X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Febi%2FEBIFetchClient.java;h=074b76c19984898df0c75cfe652e15e19b129400;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=e9aff35f16991cf53f6c13a0707efac80a1d0d1a;hpb=0eda2ac2f334f55f6e5f137789453a9f4dfe4d73;p=jalview.git diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java index e9aff35..074b76c 100644 --- a/src/jalview/ws/ebi/EBIFetchClient.java +++ b/src/jalview/ws/ebi/EBIFetchClient.java @@ -1,42 +1,42 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.ws.ebi; -import java.io.*; -import java.util.*; -import javax.xml.namespace.*; -import javax.xml.rpc.*; - -import org.apache.axis.client.Call; -import org.apache.axis.client.Service; -import org.apache.axis.encoding.*; +import java.io.BufferedInputStream; +import java.io.BufferedReader; +import java.io.File; +import java.io.FileOutputStream; +import java.io.InputStreamReader; +import java.net.URL; +import java.util.ArrayList; +import java.util.StringTokenizer; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ public class EBIFetchClient { - Call call; String format = "default"; + String style = "raw"; /** @@ -44,124 +44,94 @@ public class EBIFetchClient */ public EBIFetchClient() { - try - { - call = (Call)new Service().createCall(); - call.setTargetEndpointAddress(new java.net.URL( - "http://www.ebi.ac.uk/ws/services/Dbfetch")); - } - catch (Exception ex) - { - } } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public String[] getSupportedDBs() { - try - { - call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs")); - call.setReturnType(XMLType.SOAP_ARRAY); - - return (String[]) call.invoke(new Object[] - {}); - } - catch (Exception ex) - { - return null; - } + // TODO - implement rest call for dbfetch getSupportedDBs + throw new Error("Not yet implemented"); } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public String[] getSupportedFormats() { - try - { - call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats")); - call.setReturnType(XMLType.SOAP_ARRAY); - - return (String[]) call.invoke(new Object[] - {}); - } - catch (Exception ex) - { - return null; - } + // TODO - implement rest call for dbfetch getSupportedFormats + throw new Error("Not yet implemented"); } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public String[] getSupportedStyles() { - try - { - call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles")); - call.setReturnType(XMLType.SOAP_ARRAY); - - return (String[]) call.invoke(new Object[] - {}); - } - catch (Exception ex) - { - return null; - } + // TODO - implement rest call for dbfetch getSupportedStyles + throw new Error("Not yet implemented"); } - public File fetchDataAsFile(String ids, String f, String s) + throws OutOfMemoryError { - String[] data = fetchData(ids, f, s); File outFile = null; try { outFile = File.createTempFile("jalview", ".xml"); outFile.deleteOnExit(); - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - int index = 0; - while (index < data.length) + fetchData(ids, f, s, outFile); + if (outFile.length() == 0) { - out.println(data[index]); - index++; + outFile.delete(); + return null; } - out.close(); + } catch (Exception ex) + { } - catch (Exception ex) - {} return outFile; } /** * Single DB multiple record retrieval - * - * @param ids db:query1;query2;query3 - * @param f raw/xml - * @param s ? - * + * + * @param ids + * db:query1;query2;query3 + * @param f + * raw/xml + * @param s + * ? + * * @return Raw string array result of query set */ public String[] fetchData(String ids, String f, String s) + throws OutOfMemoryError + { + return fetchData(ids, f, s, null); + } + + public String[] fetchData(String ids, String f, String s, File outFile) + throws OutOfMemoryError { // Need to split // ids of the form uniprot:25KD_SARPE;ADHR_DROPS; + String[] rslts = new String[0]; StringTokenizer queries = new StringTokenizer(ids, ";"); String db = null; StringBuffer querystring = null; + int nq = 0; while (queries.hasMoreTokens()) { String query = queries.nextToken(); int p; - if ( (p = query.indexOf(':')) > -1) + if ((p = query.indexOf(':')) > -1) { db = query.substring(0, p); query = query.substring(p + 1); @@ -169,67 +139,90 @@ public class EBIFetchClient if (querystring == null) { querystring = new StringBuffer(query); + nq++; } else { querystring.append("," + query); + nq++; } } if (db == null) { - System.err.println("Invalid Query string : '" + ids + - "'\nShould be of form 'dbname:q1;q2;q3;q4'"); + System.err.println("Invalid Query string : '" + ids + + "'\nShould be of form 'dbname:q1;q2;q3;q4'"); + return null; + } + String[] rslt = fetchBatch(querystring.toString(), db, f, s, outFile); + if (rslt != null) + { + String[] nrslts = new String[rslt.length + rslts.length]; + System.arraycopy(rslts, 0, nrslts, 0, rslts.length); + System.arraycopy(rslt, 0, nrslts, rslts.length, rslt.length); + rslts = nrslts; } - return fetchBatch(querystring.toString(), db, f, s); + + return (rslts.length == 0 ? null : rslts); } - public String[] fetchBatch(String ids, String db, String f, String s) + public String[] fetchBatch(String ids, String db, String f, String s, + File outFile) throws OutOfMemoryError { - // max 50 ids can be added at one time + long time = System.currentTimeMillis(); + // max 200 ids can be added at one time try { - //call.setOperationName(new QName("urn:Dbfetch", "fetchData")); - call.setOperationName(new QName("urn:Dbfetch", "fetchBatch")); - call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN); - call.addParameter("db", XMLType.XSD_STRING, ParameterMode.IN); - call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN); - call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN); - call.setReturnType(XMLType.SOAP_ARRAY); + URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/" + + db.toLowerCase() + "/" + ids.toLowerCase() + + (f != null ? "/" + f : "")); - if (f != null) + BufferedInputStream is = new BufferedInputStream(rcall.openStream()); + if (outFile != null) { - format = f; + FileOutputStream fio = new FileOutputStream(outFile); + byte[] bb = new byte[32 * 1024]; + int l; + while ((l = is.read(bb)) > 0) + { + fio.write(bb, 0, l); + } + fio.close(); + is.close(); } - - if (s != null) + else { - style = s; + BufferedReader br = new BufferedReader(new InputStreamReader(is)); + String rtn; + ArrayList arl = new ArrayList(); + while ((rtn = br.readLine()) != null) + { + arl.add(rtn); + } + return arl.toArray(new String[arl.size()]); } + } catch (OutOfMemoryError er) + { - try - { - return (String[]) call.invoke(new Object[] - {ids.toLowerCase(), db.toLowerCase(), - format, style}); - } - catch (OutOfMemoryError er) - { - System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db + ":\n" + - ids); - } - return null; - } - catch (Exception ex) + System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db + + ":\n" + ids); + throw er; + } catch (Exception ex) { if (ex.getMessage().startsWith( - "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException")) + "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException")) { return null; } - System.err.println("Unexpected exception when retrieving from " + db + - "\nQuery was : '" + ids + "'"); + System.err.println("Unexpected exception when retrieving from " + db + + "\nQuery was : '" + ids + "'"); ex.printStackTrace(System.err); return null; + } finally + { + //System.err.println("Took " + (System.currentTimeMillis() - time) + // / 1000 + " secs for one call."); } + return null; } } +