tair name; tair and string annotator only annotate based on human annotated miriam data

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

@@ -208,7 +208,7 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
             String[] tairLocusNames = m.group(1).trim().split(" ");
             for (String tairLocusName : tairLocusNames) {
             	tairLocusName = tairLocusName.split("\\(")[0]; // some codes are in the form AT1G08510(FATB)
-            	MiriamData md = uniprotAnnotator.uniprotTairLocusToId(tairLocusName);
+            	MiriamData md = uniprotAnnotator.uniprotTairLocusNameToId(tairLocusName);
             	if (!md.equals(new MiriamData())){
             		result.add(md);            		
             	}

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

@@ -32,6 +32,12 @@ public class StringAnnotator extends ElementAnnotator implements IExternalServic
   /**
    * Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
    * TAIR}.
+   * Note that STRING annotation process will annotate only
+ * records which have a TAIR ID assigned by a human annotator.
+ * Otherwise, it would generate UniProt miriam records also for
+ * TAIR IDs generated from, e.g., KEGG annotator, i.e. for homologues
+ * and these UniProt IDs would be indistinguishable from the
+ * UniProt IDs describing the molecule.
    */
   private TairAnnotator tairAnnotator;
 
@@ -54,7 +60,9 @@ public class StringAnnotator extends ElementAnnotator implements IExternalServic
       throws AnnotatorException {
     List<MiriamData> mdUniprots = new ArrayList<>();
     if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) {
-      mdUniprots.addAll(tairAnnotator.tairToUniprot(identifier));
+    	if (identifier.getAnnotator() == null) {
+    		mdUniprots.addAll(tairAnnotator.tairToUniprot(identifier));
+    	}      
     } else if (identifier.getDataType().equals(MiriamType.UNIPROT)) {
       mdUniprots.add(identifier);
     } else {

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

@@ -5,6 +5,8 @@ import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import org.apache.log4j.Logger;
 import org.springframework.stereotype.Service;
@@ -28,6 +30,13 @@ import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
 
 /**
  * This is a class that implements a backend to TAIR.
+ * Note that TAIR annotation process will annotate only
+ * records which have a TAIR ID assigned by a human annotator.
+ * Otherwise, it would generate UniProt miriam records also for
+ * TAIR IDs generated from, e.g., KEGG annotator, i.e. for homologues
+ * and these UniProt IDs would be indistinguishable from the
+ * UniProt IDs describing the molecule.
+ *    
  * 
  * @author David Hoksza
  * 
@@ -39,6 +48,14 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
    * Default class logger.
    */
   private static Logger logger = Logger.getLogger(TairAnnotator.class);
+  
+  /**
+   * Pattern used for getting Tair Locus ID symbol from UniProt result page.
+   */
+  private Pattern getUniprotIdParsePattern(String tairId) {
+	  return Pattern.compile("(\\w*)\\tlocus:" + tairId);
+  }
+      
 
   /**
    * Default constructor.
@@ -74,7 +91,13 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
   @Override
   public boolean annotateElement(BioEntityProxy object, MiriamData identifier, AnnotatorData parameters)
       throws AnnotatorException {
+	  
+	  if (identifier.getAnnotator() != null) {
+		  return false;
+	  }
     if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) {
+    	//UniProt are only obained from TAIR's which were provided by the annotator (otherwise we would get
+    	//also UniProt IDs for, e.g., homologous genes' TAIR IDs obtained from KEGG
       Collection<MiriamData> collection = tairToUniprot(identifier);
       if (collection.size() > 0) {
         object.addMiriamData(collection);
@@ -97,8 +120,8 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
    * @return URL to UniProt result page with the TAIR mapping
    */
   private String getUniProtUrl(String tairId) {
-    return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair%29+" + tairId
-        + "&format=list&columns=id";
+	  return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair%29+" + tairId + "&format=tab&columns=id,database(tair)";
+//	  return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair+"+tairId+"%29&format=list&columns=id";
   }
 
   /**
@@ -110,11 +133,14 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
    *          uniprot REST API result page
    * @return uniprot identifier found on the page
    */
-  private Collection<MiriamData> parseUniprotUniprot(String pageContent) {
+  private Collection<MiriamData> parseUniprotUniprot(String pageContent, String tairId) {
     Collection<MiriamData> result = new HashSet<MiriamData>();
     if (!pageContent.isEmpty()) {
-      String[] sPageContent = pageContent.split("\\R");
-      result.add(new MiriamData(MiriamType.UNIPROT, sPageContent[0]));
+    	//the query returns a list of possible matches which needs to be pruned
+    	Matcher m = getUniprotIdParsePattern(tairId).matcher(pageContent);
+    	if (m.find()) {
+    		result.add(new MiriamData(MiriamType.UNIPROT, m.group(1)));  		
+    	} 
     }
     return result;
   }
@@ -144,7 +170,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
     try {
       String accessUrl = getUniProtUrl(tair.getResource());
       String pageContent = getWebPageContent(accessUrl);
-      return parseUniprotUniprot(pageContent);
+      return parseUniprotUniprot(pageContent, tair.getResource());
     } catch (WrongResponseCodeIOException exception) {
       logger.warn("Wrong reponse code when accessing tair data with id: " + tair.getResource());
       return null;
@@ -185,7 +211,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
 
   @Override
   public MiriamData getExampleValidAnnotation() {
-    return new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030");
+    return new MiriamData(MiriamType.TAIR_LOCUS, "2200950");
   }
 
