Comment out start and end refs

[jalview.git] / src / jalview / io / EBIFetchClient.java

diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java
index eebbfc8..a6c3ed2 100755 (executable)
--- a/src/jalview/io/EBIFetchClient.java
+++ b/src/jalview/io/EBIFetchClient.java
@@ -18,13 +18,10 @@
 */\r
 package jalview.io;\r
 \r
-import org.apache.axis.AxisFault;\r
+import java.io.*;\r
+\r
 import org.apache.axis.client.*;\r
 import org.apache.axis.encoding.XMLType;\r
-import org.apache.axis.encoding.ser.JAFDataHandlerDeserializerFactory;\r
-import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;\r
-\r
-import javax.activation.DataHandler;\r
 \r
 import javax.xml.namespace.QName;\r
 import javax.xml.rpc.ParameterMode;\r
@@ -118,6 +115,46 @@ public class EBIFetchClient
         }\r
     }\r
 \r
+    public static void main (String [] args)\r
+    {\r
+      EBIFetchClient ebi = new EBIFetchClient();\r
+      String[] result = ebi.fetchData("uniprot:25K89D_SARPE;G6PblobD_HUMAN",\r
+                           "xml", null);\r
+\r
+     try{\r
+       java.io.PrintWriter out = new java.io.PrintWriter(\r
+      new java.io.FileWriter("out.xml"));\r
+\r
+\r
+       for(int i=0; i<result.length; i++)\r
+       {\r
+         out.println(result[i]);\r
+       }\r
+       out.close();\r
+     }catch(Exception ex){ex.printStackTrace();}\r
+\r
+    }\r
+\r
+\r
+    public File fetchDataAsFile(String ids, String f, String s)\r
+    {\r
+      String [] data = fetchData(ids, f, s);\r
+      File outFile = null;\r
+      try{\r
+        outFile = File.createTempFile("jalview", ".xml");\r
+        outFile.deleteOnExit();\r
+        PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
+        int index=0;\r
+        while( index < data.length )\r
+        {\r
+          out.println(data[index]);\r
+          index++;\r
+        }\r
+        out.close();\r
+      }catch(Exception ex){}\r
+      return outFile;\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -156,98 +193,4 @@ public class EBIFetchClient
             return null;\r
         }\r
     }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param arg DOCUMENT ME!\r
-     * @param f DOCUMENT ME!\r
-     * @param s DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public String fetchDataFile(String arg, String f, String s)\r
-    {\r
-        if (f != null)\r
-        {\r
-            format = f;\r
-        }\r
-\r
-        if (s != null)\r
-        {\r
-            style = s;\r
-        }\r
-\r
-        call.setOperationName(new QName("urn:Dbfetch", "fetchDataFile"));\r
-        call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);\r
-        call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);\r
-        call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);\r
-\r
-        QName qnameAttachment = new QName("urn:Dbfetch", "DataHandler");\r
-        call.registerTypeMapping(javax.activation.DataSource.class,\r
-            qnameAttachment, JAFDataHandlerSerializerFactory.class,\r
-            JAFDataHandlerDeserializerFactory.class);\r
-\r
-        call.setReturnType(qnameAttachment);\r
-\r
-        try\r
-        {\r
-            Object ret = call.invoke(new Object[] { arg, format, style });\r
-\r
-            if (null == ret)\r
-            {\r
-                System.err.println("Received null ");\r
-                throw new AxisFault("", "Received null", null, null);\r
-            }\r
-\r
-            if (ret instanceof String)\r
-            {\r
-                System.err.println("Received problem response from server: " +\r
-                    ret);\r
-                throw new AxisFault("", (String) ret, null, null);\r
-            }\r
-\r
-            if (!(ret instanceof DataHandler))\r
-            {\r
-                //The wrong type of object that what was expected.\r
-                System.err.println("Received problem response from server:" +\r
-                    ret.getClass().getName());\r
-                throw new AxisFault("",\r
-                    "Received problem response from server:" +\r
-                    ret.getClass().getName(), null, null);\r
-            }\r
-\r
-            //Still here, so far so good.\r
-            DataHandler rdh = (DataHandler) ret;\r
-\r
-            //From here we'll just treat the data resource as file.\r
-            String receivedfileName = rdh.getName(); //Get the filename.\r
-\r
-            if (receivedfileName == null)\r
-            {\r
-                System.err.println("Could not get the file name.");\r
-                throw new AxisFault("", "Could not get the file name.", null,\r
-                    null);\r
-            }\r
-\r
-            if (arg.equalsIgnoreCase("medline"))\r
-            {\r
-                return receivedfileName;\r
-            }\r
-            else if (arg.equalsIgnoreCase("interpro"))\r
-            {\r
-                return receivedfileName;\r
-            }\r
-            else\r
-            {\r
-                System.err.println(receivedfileName);\r
-            }\r
-        }\r
-        catch (Exception ex)\r
-        {\r
-            ex.printStackTrace();\r
-        }\r
-\r
-        return "ERROR";\r
-    }\r
 }\r