diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
index d41fe7960806ce241dbc6fc0bc2ccca5d7b973f7..1fb4da6e601ab07a3c7ac41eb132c059cddaf4ff 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
@@ -1,317 +1,333 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.InputStream;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.xpath.XPath;
-import javax.xml.xpath.XPathConstants;
-import javax.xml.xpath.XPathFactory;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.w3c.dom.Document;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.annotation.cache.CachableInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.XmlSerializer;
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * This class is a backend to publically available pubmed API in
- * <a href="http://europepmc.org/RestfulWebService">Europe PubMed Central </a>.
- *
- * @author Piotr Gawron
- *
- */
-public class PubmedParser extends CachableInterface implements IExternalService {
-
- /**
- * Pubmed identifier used to check the status of service (functionality from
- * {@link IExternalService}).
- */
- private static final int SERVICE_STATUS_PUBMED_ID = 12345;
-
- /**
- * Prefix used for caching elements with pubmed identifier as a key.
- */
- private static final String PUBMED_PREFIX = "pubmed: ";
-
- /**
- * Length of {@link #PUBMED_PREFIX} string.
- */
- private static final int PUBMED_PREFIX_LENGTH = PUBMED_PREFIX.length();
-
- /**
- * Connector used for accessing data from miriam registry.
- */
- @Autowired
- private MiriamConnector miriamConnector;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PubmedParser.class);
-
- /**
- * Object that allows to serialize {@link Article} elements into xml string
- * and deserialize xml into {@link Article} objects.
- */
- private XmlSerializer<Article> articleSerializer;
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String name;
- String result = null;
- if (query instanceof String) {
- name = (String) query;
- if (name.startsWith(PUBMED_PREFIX)) {
- Integer id = Integer.valueOf(name.substring(PUBMED_PREFIX_LENGTH));
- result = articleSerializer.objectToString(getPubmedArticleById(id));
- } else {
- throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
-
- return result;
- }
-
- /**
- * Default constructor. Initializes structures used for transforming
- * {@link Article} from/to xml.
- */
- public PubmedParser() {
- super(PubmedParser.class);
- articleSerializer = new XmlSerializer<>(Article.class);
- }
-
- /**
- * Returns article data for given pubmed identifier.
- *
- * @param id
- * pubmed identifier
- * @return article data
- */
- public Article getPubmedArticleById(Integer id) {
- String queryString = "pubmed: " + id;
- Article result = articleSerializer.xmlToObject(getCacheNode(queryString));
- if (result != null && result.getTitle() != null) {
- return result;
- } else {
- logger.debug("Pubmed article (id=" + id + ") not found in cache. Accessing WebService...");
- }
-
- result = new Article();
- InputStream mainStream = null;
- // InputStream citationStream = null;
- try {
- String url = "http://www.ebi.ac.uk/europepmc/webservices/rest/search/resulttype=core&query="
- + java.net.URLEncoder.encode("src:med ext_id:" + id, "UTF-8");
-
- mainStream = new URL(url).openStream();
- // citationStream = new
- // URL("http://www.ebi.ac.uk/europepmc/webservices/rest/MED/" + id +
- // "/citations/1/xml")
- // .openStream();
- DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
- DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
- Document mainDoc = dBuilder.parse(mainStream);
- // Document citationDoc = dBuilder.parse(citationStream);
- mainDoc.getDocumentElement().normalize();
- // citationDoc.getDocumentElement().normalize();
- XPathFactory xPathFactory = XPathFactory.newInstance();
- XPath xpath = xPathFactory.newXPath();
- NodeList nodeList = null;
- // Hit Count
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/citedByCount").evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- try {
- result.setCitationCount(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
- } catch (Exception e) {
- }
- }
- // Title
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/title").evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- result.setTitle(nodeList.item(0).getFirstChild().getNodeValue());
- }
- // Year
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/yearOfPublication").evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- try {
- result.setYear(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
- } catch (Exception e) {
- }
- }
- // Journal
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/journal/title").evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- result.setJournal(nodeList.item(0).getFirstChild().getNodeValue());
- }
- // Authors
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/authorString").evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- List<String> authors = new ArrayList<String>();
- String value = nodeList.item(0).getFirstChild().getNodeValue();
- if (value != null && !value.isEmpty()) {
- authors = Arrays.asList(value.split(","));
- }
- result.setAuthors(authors);
- }
- result.setLink(miriamConnector.getUrlString(new MiriamData(MiriamType.PUBMED, id + "")));
- result.setId(id + "");
-
- if (result.getTitle() != null && !result.getTitle().trim().isEmpty()) {
- setCacheValue(queryString, articleSerializer.objectToString(result));
- } else {
- result = null;
- }
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- } finally {
- try {
- if (mainStream != null) {
- mainStream.close();
- }
- /*
- * if (citationStream != null) { citationStream.close(); }
- */
- } catch (Exception ex) {
- }
- }
- return result;
- }
-
- /**
- * This method return html \< a\ > tag with link for pubmed id (with some
- * additional information).
- *
- * @param id
- * pubmed identifier
- * @param withTextPrefix
- * should prefix be added to the tag
- * @return link to webpage with pubmed article
- */
- public String getHtmlFullLinkForId(Integer id, boolean withTextPrefix) {
- String result = "";
- Article article = getPubmedArticleById(id);
- result += "<div style=\"float:left;\" title=\"" + article.getTitle() + ", ";
- result += article.getStringAuthors() + ", ";
- result += article.getYear() + ", ";
- result += article.getJournal() + "\">";
- if (withTextPrefix) {
- result += "pubmed: ";
- }
- result += "<a target=\"_blank\" href = \"" + article.getLink() + "\">" + id + "</a> </div>";
- return result;
- }
-
- /**
- * This method return html \< a\ > tag with link for pubmed id (with some
- * additional information).
- *
- * @param id
- * pubmed identifier
- * @return link to webpage with pubmed article
- */
- public String getHtmlFullLinkForId(Integer id) {
- return getHtmlFullLinkForId(id, true);
- }
-
- /**
- * Get the summary of the article.
- *
- * @param id
- * pubmed identifier
- * @return summary of the article.
- */
- public String getSummary(Integer id) {
- Article article = getPubmedArticleById(id);
- if (article == null) {
- return null;
- }
- String result = article.getTitle() + ", " + article.getStringAuthors() + ", " + article.getYear() + ", " + article.getJournal();
- return result;
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("Europe PubMed Central", "http://europepmc.org/RestfulWebService");
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- Article art = getPubmedArticleById(SERVICE_STATUS_PUBMED_ID);
- status.setStatus(ExternalServiceStatusType.OK);
- if (art == null) {
- status.setStatus(ExternalServiceStatusType.DOWN);
- } else if (art.getTitle() == null) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else if (art.getTitle().equals("")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- /**
- * Get the summary of the article.
- *
- * @param id
- * pubmed identifier
- * @return summary of the article.
- */
- public String getSummary(String id) {
- return getSummary(Integer.valueOf(id));
- }
-
- /**
- * @return the miriamConnector
- * @see #miriamConnector
- */
- public MiriamConnector getMiriamConnector() {
- return miriamConnector;
- }
-
- /**
- * @param miriamConnector
- * the miriamConnector to set
- * @see #miriamConnector
- */
- public void setMiriamConnector(MiriamConnector miriamConnector) {
- this.miriamConnector = miriamConnector;
- }
-
- /**
- * @return the articleSerializer
- * @see #articleSerializer
- */
- protected XmlSerializer<Article> getArticleSerializer() {
- return articleSerializer;
- }
-
- /**
- * @param articleSerializer
- * the articleSerializer to set
- * @see #articleSerializer
- */
- protected void setArticleSerializer(XmlSerializer<Article> articleSerializer) {
- this.articleSerializer = articleSerializer;
- }
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.io.InputStream;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathFactory;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.data.Article;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * This class is a backend to publically available pubmed API in
+ * <a href="http://europepmc.org/RestfulWebService">Europe PubMed Central </a>.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PubmedParser extends CachableInterface implements IExternalService {
+
+ /**
+ * Pubmed identifier used to check the status of service (functionality from
+ * {@link IExternalService}).
+ */
+ private static final int SERVICE_STATUS_PUBMED_ID = 12345;
+
+ /**
+ * Prefix used for caching elements with pubmed identifier as a key.
+ */
+ private static final String PUBMED_PREFIX = "pubmed: ";
+
+ /**
+ * Length of {@link #PUBMED_PREFIX} string.
+ */
+ private static final int PUBMED_PREFIX_LENGTH = PUBMED_PREFIX.length();
+
+ /**
+ * Connector used for accessing data from miriam registry.
+ */
+ @Autowired
+ private MiriamConnector miriamConnector;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PubmedParser.class);
+
+ /**
+ * Object that allows to serialize {@link Article} elements into xml string
+ * and deserialize xml into {@link Article} objects.
+ */
+ private XmlSerializer<Article> articleSerializer;
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(PUBMED_PREFIX)) {
+ Integer id = Integer.valueOf(name.substring(PUBMED_PREFIX_LENGTH));
+ result = articleSerializer.objectToString(getPubmedArticleById(id));
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (PubmedSearchException e) {
+ throw new SourceNotAvailable(e);
+ }
+
+ return result;
+ }
+
+ /**
+ * Default constructor. Initializes structures used for transforming
+ * {@link Article} from/to xml.
+ */
+ public PubmedParser() {
+ super(PubmedParser.class);
+ articleSerializer = new XmlSerializer<>(Article.class);
+ }
+
+ /**
+ * Returns article data for given pubmed identifier.
+ *
+ * @param id
+ * pubmed identifier
+ * @return article data
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public Article getPubmedArticleById(Integer id) throws PubmedSearchException {
+ String queryString = "pubmed: " + id;
+ Article result = articleSerializer.xmlToObject(getCacheNode(queryString));
+ if (result != null && result.getTitle() != null) {
+ return result;
+ } else {
+ logger.debug("Pubmed article (id=" + id + ") not found in cache. Accessing WebService...");
+ }
+
+ result = new Article();
+ InputStream mainStream = null;
+ // InputStream citationStream = null;
+ try {
+ String url = "http://www.ebi.ac.uk/europepmc/webservices/rest/search/resulttype=core&query="
+ + java.net.URLEncoder.encode("src:med ext_id:" + id, "UTF-8");
+
+ mainStream = new URL(url).openStream();
+ // citationStream = new
+ // URL("http://www.ebi.ac.uk/europepmc/webservices/rest/MED/" + id +
+ // "/citations/1/xml")
+ // .openStream();
+ DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
+ Document mainDoc = dBuilder.parse(mainStream);
+ // Document citationDoc = dBuilder.parse(citationStream);
+ mainDoc.getDocumentElement().normalize();
+ // citationDoc.getDocumentElement().normalize();
+ XPathFactory xPathFactory = XPathFactory.newInstance();
+ XPath xpath = xPathFactory.newXPath();
+ NodeList nodeList = null;
+ // Hit Count
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/citedByCount").evaluate(mainDoc, XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ try {
+ result.setCitationCount(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
+ } catch (Exception e) {
+ }
+ }
+ // Title
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/title").evaluate(mainDoc, XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ result.setTitle(nodeList.item(0).getFirstChild().getNodeValue());
+ }
+ // Year
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/yearOfPublication").evaluate(mainDoc, XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ try {
+ result.setYear(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
+ } catch (Exception e) {
+ }
+ }
+ // Journal
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/journal/title").evaluate(mainDoc, XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ result.setJournal(nodeList.item(0).getFirstChild().getNodeValue());
+ }
+ // Authors
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/authorString").evaluate(mainDoc, XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ List<String> authors = new ArrayList<String>();
+ String value = nodeList.item(0).getFirstChild().getNodeValue();
+ if (value != null && !value.isEmpty()) {
+ authors = Arrays.asList(value.split(","));
+ }
+ result.setAuthors(authors);
+ }
+ result.setLink(miriamConnector.getUrlString(new MiriamData(MiriamType.PUBMED, id + "")));
+ result.setId(id + "");
+
+ if (result.getTitle() != null && !result.getTitle().trim().isEmpty()) {
+ setCacheValue(queryString, articleSerializer.objectToString(result));
+ } else {
+ result = null;
+ }
+
+ } catch (Exception e) {
+ throw new PubmedSearchException(e);
+ } finally {
+ try {
+ if (mainStream != null) {
+ mainStream.close();
+ }
+ } catch (Exception ex) {
+ logger.error("Problem with closing stream", ex);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * This method return html \< a\ > tag with link for pubmed id (with some
+ * additional information).
+ *
+ * @param id
+ * pubmed identifier
+ * @param withTextPrefix
+ * should prefix be added to the tag
+ * @return link to webpage with pubmed article
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getHtmlFullLinkForId(Integer id, boolean withTextPrefix) throws PubmedSearchException {
+ String result = "";
+ Article article = getPubmedArticleById(id);
+ result += "<div style=\"float:left;\" title=\"" + article.getTitle() + ", ";
+ result += article.getStringAuthors() + ", ";
+ result += article.getYear() + ", ";
+ result += article.getJournal() + "\">";
+ if (withTextPrefix) {
+ result += "pubmed: ";
+ }
+ result += "<a target=\"_blank\" href = \"" + article.getLink() + "\">" + id + "</a> </div>";
+ return result;
+ }
+
+ /**
+ * This method return html \< a\ > tag with link for pubmed id (with some
+ * additional information).
+ *
+ * @param id
+ * pubmed identifier
+ * @return link to webpage with pubmed article
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getHtmlFullLinkForId(Integer id) throws PubmedSearchException {
+ return getHtmlFullLinkForId(id, true);
+ }
+
+ /**
+ * Get the summary of the article.
+ *
+ * @param id
+ * pubmed identifier
+ * @return summary of the article.
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getSummary(Integer id) throws PubmedSearchException {
+ Article article = getPubmedArticleById(id);
+ if (article == null) {
+ return null;
+ }
+ String result = article.getTitle() + ", " + article.getStringAuthors() + ", " + article.getYear() + ", " + article.getJournal();
+ return result;
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus("Europe PubMed Central", "http://europepmc.org/RestfulWebService");
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ Article art = getPubmedArticleById(SERVICE_STATUS_PUBMED_ID);
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (art == null) {
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ } else if (art.getTitle() == null) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else if (art.getTitle().equals("")) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ /**
+ * Get the summary of the article.
