ReferenceGenomeSerializer implemented

model/src/main/java/lcsb/mapviewer/modelutils/serializer/model/map/layout/ReferenceGenomeSerializer.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.ReferenceGenome;
+
+public class ReferenceGenomeSerializer extends JsonSerializer<ReferenceGenome> {
+
+  private Function<String, String> getLocalUrl;
+
+  public ReferenceGenomeSerializer(Function<String, String> getLocalUrl) {
+    this.getLocalUrl = getLocalUrl;
+  }
+
+  @Override
+  public void serialize(final ReferenceGenome genome, final JsonGenerator gen,
+      final SerializerProvider serializers)
+      throws IOException {
+    gen.writeStartObject();
+    
+    gen.writeObjectField("organism", genome.getOrganism());
+    gen.writeStringField("version", genome.getVersion());
+    gen.writeObjectField("type", genome.getType());
+    gen.writeNumberField("downloadProgress", genome.getDownloadProgress());
+    gen.writeStringField("sourceUrl", genome.getSourceUrl());
+    gen.writeStringField("localUrl", getLocalUrl.apply(genome.getSourceUrl()));
+    gen.writeNumberField("idObject", genome.getId());
+    gen.writeObjectField("geneMapping", genome.getGeneMapping());
+    gen.writeEndObject();
+
+  }
+}
\ No newline at end of file

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

 package lcsb.mapviewer.api.genomics;
 
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.net.URISyntaxException;
 import java.util.ArrayList;
@@ -9,10 +8,7 @@ import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.TreeMap;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -34,7 +30,6 @@ import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
 import lcsb.mapviewer.services.ObjectExistsException;
 import lcsb.mapviewer.services.ObjectNotFoundException;
 import lcsb.mapviewer.services.QueryException;
-import lcsb.mapviewer.services.interfaces.IFileService;
 import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
 import lcsb.mapviewer.services.utils.ReferenceGenomeExistsException;
 
@@ -42,19 +37,15 @@ import lcsb.mapviewer.services.utils.ReferenceGenomeExistsException;
 @RequestMapping(value = "/api/genomics", produces = MediaType.APPLICATION_JSON_VALUE)
 public class ReferenceGenomeController extends BaseController {
 
-  private Logger logger = LogManager.getLogger();
-
   private IReferenceGenomeService referenceGenomeService;
-  private IFileService fileService;
 
   @Autowired
-  public ReferenceGenomeController(IReferenceGenomeService referenceGenomeService, IFileService fileService) {
+  public ReferenceGenomeController(IReferenceGenomeService referenceGenomeService) {
     this.referenceGenomeService = referenceGenomeService;
-    this.fileService = fileService;
   }
 
   @GetMapping(value = "/taxonomies/{organismId}/genomeTypes/{type}/versions/{version}/")
-  public Map<String, Object> getGenomesByQuery(@PathVariable(value = "organismId") String organismId, @PathVariable(value = "type") String type,
+  public ReferenceGenome getGenomesByQuery(@PathVariable(value = "organismId") String organismId, @PathVariable(value = "type") String type,
       @PathVariable(value = "version") String version) throws QueryException {
     MiriamData organism;
     if (organismId != null && !organismId.isEmpty()) {
@@ -69,36 +60,12 @@ public class ReferenceGenomeController extends BaseController {
       if (genome == null) {
         throw new ObjectNotFoundException("Cannot find requested reference genome");
       }
-      return genomeToMap(genome);
+      return genome;
     } catch (IllegalArgumentException e) {
       throw new QueryException("Cannot find type: " + type);
     }
   }
 
-  private Map<String, Object> genomeToMap(ReferenceGenome genome) {
-    Map<String, Object> result = new TreeMap<>();
-    result.put("organism", genome.getOrganism());
-    result.put("version", genome.getVersion());
-    result.put("type", genome.getType());
-    result.put("downloadProgress", genome.getDownloadProgress());
-    result.put("sourceUrl", genome.getSourceUrl());
-    result.put("localUrl", getLocalUrl(genome.getSourceUrl()));
-    result.put("idObject", genome.getId());
-    result.put("geneMapping", genome.getGeneMapping());
-
-    return result;
-  }
-
-  private String getLocalUrl(String sourceUrl) {
-    String url = null;
-    try {
-      url = "../" + fileService.getLocalPathForFile(sourceUrl);
-    } catch (FileNotFoundException e) {
-      logger.warn("Cannot find local file", e);
-    }
-    return url;
-  }
-
   static class RemoteUrl {
     public String url;
   }
@@ -111,7 +78,7 @@ public class ReferenceGenomeController extends BaseController {
       throw new QueryException("Unknown taxonomy organism: " + organismId);
     }
     MiriamData organism = new MiriamData(MiriamType.TAXONOMY, organismId);
-    if (genomeType==null) {
+    if (genomeType == null) {
       throw new QueryException("Unknown genome type");
     }
     String url = referenceGenomeService.getUrlForGenomeVersion(genomeType, organism, version);
@@ -160,12 +127,8 @@ public class ReferenceGenomeController extends BaseController {
   }
 
   @GetMapping(value = "/")
-  public List<Map<String, Object>> getDownloaded() {
-    List<Map<String, Object>> result = new ArrayList<>();
-    for (ReferenceGenome genome : referenceGenomeService.getDownloadedGenomes()) {
-      result.add(genomeToMap(genome));
-    }
-    return result;
+  public List<ReferenceGenome> getDownloaded() {
+    return referenceGenomeService.getDownloadedGenomes();
   }
 
   static class OrganismType {

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

@@ -37,6 +37,7 @@ 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.ReferenceGenome;
 import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
@@ -45,6 +46,7 @@ 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.modelutils.serializer.model.map.layout.ReferenceGenomeSerializer;
 import lcsb.mapviewer.services.interfaces.IElementService;
 import lcsb.mapviewer.services.interfaces.IFileService;
 import lcsb.mapviewer.services.interfaces.IMeshService;
@@ -149,6 +151,20 @@ public class SpringWebConfig implements WebMvcConfigurer {
               }
             }));
 
+        module.addSerializer(ReferenceGenome.class, new ReferenceGenomeSerializer(
+            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);
       }
     }