityHistorySummary().changes() != null && response.entityHistorySummary().changes().size() > 0) {
-                        response.entityHistorySummary().changes().sort(Comparator.comparing(EntityChange::dateTime).reversed());
-                        return response.entityHistorySummary().changes().get(0).dateTime();
+                        response.entityHistorySummary().changes().sort(Comparator.comparing(EntityChange::timestamp).reversed());
+                        return response.entityHistorySummary().changes().get(0).timestamp();
                     }
                     return LocalDateTime.MIN;
                 });

src/main/java/edu/stanford/protege/gateway/linearization/EntityLinearizationService.java

@@ -45,8 +45,9 @@ public CompletableFuture<EntityLinearizationWrapperDto> getEntityLinearizationDt
     @Async
     public CompletableFuture<EntityLinearizationWrapperDto> getEntityLinearizationDto(String entityIri, String projectId, ExecutionContext executionContext) {
         try {
+            List<LinearizationDefinition> linDef = this.getDefinitionList(executionContext);
             return entityLinearizationCommand.execute(new GetEntityLinearizationsRequest(entityIri, ProjectId.valueOf(projectId)), executionContext)
-                    .thenApply(response -> LinearizationMapper.mapFromResponse(response.linearizationSpecification(), response.lastRevisionDate()));
+                    .thenApply(response -> LinearizationMapper.mapFromResponse(response.linearizationSpecification(), response.lastRevisionDate(), linDef));
         } catch (Exception e) {
             LOGGER.error("Error fetching linearization of entity " + entityIri, e);
             throw new ApplicationException("Error fetching linearization of entity " + entityIri);
@@ -60,7 +61,8 @@ public List<LinearizationDefinition> getDefinitionList(ExecutionContext executio
 
     public void updateEntityLinearization(OWLEntityDto owlEntityDto, ProjectId projectId, ChangeRequestId changeRequestId) {
         try {
-            WhoficEntityLinearizationSpecification linearizationSpecification = LinearizationMapper.mapFromDto(owlEntityDto.entityIRI(), owlEntityDto.entityLinearizations());
+            List<LinearizationDefinition> linDef = this.getDefinitionList(SecurityContextHelper.getExecutionContext());
+            WhoficEntityLinearizationSpecification linearizationSpecification = LinearizationMapper.mapFromDto(owlEntityDto.entityIRI(), owlEntityDto.entityLinearizations(), linDef);
             saveLinearizationCommand.execute(new SaveEntityLinearizationRequest(projectId, linearizationSpecification, changeRequestId), SecurityContextHelper.getExecutionContext()).get();
         } catch (Exception e) {
             LOGGER.error("Error updating linearization for entity " + owlEntityDto.entityIRI(), e);

src/main/java/edu/stanford/protege/gateway/linearization/commands/LinearizationDefinition.java

@@ -7,13 +7,13 @@
 public class LinearizationDefinition {
 
 
-    @JsonProperty("Id")
-    private final String id;
+    @JsonProperty("linearizationId")
+    private final String linearizationId;
 
-    @JsonProperty("whoficEntityIri")
-    private final String whoficEntityIri;
+    @JsonProperty("linearizationUri")
+    private final String linearizationUri;
 
-    @JsonProperty("Description")
+    @JsonProperty("description")
     private final String description;
 
     @JsonProperty("linearizationMode")
@@ -28,25 +28,25 @@ public class LinearizationDefinition {
     @JsonProperty("sortingCode")
     private final String sortingCode;
 
-    @JsonProperty("DisplayLabel")
+    @JsonProperty("displayLabel")
     private final String displayLabel;
 
     @JsonProperty("oldId")
     private final String oldId;
 