+ *
+ * @param id
+ * pubmed identifier
+ * @return summary of the article.
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getSummary(String id) throws PubmedSearchException {
+ return getSummary(Integer.valueOf(id));
+ }
+
+ /**
+ * @return the miriamConnector
+ * @see #miriamConnector
+ */
+ public MiriamConnector getMiriamConnector() {
+ return miriamConnector;
+ }
+
+ /**
+ * @param miriamConnector
+ * the miriamConnector to set
+ * @see #miriamConnector
+ */
+ public void setMiriamConnector(MiriamConnector miriamConnector) {
+ this.miriamConnector = miriamConnector;
+ }
+
+ /**
+ * @return the articleSerializer
+ * @see #articleSerializer
+ */
+ protected XmlSerializer<Article> getArticleSerializer() {
+ return articleSerializer;
+ }
+
+ /**
+ * @param articleSerializer
+ * the articleSerializer to set
+ * @see #articleSerializer
+ */
+ protected void setArticleSerializer(XmlSerializer<Article> articleSerializer) {
+ this.articleSerializer = articleSerializer;
+ }
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedSearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedSearchException.java
new file mode 100644
index 0000000000000000000000000000000000000000..65e29dd0c3b9cbac236ba51805a84434111cfb00
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedSearchException.java
@@ -0,0 +1,48 @@
+package lcsb.mapviewer.annotation.services;
+
+/**
+ * Exception thrown when there was a problem when searching for a pubmed data.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PubmedSearchException extends Exception {
+
+ /**
+ * Default constructor.
+ *
+ * @param string
+ * exception message
+ */
+ public PubmedSearchException(String string) {
+ super(string);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception
+ */
+ public PubmedSearchException(Exception e) {
+ super(e);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * source exception
+ */
+ public PubmedSearchException(String message, Exception e) {
+ super(message, e);
+ }
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
index 31204c76a806ba03e549dcae47c7bd1d4f766167..1dd83f20b8c485ca10c8d6dc347190ef97ac328d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
@@ -1,236 +1,236 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-public class PubmedParserTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(PubmedParserTest.class);
- private boolean status;
- private boolean status2;
- @Autowired
- PubmedParser pubmedParser;
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- status = Configuration.isDbCacheOn();
- status2 = Configuration.isApplicationCacheOn();
- }
-
- @After
- public void tearDown() throws Exception {
- Configuration.setDbCacheOn(status);
- Configuration.setApplicationCacheOn(status2);
- }
-
- @Test
- public void test() {
- try {
- Configuration.setDbCacheOn(false);
- Configuration.setApplicationCacheOn(false);
- Article art = pubmedParser.getPubmedArticleById(9481670);
- assertNotNull(art);
- assertEquals(
- "Adjacent asparagines in the NR2-subunit of the NMDA receptor channel control the voltage-dependent block by extracellular Mg2+.", art.getTitle());
- assertEquals((Integer) 1998, art.getYear());
- assertEquals("The Journal of physiology", art.getJournal());
- assertTrue(art.getStringAuthors().contains("Wollmuth"));
- assertTrue(art.getStringAuthors().contains("Kuner"));
- assertTrue(art.getStringAuthors().contains("Sakmann"));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testCache() {
- try {
- Configuration.setDbCacheOn(true);
- Configuration.setApplicationCacheOn(true);
-
- Article art = pubmedParser.getPubmedArticleById(9481671);
- assertNotNull(art);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testSerialization() {
- try {
-
- Article art = new Article();
- List<String> list = new ArrayList<String>();
- list.add("aaa");
- list.add("bbb");
- art.setTitle("ttt");
- art.setAuthors(list);
- art.setJournal("jjjj");
- art.setYear(123);
-
- String serialString = pubmedParser.getArticleSerializer().objectToString(art);
-
- assertTrue(serialString.contains("aaa"));
- assertTrue(serialString.contains("bbb"));
- assertTrue(serialString.contains("ttt"));
- assertTrue(serialString.contains("jjjj"));
- assertTrue(serialString.contains("123"));
-
- Article art2 = pubmedParser.getArticleSerializer().xmlToObject(getNodeFromXmlString(serialString));
-
- assertEquals(art.getStringAuthors(), art2.getStringAuthors());
- assertEquals(art.getTitle(), art2.getTitle());
- assertEquals(art.getJournal(), art2.getJournal());
- assertEquals(art.getYear(), art2.getYear());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occurred");
- }
- }
-
- /**
- * This case was problematic with old API used to retrieve data from pubmed
- */
- @Test
- public void testProblematicCase() {
- try {
-
- Article art = pubmedParser.getPubmedArticleById(22363258);
- assertNotNull(art);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testCitationCount() {
- try {
-
- Article art = pubmedParser.getPubmedArticleById(18400456);
- assertNotNull(art);
- assertTrue(art.getCitationCount() >= 53);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testGetSummary() {
- try {
-
- String summary = pubmedParser.getSummary(18400456);
- assertNotNull(summary);
- assertFalse(summary.isEmpty());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testGetSummary2() {
- try {
-
- String summary = pubmedParser.getSummary(23644949);
- assertNull(summary);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- // wait max 15 second
- public void testCachableInterface() throws Exception {
- String query = "pubmed: 2112";
- try {
- String newRes = "hello";
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, pubmedParser.getCacheType(), newRes);
- cache.invalidateByQuery(query, pubmedParser.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- String res = cache.getStringByQuery(query, pubmedParser.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- pubmedParser.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- pubmedParser.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetHtmlFullLinkForId() throws Exception {
- try {
- String htmlString = pubmedParser.getHtmlFullLinkForId(1234);
- assertTrue(htmlString.contains("Change in the kinetics of sulphacetamide tissue distribution"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.data.Article;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+public class PubmedParserTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(PubmedParserTest.class);
+ private boolean status;
+ private boolean status2;
+ @Autowired
+ PubmedParser pubmedParser;
+
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ @Before
+ public void setUp() throws Exception {
+ status = Configuration.isDbCacheOn();
+ status2 = Configuration.isApplicationCacheOn();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ Configuration.setDbCacheOn(status);
+ Configuration.setApplicationCacheOn(status2);
+ }
+
+ @Test
+ public void test() {
+ try {
+ Configuration.setDbCacheOn(false);
+ Configuration.setApplicationCacheOn(false);
+ Article art = pubmedParser.getPubmedArticleById(9481670);
+ assertNotNull(art);
+ assertEquals(
+ "Adjacent asparagines in the NR2-subunit of the NMDA receptor channel control the voltage-dependent block by extracellular Mg2+.", art.getTitle());
+ assertEquals((Integer) 1998, art.getYear());
+ assertEquals("The Journal of physiology", art.getJournal());
+ assertTrue(art.getStringAuthors().contains("Wollmuth"));
+ assertTrue(art.getStringAuthors().contains("Kuner"));
+ assertTrue(art.getStringAuthors().contains("Sakmann"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testCache() {
+ try {
+ Configuration.setDbCacheOn(true);
+ Configuration.setApplicationCacheOn(true);
+
+ Article art = pubmedParser.getPubmedArticleById(9481671);
+ assertNotNull(art);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+
+ Article art = new Article();
+ List<String> list = new ArrayList<String>();
+ list.add("aaa");
+ list.add("bbb");
+ art.setTitle("ttt");
+ art.setAuthors(list);
+ art.setJournal("jjjj");
+ art.setYear(123);
+
+ String serialString = pubmedParser.getArticleSerializer().objectToString(art);
+
+ assertTrue(serialString.contains("aaa"));
+ assertTrue(serialString.contains("bbb"));
+ assertTrue(serialString.contains("ttt"));
+ assertTrue(serialString.contains("jjjj"));
+ assertTrue(serialString.contains("123"));
+
+ Article art2 = pubmedParser.getArticleSerializer().xmlToObject(getNodeFromXmlString(serialString));
+
+ assertEquals(art.getStringAuthors(), art2.getStringAuthors());
+ assertEquals(art.getTitle(), art2.getTitle());
+ assertEquals(art.getJournal(), art2.getJournal());
+ assertEquals(art.getYear(), art2.getYear());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occurred");
+ }
+ }
+
+ /**
+ * This case was problematic with old API used to retrieve data from pubmed
+ */
+ @Test
+ public void testProblematicCase() {
+ try {
+
+ Article art = pubmedParser.getPubmedArticleById(22363258);
+ assertNotNull(art);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testCitationCount() {
+ try {
+
+ Article art = pubmedParser.getPubmedArticleById(18400456);
+ assertNotNull(art);
+ assertTrue(art.getCitationCount() >= 53);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testGetSummary() {
+ try {
+
+ String summary = pubmedParser.getSummary(18400456);
+ assertNotNull(summary);
+ assertFalse(summary.isEmpty());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testGetSummary2() throws Exception {
+ try {
+
+ String summary = pubmedParser.getSummary(23644949);
+ assertNull(summary);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ // wait max 15 second
+ public void testCachableInterface() throws Exception {
+ String query = "pubmed: 2112";
+ try {
+ String newRes = "hello";
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, pubmedParser.getCacheType(), newRes);
+ cache.invalidateByQuery(query, pubmedParser.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ String res = cache.getStringByQuery(query, pubmedParser.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ pubmedParser.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ pubmedParser.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetHtmlFullLinkForId() throws Exception {
+ try {
+ String htmlString = pubmedParser.getHtmlFullLinkForId(1234);
+ assertTrue(htmlString.contains("Change in the kinetics of sulphacetamide tissue distribution"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomePrediction.java b/console/src/main/java/lcsb/mapviewer/run/ReactomePrediction.java
index a3134a302ebcaa1d79893e66d6fae71cc4b5dead..22b837ca221828732808816daf90d61818d49783 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomePrediction.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomePrediction.java
@@ -1,337 +1,339 @@
-package lcsb.mapviewer.run;
-
-import java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.UnsupportedEncodingException;
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
-import lcsb.mapviewer.reactome.model.ReactomeLiteratureReference;
-import lcsb.mapviewer.reactome.model.ReactomePublication;
-import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
-import lcsb.mapviewer.reactome.model.ReactomeURL;
-import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
-import lcsb.mapviewer.reactome.utils.PredictionResult;
-import lcsb.mapviewer.reactome.utils.PredictionResult.PredictionStatus;
-import lcsb.mapviewer.reactome.utils.ReactionComparator;
-import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.PropertyConfigurator;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * This class create a raport about data that might be added to PD-map based on
- * reactome data and some text mining information.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactomePrediction {
- /**
- * How many nodes in the reaction must match on both sides (reactome and ours)
- * to consider reaction similar.
- */
- private static final int PREDICTION_THRESHOLD = 3;
-
- /**
- * Number of nanoseconds in the second.
- */
- private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
-
- /**
- * Model used for generating raport.
- */
- private Model model;
-
- /**
- * Local backend to the pubmed data.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ReactomePrediction.class);
-
- /**
- * Comparator of reactions between our model and reactome.
- */
- @Autowired
- private ReactionComparator reactionComparator;
-
- /**
- * Class used for accessing reactome data.
- */
- @Autowired
- private DataSourceUpdater rc;
-
- /**
- * Util class used for manipulating information in reactome objects.
- */
- @Autowired
- private ReactomeQueryUtil rcu;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- long startTime = System.nanoTime();
- PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
- ReactomePrediction main = new ReactomePrediction();
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ApplicationContextLoader.injectDependencies(main);
- main.run();
- long endTime = System.nanoTime();
-
- long duration = endTime - startTime;
- double sec = duration / NANOSECONDS_IN_SECOND;
- System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
- }
-
- /**
- * Generates prediction report.
- */
- public void run() {
- try {
- model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
-
- Set<ReactomeReactionlikeEvent> reactions = new HashSet<ReactomeReactionlikeEvent>();
- // problematic reaction with complex of complex of molecule
- for (Reaction reaction : model.getReactions()) {
- for (String stableIdentifier : rcu.getReactomeIdentifiersForReaction(reaction)) {
- ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
- if (obj != null) {
- if (obj instanceof ReactomeReactionlikeEvent) {
- reactions.add((ReactomeReactionlikeEvent) obj);
- }
- }
- }
- }
- List<String> pubmedIds = loadPubmedIds("testFiles/data_mining/pd_pmids.txt");
- List<PredictionResult> newReaction = new ArrayList<PredictionResult>();
- logger.debug("Structure analysis");
- newReaction.addAll(rcu.getExtendedReactionsForKnownReactions(reactions, PREDICTION_THRESHOLD));
- logger.debug("Data mining analysis");
- newReaction.addAll(rcu.getExtendedReactionsForPubmedPublicationsWithTabuReaction(pubmedIds, reactions));
- Collections.sort(newReaction, PredictionResult.SCORE_COMPARATOR);
-
- printHeader();
- for (PredictionResult prediction : newReaction) {
- printResult(prediction);
- }
- printFooter(newReaction);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- }
-
- }
-
- /**
- * Load pubmed identifiers from a file.
- *
- * @param fileName
- * file with pubmed ids
- * @return list of pubmed ids
- * @throws IOException
- * thrown when there are problems with a file
- */
- private List<String> loadPubmedIds(String fileName) throws IOException {
- List<String> result = new ArrayList<String>();
- BufferedReader br = new BufferedReader(new FileReader(fileName));
- try {
- String line;
- while ((line = br.readLine()) != null) {
- result.add(line);
- }
- } finally {
- br.close();
- }
- return result;
- }
-
- /**
- * Prints report footer.
- *
- * @param results
- * results used for generating report
- */
- private void printFooter(Collection<PredictionResult> results) {
- writer.println("</table>");
-
- writer.println("Suggested reactions: " + results.size());
-
- writer.println("</body></html>");
- writer.close();
-
- }
-
- /**
- * Object used for writing the report.
- */
- private PrintWriter writer;
-
- /**
- * Creates stream for report output and prints report header.
- *
- * @throws FileNotFoundException
- * thrown when file with the report cannot be found
- * @throws UnsupportedEncodingException
- * when there are problesm with encoding
- */
- private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
- writer = new PrintWriter("out/report/report-prediction.html", "UTF-8");
- writer.println("<html><head></head><body>");
- writer.println("<table cellspacing=\"0\">");
-
- String resultString = "<tr>";
- resultString += "<td" + style + ">Reaction</td>";
- resultString += "<td" + style + ">REACTOME ID</td>";
- resultString += "<td" + style + ">Status</td>";
- resultString += "<td" + style + ">Score</td>";
- resultString += "<td" + style + ">References:</td>";
- resultString += "</tr>";
- writer.println(resultString);
-
- }
-
- /**
- * Formater used for decimals.
