diff --git a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
index 44ba848aa094bd6ea996cbc24e314ee44dfcbb00..c947104992856bb393f310779a596aae011ba27f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
@@ -8,7 +8,6 @@ import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargetType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
@@ -19,8 +18,6 @@ import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.services.search.db.GeneRow;
-import lcsb.mapviewer.services.search.db.TargetView;
import lcsb.mapviewer.services.view.AnnotationViewFactory;
public class ElementMatcher {
@@ -37,92 +34,6 @@ public class ElementMatcher {
@Autowired
private AnnotationViewFactory annotationViewFactory;
- /**
- * Check if the target should be applied to the element.
- *
- * @param target
- * drug target to check
- * @param element
- * {@link Element} to check
- * @return <code>true</code> if drug target can target element,
- * <code>false</code> otherwise
- */
- public boolean elementMatch(TargetView target, BioEntity element) {
- if (target.getType().equals(TargetType.COMPLEX_PROTEIN.getCommonName())) {
- MiriamData targetAnnotation = annotationViewFactory.viewToObject(target.getAnnotation());
- if (MiriamType.CHEMBL_TARGET.equals(targetAnnotation.getDataType())) {
- if (element.getMiriamData().contains(targetAnnotation)) {
- return true;
- }
- }
- Collection<String> ids = new HashSet<String>();
- for (GeneRow row : target.getProteins()) {
- ids.add(row.getAnnotation().getName());
- }
-
- if (element instanceof Complex) {
- Complex complex = (Complex) element;
- Set<Species> speciesSet = complex.getAllSimpleChildren();
- if (speciesSet.size() != ids.size()) {
- return false;
- }
-
- for (Element id : speciesSet) {
- if (!ids.contains(id.getName())) {
- return false;
- }
- }
- return true;
- }
- return false;
- } else if (target.getType().equals(TargetType.SINGLE_PROTEIN.getCommonName())) {
- MiriamData targetAnnotation = null;
- if (target.getAnnotation() != null) {
- targetAnnotation = annotationViewFactory.viewToObject(target.getAnnotation());
- } else if (target.getProteins().size() > 0) {
- targetAnnotation = annotationViewFactory.viewToObject(target.getProteins().get(0).getAnnotation());
- } else {
- logger.warn("Invalid target found: " + target);
- }
- if (targetAnnotation != null && element.getMiriamData().contains(targetAnnotation)) {
- return true;
- }
- if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
- if (target.getProteins().size() > 0) {
- String hgncId = target.getProteins().get(0).getAnnotation().getName();
- if (element.getName().equalsIgnoreCase(hgncId)) {
- return true;
- }
- }
- }
- return false;
- } else if (target.getType().equals(TargetType.PROTEIN_FAMILY.getCommonName())) {
- if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
- String hgncId = target.getProteins().get(0).getAnnotation().getName();
- if (element.getName().equalsIgnoreCase(hgncId)) {
- return true;
- } else if (element.getMiriamData().contains(new MiriamData(MiriamType.HGNC_SYMBOL, hgncId))) {
- return true;
- }
- for (GeneRow protein : target.getProteins()) {
- hgncId = protein.getAnnotation().getName();
- if (element.getName().equalsIgnoreCase(hgncId)) {
- return true;
- } else if (element.getMiriamData().contains(new MiriamData(MiriamType.HGNC_SYMBOL, hgncId))) {
- return true;
- }
- }
- }
- return false;
- } else if (target.getType().equals(TargetType.OTHER.getCommonName())) {
- // in other case just compare names
- String name = target.getProteins().get(0).getAnnotation().getName();
- return element.getName().equalsIgnoreCase(name);
- } else {
- throw new InvalidArgumentException("Unknown drug target type: " + target.getType());
- }
- }
-
public boolean elementMatch(Target target, BioEntity element) {
MiriamData targetAnnotation = target.getSource();
switch (target.getType()) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
index de69745e87a1471d62bd3d19513ba9dd8c048ce1..6380639b2259edbc655afb34e53ed85a2ef5d86a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
@@ -58,57 +58,7 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
@Autowired
private ElementMatcher elementMatcher;
- /**
- * Returns detailed information about element respective to the set of targets
- * (which should be connected to single drug/mirna/chemical).
