2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.ws.ebi;
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22 import javax.xml.namespace.*;
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23 import javax.xml.rpc.*;
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25 import org.apache.axis.client.Call;
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26 import org.apache.axis.client.Service;
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27 import org.apache.axis.encoding.*;
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33 * @version $Revision$
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35 public class EBIFetchClient
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39 String format = "default";
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41 String style = "raw";
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44 * Creates a new EBIFetchClient object.
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46 public EBIFetchClient()
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50 call = (Call) new Service().createCall();
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51 call.setTargetEndpointAddress(new java.net.URL(
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52 "http://www.ebi.ac.uk/ws/services/Dbfetch"));
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53 } catch (Exception ex)
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61 * @return DOCUMENT ME!
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63 public String[] getSupportedDBs()
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67 call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
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68 call.setReturnType(XMLType.SOAP_ARRAY);
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70 return (String[]) call.invoke(new Object[]
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72 } catch (Exception ex)
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81 * @return DOCUMENT ME!
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83 public String[] getSupportedFormats()
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87 call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
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88 call.setReturnType(XMLType.SOAP_ARRAY);
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90 return (String[]) call.invoke(new Object[]
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92 } catch (Exception ex)
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101 * @return DOCUMENT ME!
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103 public String[] getSupportedStyles()
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107 call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
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108 call.setReturnType(XMLType.SOAP_ARRAY);
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110 return (String[]) call.invoke(new Object[]
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112 } catch (Exception ex)
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118 public File fetchDataAsFile(String ids, String f, String s)
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119 throws OutOfMemoryError
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121 String[] data = fetchData(ids, f, s);
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122 // TODO: after JV 2.4 - test data==null and pass error(s) back up if
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123 // possible (OutOfMemoryErrors are usual problem)
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128 File outFile = null;
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131 outFile = File.createTempFile("jalview", ".xml");
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132 outFile.deleteOnExit();
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133 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
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135 while (index < data.length)
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137 out.println(data[index]);
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141 } catch (Exception ex)
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148 * Single DB multiple record retrieval
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151 * db:query1;query2;query3
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157 * @return Raw string array result of query set
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159 public String[] fetchData(String ids, String f, String s)
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160 throws OutOfMemoryError
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163 // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
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164 StringTokenizer queries = new StringTokenizer(ids, ";");
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166 StringBuffer querystring = null;
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167 while (queries.hasMoreTokens())
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169 String query = queries.nextToken();
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171 if ((p = query.indexOf(':')) > -1)
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173 db = query.substring(0, p);
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174 query = query.substring(p + 1);
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176 if (querystring == null)
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178 querystring = new StringBuffer(query);
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182 querystring.append("," + query);
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187 System.err.println("Invalid Query string : '" + ids
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188 + "'\nShould be of form 'dbname:q1;q2;q3;q4'");
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190 return fetchBatch(querystring.toString(), db, f, s);
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193 public String[] fetchBatch(String ids, String db, String f, String s)
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194 throws OutOfMemoryError
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196 // max 50 ids can be added at one time
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199 // call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
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200 call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));
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201 call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);
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202 call.addParameter("db", XMLType.XSD_STRING, ParameterMode.IN);
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203 call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
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204 call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
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205 call.setReturnType(XMLType.SOAP_ARRAY);
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219 return (String[]) call.invoke(new Object[]
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220 { ids.toLowerCase(), db.toLowerCase(), format, style });
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221 } catch (OutOfMemoryError er)
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224 System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db
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229 } catch (Exception ex)
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231 if (ex.getMessage().startsWith(
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232 "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
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236 System.err.println("Unexpected exception when retrieving from " + db
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237 + "\nQuery was : '" + ids + "'");
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238 ex.printStackTrace(System.err);
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