- */
-
- private DecimalFormat df = new DecimalFormat("#.##");
-
- /**
- * Style used for result cell.
- */
- private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
-
- /**
- * Prints one prediction row of the result.
- *
- * @param result
- * prediction result
- */
- private void printResult(PredictionResult result) {
- String color = "#FFFFFF";
- String status = "";
- if (PredictionStatus.STRUCTURE.equals(result.getStatus())) {
- color = "#A2E037";
- status = "STRUCTURE";
- } else if (PredictionStatus.DATA_MINIG.equals(result.getStatus())) {
- color = "#DDDDDD";
- status = "DATA MINING";
- } else {
- logger.warn("Unknown type: " + result.getStatus());
- }
- String resultString = "<tr bgcolor = \"" + color + "\">";
- resultString += "<td" + style + ">" + result.getReaction().getDisplayName() + "</td>";
-
- String reactomId = result.getReaction().getStableIdentifier().getIdentifier() + "." + result.getReaction().getStableIdentifier().getIdentifierVersion();
- resultString += "<td" + style + "><a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
-
- resultString += "<td" + style + ">" + status + "</td>";
- resultString += "<td" + style + ">" + df.format(result.getScore() * IProgressUpdater.MAX_PROGRESS) + "%</td>";
- resultString += "<td" + style + ">";
- for (ReactomePublication reference : result.getReaction().getLiteratureReferences()) {
- if (reference instanceof ReactomeLiteratureReference) {
- resultString += pubmedParser.getHtmlFullLinkForId(((ReactomeLiteratureReference) reference).getPubMedIdentifier());
- } else if (reference instanceof ReactomeURL) {
- resultString += reference.getTitle() + "; " + ((ReactomeURL) reference).getUniformResourceLocator();
- } else {
- throw new InvalidArgumentException("Unknown clas type: " + reference.getClass());
- }
- }
- resultString += "</td>";
- resultString += "</tr>";
- writer.println(resultString);
- System.out.println(resultString);
- }
-
- /**
- * @return the pubmedParser
- */
- public PubmedParser getPubmedParser() {
- return pubmedParser;
- }
-
- /**
- * @param pubmedParser
- * the pubmedParser to set
- */
- public void setPubmedParser(PubmedParser pubmedParser) {
- this.pubmedParser = pubmedParser;
- }
-
- /**
- * @return the reactionComparator
- */
- public ReactionComparator getReactionComparator() {
- return reactionComparator;
- }
-
- /**
- * @param reactionComparator
- * the reactionComparator to set
- */
- public void setReactionComparator(ReactionComparator reactionComparator) {
- this.reactionComparator = reactionComparator;
- }
-
- /**
- * @return the rc
- * @see #rc
- */
- public DataSourceUpdater getRc() {
- return rc;
- }
-
- /**
- * @param rc
- * the rc to set
- * @see #rc
- */
- public void setRc(DataSourceUpdater rc) {
- this.rc = rc;
- }
-
- /**
- * @return the rcu
- * @see #rcu
- */
- public ReactomeQueryUtil getRcu() {
- return rcu;
- }
-
- /**
- * @param rcu
- * the rcu to set
- * @see #rcu
- */
- public void setRcu(ReactomeQueryUtil rcu) {
- this.rcu = rcu;
- }
-
-}
+package lcsb.mapviewer.run;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.UnsupportedEncodingException;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.PropertyConfigurator;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
+import lcsb.mapviewer.reactome.model.ReactomeLiteratureReference;
+import lcsb.mapviewer.reactome.model.ReactomePublication;
+import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
+import lcsb.mapviewer.reactome.model.ReactomeURL;
+import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
+import lcsb.mapviewer.reactome.utils.PredictionResult;
+import lcsb.mapviewer.reactome.utils.PredictionResult.PredictionStatus;
+import lcsb.mapviewer.reactome.utils.ReactionComparator;
+import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
+
+/**
+ * This class create a raport about data that might be added to PD-map based on
+ * reactome data and some text mining information.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReactomePrediction {
+ /**
+ * How many nodes in the reaction must match on both sides (reactome and ours)
+ * to consider reaction similar.
+ */
+ private static final int PREDICTION_THRESHOLD = 3;
+
+ /**
+ * Number of nanoseconds in the second.
+ */
+ private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
+
+ /**
+ * Model used for generating raport.
+ */
+ private Model model;
+
+ /**
+ * Local backend to the pubmed data.
+ */
+ @Autowired
+ private PubmedParser pubmedParser;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ReactomePrediction.class);
+
+ /**
+ * Comparator of reactions between our model and reactome.
+ */
+ @Autowired
+ private ReactionComparator reactionComparator;
+
+ /**
+ * Class used for accessing reactome data.
+ */
+ @Autowired
+ private DataSourceUpdater rc;
+
+ /**
+ * Util class used for manipulating information in reactome objects.
+ */
+ @Autowired
+ private ReactomeQueryUtil rcu;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ long startTime = System.nanoTime();
+ PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
+ ReactomePrediction main = new ReactomePrediction();
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ApplicationContextLoader.injectDependencies(main);
+ main.run();
+ long endTime = System.nanoTime();
+
+ long duration = endTime - startTime;
+ double sec = duration / NANOSECONDS_IN_SECOND;
+ System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+ }
+
+ /**
+ * Generates prediction report.
+ */
+ public void run() {
+ try {
+ model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
+
+ Set<ReactomeReactionlikeEvent> reactions = new HashSet<ReactomeReactionlikeEvent>();
+ // problematic reaction with complex of complex of molecule
+ for (Reaction reaction : model.getReactions()) {
+ for (String stableIdentifier : rcu.getReactomeIdentifiersForReaction(reaction)) {
+ ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
+ if (obj != null) {
+ if (obj instanceof ReactomeReactionlikeEvent) {
+ reactions.add((ReactomeReactionlikeEvent) obj);
+ }
+ }
+ }
+ }
+ List<String> pubmedIds = loadPubmedIds("testFiles/data_mining/pd_pmids.txt");
+ List<PredictionResult> newReaction = new ArrayList<PredictionResult>();
+ logger.debug("Structure analysis");
+ newReaction.addAll(rcu.getExtendedReactionsForKnownReactions(reactions, PREDICTION_THRESHOLD));
+ logger.debug("Data mining analysis");
+ newReaction.addAll(rcu.getExtendedReactionsForPubmedPublicationsWithTabuReaction(pubmedIds, reactions));
+ Collections.sort(newReaction, PredictionResult.SCORE_COMPARATOR);
+
+ printHeader();
+ for (PredictionResult prediction : newReaction) {
+ printResult(prediction);
+ }
+ printFooter(newReaction);
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ }
+
+ }
+
+ /**
+ * Load pubmed identifiers from a file.
+ *
+ * @param fileName
+ * file with pubmed ids
+ * @return list of pubmed ids
+ * @throws IOException
+ * thrown when there are problems with a file
+ */
+ private List<String> loadPubmedIds(String fileName) throws IOException {
+ List<String> result = new ArrayList<String>();
+ BufferedReader br = new BufferedReader(new FileReader(fileName));
+ try {
+ String line;
+ while ((line = br.readLine()) != null) {
+ result.add(line);
+ }
+ } finally {
+ br.close();
+ }
+ return result;
+ }
+
+ /**
+ * Prints report footer.
+ *
+ * @param results
+ * results used for generating report
+ */
+ private void printFooter(Collection<PredictionResult> results) {
+ writer.println("</table>");
+
+ writer.println("Suggested reactions: " + results.size());
+
+ writer.println("</body></html>");
+ writer.close();
+
+ }
+
+ /**
+ * Object used for writing the report.
+ */
+ private PrintWriter writer;
+
+ /**
+ * Creates stream for report output and prints report header.
+ *
+ * @throws FileNotFoundException
+ * thrown when file with the report cannot be found
+ * @throws UnsupportedEncodingException
+ * when there are problesm with encoding
+ */
+ private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
+ writer = new PrintWriter("out/report/report-prediction.html", "UTF-8");
+ writer.println("<html><head></head><body>");
+ writer.println("<table cellspacing=\"0\">");
+
+ String resultString = "<tr>";
+ resultString += "<td" + style + ">Reaction</td>";
+ resultString += "<td" + style + ">REACTOME ID</td>";
+ resultString += "<td" + style + ">Status</td>";
+ resultString += "<td" + style + ">Score</td>";
+ resultString += "<td" + style + ">References:</td>";
+ resultString += "</tr>";
+ writer.println(resultString);
+
+ }
+
+ /**
+ * Formater used for decimals.
+ */
+
+ private DecimalFormat df = new DecimalFormat("#.##");
+
+ /**
+ * Style used for result cell.
+ */
+ private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
+
+ /**
+ * Prints one prediction row of the result.
+ *
+ * @param result
+ * prediction result
+ * @throws Exception
+ * thrown when there is a problem with printing
+ */
+ private void printResult(PredictionResult result) throws Exception {
+ String color = "#FFFFFF";
+ String status = "";
+ if (PredictionStatus.STRUCTURE.equals(result.getStatus())) {
+ color = "#A2E037";
+ status = "STRUCTURE";
+ } else if (PredictionStatus.DATA_MINIG.equals(result.getStatus())) {
+ color = "#DDDDDD";
+ status = "DATA MINING";
+ } else {
+ logger.warn("Unknown type: " + result.getStatus());
+ }
+ String resultString = "<tr bgcolor = \"" + color + "\">";
+ resultString += "<td" + style + ">" + result.getReaction().getDisplayName() + "</td>";
+
+ String reactomId = result.getReaction().getStableIdentifier().getIdentifier() + "." + result.getReaction().getStableIdentifier().getIdentifierVersion();
+ resultString += "<td" + style + "><a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
+
+ resultString += "<td" + style + ">" + status + "</td>";
+ resultString += "<td" + style + ">" + df.format(result.getScore() * IProgressUpdater.MAX_PROGRESS) + "%</td>";
+ resultString += "<td" + style + ">";
+ for (ReactomePublication reference : result.getReaction().getLiteratureReferences()) {
+ if (reference instanceof ReactomeLiteratureReference) {
+ resultString += pubmedParser.getHtmlFullLinkForId(((ReactomeLiteratureReference) reference).getPubMedIdentifier());
+ } else if (reference instanceof ReactomeURL) {
+ resultString += reference.getTitle() + "; " + ((ReactomeURL) reference).getUniformResourceLocator();
+ } else {
+ throw new InvalidArgumentException("Unknown clas type: " + reference.getClass());
+ }
+ }
+ resultString += "</td>";
+ resultString += "</tr>";
+ writer.println(resultString);
+ System.out.println(resultString);
+ }
+
+ /**
+ * @return the pubmedParser
+ */
+ public PubmedParser getPubmedParser() {
+ return pubmedParser;
+ }
+
+ /**
+ * @param pubmedParser
+ * the pubmedParser to set
+ */
+ public void setPubmedParser(PubmedParser pubmedParser) {
+ this.pubmedParser = pubmedParser;
+ }
+
+ /**
+ * @return the reactionComparator
+ */
+ public ReactionComparator getReactionComparator() {
+ return reactionComparator;
+ }
+
+ /**
+ * @param reactionComparator
+ * the reactionComparator to set
+ */
+ public void setReactionComparator(ReactionComparator reactionComparator) {
+ this.reactionComparator = reactionComparator;
+ }
+
+ /**
+ * @return the rc
+ * @see #rc
+ */
+ public DataSourceUpdater getRc() {
+ return rc;
+ }
+
+ /**
+ * @param rc
+ * the rc to set
+ * @see #rc
+ */
+ public void setRc(DataSourceUpdater rc) {
+ this.rc = rc;
+ }
+
+ /**
+ * @return the rcu
+ * @see #rcu
+ */
+ public ReactomeQueryUtil getRcu() {
+ return rcu;
+ }
+
+ /**
+ * @param rcu
+ * the rcu to set
+ * @see #rcu
+ */
+ public void setRcu(ReactomeQueryUtil rcu) {
+ this.rcu = rcu;
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/Statistics.java b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
index 81930c619aca86358211ced48a3c86918ab904d9..90dbec74ede2b7aec6262b1aa251b2abd3e4ddd6 100644
--- a/console/src/main/java/lcsb/mapviewer/run/Statistics.java
+++ b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
@@ -1,385 +1,387 @@
-package lcsb.mapviewer.run;
-
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.annotation.services.ModelAnnotator;
-import lcsb.mapviewer.annotation.services.ProblematicAnnotation;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.persist.DbUtils;
-
-/**
- * Class used for analyzing the CellDEsigner model and generating some statistic
- * about it.
- *
- * @author Piotr Gawron
- *
- */
-public class Statistics {
- /**
- * Number of nanoseconds in second.
- */
- private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(Statistics.class.getName());
-
- /**
- * Module that allows to annotate maps.
- */
- @Autowired
- private ModelAnnotator modelAnnotator;
-
- /**
- * Local backend to the pubmed data.
- */
- @Autowired
- private PubmedParser pubmedBackend;
-
- /**
- * Utils that help to manage the sessions in custom multithreaded
- * implementation.
- */
- @Autowired
- private DbUtils dbUtils;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- try {
- String[] modelFileNames = new String[] { "testFiles/pd_full/PD_160714_2/PD_160714_2.xml", //
- "testFiles/pd_full/PD_160714_2/submaps/PARK2_substrates.xml", //
- "testFiles/pd_full/PD_160714_2/submaps/Ubiquitin_proteasome_system.xml", //
- "testFiles/pd_full/PD_160714_2/submaps/Fatty_acid_and_ketone_body_metabolism.xml", //
- };
-
- long startTime = System.nanoTime();
-
- Statistics main = new Statistics();
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ApplicationContextLoader.injectDependencies(main);
-
- main.run(modelFileNames);
- long endTime = System.nanoTime();
-
- long duration = endTime - startTime;
- double sec = duration / NANOSECONDS_IN_SECOND;
- System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- }
-
- /**
- * Generate statistics.
