drug view factory removed

service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java

@@ -13,10 +13,12 @@ import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.annotation.data.Drug;
 import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargettingStructure;
 import lcsb.mapviewer.annotation.services.ChEMBLParser;
 import lcsb.mapviewer.annotation.services.DrugSearchException;
 import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
 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;
@@ -31,7 +33,6 @@ import lcsb.mapviewer.model.map.species.Rna;
 import lcsb.mapviewer.model.map.statistics.SearchType;
 import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
 import lcsb.mapviewer.services.search.db.DbSearchCriteria;
-import lcsb.mapviewer.services.view.AnnotationView;
 
 /**
  * Implementation of the service that allows access information about drugs.
@@ -73,12 +74,6 @@ public class DrugService implements IDrugService {
 	@Autowired
 	private PubmedParser					pubmedParser;
 
-	/**
-	 * Factory object used for creation of {@link DrugView} elements.
-	 */
-	@Autowired
-	private DrugViewFactory				drugViewFactory;
-
 	/**
 	 * Service that manages search history.
 	 */
@@ -304,7 +299,6 @@ public class DrugService implements IDrugService {
 			removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
 		}
 
-
 		Collections.sort(drugList, new DrugView.NameComparator());
 		return drugList;
 	}
@@ -396,17 +390,17 @@ public class DrugService implements IDrugService {
 				try {
 					List<Drug> chemicalList = drugBankParser.getDrugListByTarget(md);
 					for (Drug chemical : chemicalList) {
-						drugViewFactory.create(chemical);
+						cacheMiriamData(chemical);
 					}
-				} catch (DrugSearchException e) {
+				} catch (DrugSearchException | AnnotatorException e) {
 					logger.error("Problem with accessing info about drugbank for target: " + md, e);
 				}
 				try {
 					List<Drug> chemicalList = chEMBLParser.getDrugListByTarget(md);
 					for (Drug chemical : chemicalList) {
-						drugViewFactory.create(chemical);
+						cacheMiriamData(chemical);
 					}
-				} catch (DrugSearchException e) {
+				} catch (DrugSearchException | AnnotatorException e) {
 					logger.error("Problem with accessing info about chembl for target: " + md, e);
 				}
 				counter += 1;
@@ -416,4 +410,25 @@ public class DrugService implements IDrugService {
 		}
 	}
 
+	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/drug/DrugViewFactory.java

