X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FEBIFetchClient.java;h=c1a03022661bcd2ebdb52d39094aac4c0bea8888;hb=08044f16da407871ea84ccbfbc09e34cceb74080;hp=3c6e5f9050109f86badd33815603eada6e06b6e4;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java
index 3c6e5f9..c1a0302 100755
--- a/src/jalview/io/EBIFetchClient.java
+++ b/src/jalview/io/EBIFetchClient.java
@@ -16,166 +16,279 @@
 * 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 org.apache.axis.client.*;
-
 import java.io.*;
 
-import javax.activation.DataHandler;
 import org.apache.axis.AxisFault;
+import org.apache.axis.client.*;
 import org.apache.axis.encoding.XMLType;
-import javax.xml.rpc.ParameterMode;
-import javax.xml.namespace.QName;
-import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;
 import org.apache.axis.encoding.ser.JAFDataHandlerDeserializerFactory;
+import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;
 
+import javax.activation.DataHandler;
 
-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){}
-  }
-
-
-  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;}
-  }
-
-  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; }
-   }
+import javax.xml.namespace.QName;
+import javax.xml.rpc.ParameterMode;
 
-   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;}
+/**
+ * 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)
+        {
+        }
     }
 
-    public String [] fetchData(String ids, String f, String s)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String[] getSupportedDBs()
     {
-      // ids should be of the form uniprot:25KD_SARPE;ADHR_DROPS;
-      // max 50 ids can be added at one time
-      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);
+        try
+        {
+            call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
+            call.setReturnType(XMLType.SOAP_ARRAY);
 
-        if (f != null)
-          format = f;
+            return (String[]) call.invoke(new Object[] {  });
+        }
+        catch (Exception ex)
+        {
+            return null;
+        }
+    }
 
-        if (s != null)
-          style = s;
+    /**
+     * 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[] {ids, format, style});
+            return (String[]) call.invoke(new Object[] {  });
+        }
+        catch (Exception ex)
+        {
+            return null;
+        }
+    }
 
-      }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 String fetchDataFile(String arg, String f, String s)
+    public static void main (String [] args)
     {
+      EBIFetchClient ebi = new EBIFetchClient();
+      String[] result = ebi.fetchData("uniprot:25K89D_SARPE;G6PblobD_HUMAN",
+                           "xml", null);
 
-      if (f != null)
-        format = f;
+     try{
+       java.io.PrintWriter out = new java.io.PrintWriter(
+      new java.io.FileWriter("out.xml"));
 
-      if (s != null)
-        style = s;
 
+       for(int i=0; i<result.length; i++)
+       {
+         out.println(result[i]);
+       }
+       out.close();
+     }catch(Exception ex){ex.printStackTrace();}
 
-      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);
 
+    public File fetchDataAsFile(String ids, String f, String s)
+    {
+      String [] data = fetchData(ids, f, s);
+      File outFile = null;
       try{
-        Object ret = call.invoke(new Object[]
-                                 {arg, format, style});
-
-        if (null == ret)
+        outFile = File.createTempFile("jalview", ".xml");
+        PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+        int index=0;
+        while( index < data.length )
         {
-          System.err.println("Received null ");
-          throw new AxisFault("", "Received null", null, null);
+          out.println(data[index]);
+          index++;
         }
-        if (ret instanceof String)
+        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
         {
-          System.err.println("Received problem response from server: " + ret);
-          throw new AxisFault("", (String) ret, null, null);
+            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)
+            {
+                format = f;
+            }
+
+            if (s != null)
+            {
+                style = s;
+            }
+
+            return (String[]) call.invoke(new Object[] { ids, format, style });
         }
-        if (! (ret instanceof DataHandler))
+        catch (Exception ex)
         {
-          //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);
-
+            return 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.
+    /**
+     * DOCUMENT ME!
+     *
+     * @param arg DOCUMENT ME!
+     * @param f DOCUMENT ME!
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String fetchDataFile(String arg, String f, String s)
+    {
+        if (f != null)
+        {
+            format = f;
+        }
 
-        if (receivedfileName == null)
+        if (s != null)
         {
-          System.err.println("Could not get the file name.");
-          throw new AxisFault("", "Could not get the file name.", null, null);
+            style = s;
         }
-        if (arg.equalsIgnoreCase("medline"))
+
+        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
         {
-          return receivedfileName;
+            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);
+            }
         }
-        else if (arg.equalsIgnoreCase("interpro"))
+        catch (Exception ex)
         {
-          return receivedfileName;
+            ex.printStackTrace();
         }
-        else
-          System.err.println(receivedfileName);
-      }catch(Exception ex)
-      {
-        ex.printStackTrace();
-      }
-
-      return "ERROR";
-    }
-
 
+        return "ERROR";
+    }
 }