- *
- * @param fileNames
- * filenames for the models used for statistic generation
- */
- public void run(String[] fileNames) {
- dbUtils.createSessionForCurrentThread();
- List<Model> models = new ArrayList<>();
- try {
- // String modelName = PdMapAnnotations.getLastPdFilename();
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- for (String name : fileNames) {
- models.add(parser.createModel(new ConverterParams().filename(name)));
- }
-
- IProgressUpdater updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- logger.debug("Progress: " + progress);
- }
- };
- for (Model model : models) {
- modelAnnotator.performAnnotations(model, updater);
- }
- // modelAnnotator.removeIncorrectAnnotations(model, updater);
-
- printStatistics(models);
-
- // printAnnotationInformation(model);
- //
- // PrintWriter writer = new PrintWriter("tmp.html", "UTF-8");
- // writer.println(createPubmedExportString(model));
- // writer.close();
- } catch (Exception e) {
- logger.error(e.getMessage());
- e.printStackTrace();
- }
-
- dbUtils.closeSessionForCurrentThread();
- }
-
- /**
- * Prints statistics for the model.
- *
- * @param models
- * models under analysis
- */
- protected void printStatistics(List<Model> models) {
- int reactionNumber = 0;
- for (Model model2 : models) {
- reactionNumber += model2.getReactions().size();
- }
- print("Reactions: ");
- print(" number: " + reactionNumber);
- Map<String, Set<String>> ids = new HashMap<String, Set<String>>();
- int pubmedReactions = 0;
- for (Model model : models) {
- for (Reaction reaction : model.getReactions()) {
- for (MiriamData md : reaction.getMiriamData()) {
- String type = md.getDataType().getCommonName();
- Set<String> set = ids.get(type);
- if (set == null) {
- set = new HashSet<String>();
- ids.put(type, set);
- }
- set.add(md.getResource());
- }
- if (reaction.getMiriamData().size() == 1) {
- if (reaction.getMiriamData().iterator().next().getDataType().equals(MiriamType.PUBMED)) {
- pubmedReactions++;
- }
- }
- }
- }
-
- for (String string : ids.keySet()) {
- print(" " + string + ": " + ids.get(string).size());
- }
- print(" pubmed reactions: " + pubmedReactions);
-
- ids.clear();
- print("-----------------------------");
- print("Elements: ");
- Set<String> names = new HashSet<String>();
- Map<String, Set<String>> typeNames = new HashMap<String, Set<String>>();
-
- for (Model model : models) {
- for (Element element : model.getElements()) {
- if (element instanceof Species) {
- names.add(((Species) element).getName());
- Set<String> tmp = typeNames.get(element.getClass().getName());
- if (tmp == null) {
- tmp = new HashSet<String>();
- typeNames.put(element.getClass().getName(), tmp);
- }
- tmp.add(((Species) element).getName());
- for (MiriamData md : ((Species) element).getMiriamData()) {
- String type = md.getDataType().getCommonName();
- Set<String> set = ids.get(type);
- if (set == null) {
- set = new HashSet<String>();
- ids.put(type, set);
- }
- set.add(md.getResource());
- }
- }
- }
- }
- print(" distinct names: " + names.size());
-
- for (String string : ids.keySet()) {
- print(" " + string + ": " + ids.get(string).size());
- }
-
- print("-----------------------------");
- print(" distinct elements types: ");
- for (String string : typeNames.keySet()) {
- print(" " + string + ": " + typeNames.get(string).size());
- }
-
- Set<String> set = new HashSet<String>();
- for (Model model : models) {
- for (Compartment comp : model.getCompartments()) {
- set.add(comp.getName());
- }
- }
- print(" compartments: " + set.size());
- }
-
- /**
- * Prints information about inproper annotations.
- *
- * @param model
- * model under analysis
- */
- protected void printAnnotationInformation(Model model) {
- print("-----------------------------");
- print("Improper annotations:");
- Collection<? extends ProblematicAnnotation> improper = modelAnnotator.findImproperAnnotations(model, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, null);
- for (ProblematicAnnotation improperAnnotation : improper) {
- print(improperAnnotation.toString());
- }
- print("-----------------------------");
- print("Missing annotations:");
- Collection<ProblematicAnnotation> missing = modelAnnotator.findMissingAnnotations(model, null);
- for (ProblematicAnnotation improperAnnotation : missing) {
- print(improperAnnotation.toString());
- }
- print("-----------------------------");
- print("Complex annotations:");
- for (Element element : model.getElements()) {
- if (element instanceof ComplexSpecies && element.getMiriamData().size() > 0) {
- print(element.getClass().getSimpleName() + ";\t\tname=" + element.getName() + ";\t\tid=" + element.getElementId());
- }
- }
- print("-----------------------------");
- print("Pubmed annotated elements:");
- // Collection<? extends ProblematicAnnotation> pubmes =
- // modelAnnotator.findPubmedAnnotatedElements(model);
- // for (ProblematicAnnotation improperAnnotation : pubmes) {
- //
- // if (improperAnnotation.getObject() != null) {
- // AnnotatedObject element = improperAnnotation.getObject();
- // String ids = "";
- // for (MiriamData md : improperAnnotation.getMd()) {
- // ids += md.getResource() + ", ";
- // }
- // print(element.getClass().getSimpleName() + ";\t\tname=" +
- // element.getName() + ";\t\tid=" + element.getElementId() + ";\t\tpubmed= "
- // + ids);
- // }
- // }
- }
-
- /**
- * Prints line of the report.
- *
- * @param string
- * text to print
- */
- void print(String string) {
- System.out.println(string);
- }
-
- /**
- * @return the modelAnnotator
- */
- public ModelAnnotator getModelAnnotator() {
- return modelAnnotator;
- }
-
- /**
- * @param modelAnnotator
- * the modelAnnotator to set
- */
- public void setModelAnnotator(ModelAnnotator modelAnnotator) {
- this.modelAnnotator = modelAnnotator;
- }
-
- /**
- * Create tab separated string with information about pubmed articles used in
- * the map.
- *
- * @param model
- * analyzed model
- * @return tab separated string with information about pubmed articles
- */
- protected String createPubmedExportString(Model model) {
- Map<String, List<String>> links = new HashMap<String, List<String>>();
- for (Element element : model.getElements()) {
- for (MiriamData md : element.getMiriamData()) {
- if (MiriamType.PUBMED.equals(md.getDataType())) {
- List<String> list = links.get(md.getResource());
- if (list == null) {
- list = new ArrayList<String>();
- links.put(md.getResource(), list);
- }
- String address = "<a href =\"" + Configuration.PUBLICALY_AVAILABLE_PD_MAP + "&search=species:" + element.getElementId() + "\">" + element.getName()
- + "</a>";
- list.add(address);
- }
- }
- }
-
- for (Reaction reaction : model.getReactions()) {
- for (MiriamData md : reaction.getMiriamData()) {
- if (MiriamType.PUBMED.equals(md.getDataType())) {
- List<String> list = links.get(md.getResource());
- if (list == null) {
- list = new ArrayList<String>();
- links.put(md.getResource(), list);
- }
- String address = "<a href =\"" + PdMapAnnotations.getLinkForReaction(reaction) + "\">Reaction: " + reaction.getIdReaction() + "</a>";
- list.add(address);
- }
- }
- }
-
- StringBuilder result = new StringBuilder();
-
- result.append("<html><head/><body><table>");
- for (String string : links.keySet()) {
- Article article = pubmedBackend.getPubmedArticleById(Integer.valueOf(string));
- result.append("<tr><td><a href =\"" + article.getLink() + "\">" + string + "</a></td>");
- result.append("<td>" + article.getTitle() + "</td>");
- result.append("<td>" + article.getStringAuthors() + "</td>");
- result.append("<td>" + article.getJournal() + "</td>");
- result.append("<td>" + article.getYear() + "</td>");
- for (String str : links.get(string)) {
- result.append("<td>");
- result.append(str);
- result.append("</td>");
- }
- result.append("</tr>\n");
- }
- result.append("</table></body></html>");
-
- return result.toString();
- }
-
- /**
- * @return the pubmedBackend
- * @see #pubmedBackend
- */
- public PubmedParser getPubmedBackend() {
- return pubmedBackend;
- }
-
- /**
- * @param pubmedBackend
- * the pubmedBackend to set
- * @see #pubmedBackend
- */
- public void setPubmedBackend(PubmedParser pubmedBackend) {
- this.pubmedBackend = pubmedBackend;
- }
-
-}
+package lcsb.mapviewer.run;
+
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.data.Article;
+import lcsb.mapviewer.annotation.services.ModelAnnotator;
+import lcsb.mapviewer.annotation.services.ProblematicAnnotation;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.ComplexSpecies;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.persist.DbUtils;
+
+/**
+ * Class used for analyzing the CellDEsigner model and generating some statistic
+ * about it.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class Statistics {
+ /**
+ * Number of nanoseconds in second.
+ */
+ private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(Statistics.class.getName());
+
+ /**
+ * Module that allows to annotate maps.
+ */
+ @Autowired
+ private ModelAnnotator modelAnnotator;
+
+ /**
+ * Local backend to the pubmed data.
+ */
+ @Autowired
+ private PubmedParser pubmedBackend;
+
+ /**
+ * Utils that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ @Autowired
+ private DbUtils dbUtils;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ try {
+ String[] modelFileNames = new String[] { "testFiles/pd_full/PD_160714_2/PD_160714_2.xml", //
+ "testFiles/pd_full/PD_160714_2/submaps/PARK2_substrates.xml", //
+ "testFiles/pd_full/PD_160714_2/submaps/Ubiquitin_proteasome_system.xml", //
+ "testFiles/pd_full/PD_160714_2/submaps/Fatty_acid_and_ketone_body_metabolism.xml", //
+ };
+
+ long startTime = System.nanoTime();
+
+ Statistics main = new Statistics();
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ApplicationContextLoader.injectDependencies(main);
+
+ main.run(modelFileNames);
+ long endTime = System.nanoTime();
+
+ long duration = endTime - startTime;
+ double sec = duration / NANOSECONDS_IN_SECOND;
+ System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ }
+
+ /**
+ * Generate statistics.
+ *
+ * @param fileNames
+ * filenames for the models used for statistic generation
+ */
+ public void run(String[] fileNames) {
+ dbUtils.createSessionForCurrentThread();
+ List<Model> models = new ArrayList<>();
+ try {
+ // String modelName = PdMapAnnotations.getLastPdFilename();
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ for (String name : fileNames) {
+ models.add(parser.createModel(new ConverterParams().filename(name)));
+ }
+
+ IProgressUpdater updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ logger.debug("Progress: " + progress);
+ }
+ };
+ for (Model model : models) {
+ modelAnnotator.performAnnotations(model, updater);
+ }
+ // modelAnnotator.removeIncorrectAnnotations(model, updater);
+
+ printStatistics(models);
+
+ // printAnnotationInformation(model);
+ //
+ // PrintWriter writer = new PrintWriter("tmp.html", "UTF-8");
+ // writer.println(createPubmedExportString(model));
+ // writer.close();
+ } catch (Exception e) {
+ logger.error(e.getMessage());
+ e.printStackTrace();
+ }
+
+ dbUtils.closeSessionForCurrentThread();
+ }
+
+ /**
+ * Prints statistics for the model.
+ *
+ * @param models
+ * models under analysis
+ */
+ protected void printStatistics(List<Model> models) {
+ int reactionNumber = 0;
+ for (Model model2 : models) {
+ reactionNumber += model2.getReactions().size();
+ }
+ print("Reactions: ");
+ print(" number: " + reactionNumber);
+ Map<String, Set<String>> ids = new HashMap<String, Set<String>>();
+ int pubmedReactions = 0;
+ for (Model model : models) {
+ for (Reaction reaction : model.getReactions()) {
+ for (MiriamData md : reaction.getMiriamData()) {
+ String type = md.getDataType().getCommonName();
+ Set<String> set = ids.get(type);
+ if (set == null) {
+ set = new HashSet<String>();
+ ids.put(type, set);
+ }
+ set.add(md.getResource());
+ }
+ if (reaction.getMiriamData().size() == 1) {
+ if (reaction.getMiriamData().iterator().next().getDataType().equals(MiriamType.PUBMED)) {
+ pubmedReactions++;
+ }
+ }
+ }
+ }
+
+ for (String string : ids.keySet()) {
+ print(" " + string + ": " + ids.get(string).size());
+ }
+ print(" pubmed reactions: " + pubmedReactions);
+
+ ids.clear();
+ print("-----------------------------");
+ print("Elements: ");
+ Set<String> names = new HashSet<String>();
+ Map<String, Set<String>> typeNames = new HashMap<String, Set<String>>();
+
+ for (Model model : models) {
+ for (Element element : model.getElements()) {
+ if (element instanceof Species) {
+ names.add(((Species) element).getName());
+ Set<String> tmp = typeNames.get(element.getClass().getName());
+ if (tmp == null) {
+ tmp = new HashSet<String>();
+ typeNames.put(element.getClass().getName(), tmp);
+ }
+ tmp.add(((Species) element).getName());
+ for (MiriamData md : ((Species) element).getMiriamData()) {
+ String type = md.getDataType().getCommonName();
+ Set<String> set = ids.get(type);
+ if (set == null) {
+ set = new HashSet<String>();
+ ids.put(type, set);
+ }
+ set.add(md.getResource());
+ }
+ }
+ }
+ }
+ print(" distinct names: " + names.size());
+
+ for (String string : ids.keySet()) {
+ print(" " + string + ": " + ids.get(string).size());
+ }
+
+ print("-----------------------------");
+ print(" distinct elements types: ");
+ for (String string : typeNames.keySet()) {
+ print(" " + string + ": " + typeNames.get(string).size());
+ }
+
+ Set<String> set = new HashSet<String>();
+ for (Model model : models) {
+ for (Compartment comp : model.getCompartments()) {
+ set.add(comp.getName());
+ }
+ }
+ print(" compartments: " + set.size());
+ }
+
+ /**
+ * Prints information about inproper annotations.