- *
- * @param element
- * element for which we are looking for detailed information
- * @param model
- * {@link Model} on which element is located
- * @param targets
- * list of targets from which detailed information should be
- * extracted
- * @return detailed information for element in the specific drug,
- * <code>null</code> if such information doesnt exist
- */
- public TargetDetails getElementInformationForResult(Collection<TargetView> targets, ElementIdentifier element, Model model) {
- if (ElementIdentifierType.REACTION.getJsName().equalsIgnoreCase(element.getType())) {
- logger.warn("Detail information for reactions not available");
- return null;
- } else if (ElementIdentifierType.POINT.getJsName().equalsIgnoreCase(element.getType())) {
- logger.warn("Detail information for points not available");
- return null;
- } else if (ElementIdentifierType.ALIAS.getJsName().equalsIgnoreCase(element.getType())) {
- Model m = model.getSubmodelById(element.getModelId());
- Element alias = m.getElementByDbId(Integer.valueOf(element.getObjectId()));
- if (alias == null) {
- logger.warn("Alias with object id = " + element.getObjectId() + " is unknown.");
- return null;
- }
- for (TargetView row : targets) {
- if (elementMatch(row, alias)) {
- TargetDetails result = new TargetDetails();
- result.setDatabaseSource(row.getAnnotation());
- for (Article article : row.getReferences()) {
- result.getReferences().add(annotationViewFactory.create(article));
- }
- for (GeneRow protein : row.getProteins()) {
- result.getReferences().add(protein.getAnnotation());
- }
- return result;
- }
- }
- } else {
- throw new InvalidArgumentException("Unknown element type: " + element.getType());
- }
- return null;
- }
- protected boolean elementMatch(TargetView target, Element element) {
- return elementMatcher.elementMatch(target, element);
- }
-
protected boolean elementMatch(Target target, Element element) {
return elementMatcher.elementMatch(target, element);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/DrugTargetViewVisibilityComparator.java b/service/src/main/java/lcsb/mapviewer/services/search/db/DrugTargetViewVisibilityComparator.java
deleted file mode 100644
index a92660b2582079489651c958657e4db93d9ae28c..0000000000000000000000000000000000000000
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/DrugTargetViewVisibilityComparator.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package lcsb.mapviewer.services.search.db;
-
-import java.util.Comparator;
-
-import lcsb.mapviewer.common.comparator.StringComparator;
-
-/**
- * Comparator class for {@link TargetView} objects. It put first elements that
- * are {@link TargetView#getSelectable() selectable} elements.
- *
- * @author Piotr Gawron
- *
- */
-public class DrugTargetViewVisibilityComparator implements Comparator<TargetView> {
-
- /**
- * Comparator class for Strings that handles nulls.
- */
- private final StringComparator stringComparator = new StringComparator();
-
- @Override
- public int compare(TargetView arg0, TargetView arg1) {
- if (arg0.getSelectable() && !arg1.getSelectable()) {
- return -1;
- }
- if (!arg0.getSelectable() && arg1.getSelectable()) {
- return 1;
- }
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/TargetViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/db/TargetViewFactory.java
deleted file mode 100644
index 994ca460ecfda84f5d97e85cf72090e226a41314..0000000000000000000000000000000000000000
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/TargetViewFactory.java
+++ /dev/null
@@ -1,158 +0,0 @@
-package lcsb.mapviewer.services.search.db;
-
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.annotation.data.ArticleCitationComparator;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargetType;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.BioEntity;
-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.ModelSubmodelConnection;
-import lcsb.mapviewer.services.view.AbstractViewFactory;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
-
-/**
- * Factory class for {@link TargetView} class.
- *
- * @author Piotr Gawron
- *
- */
-public class TargetViewFactory extends AbstractViewFactory<Target, TargetView> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(TargetViewFactory.class);
-
- /**
- * Factory object for {@link lcsb.mapviewer.services.view.AnnotationView}
- * elements.
- */
- @Autowired
- private AnnotationViewFactory annotationViewFactory;
-
- /**
- * Service accessing
- * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
- @Override
- public TargetView create(Target target) {
- return create(target, null);
- }
-
- /**
- * Creates {@link TargetView} element for given {@link Target} and places
- * links on the parameter {@link Model}.
