From fed1a7c75b40dd20d8519dd9743cc53fcc051ca2 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 24 Jul 2017 12:14:40 +0200
Subject: [PATCH] ChemicalView and ChemicalViewFactory removed
---
.../mapviewer/annotation/data/Chemical.java | 21 ++
.../search/db/chemical/ChemicalService.java | 40 ++-
.../search/db/chemical/ChemicalView.java | 319 ------------------
.../db/chemical/ChemicalViewFactory.java | 188 -----------
.../search/SearchResultFactoryTest.java | 6 +-
.../lcsb/mapviewer/bean/WebTestFunctions.java | 4 -
6 files changed, 54 insertions(+), 524 deletions(-)
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalView.java
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
index e870f1d9ca..ca53af68c3 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
@@ -2,12 +2,14 @@ package lcsb.mapviewer.annotation.data;
import java.io.Serializable;
import java.util.ArrayList;
+import java.util.Comparator;
import java.util.List;
import javax.xml.bind.annotation.XmlRootElement;
import org.apache.commons.lang3.StringUtils;
+import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.model.map.MiriamData;
/**
@@ -269,4 +271,23 @@ public class Chemical implements Serializable {
return result.toString();
}
+ /**
+ * Comparator of the objects by their name.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public static class NameComparator implements Comparator<Chemical> {
+ /**
+ * Default string comparator.
+ */
+ private StringComparator stringComparator = new StringComparator();
+
+ @Override
+ public int compare(Chemical arg0, Chemical arg1) {
+ return stringComparator.compare(arg0.getChemicalName(), arg1.getChemicalName());
+ }
+
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
index 2028155ab8..f753e549b6 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
@@ -17,8 +17,11 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.Chemical;
+import lcsb.mapviewer.annotation.data.Target;
import lcsb.mapviewer.annotation.services.ChemicalParser;
import lcsb.mapviewer.annotation.services.ChemicalSearchException;
+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;
@@ -61,16 +64,17 @@ public class ChemicalService implements IChemicalService {
private ChemicalParser chemicalParser;
/**
- * Factory object used for creation of {@link ChemicalView} elements.
+ * Object used to perform operations on {@link MiriamType#HGNC} annotations.
*/
@Autowired
- private ChemicalViewFactory chemicalViewFactory;
+ private HgncAnnotator hgncAnnotator;
/**
- * Object used to perform operations on {@link MiriamType#HGNC} annotations.
+ * Service accessing
+ * <a href="http://europepmc.org/RestfulWebService">pubmed</a>.
*/
@Autowired
- private HgncAnnotator hgncAnnotator;
+ private PubmedParser pubmedParser;
/**
* Service that manages search history.
@@ -215,7 +219,8 @@ public class ChemicalService implements IChemicalService {
if (result.size() == 0) {
return null;
} else {
-// return chemicalViewFactory.create(result.get(0), searchCriteria.getModel(), searchCriteria.getColorSet());
+ // return chemicalViewFactory.create(result.get(0),
+ // searchCriteria.getModel(), searchCriteria.getColorSet());
return result.get(0);
}
@@ -256,8 +261,7 @@ public class ChemicalService implements IChemicalService {
logger.error("Problem with accessing chemical database", e);
}
-
- Collections.sort(chemicalList, new ChemicalView.NameComparator());
+ Collections.sort(chemicalList, new Chemical.NameComparator());
return chemicalList;
}
@@ -300,13 +304,19 @@ 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) {
- chemicalViewFactory.create(chemical);
+ annotations.addAll(getAllMiriamDataForChemical(chemical));
}
- } catch (ChemicalSearchException e) {
+ for (MiriamData miriamData : annotations) {
+ if (miriamData.getDataType().equals(MiriamType.PUBMED)) {
+ pubmedParser.getPubmedArticleById(Integer.valueOf(miriamData.getResource()));
+ }
+ }
+ } catch (ChemicalSearchException | NumberFormatException | PubmedSearchException e) {
logger.error("Problem with accessing info about chemical for target: " + md, e);
}
counter += 1;
@@ -318,4 +328,16 @@ public class ChemicalService implements IChemicalService {
}
}
+ private Set<MiriamData> getAllMiriamDataForChemical(Chemical chemical) {
+ Set<MiriamData> result = new HashSet<>();
+ result.add(chemical.getCasID());
+ result.add(chemical.getChemicalId());
+ for (Target target : chemical.getInferenceNetwork()) {
+ result.addAll(target.getGenes());
+ result.addAll(target.getReferences());
+
+ }
+ return result;
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalView.java b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalView.java
deleted file mode 100644
index 305af1f420..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalView.java
+++ /dev/null
@@ -1,319 +0,0 @@
-package lcsb.mapviewer.services.search.db.chemical;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.services.search.ISearchResultView;
-import lcsb.mapviewer.services.search.db.TargetView;
-import lcsb.mapviewer.services.view.AbstractView;
-import lcsb.mapviewer.services.view.AnnotationView;
-
-/**
- * Data of the chemical from external database to be visualized in the client
- * side.