+ *
+ * @param model
+ * model under analysis
+ */
+ protected void printAnnotationInformation(Model model) {
+ print("-----------------------------");
+ print("Improper annotations:");
+ Collection<? extends ProblematicAnnotation> improper = modelAnnotator.findImproperAnnotations(model, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, null);
+ for (ProblematicAnnotation improperAnnotation : improper) {
+ print(improperAnnotation.toString());
+ }
+ print("-----------------------------");
+ print("Missing annotations:");
+ Collection<ProblematicAnnotation> missing = modelAnnotator.findMissingAnnotations(model, null);
+ for (ProblematicAnnotation improperAnnotation : missing) {
+ print(improperAnnotation.toString());
+ }
+ print("-----------------------------");
+ print("Complex annotations:");
+ for (Element element : model.getElements()) {
+ if (element instanceof ComplexSpecies && element.getMiriamData().size() > 0) {
+ print(element.getClass().getSimpleName() + ";\t\tname=" + element.getName() + ";\t\tid=" + element.getElementId());
+ }
+ }
+ print("-----------------------------");
+ print("Pubmed annotated elements:");
+ // Collection<? extends ProblematicAnnotation> pubmes =
+ // modelAnnotator.findPubmedAnnotatedElements(model);
+ // for (ProblematicAnnotation improperAnnotation : pubmes) {
+ //
+ // if (improperAnnotation.getObject() != null) {
+ // AnnotatedObject element = improperAnnotation.getObject();
+ // String ids = "";
+ // for (MiriamData md : improperAnnotation.getMd()) {
+ // ids += md.getResource() + ", ";
+ // }
+ // print(element.getClass().getSimpleName() + ";\t\tname=" +
+ // element.getName() + ";\t\tid=" + element.getElementId() + ";\t\tpubmed= "
+ // + ids);
+ // }
+ // }
+ }
+
+ /**
+ * Prints line of the report.
+ *
+ * @param string
+ * text to print
+ */
+ void print(String string) {
+ System.out.println(string);
+ }
+
+ /**
+ * @return the modelAnnotator
+ */
+ public ModelAnnotator getModelAnnotator() {
+ return modelAnnotator;
+ }
+
+ /**
+ * @param modelAnnotator
+ * the modelAnnotator to set
+ */
+ public void setModelAnnotator(ModelAnnotator modelAnnotator) {
+ this.modelAnnotator = modelAnnotator;
+ }
+
+ /**
+ * Create tab separated string with information about pubmed articles used in
+ * the map.
+ *
+ * @param model
+ * analyzed model
+ * @return tab separated string with information about pubmed articles
+ * @throws Exception
+ * thrown when there is a problem with pubmed
+ */
+ protected String createPubmedExportString(Model model) throws Exception {
+ Map<String, List<String>> links = new HashMap<String, List<String>>();
+ for (Element element : model.getElements()) {
+ for (MiriamData md : element.getMiriamData()) {
+ if (MiriamType.PUBMED.equals(md.getDataType())) {
+ List<String> list = links.get(md.getResource());
+ if (list == null) {
+ list = new ArrayList<String>();
+ links.put(md.getResource(), list);
+ }
+ String address = "<a href =\"" + Configuration.PUBLICALY_AVAILABLE_PD_MAP + "&search=species:" + element.getElementId() + "\">" + element.getName()
+ + "</a>";
+ list.add(address);
+ }
+ }
+ }
+
+ for (Reaction reaction : model.getReactions()) {
+ for (MiriamData md : reaction.getMiriamData()) {
+ if (MiriamType.PUBMED.equals(md.getDataType())) {
+ List<String> list = links.get(md.getResource());
+ if (list == null) {
+ list = new ArrayList<String>();
+ links.put(md.getResource(), list);
+ }
+ String address = "<a href =\"" + PdMapAnnotations.getLinkForReaction(reaction) + "\">Reaction: " + reaction.getIdReaction() + "</a>";
+ list.add(address);
+ }
+ }
+ }
+
+ StringBuilder result = new StringBuilder();
+
+ result.append("<html><head/><body><table>");
+ for (String string : links.keySet()) {
+ Article article = pubmedBackend.getPubmedArticleById(Integer.valueOf(string));
+ result.append("<tr><td><a href =\"" + article.getLink() + "\">" + string + "</a></td>");
+ result.append("<td>" + article.getTitle() + "</td>");
+ result.append("<td>" + article.getStringAuthors() + "</td>");
+ result.append("<td>" + article.getJournal() + "</td>");
+ result.append("<td>" + article.getYear() + "</td>");
+ for (String str : links.get(string)) {
+ result.append("<td>");
+ result.append(str);
+ result.append("</td>");
+ }
+ result.append("</tr>\n");
+ }
+ result.append("</table></body></html>");
+
+ return result.toString();
+ }
+
+ /**
+ * @return the pubmedBackend
+ * @see #pubmedBackend
+ */
+ public PubmedParser getPubmedBackend() {
+ return pubmedBackend;
+ }
+
+ /**
+ * @param pubmedBackend
+ * the pubmedBackend to set
+ * @see #pubmedBackend
+ */
+ public void setPubmedBackend(PubmedParser pubmedBackend) {
+ this.pubmedBackend = pubmedBackend;
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java b/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
index 420da1a061ac241ebd2e16104b6b18bf9b5a5a7d..c0f17f66b1a0ec97cfde5ef6f8370eca9feb61ed 100644
--- a/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
+++ b/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
@@ -1,307 +1,304 @@
-package lcsb.mapviewer.run;
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.UnsupportedEncodingException;
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.graphics.MapGenerator;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
-import lcsb.mapviewer.reactome.utils.DataFormatter;
-import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
-import lcsb.mapviewer.reactome.utils.comparators.MatchResult;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.PropertyConfigurator;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * This class prepare report of data that are not included in reactome and maybe
- * should be added.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownReactionInReactome {
- /**
- * Number of nanoseconds in a second.
- */
- private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
-
- /**
- * Model used for generating raport.
- */
- private Model model;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(UnknownReactionInReactome.class);
-
- /**
- * Util class used for manipulating information in reactome objects.
- */
- @Autowired
- private ReactomeQueryUtil rcu;
-
- /**
- * Formatter used for reaction comparison.
- */
- @Autowired
- private DataFormatter dataFormatter;
-
- /**
- * Class used for accessing data in pubmed database.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- long startTime = System.nanoTime();
- PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
- UnknownReactionInReactome main = new UnknownReactionInReactome();
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ApplicationContextLoader.injectDependencies(main);
- main.run();
- long endTime = System.nanoTime();
-
- long duration = endTime - startTime;
- double sec = duration / NANOSECONDS_IN_SECOND;
- System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
- }
-
- /**
- * Executes comparison between model and reactome to generate report.
- */
- public void run() {
- try {
- MapGenerator mg = new MapGenerator();
- model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
- new CreateHierarchyCommand(model, mg.computeZoomLevels(model), mg.computeZoomFactor(model)).execute();
- List<String> ids = new ArrayList<String>();
- for (Reaction reaction : model.getReactions()) {
- if (rcu.getReactomeIdentifierForReaction(reaction) == null) {
- ids.add(reaction.getIdReaction());
- }
- }
- Collections.sort(ids);
- printHeader();
- List<MatchResult> results = new ArrayList<MatchResult>();
- for (String string : ids) {
- boolean unknown = true;
- boolean pubmed = false;
- Reaction reaction = model.getReactionByReactionId(string);
- for (MiriamData md : reaction.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.PUBMED)) {
- pubmed = true;
- ReactomeDatabaseObject obj = rcu.getLiteratureReferenceByPubMedId(Integer.parseInt(md.getResource()));
- if (obj != null) {
- unknown = false;
- }
- }
- }
- if (pubmed && unknown) {
- MatchResult matchResult = new MatchResult();
- matchResult.setLocalReaction(reaction);
- for (ReactionNode node : reaction.getReactants()) {
- matchResult.addInvalidLocalInput((Species) node.getElement());
- }
- for (ReactionNode node : reaction.getProducts()) {
- matchResult.addInvalidLocalOutput((Species) node.getElement());
- }
- for (ReactionNode node : reaction.getModifiers()) {
- matchResult.addInvalidLocalModifier((Species) node.getElement());
- }
- results.add(matchResult);
- printResult(matchResult);
- }
- }
- printFooter(results);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- }
-
- }
-
- /**
- * Prints report footer.
- *
- * @param results
- * results used in the report
- */
- private void printFooter(List<MatchResult> results) {
-
- writer.println("</table>");
- writer.println("Reactions: " + results.size());
- writer.println("</body></html>");
-
- writer.close();
- }
-
- /**
- * Object to which the report is written.
- */
- private PrintWriter writer;
-
- /**
- * Creates report stream and prints header of the report.
- *
- * @throws FileNotFoundException
- * if there is a problem with creating report file
- * @throws UnsupportedEncodingException
- * thrown when there are problems with encoding
- */
- private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
- writer = new PrintWriter("out/report/report-export.html", "UTF-8");
- writer.println("<html><head></head><body>");
- writer.println("<table cellspacing=\"0\"");
-
- String resultString = "<tr>";
- resultString += "<td" + style + ">Reaction</td>";
- resultString += "<td" + style + ">Pubmed ids</td>";
- resultString += "<td" + style + ">Ontologies</td>";
- resultString += "<td" + style + ">Input</td>";
- resultString += "<td" + style + ">Modifier</td>";
- resultString += "<td" + style + ">Output</td>";
- resultString += "</tr>";
- writer.println(resultString);
-
- }
-
- /**
- * Style used by report cells.
- */
- private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
-
- /**
- * Prints result row.
- *
- * @param result
- * result to be printed
- * @throws IOException
- * @throws AnnotatorException
- */
- private void printResult(MatchResult result) throws IOException, AnnotatorException {
-
- Set<String> ontologies = new HashSet<String>();
-
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
- for (ReactionNode node : result.getLocalReaction().getReactionNodes()) {
- if (alias.contains(node.getAlias())) {
- if (alias instanceof ArtifitialCompartmentAlias) {
- ontologies.add(((ArtifitialCompartmentAlias) alias).getTitle());
- } else {
- ontologies.add(alias.getCompartment().getName());
- }
- break;
- }
- }
- }
-
- String color = "#FFFFFF";
- String resultString = "<tr bgcolor = \"" + color + "\">";
- String reactionId = result.getLocalReaction().getIdReaction();
- resultString += "<td" + style + "><a target=\"_blank\" href=\"" + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId
- + "</a></td>";
-
- String pubmed = "";
- for (MiriamData md : result.getLocalReaction().getMiriamData()) {
- if (md.getDataType().equals(MiriamType.PUBMED)) {
- pubmed += pubmedParser.getHtmlFullLinkForId(Integer.valueOf(md.getResource()), false) + "<br/>";
- }
- }
-
- resultString += "<td" + style + ">" + pubmed + "</td>";
-
- String ont = "";
- for (String string : ontologies) {
- if (!ont.equals("")) {
- ont += "<hr/>";
- }
- ont += string;
- }
- resultString += "<td" + style + ">" + ont + "</td>";
-
- resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + " </td>";
- resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + " </td>";
- resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + " </td>";
- resultString += "</tr>";
- writer.println(resultString);
- System.out.println(resultString);
- }
-
- /**
- * @return the dataFormatter
- */
- public DataFormatter getDataFormatter() {
- return dataFormatter;
- }
-
- /**
- * @param dataFormatter
- * the dataFormatter to set
- */
- public void setDataFormatter(DataFormatter dataFormatter) {
- this.dataFormatter = dataFormatter;
- }
-
- /**
- * @return the pubmedParser
- */
- public PubmedParser getPubmedParser() {
- return pubmedParser;
- }
-
- /**
- * @param pubmedParser
- * the pubmedParser to set
- */
- public void setPubmedParser(PubmedParser pubmedParser) {
- this.pubmedParser = pubmedParser;
- }
-
- /**
- * @return the rcu
- * @see #rcu
- */
- public ReactomeQueryUtil getRcu() {
- return rcu;
- }
-
- /**
- * @param rcu
- * the rcu to set
- * @see #rcu
- */
- public void setRcu(ReactomeQueryUtil rcu) {
- this.rcu = rcu;
- }
-
-}
+package lcsb.mapviewer.run;
+
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+import java.io.UnsupportedEncodingException;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.PropertyConfigurator;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.graphics.MapGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
+import lcsb.mapviewer.reactome.utils.DataFormatter;
+import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
+import lcsb.mapviewer.reactome.utils.comparators.MatchResult;
+
+/**
+ * This class prepare report of data that are not included in reactome and maybe
+ * should be added.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownReactionInReactome {
+ /**
+ * Number of nanoseconds in a second.
+ */
+ private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
+
+ /**
+ * Model used for generating raport.
+ */
+ private Model model;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(UnknownReactionInReactome.class);
+
+ /**
+ * Util class used for manipulating information in reactome objects.
+ */
+ @Autowired
+ private ReactomeQueryUtil rcu;
+
+ /**
+ * Formatter used for reaction comparison.
+ */
+ @Autowired
+ private DataFormatter dataFormatter;
+
+ /**
+ * Class used for accessing data in pubmed database.
+ */
+ @Autowired
+ private PubmedParser pubmedParser;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ long startTime = System.nanoTime();
+ PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
+ UnknownReactionInReactome main = new UnknownReactionInReactome();
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ApplicationContextLoader.injectDependencies(main);
+ main.run();
+ long endTime = System.nanoTime();
+
+ long duration = endTime - startTime;
+ double sec = duration / NANOSECONDS_IN_SECOND;
+ System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+ }
+
+ /**
+ * Executes comparison between model and reactome to generate report.
+ */
+ public void run() {
+ try {
+ MapGenerator mg = new MapGenerator();
+ model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
+ new CreateHierarchyCommand(model, mg.computeZoomLevels(model), mg.computeZoomFactor(model)).execute();
+ List<String> ids = new ArrayList<String>();
+ for (Reaction reaction : model.getReactions()) {
+ if (rcu.getReactomeIdentifierForReaction(reaction) == null) {
+ ids.add(reaction.getIdReaction());
+ }
+ }
+ Collections.sort(ids);
+ printHeader();
+ List<MatchResult> results = new ArrayList<MatchResult>();
+ for (String string : ids) {
+ boolean unknown = true;
+ boolean pubmed = false;
+ Reaction reaction = model.getReactionByReactionId(string);
+ for (MiriamData md : reaction.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PUBMED)) {
+ pubmed = true;
+ ReactomeDatabaseObject obj = rcu.getLiteratureReferenceByPubMedId(Integer.parseInt(md.getResource()));
+ if (obj != null) {
+ unknown = false;
+ }
+ }
+ }
+ if (pubmed && unknown) {
+ MatchResult matchResult = new MatchResult();
+ matchResult.setLocalReaction(reaction);
+ for (ReactionNode node : reaction.getReactants()) {
+ matchResult.addInvalidLocalInput((Species) node.getElement());
+ }
+ for (ReactionNode node : reaction.getProducts()) {
+ matchResult.addInvalidLocalOutput((Species) node.getElement());
+ }
+ for (ReactionNode node : reaction.getModifiers()) {
+ matchResult.addInvalidLocalModifier((Species) node.getElement());
+ }
+ results.add(matchResult);
+ printResult(matchResult);
+ }
+ }
+ printFooter(results);
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ }
+
+ }
+
+ /**
+ * Prints report footer.