 
     @JsonCreator
-    public LinearizationDefinition(@JsonProperty("Id") String id,
-                                   @JsonProperty("whoficEntityIri") String whoficEntityIri,
+    public LinearizationDefinition(@JsonProperty("linearizationId") String linearizationId,
+                                   @JsonProperty("linearizationUri") String linearizationUri,
                                    @JsonProperty("oldId") String oldId,
-                                   @JsonProperty("Description")String description,
-                                   @JsonProperty("LinearizationMode") String linearizationMode,
-                                   @JsonProperty("DisplayLabel") String displayLabel,
+                                   @JsonProperty("description")String description,
+                                   @JsonProperty("linearizationMode") String linearizationMode,
+                                   @JsonProperty("displayLabel") String displayLabel,
                                    @JsonProperty("rootId") String rootId,
-                                   @JsonProperty("CoreLinId") String coreLinId,
+                                   @JsonProperty("coreLinId") String coreLinId,
                                    @JsonProperty("sortingCode") String sortingCode) {
-        this.id = id;
-        this.whoficEntityIri = whoficEntityIri;
+        this.linearizationId = linearizationId;
+        this.linearizationUri = linearizationUri;
         this.description = description;
         this.linearizationMode = linearizationMode;
         this.rootId = rootId;
@@ -58,12 +58,12 @@ public LinearizationDefinition(@JsonProperty("Id") String id,
 
 
     @JsonIgnore
-    public String getId() {
-        return id;
+    public String getLinearizationId() {
+        return linearizationId;
     }
 
-    public String getWhoficEntityIri() {
-        return whoficEntityIri;
+    public String getLinearizationUri() {
+        return linearizationUri;
     }
 
     public String getLinearizationMode() {

src/main/java/edu/stanford/protege/gateway/linearization/commands/LinearizationMapper.java

@@ -1,19 +1,18 @@
 package edu.stanford.protege.gateway.linearization.commands;
 
-import edu.stanford.protege.gateway.dto.EntityLinearization;
-import edu.stanford.protege.gateway.dto.EntityLinearizationWrapperDto;
-import edu.stanford.protege.gateway.dto.LinearizationTitle;
+import edu.stanford.protege.gateway.dto.*;
 import org.semanticweb.owlapi.model.IRI;
 
-import java.util.Date;
-import java.util.List;
+import java.util.*;
 
 public class LinearizationMapper {
 
 
-    public static EntityLinearizationWrapperDto mapFromResponse(WhoficEntityLinearizationSpecification whoficSpecification, Date latsRevisionDate) {
+    public static EntityLinearizationWrapperDto mapFromResponse(WhoficEntityLinearizationSpecification whoficSpecification, Date latsRevisionDate, List<LinearizationDefinition> linDef) {
         List<EntityLinearization> linearizations = whoficSpecification.linearizationSpecifications()
-                .stream().map(LinearizationMapper::mapFromSpecification).toList();
+                .stream()
+                .map(specification -> LinearizationMapper.mapFromSpecification(specification, linDef))
+                .toList();
         if (whoficSpecification.linearizationResiduals() != null) {
             String suppressOtherResiduals = whoficSpecification.linearizationResiduals().suppressOtherSpecifiedResiduals() == null ? null : whoficSpecification.linearizationResiduals().suppressOtherSpecifiedResiduals().toString();
             String suppressUnspecified = whoficSpecification.linearizationResiduals().suppressUnspecifiedResiduals() == null ? null : whoficSpecification.linearizationResiduals().suppressUnspecifiedResiduals().toString();
@@ -33,33 +32,55 @@ public static EntityLinearizationWrapperDto mapFromResponse(WhoficEntityLineariz
     }
 
 
-    public static WhoficEntityLinearizationSpecification mapFromDto(String entityIri, EntityLinearizationWrapperDto dto) {
+    public static WhoficEntityLinearizationSpecification mapFromDto(String entityIri, EntityLinearizationWrapperDto dto, List<LinearizationDefinition> linDef) {
         LinearizationResiduals residuals = new LinearizationResiduals(LinearizationSpecificationStatus.getStatusFromString(dto.suppressOtherSpecifiedResiduals()),
                 LinearizationSpecificationStatus.getStatusFromString(dto.suppressUnspecifiedResiduals()),
                 dto.otherSpecifiedResidualTitle() != null ? dto.otherSpecifiedResidualTitle().label() : null,
                 dto.unspecifiedResidualTitle() != null ? dto.unspecifiedResidualTitle().label() : null);
 
-        List<LinearizationSpecification> specifications = dto.linearizations().stream().map(LinearizationMapper::mapFromDto).toList();
+        List<LinearizationSpecification> specifications = dto.linearizations().stream().map(lin -> mapFromDto(lin, linDef)).toList();
 
         return new WhoficEntityLinearizationSpecification(IRI.create(entityIri), residuals, specifications);
     }
 