- *
- * @author Ayan Rota
- *
- */
-public class ChemicalView extends AbstractView<Chemical> implements ISearchResultView, Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 91486136745430139L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ChemicalView.class);
-
- /**
- * Is the chemical selected by the client or not.
- */
- private boolean selected = false;
-
- /**
- * Name of the chemical.
- */
- private String name;
-
- /**
- * Detailed description of the MeSH object.
- */
- private String description;
-
- /**
- * List of synonyms.
- */
- private List<String> synonyms = new ArrayList<>();
-
- /**
- * Link for cas id.
- */
- private AnnotationView casLink;
-
- /**
- * The direct Evedince if any.
- */
- private String directEvidence;
-
- /**
- * List of links to extenral databases.
- */
- private List<Article> directEvidencePubs = new ArrayList<>();
-
- /**
- * Link for source.
- */
- private AnnotationView sourceLink;
-
- /**
- * List of targets for the chemical.
- */
- private List<TargetView> targetRows = new ArrayList<>();
-
- /***
- * Constructor that initialize the data with information from the
- * parameter*object.
- **
- * @param chemical
- * original Chemical from which the data will be initialized
- */
-
- protected ChemicalView(Chemical chemical) {
- // chemical is not db entity so don't pass it to super constructor
- super(null);
- }
-
- /**
- * Default constructor. Should be used only for deserialization.
- */
- protected ChemicalView() {
- }
-
- /**
- * Default constructor that creates a copy.
- *
- * @param original
- * origianl object that should be copied
- */
- public ChemicalView(ChemicalView original) {
- super(null);
- selected = original.isSelected();
- name = original.getName();
- targetRows.addAll(original.getTargetRows());
- }
-
- /**
- * Comparator of the objects by their name.
- *
- * @author Piotr Gawron
- *
- */
- public static class NameComparator implements Comparator<Chemical> {
- /**
- * Default string comparator.
- */
- private StringComparator stringComparator = new StringComparator();
-
- @Override
- public int compare(Chemical arg0, Chemical arg1) {
- return stringComparator.compare(arg0.getChemicalName(), arg1.getChemicalName());
- }
-
- }
-
- /**
- * @return the selected
- */
- public boolean isSelected() {
- return selected;
- }
-
- /**
- * @param selected
- * the selected to set
- */
- public void setSelected(boolean selected) {
- this.selected = selected;
- }
-
- /**
- * @return the name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the directEvedince
- */
- public String getDirectEvedince() {
- return directEvidence;
- }
-
- /**
- * @param directEvedince
- * the directEvedince to set
- */
- public void setDirectEvedince(String directEvedince) {
- this.directEvidence = directEvedince;
- }
-
- /**
- * @return the targetRows
- */
- public List<TargetView> getTargetRows() {
- return targetRows;
- }
-
- /**
- * @param targetRows
- * the targetRows to set
- */
- public void setTargetRows(List<TargetView> targetRows) {
- this.targetRows = targetRows;
- }
-
- /**
- * Adds object to {@link #directEvidencePubs}.