 }

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

@@ -61,7 +61,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
       .compile("EC=((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))");
   
   /**
-   * Pattern used for finding EC symbol from UniProt info page .
+   * Pattern used for getting Tair Locus ID symbol from UniProt result page.
    */
   private Pattern uniprotTairLocusToId = Pattern
       .compile("locus:(\\d*)");
@@ -151,9 +151,8 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
    *          TAIR identifier
    * @return URL to UniProt result page with the TAIR mapping
    */
-  private String getUniProtTairLocus2IdUrl(String tairLocus) {
-    return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair%29+"+tairLocus+
-    		"&format=tab&columns=id,database(tair) ";
+  private String getUniProtTairLocus2IdUrl(String tairLocusName) {
+    return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair+" + tairLocusName + "%29&format=tab&columns=id,database(tair)";
   }
 
   /**
@@ -281,7 +280,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
    * @throws UniprotSearchException
    *           thrown when there is a problem with accessing external database
    */
-  public MiriamData uniprotTairLocusToId(String tairLocus) throws UniprotSearchException {
+  public MiriamData uniprotTairLocusNameToId(String tairLocus) throws UniprotSearchException {
 	  String accessUrl = getUniProtTairLocus2IdUrl(tairLocus);
 	    try {
 	    	String pageContent = getWebPageContent(accessUrl);

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

@@ -57,12 +57,12 @@ public class StringAnnotatorTest extends AnnotationTestFunctions {
   }
 
   @Test
-  @Ignore("TAIR DB restricts queries by IP")
+//  @Ignore("TAIR DB restricts queries by IP")
   public void testAnnotateTair() throws Exception {
     try {
 
       Species bioEntity = new GenericProtein("id");
-      bioEntity.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
+      bioEntity.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "2200950"));
 
       testedAnnotator.annotateElement(bioEntity);
 
@@ -70,18 +70,35 @@ public class StringAnnotatorTest extends AnnotationTestFunctions {
 
       for (MiriamData md : bioEntity.getMiriamData()) {
         if (md.getDataType().equals(MiriamType.STRING)) {
-          mdString = md; // there should be only one EC number for that TAIR<->UNIPROT record
+          mdString = md; 
         }
       }
 
       assertTrue("No STRING annotation extracted from STRING annotator", mdString != null);
-      assertTrue("Wrong number of annotations extract from STRING annotator", bioEntity.getMiriamData().size() == 3);
+      assertTrue("Wrong number of annotations extract from STRING annotator", bioEntity.getMiriamData().size() == 2);
 
     } catch (Exception e) {
       e.printStackTrace();
       throw e;
     }
   }
+  
+  @Test
+//@Ignore("TAIR DB restricts queries by IP")
+public void testAnnotateTairOnlyFromHumanAnnotator() throws Exception {
+  try {
+
+    Species bioEntity = new GenericProtein("id");
+    bioEntity.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "2200950", KeggAnnotator.class));
+
+    testedAnnotator.annotateElement(bioEntity);
+
+    assertTrue(bioEntity.getMiriamData().size() == 1);
+  } catch (Exception e) {
+    e.printStackTrace();
+    throw e;
+  }
+}
 
   @Test
   public void testAnnotateInvalidEmpty() throws Exception {

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

 package lcsb.mapviewer.annotation.services.annotators;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
@@ -45,7 +46,7 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
 
       Species protein = new GenericProtein("id");
       protein.setName("bla");
-      protein.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
+      protein.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "2200950")); //AT1G01030
 
       tairAnnotator.annotateElement(protein);
 
@@ -74,7 +75,7 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
 
       Species protein = new GenericProtein("id");
       protein.setName("bla");
-      protein.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G15950"));
+      protein.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "2200427"));
       protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "P32246")); // Human version of the protein
 
       tairAnnotator.annotateElement(protein);
@@ -163,6 +164,22 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
       throw e;
     }
   }
+  
+  @Test
+  public void testTairToUniprotFromKEGG() throws Exception {
+	  //TAIR Loci comming from annotators should be ignored by TAIR (only TAIR LOCI provided by the human annotator should be considered)
+    try {
+    	Species protein = new GenericProtein("id");
+        protein.setName("bla");
+        protein.addMiriamData(new MiriamData(MiriamType.TAIR_LOCUS, "2200427", KeggAnnotator.class));
+        tairAnnotator.annotateElement(protein);
+        assertTrue(  protein.getMiriamData().size() == 1);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+  
 
   @Test
   // @Ignore("TAIR DB restricts queries by IP")

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

@@ -283,7 +283,7 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
   public void testUniprotTairLocusToId() throws Exception {
     try {
       assertEquals(new MiriamData(MiriamType.TAIR_LOCUS, "2201786"),
-    		  uniprotAnnotator.uniprotTairLocusToId("AT1G08510") );
+    		  uniprotAnnotator.uniprotTairLocusNameToId("AT1G08510") );
     } catch (Exception e) {
       e.printStackTrace();
       throw e;
@@ -294,7 +294,7 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
   public void testUniprotWrongTairLocusToId() throws Exception {
     try {
     	assertEquals(new MiriamData(),
-    	          uniprotAnnotator.uniprotTairLocusToId("XXXXXX"));
+    	          uniprotAnnotator.uniprotTairLocusNameToId("bla"));
     } catch (Exception e) {
       e.printStackTrace();
       throw e;