--- /dev/null
+/**
+ * Downloaded from http://code.cytoscape.org/redmine/projects/cy3-impl/repository/revisions/171d9affb3499807b14db17702176b0b82d16878/raw/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/EntrezRestClient.java
+ * Originally in package org.cytoscape.webservice.ncbi.rest;
+ * Cytoscape3 code
+ * License and author attribution currently unknown.
+ */
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentMap;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.TimeUnit;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.commons.logging.LogFactory;
+import org.apache.log4j.spi.LoggerFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.SAXException;
+
+
+public class EntrezRestClient {
+ private static final org.apache.commons.logging.Log logger = LogFactory.getLog(EntrezRestClient.class);
+ private static final String BASE_URL = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/";
+ public static final String FETCH_URL = BASE_URL + "efetch.fcgi?db=gene&retmode=xml&id=";
+ private static final String SEARCH_URL = BASE_URL + "esearch.fcgi?db=gene&retmax=100000&term=";
+ private final String regex = "\\s+";
+ private static final String ID = "Id";
+
+ private final CyTableFactory tableFactory;
+ private final CyNetworkFactory networkFactory;
+ private final CyTableManager tableManager;
+
+ public EntrezRestClient(final CyNetworkFactory networkFactory,
+ final CyTableFactory tableFactory, final CyTableManager tableManager)
+ {
+ this.networkFactory = networkFactory;
+ this.tableFactory = tableFactory;
+ this.tableManager = tableManager;
+ }
+
+ public Set<String> search(final String queryString) throws IOException, ParserConfigurationException, SAXException {
+ final URL url = createURL(SEARCH_URL, queryString);
+
+ final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ final DocumentBuilder builder = factory.newDocumentBuilder();
+ InputStream is = url.openStream();
+
+ final Document result = builder.parse(is);
+
+ final Set<String> idSet = new HashSet<String>();
+ final NodeList ids = result.getElementsByTagName(ID);
+ final int dataSize = ids.getLength();
+
+ for (int i = 0; i < dataSize; i++) {
+ Node id = ids.item(i);
+ idSet.add(id.getTextContent());
+ }
+
+ is.close();
+ is = null;
+
+ return idSet;
+ }
+
+ public CyNetwork importNetwork(final Set<String> idList) {
+
+ long startTime = System.currentTimeMillis();
+
+ final ExecutorService executer = Executors.newFixedThreadPool(4);
+
+ logger.debug("Executor initialized.");
+ // final CyNetwork newNetwork = networkFactory.getInstance();
+
+
+ final ConcurrentMap<String, CyNode> nodeName2CyNodeMap = new ConcurrentHashMap<String, CyNode>();
+
+ int group = 0;
+ int buketNum = 10;
+ String[] box = new String[buketNum];
+
+
+ for (String entrezID : idList) {
+ box[group] = entrezID;
+ group++;
+
+ if (group == buketNum) {
+ executer.submit(new EntryProcessor<String>(new ImportNetworkTask<String>(box, newNetwork, nodeName2CyNodeMap)));
+ group = 0;
+ box = new String[buketNum];
+ }
+ }
+
+ String[] newbox = new String[group];
+
+ for (int i = 0; i < group; i++)
+ newbox[i] = box[i];
+
+ executer.submit(new EntryProcessor<String>(new ImportNetworkTask<String>(box, newNetwork, nodeName2CyNodeMap)));
+
+ try {
+ executer.shutdown();
+ executer.awaitTermination(1000, TimeUnit.SECONDS);
+
+ long endTime = System.currentTimeMillis();
+ double sec = (endTime - startTime) / (1000.0);
+ System.out.println("Finished in " + sec + " sec.");
+
+// if ((canceled != null) && canceled) {
+// canceled = null;
+//
+// return null;
+// }
+ } catch( Exception ex) {
+ ex.printStackTrace();
+ }
+
+ return newNetwork;
+ }
+
+
+
+ public CyTable importDataTable(final Set<String> idList, final Set<AnnotationCategory> category) {
+ if(idList == null || idList.size() == 0)
+ throw new IllegalArgumentException("ID list is null.");
+
+ long startTime = System.currentTimeMillis();
+ final ExecutorService executer = Executors.newFixedThreadPool(4);
+
+ logger.debug("Table Import Executor initialized.");
+ final Date currentDate = new Date();
+ final CyTable table = tableFactory.createTable("NCBI Global Table: " + currentDate.toString(), CyTableEntry.NAME, String.class, true, true);
+
+ int group = 0;
+ int buketNum = 10;
+ String[] box = new String[buketNum];
+
+
+ for (String entrezID : idList) {
+ box[group] = entrezID;
+ group++;
+
+ if (group == buketNum) {
+ executer.submit(new ImportTableTask(box, category, table));
+ group = 0;
+ box = new String[buketNum];
+ }
+ }
+
+ String[] newbox = new String[group];
+
+ for (int i = 0; i < group; i++)
+ newbox[i] = box[i];
+
+ executer.submit(new ImportTableTask(box, category, table));
+
+ try {
+ executer.shutdown();
+ executer.awaitTermination(1000, TimeUnit.SECONDS);
+
+ long endTime = System.currentTimeMillis();
+ double sec = (endTime - startTime) / (1000.0);
+ System.out.println("Table Import Finished in " + sec + " sec.");
+
+// if ((canceled != null) && canceled) {
+// canceled = null;
+//
+// return null;
+// }
+ } catch( Exception ex) {
+ ex.printStackTrace();
+ }
+
+ tableManager.addTable(table);
+
+ return table;
+ }
+
+ private URL createURL(final String base, final String queryString) throws IOException {
+ final String[] parts = queryString.split(regex);
+ final StringBuilder builder = new StringBuilder();
+
+ if (parts.length != 0) {
+ for (String dTerm : parts) {
+ final String trimed = dTerm.trim();
+ builder.append(trimed + "+");
+ }
+ }
+
+ String urlString = builder.toString();
+ urlString = urlString.substring(0, urlString.length() - 1);
+ final URL url = new URL(base + urlString);
+ logger.debug("Query URL = " + url.toString());
+ return url;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff