common interface for drugs and chemicals extracted

annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java

@@ -2,6 +2,7 @@ package lcsb.mapviewer.annotation.data;
 
 import java.io.Serializable;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Comparator;
 import java.util.List;
 
@@ -19,7 +20,7 @@ import lcsb.mapviewer.model.map.MiriamData;
  * 
  */
 @XmlRootElement
-public class Chemical implements Serializable {
+public class Chemical implements Serializable, TargettingStructure {
 
 	/**
 	 * 
@@ -290,4 +291,17 @@ public class Chemical implements Serializable {
 
 	}
 
+	@Override
+	public Collection<MiriamData> getSources() {
+		List<MiriamData> sources = new ArrayList<>();
+		sources.add(getCasID());
+		sources.add(getChemicalId());
+		return sources;
+	}
+
+	@Override
+	public Collection<Target> getTargets() {
+		return getInferenceNetwork();
+	}
+
 }

annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java

@@ -18,7 +18,7 @@ import lcsb.mapviewer.model.map.MiriamData;
  * 
  */
 @XmlRootElement
-public class Drug implements Serializable {
+public class Drug implements Serializable, TargettingStructure {
 
 	/**
 	 * 

annotation/src/main/java/lcsb/mapviewer/annotation/data/TargettingStructure.java

+package lcsb.mapviewer.annotation.data;
+
+import java.util.Collection;
+
+import lcsb.mapviewer.model.map.MiriamData;
+
+public interface TargettingStructure {
+
+	Collection<MiriamData> getSources();
+
+	Collection<Target> getTargets();
+
+}

service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java

@@ -18,6 +18,7 @@ import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.annotation.data.Chemical;
 import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargettingStructure;
 import lcsb.mapviewer.annotation.services.ChemicalParser;
 import lcsb.mapviewer.annotation.services.ChemicalSearchException;
 import lcsb.mapviewer.annotation.services.PubmedParser;
@@ -304,19 +305,13 @@ public class ChemicalService implements IChemicalService {
 				}
 			}
 			double counter = 0.0;
-			Set<MiriamData> annotations = new HashSet<>();
 			for (MiriamData md : targetMiriams) {
 				try {
 					List<Chemical> chemicalList = chemicalParser.getChemicalListByTarget(md, disease);
 					for (Chemical chemical : chemicalList) {
-						annotations.addAll(getAllMiriamDataForChemical(chemical));
+						cacheMiriamData(chemical);
 					}
-					for (MiriamData miriamData : annotations) {
-						if (miriamData.getDataType().equals(MiriamType.PUBMED)) {
-							pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
-						}
-					}
-				} catch (ChemicalSearchException | NumberFormatException | PubmedSearchException e) {
+				} catch (ChemicalSearchException | AnnotatorException e) {
 					logger.error("Problem with accessing info about chemical for target: " + md, e);
 				}
 				counter += 1;
@@ -328,16 +323,25 @@ public class ChemicalService implements IChemicalService {
 		}
 	}
 
-	private Set<MiriamData> getAllMiriamDataForChemical(Chemical chemical) {
+	private void cacheMiriamData(TargettingStructure targettingStructure) throws AnnotatorException {
 		Set<MiriamData> result = new HashSet<>();
-		result.add(chemical.getCasID());
-		result.add(chemical.getChemicalId());
-		for (Target target : chemical.getInferenceNetwork()) {
+		result.addAll(targettingStructure.getSources());
+		for (Target target : targettingStructure.getTargets()) {
 			result.addAll(target.getGenes());
 			result.addAll(target.getReferences());
 
 		}
-		return result;
+		
+		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);
+				}
+			}
+		}
+		
 	}
 
 }

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

@@ -190,9 +190,6 @@ public abstract class WebTestFunctions {
 	@Autowired
 	protected ModelViewFactory				 modelViewFactory;
 
-	@Autowired
-	protected DrugViewFactory					 drugViewFactory;
-
 	@Autowired
 	protected IReferenceGenomeService	 referenceGenomeService;