src/jalview/ws/dbsources/EntrezRestClient.java

   1 /**
   2  * 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
   3  * Originally in package org.cytoscape.webservice.ncbi.rest;
   4  * Cytoscape3 code
   5  * License and author attribution currently unknown.
   6  */
   7
   8 import java.io.IOException;
   9 import java.io.InputStream;
  10 import java.net.URL;
  11 import java.util.Date;
  12 import java.util.HashSet;
  13 import java.util.Map;
  14 import java.util.Set;
  15 import java.util.concurrent.ConcurrentHashMap;
  16 import java.util.concurrent.ConcurrentMap;
  17 import java.util.concurrent.ExecutorService;
  18 import java.util.concurrent.Executors;
  19 import java.util.concurrent.TimeUnit;
  20
  21 import javax.xml.parsers.DocumentBuilder;
  22 import javax.xml.parsers.DocumentBuilderFactory;
  23 import javax.xml.parsers.ParserConfigurationException;
  24
  25 import org.apache.commons.logging.LogFactory;
  26 import org.apache.log4j.spi.LoggerFactory;
  27 import org.w3c.dom.Document;
  28 import org.w3c.dom.Node;
  29 import org.w3c.dom.NodeList;
  30 import org.xml.sax.SAXException;
  31
  32
  33 public class EntrezRestClient {
  34         private static final org.apache.commons.logging.Log logger = LogFactory.getLog(EntrezRestClient.class);
  35         private static final String BASE_URL = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/";
  36         public static final String FETCH_URL = BASE_URL + "efetch.fcgi?db=gene&retmode=xml&id=";
  37         private static final String SEARCH_URL = BASE_URL + "esearch.fcgi?db=gene&retmax=100000&term=";
  38         private final String regex = "\\s+";
  39         private static final String ID = "Id";
  40
  41         private final CyTableFactory tableFactory;
  42         private final CyNetworkFactory networkFactory;
  43         private final CyTableManager tableManager;
  44
  45         public EntrezRestClient(final CyNetworkFactory networkFactory,
  46                                 final CyTableFactory tableFactory, final CyTableManager tableManager)
  47         {
  48                 this.networkFactory = networkFactory;
  49                 this.tableFactory   = tableFactory;
  50                 this.tableManager   = tableManager;
  51         }
  52
  53         public Set<String> search(final String queryString) throws IOException, ParserConfigurationException, SAXException {
  54                 final URL url = createURL(SEARCH_URL, queryString);
  55
  56                 final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
  57                 final DocumentBuilder builder = factory.newDocumentBuilder();
  58                 InputStream is = url.openStream();
  59
  60                 final Document result = builder.parse(is);
  61
  62                 final Set<String> idSet = new HashSet<String>();
  63                 final NodeList ids = result.getElementsByTagName(ID);
  64                 final int dataSize = ids.getLength();
  65
  66                 for (int i = 0; i < dataSize; i++) {
  67                         Node id = ids.item(i);
  68                         idSet.add(id.getTextContent());
  69                 }
  70
  71                 is.close();
  72                 is = null;
  73
  74                 return idSet;
  75         }
  76
  77         public CyNetwork importNetwork(final Set<String> idList) {
  78
  79                 long startTime = System.currentTimeMillis();
  80
  81                 final ExecutorService executer = Executors.newFixedThreadPool(4);
  82
  83                 logger.debug("Executor initialized.");
  84                 // final CyNetwork newNetwork = networkFactory.getInstance();
  85
  86
  87                 final ConcurrentMap<String, CyNode> nodeName2CyNodeMap = new ConcurrentHashMap<String, CyNode>();
  88
  89                 int group = 0;
  90                 int buketNum = 10;
  91                 String[] box = new String[buketNum];
  92
  93
  94                 for (String entrezID : idList) {
  95                         box[group] = entrezID;
  96                         group++;
  97
  98                         if (group == buketNum) {
  99                                 executer.submit(new EntryProcessor<String>(new ImportNetworkTask<String>(box, newNetwork, nodeName2CyNodeMap)));
 100                                 group = 0;
 101                                 box = new String[buketNum];
 102                         }
 103                 }
 104
 105                 String[] newbox = new String[group];
 106
 107                 for (int i = 0; i < group; i++)
 108                         newbox[i] = box[i];
 109
 110                 executer.submit(new EntryProcessor<String>(new ImportNetworkTask<String>(box, newNetwork, nodeName2CyNodeMap)));
 111
 112                 try {
 113                         executer.shutdown();
 114                         executer.awaitTermination(1000, TimeUnit.SECONDS);
 115
 116                         long endTime = System.currentTimeMillis();
 117                         double sec = (endTime - startTime) / (1000.0);
 118                         System.out.println("Finished in " + sec + " sec.");
 119
 120 //                      if ((canceled != null) && canceled) {
 121 //                              canceled = null;
 122 //
 123 //                              return null;
 124 //                      }
 125                 } catch( Exception ex) {
 126                         ex.printStackTrace();
 127                 }
 128
 129                 return newNetwork;
 130         }
 131
 132
 133
 134         public CyTable importDataTable(final Set<String> idList, final Set<AnnotationCategory> category) {
 135                 if(idList == null || idList.size() == 0)
 136                         throw new IllegalArgumentException("ID list is null.");
 137
 138                 long startTime = System.currentTimeMillis();
 139                 final ExecutorService executer = Executors.newFixedThreadPool(4);
 140
 141                 logger.debug("Table Import Executor initialized.");
 142                 final Date currentDate = new Date();
 143                 final CyTable table = tableFactory.createTable("NCBI Global Table: " + currentDate.toString(), CyTableEntry.NAME, String.class, true, true);
 144
 145                 int group = 0;
 146                 int buketNum = 10;
 147                 String[] box = new String[buketNum];
 148
 149
 150                 for (String entrezID : idList) {
 151                         box[group] = entrezID;
 152                         group++;
 153
 154                         if (group == buketNum) {
 155                                 executer.submit(new ImportTableTask(box, category, table));
 156                                 group = 0;
 157                                 box = new String[buketNum];
 158                         }
 159                 }
 160
 161                 String[] newbox = new String[group];
 162
 163                 for (int i = 0; i < group; i++)
 164                         newbox[i] = box[i];
 165
 166                 executer.submit(new ImportTableTask(box, category, table));
 167
 168                 try {
 169                         executer.shutdown();
 170                         executer.awaitTermination(1000, TimeUnit.SECONDS);
 171
 172                         long endTime = System.currentTimeMillis();
 173                         double sec = (endTime - startTime) / (1000.0);
 174                         System.out.println("Table Import Finished in " + sec + " sec.");
 175
 176 //                      if ((canceled != null) && canceled) {
 177 //                              canceled = null;
 178 //
 179 //                              return null;
 180 //                      }
 181                 } catch( Exception ex) {
 182                         ex.printStackTrace();
 183                 }
 184
 185                 tableManager.addTable(table);
 186
 187                 return table;
 188         }
 189
 190         private URL createURL(final String base, final String queryString) throws IOException {
 191                 final String[] parts = queryString.split(regex);
 192                 final StringBuilder builder = new StringBuilder();
 193
 194                 if (parts.length != 0) {
 195                         for (String dTerm : parts) {
 196                                 final String trimed = dTerm.trim();
 197                                 builder.append(trimed + "+");
 198                         }
 199                 }
 200
 201                 String urlString = builder.toString();
 202                 urlString = urlString.substring(0, urlString.length() - 1);
 203                 final URL url = new URL(base + urlString);
 204                 logger.debug("Query URL = " + url.toString());
 205                 return url;
 206         }
 207 }