2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
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3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.ws.ebi;
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23 import javax.xml.namespace.*;
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24 import javax.xml.rpc.*;
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26 import org.apache.axis.client.Call;
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27 import org.apache.axis.client.Service;
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28 import org.apache.axis.encoding.*;
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34 * @version $Revision$
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36 public class EBIFetchClient
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40 String format = "default";
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42 String style = "raw";
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45 * Creates a new EBIFetchClient object.
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47 public EBIFetchClient()
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51 call = (Call) new Service().createCall();
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52 call.setTargetEndpointAddress(new java.net.URL(
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53 "http://www.ebi.ac.uk/ws/services/Dbfetch"));
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54 } catch (Exception ex)
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62 * @return DOCUMENT ME!
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64 public String[] getSupportedDBs()
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68 call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
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69 call.setReturnType(XMLType.SOAP_ARRAY);
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71 return (String[]) call.invoke(new Object[]
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73 } catch (Exception ex)
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82 * @return DOCUMENT ME!
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84 public String[] getSupportedFormats()
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89 .setOperationName(new QName("urn:Dbfetch",
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90 "getSupportedFormats"));
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91 call.setReturnType(XMLType.SOAP_ARRAY);
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93 return (String[]) call.invoke(new Object[]
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95 } catch (Exception ex)
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104 * @return DOCUMENT ME!
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106 public String[] getSupportedStyles()
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110 call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
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111 call.setReturnType(XMLType.SOAP_ARRAY);
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113 return (String[]) call.invoke(new Object[]
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115 } catch (Exception ex)
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121 public File fetchDataAsFile(String ids, String f, String s)
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122 throws OutOfMemoryError
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124 String[] data = fetchData(ids, f, s);
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125 // TODO: after JV 2.4 - test data==null and pass error(s) back up if
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126 // possible (OutOfMemoryErrors are usual problem)
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131 File outFile = null;
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134 outFile = File.createTempFile("jalview", ".xml");
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135 outFile.deleteOnExit();
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136 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
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138 while (index < data.length)
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140 out.println(data[index]);
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145 catch (Exception ex)
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152 * Single DB multiple record retrieval
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155 * db:query1;query2;query3
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160 * @return Raw string array result of query set
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162 public String[] fetchData(String ids, String f, String s)
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163 throws OutOfMemoryError
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166 // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
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167 StringTokenizer queries = new StringTokenizer(ids, ";");
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169 StringBuffer querystring = null;
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170 while (queries.hasMoreTokens())
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172 String query = queries.nextToken();
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174 if ((p = query.indexOf(':')) > -1)
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176 db = query.substring(0, p);
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177 query = query.substring(p + 1);
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179 if (querystring == null)
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181 querystring = new StringBuffer(query);
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185 querystring.append("," + query);
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190 System.err.println("Invalid Query string : '" + ids
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191 + "'\nShould be of form 'dbname:q1;q2;q3;q4'");
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193 return fetchBatch(querystring.toString(), db, f, s);
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196 public String[] fetchBatch(String ids, String db, String f, String s)
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197 throws OutOfMemoryError
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199 // max 50 ids can be added at one time
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202 // call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
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203 call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));
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204 call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);
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205 call.addParameter("db", XMLType.XSD_STRING, ParameterMode.IN);
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206 call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
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207 call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
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208 call.setReturnType(XMLType.SOAP_ARRAY);
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222 return (String[]) call.invoke(new Object[]
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223 { ids.toLowerCase(), db.toLowerCase(), format, style });
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224 } catch (OutOfMemoryError er)
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227 System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db
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232 } catch (Exception ex)
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234 if (ex.getMessage().startsWith(
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235 "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
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239 System.err.println("Unexpected exception when retrieving from " + db
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240 + "\nQuery was : '" + ids + "'");
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241 ex.printStackTrace(System.err);
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