--- /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.ws;
+
+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