Merge branch 'cellwall-annotations' into 'master'

Cellwall annotations

Closes #142

See merge request piotr.gawron/minerva!201

annotation/.classpath

@@ -30,7 +30,6 @@
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>

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

@@ -705,6 +705,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
         String uniprotId = page.substring(protienLinkPosition, j);
         MiriamData uniprotMiriam = new MiriamData(MiriamType.UNIPROT, uniprotId);
         MiriamData hgncMiriam = uniprotAnnotator.uniProtToHgnc(uniprotMiriam);
+        if (hgncMiriam != null) hgncMiriam.setAnnotator(null);
         if (hgncMiriam == null || !hgncMiriam.equals(hgncTarget)) {
           logger.debug("Invalid target found. Expected " + hgncTarget + ", but found: " + hgncMiriam + " ("
               + uniprotMiriam + ")");

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

@@ -12,19 +12,26 @@ import java.util.Set;
 
 import javax.annotation.PostConstruct;
 
+import org.apache.commons.logging.Log;
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.CazyAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.GoAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.KeggAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.PdbAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.StitchAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.StringAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.TairAnnotator;
 import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -35,6 +42,7 @@ import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.user.UserAnnotatorsParam;
 import lcsb.mapviewer.modelutils.map.ClassTreeNode;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
 
@@ -67,6 +75,12 @@ public class ModelAnnotator {
 	 * Default class logger.
 	 */
 	private static Logger					 logger						= Logger.getLogger(ModelAnnotator.class);
+	
+	/**
+	 * BRENDA annotator.
+	 */
+	@Autowired
+	private BrendaAnnotator 			brendaAnnotator;
 
 	/**
 	 * Service accessing <a href= "http://biocompendium.embl.de/" >internal
@@ -74,6 +88,12 @@ public class ModelAnnotator {
 	 */
 	@Autowired
 	private BiocompendiumAnnotator biocompendiumAnnotator;
+	
+	/**
+	 * CAZy annotator.
+	 */
+	@Autowired
+	private CazyAnnotator cazyAnnotator;
 
 	/**
 	 * Backend to the chebi database.
@@ -112,6 +132,12 @@ public class ModelAnnotator {
 	 */
 	@Autowired
 	private HgncAnnotator					 hgncAnnotator;
+	
+	/**
+	 * Service accessing <a href= "http://www.kegg.jp/" > KEGG EC Nomenclature</a>.
+	 */
+	@Autowired
+	private KeggAnnotator					 keggAnnotator;
 
 	/**
 	 * Service accessing <a href= "http://www.ncbi.nlm.nih.gov/gene/" >Entrez</a>.
@@ -124,6 +150,25 @@ public class ModelAnnotator {
 	 */
 	@Autowired
 	private EnsemblAnnotator			 ensemblAnnotator;
+	
+	/**
+	 * STITCH annotator.
+	 */
+	@Autowired
+	private StitchAnnotator				stitchAnnotator;
+	
+	/**
+	 * STRING annotator.
+	 */
+	@Autowired
+	private StringAnnotator				stringAnnotator;
+	
+	/**
+	 * TAIR annotator.
+	 */
+	@Autowired
+	private TairAnnotator				tairAnnotator;
+
 
 	/**
 	 * List of all avaliable {@link ElementAnnotator} objects.
@@ -144,15 +189,21 @@ public class ModelAnnotator {
 		availableAnnotators = new ArrayList<>();
 		defaultAnnotators = new ArrayList<>();
 
+		addAnnotator(brendaAnnotator);
 		addAnnotator(biocompendiumAnnotator);
+		addAnnotator(cazyAnnotator);
 		addAnnotator(chebiBackend);
 		addAnnotator(uniprotAnnotator);
 		addAnnotator(goAnnotator);
 		addAnnotator(hgncAnnotator);
+		addAnnotator(keggAnnotator);
 		addAnnotator(pdbAnnotator);
 		addAnnotator(reconAnnotator);
 		addAnnotator(entrezAnnotator);
 		addAnnotator(ensemblAnnotator);
+		addAnnotator(stitchAnnotator);
+		addAnnotator(stringAnnotator);
+		addAnnotator(tairAnnotator);
 	}
 
 	/**
@@ -178,7 +229,7 @@ public class ModelAnnotator {
 	 *          callback function used for updating progress of the function
 	 */
 	public void performAnnotations(Model model, final IProgressUpdater progressUpdater) {
-		performAnnotations(model, progressUpdater, null);
+		performAnnotations(model, progressUpdater, null, null);
 	}
 
 	/**
@@ -192,7 +243,8 @@ public class ModelAnnotator {
 	 * @param progressUpdater
 	 *          callback function used for updating progress of the function
 	 */
-	public void performAnnotations(Model model, final IProgressUpdater progressUpdater, Map<Class<?>, List<ElementAnnotator>> annotators) {
+	public void performAnnotations(Model model, final IProgressUpdater progressUpdater, Map<Class<?>, 
+			List<ElementAnnotator>> annotators, Map<Class<?>, List<UserAnnotatorsParam>> annotatorsParams) {
 		progressUpdater.setProgress(0);
 		List<Model> models = new ArrayList<Model>();
 		models.add(model);
@@ -215,7 +267,7 @@ public class ModelAnnotator {
 					progressUpdater
 							.setProgress(ratio * IProgressUpdater.MAX_PROGRESS + (COPYING_RATIO * IProgressUpdater.MAX_PROGRESS + progress * ANNOTATING_RATIO) / size);
 				}
-			}, annotators);
+			}, annotators, annotatorsParams);
 			counter++;
 		}
 	}
@@ -254,7 +306,7 @@ public class ModelAnnotator {
 			progressUpdater.setProgress(counter / amount * IProgressUpdater.MAX_PROGRESS);
 		}
 	}
-
+	
 	/**
 	 * Annotates all elements in the model using set of {@link ElementAnnotator}
 	 * given in the param. If the set is empty then all annotators will be used.
@@ -266,15 +318,35 @@ public class ModelAnnotator {
 	 *          model where annotation shoud be updated
 	 * @param progressUpdater
 	 *          callback function used to refresh progress of function execution
-	 */
+	 */	
 	protected void annotateModel(Model model, IProgressUpdater progressUpdater, Map<Class<?>, List<ElementAnnotator>> annotators) {
+		annotateModel(model, progressUpdater, annotators, null);
+	}
+
+	/**
+	 * Annotates all elements in the model using set of {@link ElementAnnotator}
+	 * given in the param. If the set is empty then all annotators will be used.
+	 * 
+	 * @param annotators
+	 *          this map contains lists of {@link ElementAnnotator} objects that
+	 *          should be used for a given classes
+	 * @param annotatorsParams
+	 *          this map contains lists of {@link UserAnnotatorsParam} objects that
+	 *          should be used for a given {@link ElementAnnotator} class
+	 * @param model
+	 *          model where annotation should be updated
+	 * @param progressUpdater
+	 *          callback function used to refresh progress of function execution
+	 */
+	protected void annotateModel(Model model, IProgressUpdater progressUpdater, Map<Class<?>, List<ElementAnnotator>> annotators, 
+			Map<Class<?>, List<UserAnnotatorsParam>> annotatorsParams) {
 		ElementUtils elementUtils = new ElementUtils();
 
 		progressUpdater.setProgress(0);
 
 		double counter = 0;
 		double amount = model.getElements().size() + model.getReactions().size();
-
+		
 		// annotate all elements
 		for (Element element : model.getElements()) {
 			List<ElementAnnotator> list = null;
@@ -287,7 +359,15 @@ public class ModelAnnotator {
 
 			for (ElementAnnotator elementAnnotator : list) {
 				try {
-					elementAnnotator.annotateElement(element);
+					if (annotatorsParams != null){
+						List<UserAnnotatorsParam> params = annotatorsParams.get(elementAnnotator.getClass());					
+						if (params != null) {
+							elementAnnotator.annotateElement(element, params);
+						}
+					} else {
+						elementAnnotator.annotateElement(element);
+					}
+					
 				} catch (AnnotatorException e) {
 					logger.warn(elementUtils.getElementTag(element) + " " + elementAnnotator.getCommonName() + " annotation problem: " + e.getMessage());
 				}

