JAL-636 switch to simple REST interface to dbfetch (//http://www.ebi.ac.uk/Tools...

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index b837354..48895ae 100644 (file)
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -17,14 +17,14 @@
  */\r
 package jalview.ws.ebi;\r
 \r
-import java.io.*;\r
-import java.util.*;\r
-import javax.xml.namespace.*;\r
-import javax.xml.rpc.*;\r
-\r
-import org.apache.axis.client.Call;\r
-import org.apache.axis.client.Service;\r
-import org.apache.axis.encoding.*;\r
+import java.io.BufferedInputStream;\r
+import java.io.BufferedReader;\r
+import java.io.File;\r
+import java.io.FileOutputStream;\r
+import java.io.InputStreamReader;\r
+import java.net.URL;\r
+import java.util.ArrayList;\r
+import java.util.StringTokenizer;\r
 \r
 /**\r
  * DOCUMENT ME!\r
@@ -34,8 +34,6 @@ import org.apache.axis.encoding.*;
  */\r
 public class EBIFetchClient\r
 {\r
-  Call call;\r
-\r
   String format = "default";\r
 \r
   String style = "raw";\r
@@ -45,14 +43,6 @@ public class EBIFetchClient
    */\r
   public EBIFetchClient()\r
   {\r
-    try\r
-    {\r
-      call = (Call) new Service().createCall();\r
-      call.setTargetEndpointAddress(new java.net.URL(\r
-              "http://www.ebi.ac.uk/ws/services/Dbfetch"));\r
-    } catch (Exception ex)\r
-    {\r
-    }\r
   }\r
 \r
   /**\r
@@ -62,17 +52,8 @@ public class EBIFetchClient
    */\r
   public String[] getSupportedDBs()\r
   {\r
-    try\r
-    {\r
-      call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));\r
-      call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
-      return (String[]) call.invoke(new Object[]\r
-      {});\r
-    } catch (Exception ex)\r
-    {\r
-      return null;\r
-    }\r
+    // TODO - implement rest call for dbfetch getSupportedDBs\r
+    throw new Error("Not yet implemented");\r
   }\r
 \r
   /**\r
@@ -82,17 +63,8 @@ public class EBIFetchClient
    */\r
   public String[] getSupportedFormats()\r
   {\r
-    try\r
-    {\r
-      call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));\r
-      call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
-      return (String[]) call.invoke(new Object[]\r
-      {});\r
-    } catch (Exception ex)\r
-    {\r
-      return null;\r
-    }\r
+    // TODO - implement rest call for dbfetch getSupportedFormats\r
+    throw new Error("Not yet implemented");\r
   }\r
 \r
   /**\r
@@ -102,42 +74,24 @@ public class EBIFetchClient
    */\r
   public String[] getSupportedStyles()\r
   {\r
-    try\r
-    {\r
-      call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));\r
-      call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
-      return (String[]) call.invoke(new Object[]\r
-      {});\r
-    } catch (Exception ex)\r
-    {\r
-      return null;\r
-    }\r
+    // TODO - implement rest call for dbfetch getSupportedStyles\r
+    throw new Error("Not yet implemented");\r
   }\r
 \r
   public File fetchDataAsFile(String ids, String f, String s)\r
           throws OutOfMemoryError\r
   {\r
-    String[] data = fetchData(ids, f, s);\r
-    // TODO: after JV 2.4 - test data==null and pass error(s) back up if\r
-    // possible (OutOfMemoryErrors are usual problem)\r
-    if (data == null)\r
-    {\r
-      return null;\r
-    }\r
     File outFile = null;\r
     try\r
     {\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
+      fetchData(ids, f, s, outFile);\r
+      if (outFile.length() == 0)\r
       {\r
-        out.println(data[index]);\r
-        index++;\r
+        outFile.delete();\r
+        return null;\r
       }\r
-      out.close();\r
     } catch (Exception ex)\r
     {\r
     }\r
@@ -159,11 +113,19 @@ public class EBIFetchClient
   public String[] fetchData(String ids, String f, String s)\r
           throws OutOfMemoryError\r
   {\r
+    return fetchData(ids, f, s, null);\r
+  }\r
+\r
+  public String[] fetchData(String ids, String f, String s, File outFile)\r
+          throws OutOfMemoryError\r
+  {\r
     // Need to split\r
     // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;\r
+    String[] rslts = new String[0];\r