+ *
+ * @param results
+ * results used in the report
+ */
+ private void printFooter(List<MatchResult> results) {
+
+ writer.println("</table>");
+ writer.println("Reactions: " + results.size());
+ writer.println("</body></html>");
+
+ writer.close();
+ }
+
+ /**
+ * Object to which the report is written.
+ */
+ private PrintWriter writer;
+
+ /**
+ * Creates report stream and prints header of the report.
+ *
+ * @throws FileNotFoundException
+ * if there is a problem with creating report file
+ * @throws UnsupportedEncodingException
+ * thrown when there are problems with encoding
+ */
+ private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
+ writer = new PrintWriter("out/report/report-export.html", "UTF-8");
+ writer.println("<html><head></head><body>");
+ writer.println("<table cellspacing=\"0\"");
+
+ String resultString = "<tr>";
+ resultString += "<td" + style + ">Reaction</td>";
+ resultString += "<td" + style + ">Pubmed ids</td>";
+ resultString += "<td" + style + ">Ontologies</td>";
+ resultString += "<td" + style + ">Input</td>";
+ resultString += "<td" + style + ">Modifier</td>";
+ resultString += "<td" + style + ">Output</td>";
+ resultString += "</tr>";
+ writer.println(resultString);
+
+ }
+
+ /**
+ * Style used by report cells.
+ */
+ private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
+
+ /**
+ * Prints result row.
+ *
+ * @param result
+ * result to be printed
+ * @throws Exception thrown when there is a problem with printing
+ */
+ private void printResult(MatchResult result) throws Exception {
+
+ Set<String> ontologies = new HashSet<String>();
+
+ for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (ReactionNode node : result.getLocalReaction().getReactionNodes()) {
+ if (alias.contains(node.getAlias())) {
+ if (alias instanceof ArtifitialCompartmentAlias) {
+ ontologies.add(((ArtifitialCompartmentAlias) alias).getTitle());
+ } else {
+ ontologies.add(alias.getCompartment().getName());
+ }
+ break;
+ }
+ }
+ }
+
+ String color = "#FFFFFF";
+ String resultString = "<tr bgcolor = \"" + color + "\">";
+ String reactionId = result.getLocalReaction().getIdReaction();
+ resultString += "<td" + style + "><a target=\"_blank\" href=\"" + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId
+ + "</a></td>";
+
+ String pubmed = "";
+ for (MiriamData md : result.getLocalReaction().getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PUBMED)) {
+ pubmed += pubmedParser.getHtmlFullLinkForId(Integer.valueOf(md.getResource()), false) + "<br/>";
+ }
+ }
+
+ resultString += "<td" + style + ">" + pubmed + "</td>";
+
+ String ont = "";
+ for (String string : ontologies) {
+ if (!ont.equals("")) {
+ ont += "<hr/>";
+ }
+ ont += string;
+ }
+ resultString += "<td" + style + ">" + ont + "</td>";
+
+ resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + " </td>";
+ resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + " </td>";
+ resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + " </td>";
+ resultString += "</tr>";
+ writer.println(resultString);
+ System.out.println(resultString);
+ }
+
+ /**
+ * @return the dataFormatter
+ */
+ public DataFormatter getDataFormatter() {
+ return dataFormatter;
+ }
+
+ /**
+ * @param dataFormatter
+ * the dataFormatter to set
+ */
+ public void setDataFormatter(DataFormatter dataFormatter) {
+ this.dataFormatter = dataFormatter;
+ }
+
+ /**
+ * @return the pubmedParser
+ */
+ public PubmedParser getPubmedParser() {
+ return pubmedParser;
+ }
+
+ /**
+ * @param pubmedParser
+ * the pubmedParser to set
+ */
+ public void setPubmedParser(PubmedParser pubmedParser) {
+ this.pubmedParser = pubmedParser;
+ }
+
+ /**
+ * @return the rcu
+ * @see #rcu
+ */
+ public ReactomeQueryUtil getRcu() {
+ return rcu;
+ }
+
+ /**
+ * @param rcu
+ * the rcu to set
+ * @see #rcu
+ */
+ public void setRcu(ReactomeQueryUtil rcu) {
+ this.rcu = rcu;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
index 6506dbbcd87d7812d3381246fd6797aad2ab07d3..28375a5c04c7d9b3de1188d10d197a16a1a2812e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
@@ -1,515 +1,520 @@
-package lcsb.mapviewer.services.impl;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.annotation.services.MeSHParser;
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.annotation.services.TaxonomySearchException;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.commands.CopyCommand;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.map.ModelDao;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.search.data.FullAliasView;
-import lcsb.mapviewer.services.search.data.FullAliasViewFactory;
-import lcsb.mapviewer.services.search.data.LightAliasView;
-import lcsb.mapviewer.services.search.data.LightAliasViewFactory;
-import lcsb.mapviewer.services.search.data.LightReactionView;
-import lcsb.mapviewer.services.view.LayoutView;
-import lcsb.mapviewer.services.view.ModelView;
-import lcsb.mapviewer.services.view.ModelViewFactory;
-import lcsb.mapviewer.services.view.ProjectView;
-
-/**
- * Implementation of the service that manages models.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class ModelService implements IModelService {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ModelService.class);
-
- /**
- * List of cached models.
- */
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- /**
- * List of models that are currently being loaded from databsae.
- */
- private static Set<String> modelsInLoadStage = new HashSet<>();
-
- /**
- * Data access object for models.
- */
- @Autowired
- private ModelDao modelDao;
-
- /**
- * Object allowing access to the mesh database.
- */
- @Autowired
- private MeSHParser meshParser;
-
- /**
- * Local backend to the pubmed data.
- */
- @Autowired
- private PubmedParser backend;
-
- /**
- * Service used for managing layouts.
- */
- @Autowired
- private ILayoutService layoutService;
-
- /**
- * Connector used for accessing data from miriam registry.
- */
- @Autowired
- private MiriamConnector miriamConnector;
-
- /**
- * Factory object used for creation of {@link ModelView} elements.
- */
- @Autowired
- private ModelViewFactory modelViewFactory;
-
- /**
- * Factory used to create {@link FullAliasView} elements.
- */
- @Autowired
- private FullAliasViewFactory fullAliasViewFactory;
-
- /**
- * Access point and parser for the online ctd database.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
-
- @Override
- public Model getLastModelByProjectId(String projectName) {
- if (projectName == null) {
- return null;
- }
-
- // check if model is being loaded by another thread
- boolean waitForModel = false;
- do {
- synchronized (modelsInLoadStage) {
- waitForModel = modelsInLoadStage.contains(projectName);
- }
- // if model is being loaded then wait until it's loaded
- if (waitForModel) {
- try {
- Thread.sleep(100);
- } catch (InterruptedException e) {
- logger.fatal(e, e);
- }
- }
- } while (waitForModel);
-
- Model model = models.get(projectName);
- if (model == null) {
- try {
- // mark model as being load stage, so other threads that want to access
- // it will wait
- synchronized (modelsInLoadStage) {
- modelsInLoadStage.add(projectName);
- }
- logger.debug("Unknown model, trying to load the model into memory.");
-
- ModelData modelData = modelDao.getLastModelForProjectIdentifier(projectName, false);
-
- if (modelData == null) {
- logger.debug("Model doesn't exist");
- return null;
- }
- logger.debug("Model loaded from db.");
- model = new ModelFullIndexed(modelData);
-
- // this is a trick to load all required subelements of the model... ;/
- // lets copy model - it will access all elements...
- new CopyCommand(model).execute();
-
- logger.debug("Model loaded successfullly");
- models.put(projectName, model);
- } finally {
- // model is not being loaded anymore
- synchronized (modelsInLoadStage) {
- modelsInLoadStage.remove(projectName);
- }
- }
- }
- return model;
- }
-
- @Override
- public void cacheAllPubmedIds(Model model, IProgressUpdater updater) {
- logger.debug("Caching pubmed ids...");
- if (model != null) {
- Set<Integer> pubmedIds = new HashSet<Integer>();
-
- for (Element element : model.getElements()) {
- if (element instanceof Species) {
- for (MiriamData md : ((Species) element).getMiriamData()) {
- if (MiriamType.PUBMED.equals(md.getDataType())) {
- try {
- pubmedIds.add(Integer.parseInt(md.getResource()));
- } catch (NumberFormatException e) {
- logger.error("Problem with parsing: " + e.getMessage(), e);
- }
- }
- }
- }
- }
- for (Reaction reaction : model.getReactions()) {
- for (MiriamData md : reaction.getMiriamData()) {
- if (MiriamType.PUBMED.equals(md.getDataType())) {
- try {
- pubmedIds.add(Integer.parseInt(md.getResource()));
- } catch (NumberFormatException e) {
- logger.error("Problem with parsing: " + e.getMessage(), e);
- }
- }
- }
- }
- double amount = pubmedIds.size();
- double counter = 0;
- for (Integer id : pubmedIds) {
- Article art = backend.getPubmedArticleById(id);
- if (art == null) {
- logger.warn("Cannot find pubmed article. Pubmed_id = " + id);
- }
- counter++;
- updater.setProgress(IProgressUpdater.MAX_PROGRESS * counter / amount);
- }
- }
- logger.debug("Caching finished");
- }
-
- @Override
- public void updateModel(ModelData model, ProjectView selectedProject) {
-
- for (Model cachedModel : models.values()) {
- if (cachedModel.getId().equals(selectedProject.getModelId())) {
- setModel(cachedModel.getModelData(), selectedProject);
- }
- }
- setModel(model, selectedProject);
- modelDao.update(model);
- }
-
- /**
- * Sets the data from selectedProject into model.
- *
- * @param model
- * destination of the data
- * @param selectedProject
- * source of the data
- */
- private void setModel(ModelData model, ProjectView selectedProject) {
- model.setNotes(selectedProject.getDescription());
- model.setMapVersion(selectedProject.getVersion());
- model.setNotifyEmail(selectedProject.getNotifyEmail());
- List<Layout> toRemove = new ArrayList<Layout>();
- for (Layout layout : model.getLayouts()) {
- boolean exists = false;
- for (LayoutView row : selectedProject.getLayouts()) {
- if (layout.getId() == row.getIdObject()) {
- exists = true;
- // don't allow client side to edit layouts
- // layout.setDirectory(row.getDirectory());
- layout.setTitle(row.getName());
- layout.setDescription(row.getDescription());
- }
- }
- if (!exists) {
- toRemove.add(layout);
- }
- }
- model.getLayouts().removeAll(toRemove);
-
- MiriamData disease = null;
- if (selectedProject.getNewDiseaseName() != null) {
- disease = new MiriamData(MiriamType.MESH_2012, selectedProject.getNewDiseaseName());
- }
-
- try {
- if (meshParser.isValidMeshId(disease)) {
- model.getProject().setDisease(disease);
- } else {
- model.getProject().setDisease(null);
- selectedProject.setNewDiseaseName(null);
- }
- } catch (AnnotatorException e) {
- logger.warn("Problem with accessing mesh db");
- }
-
- if (model.getProject() != null) {
- MiriamData organism = null;
- if (selectedProject.getNewOrganismName() != null && !selectedProject.getNewOrganismName().isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, selectedProject.getNewOrganismName());
- }
-
- try {
- if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
- model.getProject().setOrganism(organism);
- } else {
- model.getProject().setOrganism(null);
- }
- } catch (TaxonomySearchException e) {
- logger.error("Problem with accessing taxonomy db", e);
- model.getProject().setOrganism(null);
- }
- }
-
- }
-
- @Override
- public void removeModelFromCache(Model model) {
- models.remove(model.getProject().getProjectId());
-
- }
-
- /**
- * @return the modelDao
- * @see #modelDao
- */
- public ModelDao getModelDao() {
- return modelDao;
- }
-
- /**
- * @param modelDao
- * the modelDao to set
- * @see #modelDao
- */
- public void setModelDao(ModelDao modelDao) {
- this.modelDao = modelDao;
- }
-
- /**
- * @return the backend
- * @see #backend
- */
- public PubmedParser getBackend() {
- return backend;
- }
-
- /**
- * @param backend
- * the backend to set
- * @see #backend
- */
- public void setBackend(PubmedParser backend) {
- this.backend = backend;
- }
-
- @Override
- public void cacheAllMiriamLinks(Model model, IProgressUpdater updater) {
- logger.debug("Caching miriam ids...");
- if (model != null) {
- Set<MiriamData> pubmedIds = new HashSet<MiriamData>();
-
- for (Element element : model.getElements()) {
- pubmedIds.addAll(element.getMiriamData());
- }
- for (Reaction reaction : model.getReactions()) {
- pubmedIds.addAll(reaction.getMiriamData());
- }
- double amount = pubmedIds.size();
- double counter = 0;
- for (MiriamData md : pubmedIds) {
- miriamConnector.getUrlString(md);
- counter++;
- updater.setProgress(IProgressUpdater.MAX_PROGRESS * counter / amount);
- }
- }
- logger.debug("Caching finished");
-
- }
-
- @Override
- public ModelView getModelView(Model model, User user) {
- ModelView result = modelViewFactory.create(model);
- if (user != null) {
- result.setCustomLayouts(layoutService.getCustomLayouts(model, user));
- for (ModelView view : result.getSubmodels()) {
- view.setCustomLayouts(layoutService.getCustomLayouts(model.getSubmodelById(view.getIdObject()), user));
- }
- }
- return result;
- }
-
- @Override
- public void removeModelFromCache(ModelData model) {
- models.remove(model.getProject().getProjectId());
- }
-
- /**
- * @return the layoutService
- * @see #layoutService
- */
- public ILayoutService getLayoutService() {
- return layoutService;
- }
-
- /**
- * @param layoutService
- * the layoutService to set
- * @see #layoutService
- */
- public void setLayoutService(ILayoutService layoutService) {
- this.layoutService = layoutService;
- }
-
- @Override
- public void removeModelFromCacheByProjectId(String projectId) {
- models.remove(projectId);
- }
-
- @Override
- public List<LightAliasView> getLightAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
- LightAliasViewFactory lightAliasViewFactory = new LightAliasViewFactory();
- List<LightAliasView> result = lightAliasViewFactory.createList(getAliasesByIds(model, identifiers));
- return result;
- }
-
- /**
- * Returns list of {@link Alias aliases} for given identifiers.
