From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 18 Sep 2013 13:11:01 +0000 (+0100)
Subject: JAL-1375 initial import of EntrezClient code from Cytoscape3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dbabbe48a455467de19b953d098a9cd943f9c133;p=jalview.git

JAL-1375 initial import of EntrezClient code from Cytoscape3
---

diff --git a/src/jalview/ws/dbsources/EntrezRestClient.java b/src/jalview/ws/dbsources/EntrezRestClient.java
new file mode 100644
index 0000000..d5ad673
--- /dev/null
+++ b/src/jalview/ws/dbsources/EntrezRestClient.java
@@ -0,0 +1,207 @@
+/**
+ * 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;
+	}
+}