mirna view factory removed

service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java

@@ -15,8 +15,11 @@ import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.annotation.data.MiRNA;
 import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargettingStructure;
 import lcsb.mapviewer.annotation.services.MiRNAParser;
 import lcsb.mapviewer.annotation.services.MiRNASearchException;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.annotation.services.PubmedSearchException;
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
@@ -60,16 +63,17 @@ public class MiRNAService implements IMiRNAService {
 	private HgncAnnotator					hgncAnnotator;
 
 	/**
-	 * Factory object used for creation of {@link MiRNAView} elements.
+	 * Service that manages search history.
 	 */
 	@Autowired
-	private MiRNAViewFactory			miRNAViewFactory;
+	private ISearchHistoryService	searchHistoryService;
 
 	/**
-	 * Service that manages search history.
+	 * Service accessing
+	 * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
 	 */
 	@Autowired
-	private ISearchHistoryService	searchHistoryService;
+	private PubmedParser					pubmedParser;
 
 	/**
 	 * Default constructor.
@@ -162,7 +166,7 @@ public class MiRNAService implements IMiRNAService {
 		for (MiRNA drug : mirnaList) {
 			removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
 		}
-		
+
 		Collections.sort(mirnaList, new MiRNAView.NameComparator());
 		return mirnaList;
 	}
@@ -227,9 +231,9 @@ public class MiRNAService implements IMiRNAService {
 				try {
 					List<MiRNA> chemicalList = miRNAParser.getMiRnaListByTargets(currentList);
 					for (MiRNA chemical : chemicalList) {
-						miRNAViewFactory.create(chemical);
+						cacheMiriamData(chemical);
 					}
-				} catch (MiRNASearchException e) {
+				} catch (MiRNASearchException | AnnotatorException e) {
 					logger.error("Problem with accessing info about mirna for target: " + md, e);
 				}
 				progress = counter / (double) targetMiriams.size();
@@ -239,4 +243,25 @@ public class MiRNAService implements IMiRNAService {
 		}
 	}
 
+	private void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
+		Set<MiriamData> result = new HashSet<>();
+		result.addAll(targettingStructure.getSources());
+		for (Target target : targettingStructure.getTargets()) {
+			result.addAll(target.getGenes());
+			result.addAll(target.getReferences());
+
+		}
+
+		for (MiriamData miriamData : result) {
+			if (miriamData.getDataType().equals(MiriamType.PUBMED)) {
+				try {
+					pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
+				} catch (NumberFormatException | PubmedSearchException e) {
+					throw new AnnotatorException(e);
+				}
+			}
+		}
+
+	}
+
 }

service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java

-package lcsb.mapviewer.services.search.db.mirna;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.data.MiRNA;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.services.overlay.IconManager;
-import lcsb.mapviewer.services.overlay.IconType;
-import lcsb.mapviewer.services.search.SearchResultFactory;
-import lcsb.mapviewer.services.search.data.ElementIdentifier;
-import lcsb.mapviewer.services.search.db.DrugTargetViewVisibilityComparator;
-import lcsb.mapviewer.services.search.db.TargetView;
-import lcsb.mapviewer.services.search.db.TargetViewFactory;
-
-/**
- * Factory class for {@link MiRNAView} class.
- * 
- * @author Ayan Rota
- * 
- */
-public class MiRNAViewFactory extends SearchResultFactory<MiRNA, MiRNAView> {
-
-	/**
-	 * Default class logger.
-	 */
-	@SuppressWarnings("unused")
-	private static Logger			logger = Logger.getLogger(MiRNAViewFactory.class);
-
-	/**
-	 * Factory object for {@link TargetView} elements.
-	 */
-	@Autowired
-	private TargetViewFactory	drugTargetViewFactory;
-
-	@Override
-	public MiRNAView create(MiRNA miRNA) {
-		return create(miRNA, null, 0);
-	}
-
-	/**
-	 * Creates {@link MiRNAView}.
-	 * 
-	 * @param miRNA
-	 *          original MiRNA from which the data will be initialized
-	 * @param model
-	 *          model where the view will be presented
-	 * @param set
-	 *          which set of icons should be used
-	 * 
-	 * @return {@link MiRNAView} object for given miRNA. links are placed
-	 *         according to model given in the parameter.
-	 */
-	public MiRNAView create(MiRNA miRNA, Model model, int set) {
-		MiRNAView miRNAView = new MiRNAView(miRNA);
-		if (miRNA == null) {
-			return miRNAView;
-		}
-
-		miRNAView.setName(miRNA.getName());
-
-		List<TargetView> targetsRows = new ArrayList<>();
-		int differentNames = 0;
-		for (Target geneEntry : miRNA.getTargets()) {
-			targetsRows.add(drugTargetViewFactory.create(geneEntry, model));
-		}
-
-		Collections.sort(targetsRows, new DrugTargetViewVisibilityComparator());
-
-		for (TargetView geneTargetView : targetsRows) {
-			if (geneTargetView.getSelectable()) {
-				String icon = IconManager.getInstance().getIconForIndex(differentNames++, IconType.MI_RNA, set);
-				geneTargetView.setIcon(icon);
-				geneTargetView.setSelected(true);
-			}
-		}
-		miRNAView.setTargetRows(targetsRows);
-		return miRNAView;
-
-	}
-
-	@Override
-	public String createGson(MiRNAView object) {
-		return new Gson().toJson(object);
-	}
-
-	@Override
-	public List<ElementIdentifier> searchResultToElementIdentifier(MiRNAView searchResult, Model inputModel) {
-		List<ElementIdentifier> result = new ArrayList<>();
-
-		List<Model> models = new ArrayList<>();
-		models.addAll(inputModel.getSubmodels());
-		models.add(inputModel);
-		for (Model model : models) {
-			for (TargetView target : searchResult.getTargetRows()) {
-				if (target.getSelected() && target.getIcon() != null) {
-					for (Element element : model.getElements()) {
-						if (elementMatch(target, element)) {
-							result.add(new ElementIdentifier(element, target.getIcon()));
-						}
-					}
-				}
-			}
-		}
-		return result;
-	}
-
-}

service/src/main/resources/applicationContext-service.xml

@@ -68,7 +68,6 @@
 	<bean id="FullReactionViewFactory" class="lcsb.mapviewer.services.search.data.FullReactionViewFactory"/>
 	<bean id="LightAliasViewFactory" class="lcsb.mapviewer.services.search.data.LightAliasViewFactory"/>
 
-	<bean id="MiRNAViewFactory" class="lcsb.mapviewer.services.search.db.mirna.MiRNAViewFactory"/>
 	<bean id="TargetViewFactory" class="lcsb.mapviewer.services.search.db.TargetViewFactory"/>
 	
 	<bean id="ElementMatcher" class="lcsb.mapviewer.services.search.ElementMatcher"/>