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

+package lcsb.mapviewer.annotation.services.annotators;
+
+/**
+ * Definition of a single parameter of an annotator.
+ * 
+ * @author David Hoksza
+ * 
+ */
+public class AnnotatorParamDefinition {
+	private String name;
+	
+	private String description;
+	
+	private Class<?> type;
+
+	public AnnotatorParamDefinition(String name, Class<?> type, String description) {
+		super();
+		this.name = name;
+		this.description = description;
+		this.type = type;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public String getDescription() {
+		return description;
+	}
+
+	public Class<?> getType() {
+		return type;
+	}	
+
+}

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

@@ -83,7 +83,7 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
 		try {
 			if (query instanceof String) {
 				String name = (String) query;
-				result = getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, name));
+				result = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, name));
 			} else {
 				throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
 			}
@@ -109,7 +109,7 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
 			throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
 		}
 
-		MiriamData miriamData = new MiriamData(md);
+		MiriamData miriamData = createMiriamData(md);
 		miriamData.setResource(miriamData.getResource().replaceAll("[\n\r]+", " "));
 
 		String annotation = getCacheValue(miriamData.getResource());
@@ -282,7 +282,7 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
 		this.setCache(null);
 
 		try {
-			String annotations = getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+			String annotations = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
 
 			status.setStatus(ExternalServiceStatusType.OK);
 			if (annotations == null) {
@@ -302,7 +302,7 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
 	public void annotateElement(BioEntity element) throws AnnotatorException {
 		if (isAnnotatable(element)) {
 			try {
-				String annotationString = getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, element.getName()));
+				String annotationString = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, element.getName()));
 				if (annotationString != null) {
 					if (element.getMiriamData().size() == 0) {
 						element.addMiriamData(rap.getMiriamData(annotationString));

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

+package lcsb.mapviewer.annotation.services.annotators;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.regex.Pattern;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+
+/**
+ * This is a class that implements a backend to Brenda enzyme database.
+ * 
+ * @author David Hoksza
+ * 
+ */
+public class BrendaAnnotator extends ElementAnnotator implements IExternalService {
+
+	/**
+	 * Default class logger.
+	 */
+	private static Logger	logger					= Logger.getLogger(BrendaAnnotator.class);
+	
+	/**
+	 * Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
+	 * TAIR}.
+	 */
+	@Autowired
+	private TairAnnotator		tairAnnotator;	
+
+	/**
+	 * Default constructor.
+	 */
+	public BrendaAnnotator() {
+		super(BrendaAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
+	}
+
+	@Override
+	public ExternalServiceStatus getServiceStatus() {
+		ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+		GeneralCacheInterface cacheCopy = getCache();
+		this.setCache(null);
+
+		try {
+			Collection<MiriamData> mds = new UniprotAnnotator().uniProtToEC(createMiriamData(MiriamType.UNIPROT, "P12345"));
+
+			status.setStatus(ExternalServiceStatusType.OK);
+			List<String> ecs = new ArrayList<>();
+			if (mds != null) {
+				for (MiriamData md: mds) {
+					ecs.add(md.getResource());
+				}
+			}
+			if (mds == null || mds.size() != 2 || ecs.indexOf("2.6.1.1") < 0 || ecs.indexOf("2.6.1.7") < 0) {
+				status.setStatus(ExternalServiceStatusType.CHANGED);
+			}
+		} catch (Exception e) {
+			logger.error(status.getName() + " is down", e);
+			status.setStatus(ExternalServiceStatusType.DOWN);
+		}
+		this.setCache(cacheCopy);
+		return status;
+	}
+
+	@Override
+	public void annotateElement(BioEntity object) throws AnnotatorException {
+		if (isAnnotatable(object)) {
+			
+			MiriamData mdTair = null;			
+			for (MiriamData md : object.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.BRENDA)) {
+					return;
+				}
+				else if (md.getDataType().equals(MiriamType.TAIR_LOCUS)) {
+					mdTair = md;
+				}				
+			}			
+			
+			if (mdTair != null) {
+				tairAnnotator.annotateElement(object);
+			}
+			
+			List<MiriamData> mdUniprots = new ArrayList<MiriamData>();
+			for (MiriamData md : object.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.UNIPROT)) {
+					mdUniprots.add(md);
+				}			
+			}
+			
+			UniprotAnnotator uniprotAnnotator = new UniprotAnnotator();
+			
+			
+			List<String> ecIds = new ArrayList<String>();
+			for (MiriamData mdUniprot: mdUniprots) {
+				try {
+					Collection<MiriamData> mdECs =  uniprotAnnotator.uniProtToEC(mdUniprot);
+					if (mdECs != null) {
+						for (MiriamData mdEC: mdECs) {
+							mdEC.setAnnotator(BrendaAnnotator.class);
+							mdEC.setDataType(MiriamType.BRENDA);
+							if (ecIds.indexOf(mdEC.getResource()) == -1) {
+								ecIds.add(mdEC.getResource());
+								object.addMiriamData(mdEC);						
+							}					
+						}					
+					}
+				} catch (UniprotSearchException e) {
+					logger.warn("Cannot find EC data for UniProt id: " + mdUniprot.getResource());
+				}												
+			}			
+		}		
+	}
+	
+
+	@Override
+	public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+		String name;
+		String result = null;
+		if (query instanceof String) {
+			name = (String) query;
+			if (name.startsWith("http")) {
+				try {
+					result = getWebPageContent(name);
+				} catch (IOException e) {
+					throw new SourceNotAvailable(e);
+				}
+			} else {
+				throw new InvalidArgumentException("Don't know what to do with query: " + query);
+			}
+		} else {
+			throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+		}
+		return result;
+	}
+
+
+	
+
+	@Override
+	public String getCommonName() {
+		return MiriamType.BRENDA.getCommonName();
+	}
+
+	@Override
+	public String getUrl() {
+		return MiriamType.BRENDA.getDbHomepage();
+	}
+
+	@Override
+	protected WebPageDownloader getWebPageDownloader() {
+		return super.getWebPageDownloader();
+	}
+
+	@Override
+	protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+		super.setWebPageDownloader(webPageDownloader);
+	}
+
+}