 
-    private static LinearizationSpecification mapFromDto(EntityLinearization dto) {
+    private static LinearizationSpecification mapFromDto(EntityLinearization dto, List<LinearizationDefinition> linDef) {
         return new LinearizationSpecification(LinearizationSpecificationStatus.getStatusFromString(dto.isAuxiliaryAxisChild()),
                 LinearizationSpecificationStatus.getStatusFromString(dto.isGrouping()),
                 LinearizationSpecificationStatus.getStatusFromString(dto.isIncludedInLinearization()),
                 dto.linearizationPathParent() == null ? null : IRI.create(dto.linearizationPathParent()),
-                IRI.create(dto.linearizationId()),
+                IRI.create(getLinView(dto, linDef)),
                 dto.codingNote());
     }
 
-    private static EntityLinearization mapFromSpecification(LinearizationSpecification specification) {
+    private static EntityLinearization mapFromSpecification(LinearizationSpecification specification, List<LinearizationDefinition> linDef) {
+
         return new EntityLinearization(specification.isAuxiliaryAxisChild().toString(),
                 specification.isGrouping().toString(),
                 specification.isIncludedInLinearization().toString(),
                 specification.linearizationParent() == null ? "" : specification.linearizationParent().toString(),
-                specification.linearizationView() == null ? "" : specification.linearizationView().toString(),
+                getLinId(specification, linDef),
                 specification.codingNote());
     }
+
+    private static String getLinId(LinearizationSpecification linSpec, List<LinearizationDefinition> linDef) {
+        return linDef.stream()
+                .filter(lindef -> {
+                    if (linSpec.linearizationView() != null) {
+                        return lindef.getLinearizationUri().equals(linSpec.linearizationView().toString());
+                    }
+                    return false;
+                })
+                .findAny()
+                .map(LinearizationDefinition::getLinearizationId)
+                .orElse("");
+    }
+
+    private static String getLinView(EntityLinearization lin, List<LinearizationDefinition> linDef) {
+        return linDef.stream()
+                .filter(lindef -> lin.linearizationId().equals(lindef.getLinearizationId()))
+                .findAny()
+                .map(LinearizationDefinition::getLinearizationUri)
+                .orElse("");
+    }
 }

src/main/java/edu/stanford/protege/gateway/postcoordination/SpecificationMapper.java

@@ -1,6 +1,5 @@
 package edu.stanford.protege.gateway.postcoordination;
 
-import edu.stanford.protege.gateway.dto.EntityPostCoordinationCustomScalesDto;
 import edu.stanford.protege.gateway.dto.EntityPostCoordinationSpecificationDto;
 import edu.stanford.protege.gateway.linearization.commands.LinearizationDefinition;
 import edu.stanford.protege.gateway.postcoordination.commands.*;
@@ -15,7 +14,7 @@ public static List<EntityPostCoordinationSpecificationDto> mapFromResponse(GetEn
         List<EntityPostCoordinationSpecificationDto> resp = new ArrayList<>();
         for (PostCoordinationSpecification specification : response.postCoordinationSpecification().postcoordinationSpecifications()) {
             LinearizationDefinition definition = gedDefinitionByView(specification.getLinearizationView(), definitions);
-            EntityPostCoordinationSpecificationDto dto = new EntityPostCoordinationSpecificationDto(definition.getId(),
+            EntityPostCoordinationSpecificationDto dto = new EntityPostCoordinationSpecificationDto(definition.getLinearizationId(),
                     new ArrayList<>(),
                     new ArrayList<>(),
                     new ArrayList<>(),
@@ -48,7 +47,7 @@ public static WhoficEntityPostCoordinationSpecification mapFromDtoList(String en
 
