/*
- * 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 <http://www.gnu.org/licenses/>.
+ * 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";
/**
*/
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);
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<String> arl = new ArrayList<String>();
+ 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;
}
}
+
git://source.jalview.org / jalview.git / blobdiff