pdb annotator fixed

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java

@@ -14,8 +14,9 @@ import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.gson.Gson;
-import com.google.gson.reflect.TypeToken;
 
 import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
 import lcsb.mapviewer.annotation.cache.WebPageDownloader;
@@ -90,7 +91,8 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
       Collection<Structure> structures = uniProtToPdb(getExampleValidAnnotation());
 
       if (structures.size() > 0) {
-        if (structures.iterator().next().getPdbId() != null) { // TODO - is this id?
+        if (structures.iterator().next().getPdbId() != null) { // TODO - is this
+                                                               // id?
           status.setStatus(ExternalServiceStatusType.OK);
         } else {
           status.setStatus(ExternalServiceStatusType.CHANGED);
@@ -206,19 +208,22 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
    */
   private Collection<Structure> processMappingData(final String pageContentJson) {
     Collection<Structure> result = new HashSet<Structure>();
-    Gson g = new Gson();
-    java.lang.reflect.Type t = new TypeToken<Map<String, List<PdbBestMappingEntry>>>() {
-    }.getType();
-    Map<String, List<PdbBestMappingEntry>> m = g.fromJson(pageContentJson, t);
-    if (m != null) {
-      for (final String key : m.keySet()) {
-        for (final PdbBestMappingEntry e : m.get(key)) {
-          if (e != null) {
-            result.add(e.convertToStructure());
-            // result.add(new MiriamData(MiriamType.PDB, e.pdb_id));
+    try {
+      ObjectMapper objectMapper = new ObjectMapper();
+      Map<String, List<PdbBestMappingEntry>> m = objectMapper.readValue(pageContentJson, new TypeReference<Map<String, List<PdbBestMappingEntry>>>() {
+      });
+      if (m != null) {
+        for (final String key : m.keySet()) {
+          for (final PdbBestMappingEntry e : m.get(key)) {
+            if (e != null) {
+              result.add(e.convertToStructure());
+              // result.add(new MiriamData(MiriamType.PDB, e.pdb_id));
+            }
           }
         }
       }
+    } catch (IOException e1) {
+      logger.error(e1, e1);
     }
 
     return result;

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java

 package lcsb.mapviewer.annotation.services.annotators;
 
+import com.fasterxml.jackson.annotation.JsonProperty;
+
 import lcsb.mapviewer.model.map.species.field.Structure;
 
 /**
@@ -9,15 +11,34 @@ import lcsb.mapviewer.model.map.species.field.Structure;
  *
  */
 public class PdbBestMappingEntry {
+  @JsonProperty(value = "chain_id")
   private String chainId;
+
+  @JsonProperty(value = "experimental_method")
   private String experimentalMethod;
+  
+  @JsonProperty(value = "pdb_id")
   private String pdbId;
+  
+  @JsonProperty(value = "start")
   private int start;
+  
+  @JsonProperty(value = "end")
   private int end;
+
+  @JsonProperty(value = "unp_end")
   private int unpEnd;
+  
+  @JsonProperty(value = "coverage")
   private double coverage;
+  
+  @JsonProperty(value = "unp_start")
   private int unpStart;
+
+  @JsonProperty(value = "resolution")
   private double resolution;
+  
+  @JsonProperty(value = "tax_id")
   private int taxId;
 
   public Structure convertToStructure() {

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java

@@ -11,7 +11,6 @@ import java.util.Set;
 
 import org.junit.After;
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
 import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -48,8 +47,8 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
     Species protein = new GenericProtein("id");
     protein.setName(uniprotId);
     /*
-     * One needs to have the UniProt ID first. This tests simulates situation when
-     * the Uniprot annotator is called first.
+     * One needs to have the UniProt ID first. This tests simulates situation
+     * when the Uniprot annotator is called first.
      */
     uniprotAnnotator.annotateElement(protein);
     int cntAnnotations1 = protein.getMiriamData().size();
@@ -77,7 +76,8 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
         ur = ur1;
       }
     }
-    // Test whether there is a uniprot record with the uniprot ID which was stored
+    // Test whether there is a uniprot record with the uniprot ID which was
+    // stored
     assertNotNull(ur);
     // Test whether structures are there
     Set<Structure> ss = ur.getStructures();
@@ -88,15 +88,9 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
   }
 
   @Test
-  @Ignore
   public void testAnnotate2() throws Exception {
     Species protein = new GenericProtein("id");
-    protein.setName("P29373");
-    /*
-     * One needs to have the UniProt ID first, and Uniprot lookup through HGNC is
-     * included in PDB annotator. This tests simulates situation when the PDB
-     * annotator is called first.
-     */
+    protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "P29373"));
     pdbAnnotator.annotateElement(protein);
     int cntAnnotations = protein.getMiriamData().size();
 
@@ -114,9 +108,9 @@ public class PdbAnnotatorTest extends AnnotationTestFunctions {
   }
 
   @Test
-  @Ignore
   public void testAnnotateNotUniprotAnnodated() throws Exception {
     Species protein = new GenericProtein("id");
+    protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "P29373"));
     protein.setName("P29373");
     pdbAnnotator.annotateElement(protein);