+++ /dev/null
-/*
- * 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
- */
-package jalview.io;
-
-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.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class EBIFetchClient
-{
- Call call;
- String format = "default";
- String style = "raw";
-
- /**
- * Creates a new EBIFetchClient object.
- */
- 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;
- }
- }
-
- /**
- * 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;
- }
- }
-
- /**
- * 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;
- }
- }
-
-
- public File fetchDataAsFile(String ids, String f, String s)
- {
- 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)
- {
- out.println(data[index]);
- index++;
- }
- out.close();
- }
- catch (Exception ex)
- {}
- return outFile;
- }
-
- /**
- * Single DB multiple record retrieval
- *
- * @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)
- {
- // Need to split
- // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
- StringTokenizer queries = new StringTokenizer(ids, ";");
- String db = null;
- StringBuffer querystring = null;
- while (queries.hasMoreTokens())
- {
- String query = queries.nextToken();
- int p;
- if ( (p = query.indexOf(':')) > -1)
- {
- db = query.substring(0, p);
- query = query.substring(p + 1);
- }
- if (querystring == null)
- {
- querystring = new StringBuffer(query);
- }
- else
- {
- querystring.append("," + query);
- }
- }
- if (db == null)
- {
- System.err.println("Invalid Query string : '" + ids +
- "'\nShould be of form 'dbname:q1;q2;q3;q4'");
- }
- return fetchBatch(querystring.toString(), db, f, s);
- }
-
- public String[] fetchBatch(String ids, String db, String f, String s)
- {
- // max 50 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);
-
- if (f != null)
- {
- format = f;
- }
-
- if (s != null)
- {
- style = s;
- }
-
- 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)
- {
- if (ex.getMessage().startsWith(
- "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
- {
- return null;
- }
- System.err.println("Unexpected exception when retrieving from " + db +
- "\nQuery was : '" + ids + "'");
- ex.printStackTrace(System.err);
- return null;
- }
- }
-}
git://source.jalview.org / jalview.git / blobdiff