ReferenceGenomeGeneMappingSerializer implemented

model/src/main/java/lcsb/mapviewer/modelutils/serializer/model/map/layout/ReferenceGenomeGeneMappingSerializer.java

+package lcsb.mapviewer.modelutils.serializer.model.map.layout;
+
+import java.io.IOException;
+import java.util.function.Function;
+
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.SerializerProvider;
+
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
+
+public class ReferenceGenomeGeneMappingSerializer extends JsonSerializer<ReferenceGenomeGeneMapping> {
+
+  private Function<String, String> getLocalUrl;
+
+  public ReferenceGenomeGeneMappingSerializer(Function<String, String> getLocalUrl) {
+    this.getLocalUrl = getLocalUrl;
+  }
+
+  @Override
+  public void serialize(final ReferenceGenomeGeneMapping mapping, final JsonGenerator gen,
+      final SerializerProvider serializers)
+      throws IOException {
+    gen.writeStartObject();
+    gen.writeNumberField("downloadProgress", mapping.getDownloadProgress());
+    gen.writeStringField("localUrl", getLocalUrl.apply(mapping.getSourceUrl()));
+    gen.writeStringField("sourceUrl", mapping.getSourceUrl());
+    gen.writeStringField("name", mapping.getName());
+    gen.writeNumberField("idObject", mapping.getId());
+    gen.writeEndObject();
+
+  }
+}
\ No newline at end of file

rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java

@@ -84,7 +84,7 @@ public class ReferenceGenomeController extends BaseController {
     result.put("sourceUrl", genome.getSourceUrl());
     result.put("localUrl", getLocalUrl(genome.getSourceUrl()));
     result.put("idObject", genome.getId());
-    result.put("geneMapping", geneMappingToMaps(genome.getGeneMapping()));
+    result.put("geneMapping", genome.getGeneMapping());
 
     return result;
   }
@@ -99,25 +99,6 @@ public class ReferenceGenomeController extends BaseController {
     return url;
   }
 
-  private List<Map<String, Object>> geneMappingToMaps(List<ReferenceGenomeGeneMapping> geneMapping) {
-    List<Map<String, Object>> result = new ArrayList<>();
-    for (ReferenceGenomeGeneMapping referenceGenomeGeneMapping : geneMapping) {
-      result.add(geneMappingToMap(referenceGenomeGeneMapping));
-    }
-
-    return result;
-  }
-
-  private Map<String, Object> geneMappingToMap(ReferenceGenomeGeneMapping mapping) {
-    Map<String, Object> result = new TreeMap<>();
-    result.put("downloadProgress", mapping.getDownloadProgress());
-    result.put("localUrl", getLocalUrl(mapping.getSourceUrl()));
-    result.put("sourceUrl", mapping.getSourceUrl());
-    result.put("name", mapping.getName());
-    result.put("idObject", mapping.getId());
-    return result;
-  }
-
   static class RemoteUrl {
     public String url;
   }

web/src/main/java/lcsb/mapviewer/web/config/SpringWebConfig.java

 package lcsb.mapviewer.web.config;
 
 import java.awt.Color;
+import java.io.FileNotFoundException;
 import java.util.Calendar;
 import java.util.List;
 import java.util.function.Function;
@@ -36,13 +37,16 @@ import lcsb.mapviewer.api.SpringRestApiConfig;
 import lcsb.mapviewer.model.Article;
 import lcsb.mapviewer.model.map.Comment;
 import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.modelutils.serializer.CalendarSerializer;
 import lcsb.mapviewer.modelutils.serializer.ColorSerializer;
 import lcsb.mapviewer.modelutils.serializer.model.map.CommentSerializer;
 import lcsb.mapviewer.modelutils.serializer.model.map.MiriamDataSerializer;
+import lcsb.mapviewer.modelutils.serializer.model.map.layout.ReferenceGenomeGeneMappingSerializer;
 import lcsb.mapviewer.services.interfaces.IElementService;
+import lcsb.mapviewer.services.interfaces.IFileService;
 import lcsb.mapviewer.services.interfaces.IMeshService;
 import lcsb.mapviewer.services.interfaces.IMiriamService;
 import lcsb.mapviewer.services.interfaces.IReactionService;
@@ -61,15 +65,17 @@ public class SpringWebConfig implements WebMvcConfigurer {
   private IMeshService meshService;
   private IElementService elementService;
   private IReactionService reactionService;
+  private IFileService fileService;
 
