/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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
+ * 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.Enumeration;
-import java.util.Hashtable;
-import java.util.StringTokenizer;
-
-import org.apache.axis.client.*;
-import org.apache.axis.encoding.XMLType;
-
-import javax.xml.namespace.QName;
-import javax.xml.rpc.ParameterMode;
+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!
*/
public class EBIFetchClient
{
- Call call;
- String format = "default";
- String style = "raw";
-
- /**
- * Creates a new EBIFetchClient object.
- */
- public EBIFetchClient()
+ Call call;
+ String format = "default";
+ String style = "raw";
+
+ /**
+ * Creates a new EBIFetchClient object.
+ */
+ public EBIFetchClient()
+ {
+ try
{
- try
- {
- call = (Call) new Service().createCall();
- call.setTargetEndpointAddress(new java.net.URL(
- "http://www.ebi.ac.uk/ws/services/Dbfetch"));
- }
- catch (Exception ex)
- {
- }
+ call = (Call)new Service().createCall();
+ call.setTargetEndpointAddress(new java.net.URL(
+ "http://www.ebi.ac.uk/ws/services/Dbfetch"));
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String[] getSupportedDBs()
+ catch (Exception ex)
{
- 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()
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedDBs()
+ {
+ try
{
- try
- {
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
- call.setReturnType(XMLType.SOAP_ARRAY);
-
- return (String[]) call.invoke(new Object[] { });
- }
- catch (Exception ex)
- {
- return null;
- }
+ 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[] getSupportedStyles()
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedFormats()
+ {
+ try
{
- try
- {
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
- call.setReturnType(XMLType.SOAP_ARRAY);
-
- return (String[]) call.invoke(new Object[] { });
- }
- catch (Exception ex)
- {
- return null;
- }
+ 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);
- public static void main (String [] args)
+ return (String[]) call.invoke(new Object[]
+ {});
+ }
+ catch (Exception ex)
{
- EBIFetchClient ebi = new EBIFetchClient();
- String[] result = ebi.fetchData("uniprot:25KD_SARPE;G6PD_HUMAN",
- "xml", null);
+ return null;
+ }
+ }
+
+ public static void main(String[] args)
+ {
+ EBIFetchClient ebi = new EBIFetchClient();
+ String[] result = ebi.fetchData("uniprot:25KD_SARPE;G6PD_HUMAN",
+ "xml", null);
- try{
- java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter("out.xml"));
+ try
+ {
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter("out.xml"));
+ for (int i = 0; i < result.length; i++)
+ {
+ out.println(result[i]);
+ }
+ out.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
- for(int i=0; i<result.length; i++)
- {
- out.println(result[i]);
- }
- out.close();
- }catch(Exception ex){ex.printStackTrace();}
+ }
+ 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;
- public File fetchDataAsFile(String ids, String f, String s)
+ 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 && (p + 3 < query.length()))
+ {
+ db = query.substring(0, p);
+ query = query.substring(p + 1);
+ }
+ if (querystring == null)
+ {
+ querystring = new StringBuffer(query);
+ }
+ else
+ {
+ querystring.append("," + query);
+ }
+ }
+ if (db == null)
{
- 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;
+ System.err.println("Invalid Query string : '" + ids +
+ "'\nShould be of form 'dbname:q1;q2;q3;q4'");
}
+ return fetchBatch(querystring.toString(), db, f, s);
+ }
- /**
- * 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)
+ public String[] fetchBatch(String ids, String db, String f, String s)
+ {
+ // max 50 ids can be added at one time
+ try
{
- // 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 && (p+3<query.length())) {
- 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);
+ //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;
}
- 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;
- }
+ 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