Passing annotator parameters from client to server

annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java

@@ -363,9 +363,7 @@ public class ModelAnnotator {
 
 			for (ElementAnnotator elementAnnotator : list) {
 				try {
-					List<UserAnnotatorsParam> params = annotatorsParams.get(elementAnnotator.getClass());
-					logger.debug("params");
-					logger.debug(params);
+					List<UserAnnotatorsParam> params = annotatorsParams.get(elementAnnotator.getClass());					
 					if (params != null) {
 						elementAnnotator.annotateElement(element, params);						
 					} else {

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

@@ -4,6 +4,7 @@ package lcsb.mapviewer.annotation.services.annotators;
 import java.io.IOException;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -27,6 +28,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Protein;
 import lcsb.mapviewer.model.map.species.Rna;
 import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.user.UserAnnotatorsParam;
 
 /**
  * This is a class that implements KEGG annotator which extract from KEGG 
@@ -48,6 +50,11 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
 	 */
 	private Pattern				pubmedMatcher	= Pattern.compile("\\[PMID:(\\d+)\\]");
 
+	/**
+	 * Pattern used for finding ATH orghologs in KEGG GENE sectionpage.
+	 */
+	private Pattern				athOrthologMatcher	= Pattern.compile(" *ATH: (.*)");
+
 	
 	/**
 	 * Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS TAIR}.
@@ -73,14 +80,6 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
 				+ " (GENE section in the KEGG enzyme record) should be imported."
 				+ " Currently ATH (Arabidopsis Thaliana) is supported.");
 		this.addParameterDefinition(paramDef);
-		
-		this.addParameterDefinition(new AnnotatorParamDefinition("test string1", String.class, "test string1 comment"));
-		this.addParameterDefinition(new AnnotatorParamDefinition("test int1", Integer.class, "int1 comment"));
-		this.addParameterDefinition(new AnnotatorParamDefinition("test bool1", Boolean.class, "boolean comment"));
-		this.addParameterDefinition(new AnnotatorParamDefinition("test bool2", Boolean.class, "boolean comment 2"));
-		this.addParameterDefinition(new AnnotatorParamDefinition("test int2", Integer.class, "int2 comment"));
-		this.addParameterDefinition(new AnnotatorParamDefinition("test int3", Integer.class, "int3 comment"));
-		this.addParameterDefinition(new AnnotatorParamDefinition("test string2", String.class, "test string2 comment"));
 	}
 
 	@Override
@@ -122,61 +121,66 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
 	
 	
 	@Override
-	public void annotateElement(BioEntity object) throws AnnotatorException {
-		if (isAnnotatable(object)) {
+	public void annotateElement(BioEntity object, List<UserAnnotatorsParam> params) throws AnnotatorException {
+		
+		if (!isAnnotatable(object)) { return; }
 			
-			MiriamData mdTair = null;
-			for (MiriamData md : object.getMiriamData()) {
-				Class<?> annotator =  md.getAnnotator();
-				if (annotator == this.getClass()) {
-					//this annotator was already used
-					return;
-				}
-				else if (md.getDataType().equals(MiriamType.TAIR_LOCUS) && 
-				 		(annotator == null ) ) {
-				 	mdTair = md;
-				}				
+		MiriamData mdTair = null;
+		for (MiriamData md : object.getMiriamData()) {
+			Class<?> annotator =  md.getAnnotator();
+			if (annotator == this.getClass()) {
+				//this annotator was already used
+				return;
 			}
-			
-			if (mdTair != null) tairAnnotator.annotateElement(object);
-			
-			MiriamData mdUniprot = null;
-			for (MiriamData md : object.getMiriamData()) {
-				if (md.getDataType().equals(MiriamType.UNIPROT) ) {
-				 	mdUniprot = md;
-				}
+			else if (md.getDataType().equals(MiriamType.TAIR_LOCUS) && 
+			 		(annotator == null ) ) {
+			 	mdTair = md;
+			}				
+		}
+		
+		if (mdTair != null) tairAnnotator.annotateElement(object);
+		
+		MiriamData mdUniprot = null;
+		for (MiriamData md : object.getMiriamData()) {
+			if (md.getDataType().equals(MiriamType.UNIPROT) ) {
+			 	mdUniprot = md;
 			}
-			if (mdUniprot != null) uniprotAnnotator.annotateElement(object);
-			
-			Set<String> ecs = new HashSet<String>();						
-			for (MiriamData md : object.getMiriamData()) {
-				if (md.getDataType().equals(MiriamType.EC)) {					
-					ecs.add(md.getResource());
-				}
+		}
+		if (mdUniprot != null) uniprotAnnotator.annotateElement(object);
+		
+		Set<String> ecs = new HashSet<String>();						
+		for (MiriamData md : object.getMiriamData()) {
+			if (md.getDataType().equals(MiriamType.EC)) {					
+				ecs.add(md.getResource());
 			}
+		}
+		
+		if (ecs.size() == 0) {				 
+			return;
+		}			
+								
+		//annotate from KEGG
+		Set<MiriamData> annotations = new HashSet<MiriamData>();
+		for (String ec: ecs) {
 			