   @Autowired
   public SpringWebConfig(List<HandlerInterceptor> interceptors, IMiriamService miriamConnector, IMeshService meshService,
-      IElementService elementService, IReactionService reactionService) {
+      IElementService elementService, IReactionService reactionService, IFileService fileService) {
     this.interceptors = interceptors;
     this.miriamService = miriamConnector;
     this.meshService = meshService;
     this.elementService = elementService;
     this.reactionService = reactionService;
+    this.fileService = fileService;
   }
 
   @Override
@@ -129,6 +135,20 @@ public class SpringWebConfig implements WebMvcConfigurer {
               }
             }));
 
+        module.addSerializer(ReferenceGenomeGeneMapping.class, new ReferenceGenomeGeneMappingSerializer(
+            new Function<String, String>() {
+              @Override
+              public String apply(String sourceUrl) {
+                String url = null;
+                try {
+                  url = "../" + fileService.getLocalPathForFile(sourceUrl);
+                } catch (FileNotFoundException e) {
+                  logger.warn("Cannot find local file", e);
+                }
+                return url;
+              }
+            }));
+
         m.getObjectMapper().registerModule(module);
       }
     }

web/src/test/java/lcsb/mapviewer/web/GenomicsControllerIntegrationTest.java

@@ -30,6 +30,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.mock.web.MockHttpSession;
 import org.springframework.restdocs.payload.FieldDescriptor;
+import org.springframework.restdocs.payload.JsonFieldType;
 import org.springframework.test.context.ActiveProfiles;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.test.web.servlet.RequestBuilder;
@@ -244,6 +245,11 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
     genome.setDownloadProgress(100.0);
     genome.setType(ReferenceGenomeType.UCSC);
     genome.setVersion("eboVir3");
+    ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
+    mapping.setName("xy");
+    mapping.setSourceUrl("https://minerva-dev.lcsb.uni.lu/tmp/refGene.bb");
+    genome.addReferenceGenomeGeneMapping(mapping);
+
     return callInSeparateThread(() -> {
       referenceGenomeDao.add(genome);
       return genome;
@@ -296,22 +302,36 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
         .type("double"),
         fieldWithPath("geneMapping")
             .description("list of available gene mappings for given genome")
-            .type("array"),
+            .type(JsonFieldType.ARRAY),
+        fieldWithPath("geneMapping[].name")
+            .description("name of the gene mapping")
+            .type(JsonFieldType.STRING),
+        fieldWithPath("geneMapping[].sourceUrl")
+            .description("source url of the gene mapping")
+            .type(JsonFieldType.STRING),
+        fieldWithPath("geneMapping[].localUrl")
+            .description("url with local copy of the mapping")
+            .type(JsonFieldType.STRING),
+        fieldWithPath("geneMapping[].downloadProgress")
+            .description("download progress")
+            .type(JsonFieldType.NUMBER),
+        fieldWithPath("geneMapping[].idObject")
+            .ignored(),
         fieldWithPath("idObject")
             .description("unique id of genome in minerva")
-            .type("number"),
+            .type(JsonFieldType.NUMBER),
         fieldWithPath("localUrl")
             .description("url on minerva where local copy of genome can be accessed")
-            .type("string"),
+            .type(JsonFieldType.STRING),
         fieldWithPath("organism")
             .description("organism identifier")
-            .type("object"),
+            .type(JsonFieldType.OBJECT),
         fieldWithPath("organism.resource")
             .description("organism identifier")
-            .type("string"),
+            .type(JsonFieldType.STRING),
         fieldWithPath("organism.type")
             .description("organism identifier type (usually " + MiriamType.TAXONOMY + ")")
-            .type("string"),
+            .type(JsonFieldType.STRING),
         fieldWithPath("organism.annotatorClassName")
             .ignored(),
         fieldWithPath("organism.id")
@@ -320,13 +340,13 @@ public class GenomicsControllerIntegrationTest extends ControllerIntegrationTest
             .ignored(),
         fieldWithPath("sourceUrl")
             .description("genome source url")
-            .type("string"),
+            .type(JsonFieldType.STRING),
         fieldWithPath("type")
             .description("type of genome (database from which it was downloaded)")
-            .type("string"),
+            .type(JsonFieldType.STRING),
         fieldWithPath("version")
             .description("genome version")
-            .type("string"));
+            .type(JsonFieldType.STRING));
   }
 
   @Test