From fb0b0f2434cf4af0cee7a146bc3d7ef37299a901 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 7 Feb 2005 17:09:57 +0000
Subject: [PATCH] New class

---
 src/jalview/io/EBIFetchClient.java |  160 ++++++++++++++++++++++++++++++++++++
 1 file changed, 160 insertions(+)
 create mode 100755 src/jalview/io/EBIFetchClient.java

diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java
new file mode 100755
index 0000000..be2f01e
--- /dev/null
+++ b/src/jalview/io/EBIFetchClient.java
@@ -0,0 +1,160 @@
+package jalview.io;
+
+import org.apache.axis.client.*;
+
+import java.io.*;
+
+import javax.activation.DataHandler;
+import org.apache.axis.AxisFault;
+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;
+
+
+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; }
+   }
+
+   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 [] 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{
+        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});
+
+      }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.out.println("Received null ");
+          throw new AxisFault("", "Received null", null, null);
+        }
+        if (ret instanceof String)
+        {
+          System.out.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.out.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.out.println(receivedfileName);
+      }catch(Exception ex)
+      {}
+
+      return "ERROR";
+    }
+
+
+}
-- 
1.7.10.2