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Commit fed1a7c7 authored by Piotr Gawron's avatar Piotr Gawron
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ChemicalView and ChemicalViewFactory removed

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1 merge request!75Resolve "MiRNA - Show all - duplicated entries"
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annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
+ 21
− 0
View file @ fed1a7c7
......@@ -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());
}
}
}
service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
+ 31
− 9
View file @ fed1a7c7
......@@ -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;
}
}
service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalView.java deleted 100644 → 0
+ 0
− 319
View file @ 5b7ffad1
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;
}
}
service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java deleted 100644 → 0
+ 0
− 188
View file @ 5b7ffad1
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;
}
}
service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
+ 2
− 4
View file @ fed1a7c7
......@@ -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;
......
web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
+ 0
− 4
View file @ fed1a7c7
......@@ -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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