         List<PostCoordinationSpecification> specifications = dtos.stream().map(dto -> {
             LinearizationDefinition definition = getDefinitionByLinearizationId(dto.linearizationId(), definitions);
-            PostCoordinationSpecification spec = new PostCoordinationSpecification(definition.getWhoficEntityIri(),
+            PostCoordinationSpecification spec = new PostCoordinationSpecification(definition.getLinearizationUri(),
                     new ArrayList<>(),
                     new ArrayList<>(),
                     new ArrayList<>(),
@@ -98,13 +97,13 @@ private static boolean isMainAxis(LinearizationDefinition linearizationDefinitio
     }
 
     private static LinearizationDefinition getDefinitionByLinearizationId(String linearizationId, List<LinearizationDefinition> definitions) {
-        return definitions.stream().filter(def -> def.getId().equalsIgnoreCase(linearizationId))
+        return definitions.stream().filter(def -> def.getLinearizationId().equalsIgnoreCase(linearizationId))
                 .findFirst()
                 .orElseThrow(() -> new RuntimeException("Error finding definition with id " + linearizationId));
     }
 
     private static LinearizationDefinition gedDefinitionByView(String linearizationView, List<LinearizationDefinition> definitions) {
-        return definitions.stream().filter(def -> def.getWhoficEntityIri().equalsIgnoreCase(linearizationView))
+        return definitions.stream().filter(def -> def.getLinearizationUri().equalsIgnoreCase(linearizationView))
                 .findFirst()
                 .orElseThrow(() -> new RuntimeException("Error finding definition with id " + linearizationView));
     }

src/main/resources/application.yaml

@@ -7,7 +7,7 @@ logging:
     root: DEBUG
 
 icatx:
-  formId: 013d9d4a-9dac-4d2f-aa52-2a40fad73b77
+  formId: 0612d01f-a60f-4fe7-8421-d404915685d7
 
 springdoc:
   swagger-ui:
@@ -18,7 +18,7 @@ spring:
   application:
     name: icatx-api-gateway
   rabbitmq:
-    host: localhost
+    host: rabbitmq
     port: 5672
     username: guest
     password: guest

src/test/java/edu/stanford/protege/gateway/linearization/EntityLinearizationMapperTest.java

@@ -1,36 +1,44 @@
 package edu.stanford.protege.gateway.linearization;
 
-import edu.stanford.protege.gateway.dto.EntityLinearization;
-import edu.stanford.protege.gateway.dto.EntityLinearizationWrapperDto;
-import edu.stanford.protege.gateway.dto.LinearizationTitle;
-import edu.stanford.protege.gateway.linearization.commands.LinearizationMapper;
-import edu.stanford.protege.gateway.linearization.commands.LinearizationSpecificationStatus;
-import edu.stanford.protege.gateway.linearization.commands.WhoficEntityLinearizationSpecification;
-import org.junit.jupiter.api.Test;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import edu.stanford.protege.gateway.config.ApplicationBeans;
+import edu.stanford.protege.gateway.dto.*;
+import edu.stanford.protege.gateway.linearization.commands.*;
+import org.junit.jupiter.api.*;
 
-import java.util.Collections;
+import java.io.*;
+import java.util.*;
 
 import static org.junit.jupiter.api.Assertions.*;
 
 public class EntityLinearizationMapperTest {
 
+    private List<LinearizationDefinition> definitionList;
 
+    @BeforeEach
+    public void setUp() throws IOException {
+        ObjectMapper objectMapper = new ApplicationBeans().objectMapper();
+        File defFile = new File("src/test/resources/LinearizationDefinitions.json");
+        definitionList = objectMapper.readValue(defFile, new TypeReference<>() {
+        });
+    }
 
 
     @Test
     public void GIVEN_scrambledLinearizationDTO_WHEN_mapToRequest_THEN_fieldsAreCorrectlyMapped() {
         EntityLinearization entityLinearization = new EntityLinearization("true",
                 "fAlSE",
-                "unKnown",null,
-                "http://id.who.int/icd/release/11/pcl",null);
+                "unKnown", null,
+                "PCL", null);
 
         EntityLinearizationWrapperDto dto = new EntityLinearizationWrapperDto(null,
                 "UnKnown",
                 null,
                 null,
                 new LinearizationTitle("test"), Collections.singletonList(entityLinearization));
 
-        WhoficEntityLinearizationSpecification spec = LinearizationMapper.mapFromDto("http://id.who.int/icd/entity/694903163", dto);
+        WhoficEntityLinearizationSpecification spec = LinearizationMapper.mapFromDto("http://id.who.int/icd/entity/694903163", dto, definitionList);
 
         assertNotNull(spec);
         assertNotNull(spec.linearizationResiduals());