     StringTokenizer queries = new StringTokenizer(ids, ";");\r
     String db = null;\r
     StringBuffer querystring = null;\r
+    int nq = 0;\r
     while (queries.hasMoreTokens())\r
     {\r
       String query = queries.nextToken();\r
@@ -176,56 +138,73 @@ public class EBIFetchClient
       if (querystring == null)\r
       {\r
         querystring = new StringBuffer(query);\r
+        nq++;\r
       }\r
       else\r
       {\r
         querystring.append("," + query);\r
+        nq++;\r
       }\r
     }\r
     if (db == null)\r
     {\r
       System.err.println("Invalid Query string : '" + ids\r
               + "'\nShould be of form 'dbname:q1;q2;q3;q4'");\r
+      return null;\r
     }\r
-    return fetchBatch(querystring.toString(), db, f, s);\r
+    String[] rslt = fetchBatch(querystring.toString(), db, f, s, outFile);\r
+    if (rslt != null)\r
+    {\r
+      String[] nrslts = new String[rslt.length + rslts.length];\r
+      System.arraycopy(rslts, 0, nrslts, 0, rslts.length);\r
+      System.arraycopy(rslt, 0, nrslts, rslts.length, rslt.length);\r
+      rslts = nrslts;\r
+    }\r
+\r
+    return (rslts.length == 0 ? null : rslts);\r
   }\r
 \r
-  public String[] fetchBatch(String ids, String db, String f, String s)\r
-          throws OutOfMemoryError\r
+  public String[] fetchBatch(String ids, String db, String f, String s,\r
+          File outFile) throws OutOfMemoryError\r
   {\r
-    // max 50 ids can be added at one time\r
+    long time = System.currentTimeMillis();\r
+    // max 200 ids can be added at one time\r
     try\r
     {\r
-      // call.setOperationName(new QName("urn:Dbfetch", "fetchData"));\r
-      call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));\r
-      call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);\r
-      call.addParameter("db", XMLType.XSD_STRING, ParameterMode.IN);\r
-      call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);\r
-      call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);\r
-      call.setReturnType(XMLType.SOAP_ARRAY);\r
+      URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"\r
+              + db.toLowerCase() + "/" + ids.toLowerCase()\r
+              + (f != null ? "/" + f : ""));\r
 \r
-      if (f != null)\r
+      BufferedInputStream is = new BufferedInputStream(rcall.openStream());\r
+      if (outFile != null)\r
       {\r
-        format = f;\r
+        FileOutputStream fio = new FileOutputStream(outFile);\r
+        byte[] bb = new byte[32 * 1024];\r
+        int l;\r
+        while ((l = is.read(bb)) > 0)\r
+        {\r
+          fio.write(bb, 0, l);\r
+        }\r
+        fio.close();\r
+        is.close();\r
       }\r
-\r
-      if (s != null)\r
+      else\r
       {\r
-        style = s;\r
+        BufferedReader br = new BufferedReader(new InputStreamReader(is));\r
+        String rtn;\r
+        ArrayList<String> arl = new ArrayList<String>();\r
+        while ((rtn = br.readLine()) != null)\r
+        {\r
+          arl.add(rtn);\r
+        }\r
+        return arl.toArray(new String[arl.size()]);\r
       }\r
+    } catch (OutOfMemoryError er)\r
+    {\r
 \r
-      try\r
-      {\r
-        return (String[]) call.invoke(new Object[]\r
-        { ids.toLowerCase(), db.toLowerCase(), format, style });\r
-      } catch (OutOfMemoryError er)\r
-      {\r
-\r
-        System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db\r
-                + ":\n" + ids);\r
-        throw er;\r
-      }\r
-      // return null;\r
+      System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db\r
+              + ":\n" + ids);\r
+      throw er;\r
     } catch (Exception ex)\r
     {\r
       if (ex.getMessage().startsWith(\r
@@ -237,6 +216,11 @@ public class EBIFetchClient
               + "\nQuery was : '" + ids + "'");\r
       ex.printStackTrace(System.err);\r
       return null;\r
+    } finally\r
+    {\r
+      //System.err.println("Took " + (System.currentTimeMillis() - time)\r
+      //        / 1000 + " secs for one call.");\r
     }\r
+    return null;\r
   }\r
 }\r