From 9c72feed5c2adc657626c585153160433a193f4d Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 20 Feb 2018 17:13:01 +0100
Subject: [PATCH] unused PubmedAnnotatedElementsViewFactory removed
---
.../view/PubmedAnnotatedElementsView.java | 108 ------------------
.../PubmedAnnotatedElementsViewFactory.java | 88 --------------
.../resources/applicationContext-service.xml | 1 -
3 files changed, 197 deletions(-)
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java b/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java
deleted file mode 100644
index fa8eb02646..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java
+++ /dev/null
@@ -1,108 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.services.impl.SearchService;
-
-/**
- * View object for pubmed article for a given model. It contains information
- * about article and list of elements annotated by this
- * {@link lcsb.mapviewer.model.map.MiriamType#PUBMED article}.
- *
- * @author Piotr Gawron
- *
- */
-public class PubmedAnnotatedElementsView extends AbstractView<MiriamData> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Article for which this pubmed summary is created.
- */
- private Article article;
-
- /**
- * List of elements that are annotated the publication. {@link Pair#left}
- * refers to human readable name and {@link Pair#right} is search string that
- * can be used to access element on the model.
- */
- private List<Pair<String, String>> elements = new ArrayList<>();
-
- /**
- * Default constructor.
- *
- * @param element
- * {@link MiriamData} that represents publication for this object.
- *
- * @see #article
- */
- public PubmedAnnotatedElementsView(MiriamData element) {
- super(element);
- }
-
- /**
- * @return the article
- * @see #article
- */
- public Article getArticle() {
- return article;
- }
-
- /**
- * @param article
- * the article to set
- * @see #article
- */
- public void setArticle(Article article) {
- this.article = article;
- }
-
- /**
- * @return the elements
- * @see #elements
- */
- public List<Pair<String, String>> getElements() {
- return elements;
- }
-
- /**
- * @param elements
- * the elements to set
- * @see #elements
- */
- public void setElements(List<Pair<String, String>> elements) {
- this.elements = elements;
- }
-
- /**
- * Adds element annotratd by {@link #article}.
- *
- * @param annotatedObject
- * object to add
- */
- public void addElement(BioEntity annotatedObject) {
- if (annotatedObject instanceof Element) {
- Element alias = (Element) annotatedObject;
- elements.add(new Pair<String, String>(alias.getName(), SearchService.SPECIES_SEARCH_PREFIX + ":" + alias.getElementId()));
- } else if (annotatedObject instanceof Reaction) {
- Reaction reaction = (Reaction) annotatedObject;
- elements.add(
- new Pair<>(
- SearchService.REACTION_SEARCH_PREFIX + ":" + reaction.getIdReaction(), SearchService.REACTION_SEARCH_PREFIX + ":" + reaction.getIdReaction()));
- } else {
- throw new InvalidStateException("Unknown subtype of " + BioEntity.class.getName() + ": " + annotatedObject.getClass().getName());
- }
-
- }
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java
deleted file mode 100644
index f743b95b3a..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java
+++ /dev/null
@@ -1,88 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-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.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-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;
-
-/**
- * Factory class for {@link LayoutView} class.
- *
- * @author Piotr Gawron
- *
- */
-public class PubmedAnnotatedElementsViewFactory extends AbstractViewFactory<MiriamData, PubmedAnnotatedElementsView> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(PubmedAnnotatedElementsViewFactory.class);
-
- /**
- * Local backend to the pubmed data.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
- @Override
- public PubmedAnnotatedElementsView create(MiriamData element) {
- PubmedAnnotatedElementsView result = new PubmedAnnotatedElementsView(element);
- if (element == null) {
- return result;
- } else if (!MiriamType.PUBMED.equals(element.getDataType())) {
- throw new InvalidArgumentException("Only " + MiriamType.PUBMED + " types are valid");
- }
- try {
- result.setArticle(pubmedParser.getPubmedArticleById(Integer.valueOf(element.getResource())));
- } catch (PubmedSearchException e) {
- Article article = new Article();
- article.setTitle("N/A");
- result.setArticle(article);
- logger.error(e, e);
- }
- return result;
- }
-
- /**
- * Creates publication summary for a given model.
- *
- * @param miriamData
- * {@link MiriamData} representing article
- * @param model
- * model for which summary will be prepared
- * @return publication summary for a given model and publication
- */
- public PubmedAnnotatedElementsView create(MiriamData miriamData, Model model) {
- PubmedAnnotatedElementsView result = create(miriamData);
- Set<BioEntity> elements = model.getElementsByAnnotation(miriamData);
- for (Model submodel : model.getSubmodels()) {
- elements.addAll(submodel.getElementsByAnnotation(miriamData));
- }
- for (BioEntity annotatedObject : elements) {
- result.addElement(annotatedObject);
- }
- return result;
- }
-
- @Override
- public String createGson(PubmedAnnotatedElementsView object) {
- return new Gson().toJson(object);
- }
-
- @Override
- public MiriamData viewToObject(PubmedAnnotatedElementsView view) {
- throw new NotImplementedException();
- }
-}
diff --git a/service/src/main/resources/applicationContext-service.xml b/service/src/main/resources/applicationContext-service.xml
index 45127552d3..60ec25e594 100644
--- a/service/src/main/resources/applicationContext-service.xml
+++ b/service/src/main/resources/applicationContext-service.xml
@@ -57,7 +57,6 @@
<bean id="OverviewLinkViewFactory" class="lcsb.mapviewer.services.view.OverviewLinkViewFactory"/>
<bean id="PrivilegeViewFactory" class="lcsb.mapviewer.services.view.PrivilegeViewFactory"/>
<bean id="ProjectViewFactory" class="lcsb.mapviewer.services.view.ProjectViewFactory"/>
- <bean id="PubmedAnnotatedElementsViewFactory" class="lcsb.mapviewer.services.view.PubmedAnnotatedElementsViewFactory"/>
<bean id="ReferenceGenomeViewFactory" class="lcsb.mapviewer.services.view.ReferenceGenomeViewFactory"/>
<bean id="ReferenceGenomeGeneMappingViewFactory" class="lcsb.mapviewer.services.view.ReferenceGenomeGeneMappingViewFactory"/>
--
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