-			if (ecs.size() == 0) {				 
-				return;
-			}			
-									
-			//annotate from KEGG
-			Set<MiriamData> annotations = new HashSet<MiriamData>();
-			for (String ec: ecs) {
-				
-				String accessUrl = getKeggUrl(ec);
-				
-				try {
-					String pageContent = getWebPageContent(accessUrl);
-					annotations.addAll(parseKegg(pageContent));
-						
-				} catch (WrongResponseCodeIOException exception) {
-					logger.warn("Cannot find kegg data for id: " + ec);
-				} catch (IOException exception) {
-					throw new AnnotatorException(exception);
-				}
+			String accessUrl = getKeggUrl(ec);
+			
+			try {
+				String pageContent = getWebPageContent(accessUrl);
+				annotations.addAll(parseKegg(pageContent, params));
+					
+			} catch (WrongResponseCodeIOException exception) {
+				logger.warn("Cannot find kegg data for id: " + ec);
+			} catch (IOException exception) {
+				throw new AnnotatorException(exception);
 			}
-			object.addMiriamData(annotations);
-		}		
+		}
+		object.addMiriamData(annotations);
+	}
+	
+	@Override
+	public void annotateElement(BioEntity object) throws AnnotatorException {
+		this.annotateElement(object, null);				
 	}
 	
 	/**
@@ -196,9 +200,16 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
 	 * 
 	 * @param pageContent
 	 *          Kegg page
-	 * @return {@link MiriamType#PUBMED}s found on the page
+	 * @param params
+	 * 			List of {@link UserAnnotatorsParam} to be used 
+	 * 			for parameterization. Should contain only at most 
+	 * 			one record with space separated KEGG organisms names.
+	 * 			If the value has not been set by the user, 
+	 * 			null will be passed. 
+	 * @return 
+	 * 			{@link MiriamType#PUBMED}s found on the page
 	 */
-	private Collection<MiriamData> parseKegg(String pageContent) {
+	private Collection<MiriamData> parseKegg(String pageContent, List<UserAnnotatorsParam> params) {
 		
 		//Retrieve Pubmeds
 		Collection<MiriamData> result = new HashSet<MiriamData>();
@@ -208,6 +219,23 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
 		}
 		
 		//Retrieve homologous organisms based on parameterization	
+		if (params != null) {
+			String[] keggOrgnismCodes = params.get(0).getParamValue().trim().split(" +");
+			for (String code: keggOrgnismCodes) {
+				if (code.toUpperCase() != "ATH") {
+					logger.warn("KEGG annotator currently supports only ATH");
+				} else {
+					m = athOrthologMatcher.matcher(pageContent);
+					if (m.find()) {
+						String[] tairCodes = m.group(1).trim().split(" ");
+						for (String tairCode: tairCodes) {
+							tairCode = tairCode.split("\\(")[0]; //some codes are in the form AT1G08510(FATB)
+							result.add(createMiriamData(MiriamType.TAIR_LOCUS, tairCode));
+			            }
+					}
+				}
+			}
+		}
 		
 		return result;
 	}

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

@@ -2,23 +2,15 @@ package lcsb.mapviewer.annotation.services.annotators;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.util.Collection;
-import java.io.IOException;
 
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
-import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
 import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.map.MiriamData;

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

@@ -11,6 +11,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
 
 import org.junit.After;
@@ -27,6 +28,7 @@ import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.user.UserAnnotatorsParam;
 
 public class KeggAnnotatorTest extends AnnotationTestFunctions {
 	
@@ -71,7 +73,7 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
 		
 
 	@Test
-	public void testAnnotateFromUniprot() throws Exception {
+	public void testAnnotateFromUniprotWithoutParams() throws Exception {
 		try {
 
 			Species protein = new GenericProtein("id");
@@ -89,6 +91,82 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
 		}
 	}
 	