- *
- * @param target
- * object for which {@link TargetView} is created
- * @param model
- * {@link Model} where links will be placed
- * @return {@link TargetView} element for given {@link Target}
- */
- public TargetView create(Target target, Model model) {
- TargetView result = new TargetView();
- if (target == null) {
- return result;
- }
- result.setName(target.getName());
- if (target.getType() == null) {
- logger.warn("Unknown type of target: " + target.getName() + ", target name: " + target.getName());
- } else {
- result.setType(target.getType().getCommonName());
- }
-
- if (target.getType() == TargetType.SINGLE_PROTEIN || target.getType() == TargetType.COMPLEX_PROTEIN || target.getType() == TargetType.PROTEIN_FAMILY) {
- result.setVisible(true);
- result.setSelectable(false);
- }
-
- for (MiriamData md : target.getGenes()) {
- GeneRow geneRow = new GeneRow();
- geneRow.setAnnotation(annotationViewFactory.create(md));
- if (model != null) {
- Set<BioEntity> list = new HashSet<>();
- list.addAll(model.getElementsByName(md.getResource()));
- list.addAll(model.getElementsByAnnotation(md));
-
- int countInTopModel = list.size();
- for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- list.addAll(submodel.getSubmodel().getModel().getElementsByName(md.getResource()));
- list.addAll(submodel.getSubmodel().getModel().getElementsByAnnotation(md));
- }
- int counter = list.size();
- geneRow.setSelectable(counter > 0);
-
- if (counter > 0) {
- geneRow.setSelectable(true);
- if (target.getType() == TargetType.SINGLE_PROTEIN || target.getType() == TargetType.PROTEIN_FAMILY) {
- result.setSelectable(true);
- }
- if (countInTopModel < counter) {
- result.setAvailableInSubmodel(true);
- }
- }
- }
- result.addProtein(geneRow);
- }
-
- // this should be fixed
- // if (target.getType() == TargetType.COMPLEX_PROTEIN) {
- //
- // if (complexToOverlayList(target, null).size() > 0) {
- // row.setSelectable(true);
- // }
- // }
-
- if (target.getSource() != null) {
- result.setAnnotation(annotationViewFactory.create(target.getSource()));
- }
- for (MiriamData md : target.getReferences()) {
- if (md.getDataType().equals(MiriamType.PUBMED)) {
- try {
- Integer id = Integer.parseInt(md.getResource());
- Article reference = pubmedParser.getPubmedArticleById(id);
- if (reference != null) {
- result.addReference(reference);
- }
- } catch (NumberFormatException e) {
- logger.warn("Invalid pubmed reference: " + md);
- } catch (PubmedSearchException e) {
- logger.warn("Problem with accessing info about pubmed: " + md, e);
- }
- } else {
- logger.warn("Unknown reference type: " + md);
- }
- }
- Collections.sort(result.getReferences(), new ArticleCitationComparator());
-
- return result;
-
- }
-
- @Override
- public String createGson(TargetView object) {
- return new Gson().toJson(object);
- }
-
- @Override
- public Target viewToObject(TargetView view) {
- throw new NotImplementedException();
- }
-}
diff --git a/service/src/main/resources/applicationContext-service.xml b/service/src/main/resources/applicationContext-service.xml
index c40be7af7591eb74805a56c5775174aa273d0535..7d133276baca0b90b4f182c4120f431a268bb381 100644
--- a/service/src/main/resources/applicationContext-service.xml
+++ b/service/src/main/resources/applicationContext-service.xml
@@ -68,8 +68,6 @@
<bean id="FullReactionViewFactory" class="lcsb.mapviewer.services.search.data.FullReactionViewFactory"/>
<bean id="LightAliasViewFactory" class="lcsb.mapviewer.services.search.data.LightAliasViewFactory"/>
- <bean id="TargetViewFactory" class="lcsb.mapviewer.services.search.db.TargetViewFactory"/>
-
<bean id="ElementMatcher" class="lcsb.mapviewer.services.search.ElementMatcher"/>
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/db/AllSearchDbTests.java b/service/src/test/java/lcsb/mapviewer/services/search/db/AllSearchDbTests.java
index dbcdf6e6c209ae879d32867da131c2ff7e004757..7a0f88d8154271df156c9f42b462aad2415117b7 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/db/AllSearchDbTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/db/AllSearchDbTests.java
@@ -12,7 +12,6 @@ import lcsb.mapviewer.services.search.db.mirna.MiRNAServiceTest;
@SuiteClasses({ AllSearchDrugTests.class, //
ChemicalServiceTest.class, //
MiRNAServiceTest.class, //
- TargetViewFactoryTest.class, //
TargetViewTest.class,//
})
public class AllSearchDbTests {
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/db/TargetViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/db/TargetViewFactoryTest.java
deleted file mode 100644
index 6146b57cf683c9c0990364d32bc34e880b3b1efd..0000000000000000000000000000000000000000
--- a/service/src/test/java/lcsb/mapviewer/services/search/db/TargetViewFactoryTest.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package lcsb.mapviewer.services.search.db;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.search.db.TargetView;
-import lcsb.mapviewer.services.search.db.TargetViewFactory;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-public class TargetViewFactoryTest extends ServiceTestFunctions{
-
- @Autowired
- TargetViewFactory targetViewFactory;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCreateEmpty() throws Exception {
- try {
- Object object = targetViewFactory.create(null);
- assertNotNull(object);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateGson() throws Exception {
- try {
- TargetView object = targetViewFactory.create(null);
- assertNotNull(targetViewFactory.createGson(object));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}