-package lcsb.mapviewer.services.search.db.drug;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargetType;
-import lcsb.mapviewer.model.map.MiriamData;
-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.GeneRow;
-import lcsb.mapviewer.services.search.db.TargetView;
-import lcsb.mapviewer.services.search.db.TargetViewFactory;
-import lcsb.mapviewer.services.view.AnnotationView;
-
-/**
- * Factory class for {@link DrugView} class.
- * 
- * @author Piotr Gawron
- * 
- */
-public class DrugViewFactory extends SearchResultFactory<Drug, DrugView> {
-	/**
-	 * Default class logger.
-	 */
-	private static Logger			logger = Logger.getLogger(DrugViewFactory.class);
-
-	/**
-	 * Factory object used for creation of {@link TargetView} elements.
-	 */
-	@Autowired
-	private TargetViewFactory	targetViewFactory;
-
-	@Override
-	public DrugView create(Drug drug) {
-		return create(drug, null, 0);
-	}
-
-	/**
-	 * Creates {@link DrugView}.
-	 * 
-	 * @param drug
-	 *          original Drug 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 DrugView} object for given drug. links are placed according
-	 *         to model given in the parameter.
-	 */
-	public DrugView create(Drug drug, Model model, int set) {
-		DrugView result = new DrugView(drug);
-		if (drug == null) {
-			return result;
-		}
-		result.setName(drug.getName());
-		for (MiriamData md : drug.getSources()) {
-			AnnotationView view = getAnnotationViewFactory().create(md);
-			result.addDrugLink(view);
-
-		}
-		result.setDescription(drug.getDescription());
-		result.setBloodBrainBarrier(drug.getBloodBrainBarrier());
-		result.addBrandNames(drug.getBrandNames());
-		result.addSynonyms(drug.getSynonyms());
-
-		int differentNames = 0;
-
-		for (Target target : drug.getTargets()) {
-			result.addTargetRow(targetViewFactory.create(target, model));
-		}
-		Collections.sort(result.getTargetRows(), new DrugTargetViewVisibilityComparator());
-		for (TargetView row : result.getTargetRows()) {
-			if (row.getVisible()) {
-				String icon;
-				icon = IconManager.getInstance().getIconForIndex(differentNames++, IconType.DRUG, set);
-				row.setIcon(icon);
-				if (row.getSelectable()) {
-					row.setSelected(true);
-				}
-			}
-		}
-
-		Map<String, Integer> dbEntries = new HashMap<String, Integer>();
-		for (AnnotationView dl : result.getDrugLinks()) {
-			Integer counter = dbEntries.get(dl.getName());
-			if (counter == null) {
-				counter = 1;
-			} else {
-				counter += 1;
-			}
-			dbEntries.put(dl.getName(), counter);
-		}
-		for (Entry<String, Integer> entry : dbEntries.entrySet()) {
-			if (entry.getValue() == 1) {
-				entry.setValue(null);
-			} else {
-				entry.setValue(0);
-			}
-		}
-		for (AnnotationView dl : result.getDrugLinks()) {
-			Integer counter = dbEntries.get(dl.getName());
-			if (counter != null) {
-				counter += 1;
-				dbEntries.put(dl.getName(), counter);
-				dl.setName(dl.getName() + " (" + counter + ")");
-			}
-		}
-		return result;
-	}
-
-	@Override
-	public String createGson(DrugView object) {
-		return new Gson().toJson(object);
-	}
-
-	/**
-	 * Creates list of markers for the given geneName.
-	 * 
-	 * @param annotation
-	 *          annotation of a gene (hgnc)
-	 * @param icon
-	 *          what icon should be used by markers
-	 * @param models
-	 *          list of models where we want to create markers
-	 * @return list of markers to be presented on the client side for the given
-	 *         geneName
-	 */
-	protected List<ElementIdentifier> geneToOverlayList(AnnotationView annotation, String icon, List<Model> models) {
-		List<ElementIdentifier> result = new ArrayList<>();
-
-		for (Model m : models) {
-			List<Element> species = m.getElementsByName(annotation.getName());
-			for (Element species2 : species) {
-				result.add(new ElementIdentifier(species2, icon));
-			}
-		}
-		return result;
-	}
-
-	/**
-	 * Creates list of markers for the given chembl target.
-	 * 
-	 * @param complexTarget
-	 *          chembl target
-	 * @param models
-	 *          list of models where we want to create markers
-	 * @return list of markers to be presented on the client side for the given
-	 *         chembl target
-	 */
-	protected List<ElementIdentifier> complexToOverlayList(TargetView complexTarget, Collection<Model> models) {
-		List<ElementIdentifier> result = new ArrayList<>();
-
-		for (Model m : models) {
-			for (Element element : m.getElements()) {
-				if (elementMatch(complexTarget, element)) {
-					result.add(new ElementIdentifier(element, complexTarget.getIcon()));
-				}
-			}
-		}
-		return result;
-	}
-
-	@Override
-	public List<ElementIdentifier> searchResultToElementIdentifier(DrugView drug, Model model) {
-		List<ElementIdentifier> result = new ArrayList<>();
-
-		List<Model> models = new ArrayList<>();
-		models.add(model);
-		models.addAll(model.getSubmodels());
-
-		// to be more specific add markers for targets
-		for (TargetView row : drug.getTargetRows()) {
-			// check if target should be vizualized
-			if (row.getSelected()) {
-				// depending on the type vizualize:
-				if (row.getType().equals(TargetType.COMPLEX_PROTEIN.getCommonName())) {
-					// complex children
-					result.addAll(complexToOverlayList(row, models));
-				} else if (row.getType().equals(TargetType.SINGLE_PROTEIN.getCommonName())) {
-					// single protein
-					if (row.getProteins().size() > 0) {
-						result.addAll(geneToOverlayList(row.getProteins().get(0).getAnnotation(), row.getIcon(), models));
-					}
-				} else if (row.getType().equals(TargetType.PROTEIN_FAMILY.getCommonName())) {
-					// all proteins in the family
-					for (GeneRow geneRow : row.getProteins()) {
-						result.addAll(geneToOverlayList(geneRow.getAnnotation(), row.getIcon(), models));
-					}
-				} else {
-					logger.error("Unknown target type: " + row.getType());
-				}
-			} else { // if the whole target wasn't selected then maybe only some
-							 // proteins within it were selected
-				for (GeneRow geneRow : row.getProteins()) {
-					if (geneRow.getSelected()) {
-						result.addAll(geneToOverlayList(geneRow.getAnnotation(), row.getIcon(), models));
-					}
-				}
-			}
-		}
-
-		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="DrugViewFactory" class="lcsb.mapviewer.services.search.db.drug.DrugViewFactory"/>
 	<bean id="MiRNAViewFactory" class="lcsb.mapviewer.services.search.db.mirna.MiRNAViewFactory"/>
 	<bean id="TargetViewFactory" class="lcsb.mapviewer.services.search.db.TargetViewFactory"/>
 	

service/src/test/java/lcsb/mapviewer/services/search/db/drug/AllSearchDrugTests.java

@@ -6,7 +6,6 @@ import org.junit.runners.Suite.SuiteClasses;
 
 @RunWith(Suite.class)
 @SuiteClasses({ DrugServiceTest.class, //
-		DrugViewFactoryTest.class, //
 		DrugViewTest.class,//
 