+	@Test
+	public void testAnnotateFromUniprotWithParams() throws Exception {
+		try {
+
+			Species protein = new GenericProtein("id");
+			protein.setName("bla");
+			protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q42561"));
+			
+			UserAnnotatorsParam ap = new UserAnnotatorsParam(String.class, "KEGG organism identifier", "ATH");
+			List<UserAnnotatorsParam> aps = new ArrayList<>();
+			aps.add(ap);
+			keggAnnotator.annotateElement(protein, aps);
+			
+			int cntTairs = 0;
+			for (MiriamData md : protein.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.TAIR_LOCUS)) {
+					cntTairs++;
+				}
+			}
+			
+			assertTrue("Invalid number of TAIR annotators from KEGG", cntTairs == 3);
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	
+	@Test
+	public void testAnnotateFromUniprotWithWrongParams1() throws Exception {
+		try {
+
+			Species protein = new GenericProtein("id");
+			protein.setName("bla");
+			protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q42561"));
+			
+			UserAnnotatorsParam ap = new UserAnnotatorsParam(String.class, "XXX", "XXX");
+			List<UserAnnotatorsParam> aps = new ArrayList<>();
+			aps.add(ap);
+			keggAnnotator.annotateElement(protein, aps);
+			
+			assertEquals("There should be warning about unsupported parameter", 1, getWarnings().size());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	
+	@Test
+	public void testAnnotateFromUniprotWithWrongParams2() throws Exception {
+		try {
+
+			Species protein = new GenericProtein("id");
+			protein.setName("bla");
+			protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q42561"));
+			List<UserAnnotatorsParam> aps = new ArrayList<>();
+			aps.add(new UserAnnotatorsParam(String.class, "KEGG organism identifier", "ATH XXX"));
+			keggAnnotator.annotateElement(protein, aps);
+			
+			int cntTairs = 0;
+			for (MiriamData md : protein.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.TAIR_LOCUS)) {
+					cntTairs++;
+				}
+			}
+			
+			assertTrue("Invalid number of TAIR annotators from KEGG", cntTairs == 3);
+			assertEquals("There should be warning about unsupported parameter", 1, getWarnings().size());
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+	
 	@Test
 	public void testAnnotateFromEc() throws Exception {
 		try {
@@ -101,7 +179,6 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
 			
 			Evaluate_3_1_2_14(protein);
 			
-
 		} catch (Exception e) {
 			e.printStackTrace();
 			throw e;

frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js

@@ -65,7 +65,8 @@ function onChangeParameterValue(element, user){
 
   var annotatorsParams = {};
   annotatorsParams[annotatorClassName] = {};
-  annotatorsParams[annotatorClassName][name] = element.value;
+  if (element.type == 'checkbox') annotatorsParams[annotatorClassName][name] = element.checked.toString();
+  else annotatorsParams[annotatorClassName][name] = element.value;
   data.setAnnotatorsParameters(annotatorsParams);
 
   return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);  
@@ -95,6 +96,7 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
     var selectedAnnotators = user.getPreferences().getElementAnnotators(elementType.className);
     var existingAnnotatorsParameters = user.getPreferences().getAnnotatorsParameters();
 
+
     for (var i = 0; i < annotators.length; i++) {
       var annotator = annotators[i];
       var selected = false;
@@ -157,12 +159,14 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
                   inputType: "number",
                   onchange: function(){return onChangeParameterValue(this, user);}
                 });
+                if (existingParamValue) paramValue.value = existingParamValue;
               } else if (param.type.indexOf("Boolean") >= 0) {
                 paramValue = Functions.createElement({
                   type: "input",
                   inputType: "checkbox",
                   onchange: function(){return onChangeParameterValue(this, user);}
                 });
+                paramValue.checked = (existingParamValue && existingParamValue === 'true');
               } else {
                 throw new InvalidAlgorithmError("Unknown annotator parameter type");
               }              

model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java

@@ -248,17 +248,12 @@ public class UserAnnotationSchema implements Serializable {
 			if (params.getAnnotatorClassName().equals(ap.getAnnotatorClassName()) && 
 					params.getParamName().equals(ap.getParamName())) {				
 				this.annotatorsParams.get(i).setParamValue(ap.getParamValue());
-			} else {
-				ap.setAnnotationSchema(this);
-				this.annotatorsParams.add(ap);				
+				return;
 			}
 		}
-		
-		if (this.annotatorsParams.size() == 0) {
-			ap.setAnnotationSchema(this);
-			this.annotatorsParams.add(ap);			
-		}
-		
+	
+		ap.setAnnotationSchema(this);
+		this.annotatorsParams.add(ap);			
 	}
 
 	/**

service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java

@@ -1469,7 +1469,16 @@ public class ProjectService implements IProjectService {
 		 dbUser.setAnnotationSchema(annotationSchema);
 	 }
 	 
-	 return annotationSchema.getAnnotatorsParams();
+	 /*
+	  * Hibernate lazy loads collections so each element needs to be accessed 
+	  * to be loaded now or otherwise the data might not be available
+	  * when accessed because the session might not be available at that time.
+	  */
+	 List<UserAnnotatorsParam> aps = new ArrayList<>();	 
+	 for (UserAnnotatorsParam ap: annotationSchema.getAnnotatorsParams()){		 
+		 aps.add(ap);
+	 }	 
+	 return aps;
   }
 
   /**