diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
index c79e10ca98485ea4f4c3235362e35aaf5f11ccc1..9d2b1b10da174fd0ba697412b377746105025eae 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
+++ b/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);
+ }
+ }
+ }
+
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java
deleted file mode 100644
index 235a3a68240f5404e7e4d8f676ae9769065e2d24..0000000000000000000000000000000000000000
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java
+++ /dev/null
@@ -1,116 +0,0 @@
-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;
- }
-
-}
diff --git a/service/src/main/resources/applicationContext-service.xml b/service/src/main/resources/applicationContext-service.xml
index bf0ea8495fbd544392a02ebf4b2f31d0f60ce1b1..c40be7af7591eb74805a56c5775174aa273d0535 100644
--- a/service/src/main/resources/applicationContext-service.xml
+++ b/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"/>