- *
- * @param model
- * model where aliases are located
- * @param identifiers
- * list of alias identifiers in a given submodel. Every {@link Pair}
- * contains information about {@link Model#getId() model identifier}
- * (in {@link Pair#left}) and
- * {@link lcsb.mapviewer.model.map.layout.alias.Alias#getId() alias
- * identifier} (in {@link Pair#right}).
- * @return list of {@link Alias aliases} for given identifiers
- */
- private List<Alias> getAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
- Map<Integer, Set<Integer>> identifiersForMap = new HashMap<>();
- for (Pair<Integer, Integer> pair : identifiers) {
- Set<Integer> set = identifiersForMap.get(pair.getLeft());
- if (set == null) {
- set = new HashSet<>();
- identifiersForMap.put(pair.getLeft(), set);
- }
- set.add(pair.getRight());
- }
-
- List<Alias> result = new ArrayList<>();
- List<Model> models = new ArrayList<>();
- models.add(model);
- models.addAll(model.getSubmodels());
- for (Model model2 : models) {
- Set<Integer> set = identifiersForMap.get(model2.getModelData().getId());
- if (set != null) {
- for (Alias alias : model2.getAliases()) {
- if (set.contains(alias.getId())) {
- result.add(alias);
- set.remove(alias.getId());
- }
- if (set.size() == 0) {
- break;
- }
- }
- if (set.size() > 0) {
- Integer aliasId = set.iterator().next();
- throw new InvalidArgumentException("Cannot find alias (id: " + aliasId + ") in a model (id: " + model2.getModelData().getId() + ")");
- }
- identifiersForMap.remove(model2.getModelData().getId());
- }
- }
- if (identifiersForMap.keySet().size() > 0) {
- Integer modelId = identifiersForMap.keySet().iterator().next();
- Integer aliasId = identifiersForMap.get(modelId).iterator().next();
- throw new InvalidArgumentException("Cannot find alias (id: " + aliasId + ") in a model (id: " + modelId + "). Model doesn't exist.");
- }
- return result;
- }
-
- @Override
- public List<LightReactionView> getLightReactionsByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
-
- Map<Integer, Set<Integer>> identifiersForMap = new HashMap<>();
- for (Pair<Integer, Integer> pair : identifiers) {
- Set<Integer> set = identifiersForMap.get(pair.getLeft());
- if (set == null) {
- set = new HashSet<>();
- identifiersForMap.put(pair.getLeft(), set);
- }
- set.add(pair.getRight());
- }
-
- List<LightReactionView> result = new ArrayList<>();
- List<Model> models = new ArrayList<>();
- models.add(model);
- models.addAll(model.getSubmodels());
- for (Model model2 : models) {
- Set<Integer> set = identifiersForMap.get(model2.getModelData().getId());
- if (set != null) {
- for (Reaction reaction : model2.getReactions()) {
- if (set.contains(reaction.getId())) {
- result.add(new LightReactionView(reaction));
- set.remove(reaction.getId());
- }
- if (set.size() == 0) {
- break;
- }
- }
- if (set.size() > 0) {
- Integer aliasId = set.iterator().next();
- throw new InvalidArgumentException("Cannot find reaction (id: " + aliasId + ") in a model (id: " + model2.getModelData().getId() + ")");
- }
- identifiersForMap.remove(model2.getModelData().getId());
- }
- }
- if (identifiersForMap.keySet().size() > 0) {
- Integer modelId = identifiersForMap.keySet().iterator().next();
- Integer aliasId = identifiersForMap.get(modelId).iterator().next();
- throw new InvalidArgumentException("Cannot find reaction (id: " + aliasId + ") in a model (id: " + modelId + "). Model doesn't exist.");
- }
- return result;
- }
-
- @Override
- public List<FullAliasView> getFullAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
- List<FullAliasView> result = fullAliasViewFactory.createList(getAliasesByIds(model, identifiers));
- return result;
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.Article;
+import lcsb.mapviewer.annotation.services.MeSHParser;
+import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.annotation.services.PubmedSearchException;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.annotation.services.TaxonomySearchException;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.commands.CopyCommand;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.map.ModelDao;
+import lcsb.mapviewer.services.interfaces.ILayoutService;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.search.data.FullAliasView;
+import lcsb.mapviewer.services.search.data.FullAliasViewFactory;
+import lcsb.mapviewer.services.search.data.LightAliasView;
+import lcsb.mapviewer.services.search.data.LightAliasViewFactory;
+import lcsb.mapviewer.services.search.data.LightReactionView;
+import lcsb.mapviewer.services.view.LayoutView;
+import lcsb.mapviewer.services.view.ModelView;
+import lcsb.mapviewer.services.view.ModelViewFactory;
+import lcsb.mapviewer.services.view.ProjectView;
+
+/**
+ * Implementation of the service that manages models.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class ModelService implements IModelService {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ModelService.class);
+
+ /**
+ * List of cached models.
+ */
+ private static Map<String, Model> models = new HashMap<String, Model>();
+
+ /**
+ * List of models that are currently being loaded from databsae.
+ */
+ private static Set<String> modelsInLoadStage = new HashSet<>();
+
+ /**
+ * Data access object for models.
+ */
+ @Autowired
+ private ModelDao modelDao;
+
+ /**
+ * Object allowing access to the mesh database.
+ */
+ @Autowired
+ private MeSHParser meshParser;
+
+ /**
+ * Local backend to the pubmed data.
+ */
+ @Autowired
+ private PubmedParser backend;
+
+ /**
+ * Service used for managing layouts.
+ */
+ @Autowired
+ private ILayoutService layoutService;
+
+ /**
+ * Connector used for accessing data from miriam registry.
+ */
+ @Autowired
+ private MiriamConnector miriamConnector;
+
+ /**
+ * Factory object used for creation of {@link ModelView} elements.
+ */
+ @Autowired
+ private ModelViewFactory modelViewFactory;
+
+ /**
+ * Factory used to create {@link FullAliasView} elements.
+ */
+ @Autowired
+ private FullAliasViewFactory fullAliasViewFactory;
+
+ /**
+ * Access point and parser for the online ctd database.
+ */
+ @Autowired
+ private TaxonomyBackend taxonomyBackend;
+
+ @Override
+ public Model getLastModelByProjectId(String projectName) {
+ if (projectName == null) {
+ return null;
+ }
+
+ // check if model is being loaded by another thread
+ boolean waitForModel = false;
+ do {
+ synchronized (modelsInLoadStage) {
+ waitForModel = modelsInLoadStage.contains(projectName);
+ }
+ // if model is being loaded then wait until it's loaded
+ if (waitForModel) {
+ try {
+ Thread.sleep(100);
+ } catch (InterruptedException e) {
+ logger.fatal(e, e);
+ }
+ }
+ } while (waitForModel);
+
+ Model model = models.get(projectName);
+ if (model == null) {
+ try {
+ // mark model as being load stage, so other threads that want to access
+ // it will wait
+ synchronized (modelsInLoadStage) {
+ modelsInLoadStage.add(projectName);
+ }
+ logger.debug("Unknown model, trying to load the model into memory.");
+
+ ModelData modelData = modelDao.getLastModelForProjectIdentifier(projectName, false);
+
+ if (modelData == null) {
+ logger.debug("Model doesn't exist");
+ return null;
+ }
+ logger.debug("Model loaded from db.");
+ model = new ModelFullIndexed(modelData);
+
+ // this is a trick to load all required subelements of the model... ;/
+ // lets copy model - it will access all elements...
+ new CopyCommand(model).execute();
+
+ logger.debug("Model loaded successfullly");
+ models.put(projectName, model);
+ } finally {
+ // model is not being loaded anymore
+ synchronized (modelsInLoadStage) {
+ modelsInLoadStage.remove(projectName);
+ }
+ }
+ }
+ return model;
+ }
+
+ @Override
+ public void cacheAllPubmedIds(Model model, IProgressUpdater updater) {
+ logger.debug("Caching pubmed ids...");
+ if (model != null) {
+ Set<Integer> pubmedIds = new HashSet<Integer>();
+
+ for (Element element : model.getElements()) {
+ if (element instanceof Species) {
+ for (MiriamData md : ((Species) element).getMiriamData()) {
+ if (MiriamType.PUBMED.equals(md.getDataType())) {
+ try {
+ pubmedIds.add(Integer.parseInt(md.getResource()));
+ } catch (NumberFormatException e) {
+ logger.error("Problem with parsing: " + e.getMessage(), e);
+ }
+ }
+ }
+ }
+ }
+ for (Reaction reaction : model.getReactions()) {
+ for (MiriamData md : reaction.getMiriamData()) {
+ if (MiriamType.PUBMED.equals(md.getDataType())) {
+ try {
+ pubmedIds.add(Integer.parseInt(md.getResource()));
+ } catch (NumberFormatException e) {
+ logger.error("Problem with parsing: " + e.getMessage(), e);
+ }
+ }
+ }
+ }
+ double amount = pubmedIds.size();
+ double counter = 0;
+ for (Integer id : pubmedIds) {
+ try {
+ Article art = backend.getPubmedArticleById(id);
+ if (art == null) {
+ logger.warn("Cannot find pubmed article. Pubmed_id = " + id);
+ }
+ } catch (PubmedSearchException e) {
+ logger.warn("Problem with accessing info about pubmed: " + id, e);
+ }
+ counter++;
+ updater.setProgress(IProgressUpdater.MAX_PROGRESS * counter / amount);
+ }
+ }
+ logger.debug("Caching finished");
+ }
+
+ @Override
+ public void updateModel(ModelData model, ProjectView selectedProject) {
+
+ for (Model cachedModel : models.values()) {
+ if (cachedModel.getId().equals(selectedProject.getModelId())) {
+ setModel(cachedModel.getModelData(), selectedProject);
+ }
+ }
+ setModel(model, selectedProject);
+ modelDao.update(model);
+ }
+
+ /**
+ * Sets the data from selectedProject into model.
+ *
+ * @param model
+ * destination of the data
+ * @param selectedProject
+ * source of the data
+ */
+ private void setModel(ModelData model, ProjectView selectedProject) {
+ model.setNotes(selectedProject.getDescription());
+ model.setMapVersion(selectedProject.getVersion());
+ model.setNotifyEmail(selectedProject.getNotifyEmail());
+ List<Layout> toRemove = new ArrayList<Layout>();
+ for (Layout layout : model.getLayouts()) {
+ boolean exists = false;
+ for (LayoutView row : selectedProject.getLayouts()) {
+ if (layout.getId() == row.getIdObject()) {
+ exists = true;
+ // don't allow client side to edit layouts
+ // layout.setDirectory(row.getDirectory());
+ layout.setTitle(row.getName());
+ layout.setDescription(row.getDescription());
+ }
+ }
+ if (!exists) {
+ toRemove.add(layout);
+ }
+ }
+ model.getLayouts().removeAll(toRemove);
+
+ MiriamData disease = null;
+ if (selectedProject.getNewDiseaseName() != null) {
+ disease = new MiriamData(MiriamType.MESH_2012, selectedProject.getNewDiseaseName());
+ }
+
+ try {
+ if (meshParser.isValidMeshId(disease)) {
+ model.getProject().setDisease(disease);
+ } else {
+ model.getProject().setDisease(null);
+ selectedProject.setNewDiseaseName(null);
+ }
+ } catch (AnnotatorException e) {
+ logger.warn("Problem with accessing mesh db");
+ }
+
+ if (model.getProject() != null) {
+ MiriamData organism = null;
+ if (selectedProject.getNewOrganismName() != null && !selectedProject.getNewOrganismName().isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, selectedProject.getNewOrganismName());
+ }
+
+ try {
+ if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
+ model.getProject().setOrganism(organism);
+ } else {
+ model.getProject().setOrganism(null);
+ }
+ } catch (TaxonomySearchException e) {
+ logger.error("Problem with accessing taxonomy db", e);
+ model.getProject().setOrganism(null);
+ }
+ }
+
+ }
+
+ @Override
+ public void removeModelFromCache(Model model) {
+ models.remove(model.getProject().getProjectId());
+
+ }
+
+ /**
+ * @return the modelDao
+ * @see #modelDao
+ */
+ public ModelDao getModelDao() {
+ return modelDao;
+ }
+
+ /**
+ * @param modelDao
+ * the modelDao to set
+ * @see #modelDao
+ */
+ public void setModelDao(ModelDao modelDao) {
+ this.modelDao = modelDao;
+ }
+
+ /**
+ * @return the backend
+ * @see #backend
+ */
+ public PubmedParser getBackend() {
+ return backend;
+ }
+
+ /**
+ * @param backend
+ * the backend to set
+ * @see #backend
+ */
+ public void setBackend(PubmedParser backend) {
+ this.backend = backend;
+ }
+
+ @Override
+ public void cacheAllMiriamLinks(Model model, IProgressUpdater updater) {
+ logger.debug("Caching miriam ids...");
+ if (model != null) {
+ Set<MiriamData> pubmedIds = new HashSet<MiriamData>();
+
+ for (Element element : model.getElements()) {
+ pubmedIds.addAll(element.getMiriamData());
+ }
+ for (Reaction reaction : model.getReactions()) {
+ pubmedIds.addAll(reaction.getMiriamData());
+ }
+ double amount = pubmedIds.size();
+ double counter = 0;
+ for (MiriamData md : pubmedIds) {
+ miriamConnector.getUrlString(md);
+ counter++;
+ updater.setProgress(IProgressUpdater.MAX_PROGRESS * counter / amount);
+ }
+ }
+ logger.debug("Caching finished");
+
+ }
+
+ @Override
+ public ModelView getModelView(Model model, User user) {
+ ModelView result = modelViewFactory.create(model);
+ if (user != null) {
+ result.setCustomLayouts(layoutService.getCustomLayouts(model, user));
+ for (ModelView view : result.getSubmodels()) {
+ view.setCustomLayouts(layoutService.getCustomLayouts(model.getSubmodelById(view.getIdObject()), user));
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public void removeModelFromCache(ModelData model) {
+ models.remove(model.getProject().getProjectId());
+ }
+
+ /**
+ * @return the layoutService
+ * @see #layoutService
+ */
+ public ILayoutService getLayoutService() {
+ return layoutService;
+ }
+
+ /**
+ * @param layoutService
+ * the layoutService to set
+ * @see #layoutService
+ */
+ public void setLayoutService(ILayoutService layoutService) {
+ this.layoutService = layoutService;
+ }
+
+ @Override
+ public void removeModelFromCacheByProjectId(String projectId) {
+ models.remove(projectId);
+ }
+
+ @Override
+ public List<LightAliasView> getLightAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
+ LightAliasViewFactory lightAliasViewFactory = new LightAliasViewFactory();
+ List<LightAliasView> result = lightAliasViewFactory.createList(getAliasesByIds(model, identifiers));
+ return result;
+ }
+
+ /**
+ * Returns list of {@link Alias aliases} for given identifiers.
