2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.ws.ebi;
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20 import java.io.BufferedInputStream;
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21 import java.io.BufferedReader;
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22 import java.io.File;
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23 import java.io.FileOutputStream;
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24 import java.io.InputStreamReader;
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25 import java.net.URL;
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26 import java.util.ArrayList;
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27 import java.util.StringTokenizer;
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33 * @version $Revision$
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35 public class EBIFetchClient
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37 String format = "default";
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39 String style = "raw";
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42 * Creates a new EBIFetchClient object.
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44 public EBIFetchClient()
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51 * @return DOCUMENT ME!
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53 public String[] getSupportedDBs()
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55 // TODO - implement rest call for dbfetch getSupportedDBs
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56 throw new Error("Not yet implemented");
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62 * @return DOCUMENT ME!
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64 public String[] getSupportedFormats()
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66 // TODO - implement rest call for dbfetch getSupportedFormats
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67 throw new Error("Not yet implemented");
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73 * @return DOCUMENT ME!
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75 public String[] getSupportedStyles()
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77 // TODO - implement rest call for dbfetch getSupportedStyles
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78 throw new Error("Not yet implemented");
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81 public File fetchDataAsFile(String ids, String f, String s)
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82 throws OutOfMemoryError
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84 File outFile = null;
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87 outFile = File.createTempFile("jalview", ".xml");
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88 outFile.deleteOnExit();
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89 fetchData(ids, f, s, outFile);
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90 if (outFile.length() == 0)
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95 } catch (Exception ex)
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102 * Single DB multiple record retrieval
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105 * db:query1;query2;query3
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111 * @return Raw string array result of query set
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113 public String[] fetchData(String ids, String f, String s)
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114 throws OutOfMemoryError
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116 return fetchData(ids, f, s, null);
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119 public String[] fetchData(String ids, String f, String s, File outFile)
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120 throws OutOfMemoryError
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123 // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
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124 String[] rslts = new String[0];
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125 StringTokenizer queries = new StringTokenizer(ids, ";");
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127 StringBuffer querystring = null;
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129 while (queries.hasMoreTokens())
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131 String query = queries.nextToken();
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133 if ((p = query.indexOf(':')) > -1)
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135 db = query.substring(0, p);
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136 query = query.substring(p + 1);
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138 if (querystring == null)
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140 querystring = new StringBuffer(query);
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145 querystring.append("," + query);
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151 System.err.println("Invalid Query string : '" + ids
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152 + "'\nShould be of form 'dbname:q1;q2;q3;q4'");
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155 String[] rslt = fetchBatch(querystring.toString(), db, f, s, outFile);
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158 String[] nrslts = new String[rslt.length + rslts.length];
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159 System.arraycopy(rslts, 0, nrslts, 0, rslts.length);
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160 System.arraycopy(rslt, 0, nrslts, rslts.length, rslt.length);
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164 return (rslts.length == 0 ? null : rslts);
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167 public String[] fetchBatch(String ids, String db, String f, String s,
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168 File outFile) throws OutOfMemoryError
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170 long time = System.currentTimeMillis();
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171 // max 200 ids can be added at one time
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174 URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
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175 + db.toLowerCase() + "/" + ids.toLowerCase()
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176 + (f != null ? "/" + f : ""));
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178 BufferedInputStream is = new BufferedInputStream(rcall.openStream());
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179 if (outFile != null)
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181 FileOutputStream fio = new FileOutputStream(outFile);
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182 byte[] bb = new byte[32 * 1024];
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184 while ((l = is.read(bb)) > 0)
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186 fio.write(bb, 0, l);
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193 BufferedReader br = new BufferedReader(new InputStreamReader(is));
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195 ArrayList<String> arl = new ArrayList<String>();
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196 while ((rtn = br.readLine()) != null)
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200 return arl.toArray(new String[arl.size()]);
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202 } catch (OutOfMemoryError er)
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205 System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db
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208 } catch (Exception ex)
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210 if (ex.getMessage().startsWith(
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211 "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
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215 System.err.println("Unexpected exception when retrieving from " + db
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216 + "\nQuery was : '" + ids + "'");
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217 ex.printStackTrace(System.err);
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221 //System.err.println("Took " + (System.currentTimeMillis() - time)
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222 // / 1000 + " secs for one call.");
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