 })

service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugServiceTest.java

@@ -19,24 +19,16 @@ import org.junit.Test;
 import lcsb.mapviewer.annotation.data.Drug;
 import lcsb.mapviewer.annotation.data.Target;
 import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.converter.ComplexZipConverter;
-import lcsb.mapviewer.converter.ComplexZipConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.SubmodelType;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Protein;
 import lcsb.mapviewer.services.ServiceTestFunctions;
 import lcsb.mapviewer.services.search.db.DbSearchCriteria;
-import lcsb.mapviewer.services.search.db.GeneRow;
-import lcsb.mapviewer.services.search.db.TargetView;
 
 public class DrugServiceTest extends ServiceTestFunctions {
 	Logger logger = Logger.getLogger(DrugServiceTest.class);

service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactoryTest.java

-package lcsb.mapviewer.services.search.db.drug;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargetType;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.overlay.IconManager;
-import lcsb.mapviewer.services.search.data.ElementIdentifier;
-import lcsb.mapviewer.services.search.db.TargetDetails;
-import lcsb.mapviewer.services.search.db.TargetView;
-import lcsb.mapviewer.services.search.db.TargetViewFactory;
-import lcsb.mapviewer.services.view.AnnotationView;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
-
-public class DrugViewFactoryTest extends ServiceTestFunctions {
-
-	@Autowired
-	TargetViewFactory			targetViewFactory;
-
-	Logger								logger = Logger.getLogger(DrugViewFactoryTest.class);
-
-	@Autowired
-	AnnotationViewFactory	avFactory;
-
-	@Autowired
-	DrugViewFactory				dvf;
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testGeneToOverlayList() throws Exception {
-		try {
-			Model model = getModelForFile("testFiles/drug_target.xml", true);
-			model.setTileSize(256);
-			List<Model> models = new ArrayList<>();
-			models.add(model);
-
-			AnnotationView annotation = avFactory.create(new MiriamData());
-			annotation.setName("M");
-
-			List<ElementIdentifier> overlays = dvf.geneToOverlayList(annotation, IconManager.getInstance().getEmpyIcon(), models);
-			assertEquals(1, overlays.size());
-
-			annotation.setName("GRIN2B");
-			overlays = dvf.geneToOverlayList(annotation, IconManager.getInstance().getEmpyIcon(), models);
-			assertEquals(3, overlays.size());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testComplexToOverlayList() throws Exception {
-		try {
-			Drug drug = chemblParser.findDrug("AMANTADINE");
-			Target exampleTarget = null;
-			assertTrue(drug.getTargets().size() > 0);
-			for (Target target : drug.getTargets()) {
-				if (target.getName().equals("Glutamate [NMDA] receptor")) {
-					target.setType(TargetType.COMPLEX_PROTEIN);
-					exampleTarget = target;
-				}
-				logger.debug(target);
-			}
-			assertNotNull(exampleTarget);
-			Model model = getModelForFile("testFiles/drug_target.xml", true);
-			model.setTileSize(256);
-			List<Model> models = new ArrayList<>();
-			models.add(model);
-			TargetView view = targetViewFactory.create(exampleTarget);
-			view.setIcon(IconManager.getInstance().getEmpyIcon());
-
-			List<ElementIdentifier> overlays = dvf.complexToOverlayList(view, models);
-			assertEquals(2, overlays.size());
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testgetElementInformationForResult() throws Exception {
-		try {
-			Drug drug = chemblParser.findDrug("AMANTADINE");
-			Model model = getModelForFile("testFiles/drug_target.xml", false);
-			Element alias = model.getElementByElementId("sa9");
-			alias.setName("M");
-			alias.setId(12);
-			model.removeElement(alias);
-			model.addElement(alias);
-			ElementIdentifier ei = new ElementIdentifier(alias, null);
-			model.setTileSize(256);
-			List<Model> models = new ArrayList<>();
-			models.add(model);
-			DrugView view = dvf.create(drug);
-			TargetDetails result = dvf.getElementInformationForResult(view.getTargetRows(), ei, model);
-			assertNotNull(result);
-			assertFalse(result.getDatabaseSource().equals(result.getReferences().get(0)));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCreateEmpty() throws Exception {
-		try {
-			Object object = dvf.create(null);
-			assertNotNull(object);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testCreateGson() throws Exception {
-		try {
-			DrugView object = dvf.create(null);
-			assertNotNull(dvf.createGson(object));
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-}

web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java

@@ -80,7 +80,6 @@ import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
 import lcsb.mapviewer.services.interfaces.ISearchService;
 import lcsb.mapviewer.services.interfaces.IUserService;
 import lcsb.mapviewer.services.search.db.chemical.IChemicalService;
-import lcsb.mapviewer.services.search.db.drug.DrugViewFactory;
 import lcsb.mapviewer.services.search.db.drug.IDrugService;
 import lcsb.mapviewer.services.view.AuthenticationToken;
 import lcsb.mapviewer.services.view.ModelViewFactory;