+ *
+ * @param model
+ * model where aliases are located
+ * @param identifiers
+ * list of alias identifiers in a given submodel. Every {@link Pair}
+ * contains information about {@link Model#getId() model identifier}
+ * (in {@link Pair#left}) and
+ * {@link lcsb.mapviewer.model.map.layout.alias.Alias#getId() alias
+ * identifier} (in {@link Pair#right}).
+ * @return list of {@link Alias aliases} for given identifiers
+ */
+ private List<Alias> getAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
+ Map<Integer, Set<Integer>> identifiersForMap = new HashMap<>();
+ for (Pair<Integer, Integer> pair : identifiers) {
+ Set<Integer> set = identifiersForMap.get(pair.getLeft());
+ if (set == null) {
+ set = new HashSet<>();
+ identifiersForMap.put(pair.getLeft(), set);
+ }
+ set.add(pair.getRight());
+ }
+
+ List<Alias> result = new ArrayList<>();
+ List<Model> models = new ArrayList<>();
+ models.add(model);
+ models.addAll(model.getSubmodels());
+ for (Model model2 : models) {
+ Set<Integer> set = identifiersForMap.get(model2.getModelData().getId());
+ if (set != null) {
+ for (Alias alias : model2.getAliases()) {
+ if (set.contains(alias.getId())) {
+ result.add(alias);
+ set.remove(alias.getId());
+ }
+ if (set.size() == 0) {
+ break;
+ }
+ }
+ if (set.size() > 0) {
+ Integer aliasId = set.iterator().next();
+ throw new InvalidArgumentException("Cannot find alias (id: " + aliasId + ") in a model (id: " + model2.getModelData().getId() + ")");
+ }
+ identifiersForMap.remove(model2.getModelData().getId());
+ }
+ }
+ if (identifiersForMap.keySet().size() > 0) {
+ Integer modelId = identifiersForMap.keySet().iterator().next();
+ Integer aliasId = identifiersForMap.get(modelId).iterator().next();
+ throw new InvalidArgumentException("Cannot find alias (id: " + aliasId + ") in a model (id: " + modelId + "). Model doesn't exist.");
+ }
+ return result;
+ }
+
+ @Override
+ public List<LightReactionView> getLightReactionsByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
+
+ Map<Integer, Set<Integer>> identifiersForMap = new HashMap<>();
+ for (Pair<Integer, Integer> pair : identifiers) {
+ Set<Integer> set = identifiersForMap.get(pair.getLeft());
+ if (set == null) {
+ set = new HashSet<>();
+ identifiersForMap.put(pair.getLeft(), set);
+ }
+ set.add(pair.getRight());
+ }
+
+ List<LightReactionView> result = new ArrayList<>();
+ List<Model> models = new ArrayList<>();
+ models.add(model);
+ models.addAll(model.getSubmodels());
+ for (Model model2 : models) {
+ Set<Integer> set = identifiersForMap.get(model2.getModelData().getId());
+ if (set != null) {
+ for (Reaction reaction : model2.getReactions()) {
+ if (set.contains(reaction.getId())) {
+ result.add(new LightReactionView(reaction));
+ set.remove(reaction.getId());
+ }
+ if (set.size() == 0) {
+ break;
+ }
+ }
+ if (set.size() > 0) {
+ Integer aliasId = set.iterator().next();
+ throw new InvalidArgumentException("Cannot find reaction (id: " + aliasId + ") in a model (id: " + model2.getModelData().getId() + ")");
+ }
+ identifiersForMap.remove(model2.getModelData().getId());
+ }
+ }
+ if (identifiersForMap.keySet().size() > 0) {
+ Integer modelId = identifiersForMap.keySet().iterator().next();
+ Integer aliasId = identifiersForMap.get(modelId).iterator().next();
+ throw new InvalidArgumentException("Cannot find reaction (id: " + aliasId + ") in a model (id: " + modelId + "). Model doesn't exist.");
+ }
+ return result;
+ }
+
+ @Override
+ public List<FullAliasView> getFullAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
+ List<FullAliasView> result = fullAliasViewFactory.createList(getAliasesByIds(model, identifiers));
+ return result;
+ }
+
+}
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
index 69953b6392e0d942780fd214d2704b723accfe38..617961809d3857368b379a4ed8f972b840a786a5 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/TargetViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/TargetViewFactory.java
@@ -1,155 +1,158 @@
-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.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
-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<AnnotatedObject> list = new HashSet<>();
- list.addAll(model.getSpeciesByName(md.getResource()));
- list.addAll(model.getElementsByAnnotation(md));
-
- int countInTopModel = list.size();
- for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- list.addAll(submodel.getSubmodel().getModel().getSpeciesByName(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);
- }
- } 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();
- }
-}
+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.AnnotatedObject;
+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<AnnotatedObject> list = new HashSet<>();
+ list.addAll(model.getSpeciesByName(md.getResource()));
+ list.addAll(model.getElementsByAnnotation(md));
+
+ int countInTopModel = list.size();
+ for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
+ list.addAll(submodel.getSubmodel().getModel().getSpeciesByName(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/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java
index 107a22c1e3dd155b673a77c5e2df0c9061c9f9b1..69f2559cdddcfd0c94ee3758c656c1d0ba0c4ec7 100644
--- 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
@@ -1,188 +1,193 @@
-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.annotators.AnnotatorException;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-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.getSynonymsString());
- } else {
- chemicalView.setDescription("Mesh term not available");
- chemicalView.setSynonyms("N/A");
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with accessing mesh database", e);
- chemicalView.setDescription("Mesh term not available");
- chemicalView.setSynonyms("N/A");
- }
- }
-
- 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());
- Article article = pubmedParser.getPubmedArticleById(id);
- if (article != null) {
- articles.add(article);
- }
- } 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)) {
- for (Alias alias : model.getAliasesForElement(element)) {
- result.add(new ElementIdentifier(alias, target.getIcon()));
- }
- }
- }
- }
- }
- }
- return result;
- }
-}
+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.Element;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.model.Model;
+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.getSynonymsString());
+ } else {
+ chemicalView.setDescription("Mesh term not available");
+ chemicalView.setSynonyms("N/A");
+ }
+ } catch (AnnotatorException e) {
+ logger.error("Problem with accessing mesh database", e);
+ chemicalView.setDescription("Mesh term not available");
+ chemicalView.setSynonyms("N/A");
+ }
+ }
+
+ 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)) {
+ for (Alias alias : model.getAliasesForElement(element)) {
+ result.add(new ElementIdentifier(alias, target.getIcon()));
+ }
+ }
+ }
+ }
+ }
+ }
+ return result;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/AnnotationViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/AnnotationViewFactory.java
index 39f49c3ac250e632c8a76f1f717e32fd08fbdfbb..c0a20024454f6626eaedeb748177b0c6097d5cf1 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/AnnotationViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/AnnotationViewFactory.java
@@ -1,102 +1,108 @@
-package lcsb.mapviewer.services.view;
-
-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.MiriamConnector;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.graph.DataMiningType;
-
-/**
- * Factory class for {@link AnnotationView} class.
- *
- * @author Piotr Gawron
- *
- */
-public class AnnotationViewFactory extends AbstractViewFactory<MiriamData, AnnotationView> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(AnnotationViewFactory.class);
-
- /**
- * Local backend to the pubmed data.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
- /**
- * Local backend to the miriam registry.
- */
- @Autowired
- private MiriamConnector miriamConnector;
-
- @Override
- public AnnotationView create(MiriamData object) {
- AnnotationView result = new AnnotationView(object);
- if (object != null && object.getDataType() != null) {
- if (object.getDataType().getUris().size() > 0) {
- try {
- result.setLink(miriamConnector.getUrlString(object));
- } catch (Exception e) {
- logger.error("Problem with miriam: " + object, e);
- }
- }
- if (MiriamType.PUBMED.equals(object.getDataType())) {
- String summary = pubmedParser.getSummary(object.getResource());
- // workaround,
- // tak a look at Bug #461
- if (summary != null) {
- result.setSummary(summary.replace("\\", "\\\\"));
- }
- }
- result.setType(object.getDataType().getCommonName());
- result.setName(object.getResource());
- }
- return result;
- }
-
- /**
- * Creates {@link AnnotationView} for {@link DataMiningType} object.
- *
- * @param dataMiningType
- * type of datamining element
- * @return {@link AnnotationView} for {@link DataMiningType} object
- */
- public AnnotationView create(DataMiningType dataMiningType) {
- AnnotationView result = new AnnotationView(null);
- result.setName(dataMiningType.getCommonName());
- if (dataMiningType.getSource() != null) {
- result.setLink(DataMiningType.STRUCTURE_ANALYSIS.getSource());
- }
- return result;
- }
-
- @Override
- public String createGson(AnnotationView object) {
- return new Gson().toJson(object);
- }
-
- @Override
- public MiriamData viewToObject(AnnotationView view) {
- MiriamType type = MiriamType.getTypeByCommonName(view.getType());
- return new MiriamData(type, view.getName());
- }
-
- /**
- * Creates {@link AnnotationView} from an {@link Article}.
- *
- * @param article
- * object from which we create {@link AnnotationView}
- * @return {@link AnnotationView} from an {@link Article}
- */
- public AnnotationView create(Article article) {
- return create(new MiriamData(MiriamType.PUBMED, article.getId()));
- }
-
-}
+package lcsb.mapviewer.services.view;
+
+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.MiriamConnector;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.annotation.services.PubmedSearchException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.graph.DataMiningType;
+
+/**
+ * Factory class for {@link AnnotationView} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AnnotationViewFactory extends AbstractViewFactory<MiriamData, AnnotationView> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(AnnotationViewFactory.class);
+
+ /**
+ * Local backend to the pubmed data.
+ */
+ @Autowired
+ private PubmedParser pubmedParser;
+
+ /**
+ * Local backend to the miriam registry.
+ */
+ @Autowired
+ private MiriamConnector miriamConnector;
+
+ @Override
+ public AnnotationView create(MiriamData object) {
+ AnnotationView result = new AnnotationView(object);
+ if (object != null && object.getDataType() != null) {
+ if (object.getDataType().getUris().size() > 0) {
+ try {
+ result.setLink(miriamConnector.getUrlString(object));
+ } catch (Exception e) {
+ logger.error("Problem with miriam: " + object, e);
+ }
+ }
+ if (MiriamType.PUBMED.equals(object.getDataType())) {
+ try {
+ String summary = pubmedParser.getSummary(object.getResource());
+ // workaround,
+ // tak a look at Bug #461
+ if (summary != null) {
+ result.setSummary(summary.replace("\\", "\\\\"));
+ }
+ } catch (PubmedSearchException e) {
+ logger.error("Problem with accessing info about pubmed", e);
+ result.setSummary("N/A");
+ }
+ }
+ result.setType(object.getDataType().getCommonName());
+ result.setName(object.getResource());
+ }
+ return result;
+ }
+
+ /**
+ * Creates {@link AnnotationView} for {@link DataMiningType} object.
+ *
+ * @param dataMiningType
+ * type of datamining element
+ * @return {@link AnnotationView} for {@link DataMiningType} object
+ */
+ public AnnotationView create(DataMiningType dataMiningType) {
+ AnnotationView result = new AnnotationView(null);
+ result.setName(dataMiningType.getCommonName());
+ if (dataMiningType.getSource() != null) {
+ result.setLink(DataMiningType.STRUCTURE_ANALYSIS.getSource());
+ }
+ return result;
+ }
+
+ @Override
+ public String createGson(AnnotationView object) {
+ return new Gson().toJson(object);
+ }
+
+ @Override
+ public MiriamData viewToObject(AnnotationView view) {
+ MiriamType type = MiriamType.getTypeByCommonName(view.getType());
+ return new MiriamData(type, view.getName());
+ }
+
+ /**
+ * Creates {@link AnnotationView} from an {@link Article}.
+ *
+ * @param article
+ * object from which we create {@link AnnotationView}
+ * @return {@link AnnotationView} from an {@link Article}
+ */
+ public AnnotationView create(Article article) {
+ return create(new MiriamData(MiriamType.PUBMED, article.getId()));
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java
index 20663ff1bf763ab9a9f845388df7a2e63ff6ece8..54dc5b2e7b5a03891c2d3a24c47165108c220341 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java
@@ -1,79 +1,88 @@
-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.services.PubmedParser;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
-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.
- */
- @SuppressWarnings("unused")
- 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");
- }
- result.setArticle(pubmedParser.getPubmedArticleById(Integer.valueOf(element.getResource())));
- 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<AnnotatedObject> elements = model.getElementsByAnnotation(miriamData);
- for (Model submodel : model.getSubmodels()) {
- elements.addAll(submodel.getElementsByAnnotation(miriamData));
- }
- for (AnnotatedObject 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();
- }
-}
+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.AnnotatedObject;
+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<AnnotatedObject> elements = model.getElementsByAnnotation(miriamData);
+ for (Model submodel : model.getSubmodels()) {
+ elements.addAll(submodel.getElementsByAnnotation(miriamData));
+ }
+ for (AnnotatedObject 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();
+ }
+}