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

+package lcsb.mapviewer.annotation.services.annotators;
+
+import java.io.IOException;
+import java.util.ArrayList;
+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.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+
+/**
+ * This is a class that implements a backend to CAZy.
+ * 
+ * @author David Hoksza
+ * 
+ */
+public class CazyAnnotator extends ElementAnnotator implements IExternalService {
+
+	/**
+	 * Default class logger.
+	 */
+	private static Logger	logger					= Logger.getLogger(CazyAnnotator.class);
+	
+	/**
+	 * Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
+	 * tair}.
+	 */
+	@Autowired
+	private TairAnnotator		tairAnnotator;
+
+	/**
+	 * Pattern used for finding UniProt symbol from TAIR info page .
+	 */
+	private Pattern				cazyIdMatcher		= Pattern.compile("\\/((GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?)\\.html");
+
+	/**
+	 * Default constructor.
+	 */
+	public CazyAnnotator() {
+		super(CazyAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
+	}
+
+	@Override
+	public ExternalServiceStatus getServiceStatus() { 
+		ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+		GeneralCacheInterface cacheCopy = getCache();
+		this.setCache(null);
+
+		try {
+			MiriamData md = uniprotToCazy(createMiriamData(MiriamType.UNIPROT, "Q9SG95"));
+
+			status.setStatus(ExternalServiceStatusType.OK);
+			if (md == null || !md.getResource().equalsIgnoreCase("GH5_7")) {
+				status.setStatus(ExternalServiceStatusType.CHANGED);
+			}
+		} catch (Exception e) {
+			logger.error(status.getName() + " is down", e);
+			status.setStatus(ExternalServiceStatusType.DOWN);
+		}
+		this.setCache(cacheCopy);
+		return status;
+	}
+
+	@Override
+	public void annotateElement(BioEntity object) throws AnnotatorException {
+		if (isAnnotatable(object)) {
+			
+			MiriamData mdTair = null;
+			MiriamData mdCazy = null;
+			for (MiriamData md : object.getMiriamData()) {
+				if (md.getDataType().equals(MiriamType.CAZY)) {
+					mdCazy = md;
+				}
+				else if (md.getDataType().equals(MiriamType.TAIR_LOCUS)) {
+					mdTair = md;
+				}				
+			}
+