- *
- * @param article
- * object to add
- */
- public void addDirectEvidence(Article article) {
- directEvidencePubs.add(article);
- }
-
- /**
- * @return casLink
- */
- public AnnotationView getCasLink() {
- return casLink;
- }
-
- /**
- * @param casLink
- * a link to Cas
- */
- public void setCasLink(AnnotationView casLink) {
- this.casLink = casLink;
- }
-
- /**
- * @return direct evidence.
- */
- public String getDirectEvidence() {
- return directEvidence;
- }
-
- /**
- * @param directEvidence
- * a text to indicate if there is direct evidence found.
- */
- public void setDirectEvidence(String directEvidence) {
- this.directEvidence = directEvidence;
- }
-
- /**
- * @return the link to the source database of chemicals.
- */
- public AnnotationView getSourceLink() {
- return sourceLink;
- }
-
- /**
- * @param sourceLink
- * the link to database of chemicals.
- */
- public void setSourceLink(AnnotationView sourceLink) {
- this.sourceLink = sourceLink;
- }
-
- /**
- * Returns link to pubmed that enlist all references.
- *
- * @return link to pubmed that enlist all references
- */
- public String getAllDirectEvidenceLinks() {
- String result = "http://www.ncbi.nlm.nih.gov/pubmed/?term=";
- for (Article publication : directEvidencePubs) {
- result += publication.getId() + " ";
- }
- return result;
- }
-
- /**
- * @return all articles/publications associated with the chemical direct
- * evidence.
- */
- public List<Article> getDirectEvidencePubs() {
- return directEvidencePubs;
- }
-
- /**
- * @param directEvidencePubs
- * all articles/publications associated with the chemical direct
- * evidence.
- */
- public void setDirectEvidencePubs(List<Article> directEvidencePubs) {
- this.directEvidencePubs = directEvidencePubs;
- }
-
- /**
- * @param description
- * description of the Chemicals.
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @return description of Chemical.
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @return list of Synonyms.
- */
- public List<String> getSynonyms() {
- return synonyms;
- }
-
- /**
- * @param synonyms
- * list of Synonyms.
- */
- public void setSynonyms(List<String> synonyms) {
- this.synonyms = synonyms;
- }
-
- @Override
- public String getUniqueId() {
- return name;
- }
-
- @Override
- public void setUniqueId(String uniqueId) {
- this.name = uniqueId;
- }
-
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java
deleted file mode 100644
index dee6222cc6..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java
+++ /dev/null
@@ -1,188 +0,0 @@
-package lcsb.mapviewer.services.search.db.chemical;
-
-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.Article;
-import lcsb.mapviewer.annotation.data.ArticleCitationComparator;
-import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.data.MeSH;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.services.MeSHParser;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-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;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
-
-/**
- * Factory class for {@link ChemicalView} class.
- *
- * @author Ayan Rota
- *
- */
-public class ChemicalViewFactory extends SearchResultFactory<Chemical, ChemicalView> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ChemicalViewFactory.class);
-
- /**
- * Factory object used for creation of
- * {@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;
-
- /**
- * Factory object used for creation of {@link TargetView} elements.
- */
- @Autowired
- private TargetViewFactory drugTargetViewFactory;
-
- /**
- * Service accessing <a href="http://europepmc.org/RestfulWebService">mesh</a>
- * .
- */
- @Autowired
- private MeSHParser meSHParser;
-
- @Override
- public ChemicalView create(Chemical chemical) {
- return create(chemical, null, 0);
- }
-
- /**
- * Creates {@link ChemicalView}.
- *
- * @param chemical
- * original Chemical 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 ChemicalView} object for given chemical. links are placed
- * according to model given in the parameter.
