X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FEBIFetchClient.java;h=893608479348c6b88fd99fa9ca6ac6a089ab0b23;hb=5487f5075a649e1e638d10159825c5ca292fa822;hp=5b21bfe092515f97283c01493969dcf18073d963;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java
index 5b21bfe..8936084 100755
--- a/src/jalview/io/EBIFetchClient.java
+++ b/src/jalview/io/EBIFetchClient.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* 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
@@ -18,158 +18,179 @@
 */
 package jalview.io;
 
-import org.apache.axis.AxisFault;
-import org.apache.axis.client.*;
-import org.apache.axis.encoding.XMLType;
-import org.apache.axis.encoding.ser.JAFDataHandlerDeserializerFactory;
-import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;
-
 import java.io.*;
 
-import javax.activation.DataHandler;
+import org.apache.axis.client.*;
+import org.apache.axis.encoding.XMLType;
 
 import javax.xml.namespace.QName;
 import javax.xml.rpc.ParameterMode;
 
 
-public class EBIFetchClient {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class EBIFetchClient
+{
     Call call;
     String format = "default";
     String style = "raw";
 
-    public EBIFetchClient() {
-        try {
+    /**
+     * 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) {
+        }
+        catch (Exception ex)
+        {
         }
     }
 
-    public String[] getSupportedDBs() {
-        try {
+    /**
+     * 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) {
+        }
+        catch (Exception ex)
+        {
             return null;
         }
     }
 
-    public String[] getSupportedFormats() {
-        try {
+    /**
+     * 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) {
+        }
+        catch (Exception ex)
+        {
             return null;
         }
     }
 
-    public String[] getSupportedStyles() {
-        try {
+    /**
+     * 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) {
+        }
+        catch (Exception ex)
+        {
             return null;
         }
     }
 
-    public String[] fetchData(String ids, String f, String s) {
+    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"));
+
+
+       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;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ids DOCUMENT ME!
+     * @param f DOCUMENT ME!
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String[] fetchData(String ids, String f, String s)
+    {
         // ids should be of the form uniprot:25KD_SARPE;ADHR_DROPS;
         // max 50 ids can be added at one time
-        try {
+        try
+        {
             call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
             call.addParameter("query", 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) {
+            if (f != null)
+            {
                 format = f;
             }
 
-            if (s != null) {
+            if (s != null)
+            {
                 style = s;
             }
 
             return (String[]) call.invoke(new Object[] { ids, format, style });
-        } catch (Exception ex) {
-            return null;
         }
-    }
-
-    public String fetchDataFile(String arg, String f, String s) {
-        if (f != null) {
-            format = f;
-        }
-
-        if (s != null) {
-            style = s;
-        }
-
-        call.setOperationName(new QName("urn:Dbfetch", "fetchDataFile"));
-        call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);
-        call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
-        call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
-
-        QName qnameAttachment = new QName("urn:Dbfetch", "DataHandler");
-        call.registerTypeMapping(javax.activation.DataSource.class,
-            qnameAttachment, JAFDataHandlerSerializerFactory.class,
-            JAFDataHandlerDeserializerFactory.class);
-
-        call.setReturnType(qnameAttachment);
-
-        try {
-            Object ret = call.invoke(new Object[] { arg, format, style });
-
-            if (null == ret) {
-                System.err.println("Received null ");
-                throw new AxisFault("", "Received null", null, null);
-            }
-
-            if (ret instanceof String) {
-                System.err.println("Received problem response from server: " +
-                    ret);
-                throw new AxisFault("", (String) ret, null, null);
-            }
-
-            if (!(ret instanceof DataHandler)) {
-                //The wrong type of object that what was expected.
-                System.err.println("Received problem response from server:" +
-                    ret.getClass().getName());
-                throw new AxisFault("",
-                    "Received problem response from server:" +
-                    ret.getClass().getName(), null, null);
-            }
-
-            //Still here, so far so good.
-            DataHandler rdh = (DataHandler) ret;
-
-            //From here we'll just treat the data resource as file.
-            String receivedfileName = rdh.getName(); //Get the filename.
-
-            if (receivedfileName == null) {
-                System.err.println("Could not get the file name.");
-                throw new AxisFault("", "Could not get the file name.", null,
-                    null);
-            }
-
-            if (arg.equalsIgnoreCase("medline")) {
-                return receivedfileName;
-            } else if (arg.equalsIgnoreCase("interpro")) {
-                return receivedfileName;
-            } else {
-                System.err.println(receivedfileName);
-            }
-        } catch (Exception ex) {
-            ex.printStackTrace();
+        catch (Exception ex)
+        {
+            return null;
         }
-
-        return "ERROR";
     }
 }