- */
- public ChemicalView create(Chemical chemical, Model model, int set) {
- ChemicalView chemicalView = new ChemicalView(chemical);
- if (chemical == null) {
- return chemicalView;
- }
-
- chemicalView.setName(chemical.getChemicalName());
- if (chemical.getDirectEvidence() != null) {
- chemicalView.setDirectEvedince(chemical.getDirectEvidence().getValue());
- }
-
- if (chemical.getChemicalId() != null) {
- chemicalView.setSourceLink(annotationViewFactory.create(chemical.getChemicalId()));
- try {
- MeSH mesh = meSHParser.getMeSH(chemical.getChemicalId());
- if (mesh != null) {
- chemicalView.setDescription(mesh.getDescription());
- chemicalView.setSynonyms(mesh.getSynonyms());
- } else {
- chemicalView.setDescription("Mesh term not available");
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with accessing mesh database", e);
- chemicalView.setDescription("Mesh term not available");
- }
- }
-
- if (chemical.getCasID() != null) {
- chemicalView.setCasLink(annotationViewFactory.create(chemical.getCasID()));
- }
-
- List<Article> articles = new ArrayList<Article>();
- for (MiriamData publication : chemical.getDirectEvidencePublication()) {
- if (publication.getDataType().equals(MiriamType.PUBMED)) {
- Integer id = Integer.parseInt(publication.getResource());
- try {
- Article article = pubmedParser.getPubmedArticleById(id);
- if (article != null) {
- articles.add(article);
- }
- } catch (PubmedSearchException e) {
- logger.error("Problem with accessing info about pubmed", e);
- }
- } else {
- logger.warn("Unknown publication type: " + publication);
- }
- }
- Collections.sort(articles, new ArticleCitationComparator());
- chemicalView.setDirectEvidencePubs(articles);
-
- List<TargetView> targetsRows = new ArrayList<>();
-
- int differentNames = 0;
- for (Target geneEntry : chemical.getInferenceNetwork()) {
- 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.CHEMICAL, set);
- geneTargetView.setIcon(icon);
- geneTargetView.setSelected(true);
- }
- }
- chemicalView.setTargetRows(targetsRows);
- return chemicalView;
-
- }
-
- @Override
- public String createGson(ChemicalView object) {
- return new Gson().toJson(object);
- }
-
- @Override
- public List<ElementIdentifier> searchResultToElementIdentifier(ChemicalView chemical, 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 : chemical.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/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
index 423e18eaad..7a310be346 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
@@ -15,10 +15,8 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.search.comment.FullCommentViewFactory;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
-import lcsb.mapviewer.services.search.db.GeneRow;
-import lcsb.mapviewer.services.search.db.TargetView;
-import lcsb.mapviewer.services.search.db.chemical.ChemicalViewFactory;
import lcsb.mapviewer.services.search.db.chemical.IChemicalService;
public class SearchResultFactoryTest extends ServiceTestFunctions {
@@ -26,7 +24,7 @@ public class SearchResultFactoryTest extends ServiceTestFunctions {
Logger logger = Logger.getLogger(SearchResultFactoryTest.class);
@Autowired
- ChemicalViewFactory factory;
+ FullCommentViewFactory factory;
@Autowired
IChemicalService chemicalService;
diff --git a/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java b/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
index 4e4f8ba30d..1f91278fa0 100644
--- a/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
+++ b/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
@@ -79,7 +79,6 @@ import lcsb.mapviewer.services.interfaces.IProjectService;
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.ChemicalViewFactory;
import lcsb.mapviewer.services.search.db.chemical.IChemicalService;
import lcsb.mapviewer.services.search.db.drug.DrugViewFactory;
import lcsb.mapviewer.services.search.db.drug.IDrugService;
@@ -194,9 +193,6 @@ public abstract class WebTestFunctions {
@Autowired
protected DrugViewFactory drugViewFactory;
- @Autowired
- protected ChemicalViewFactory chemicalViewFactory;
-
@Autowired
protected IReferenceGenomeService referenceGenomeService;
--
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