From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 4 Oct 2012 15:56:41 +0000 (+0100)
Subject: JAL-636 switch to simple REST interface to dbfetch (//http://www.ebi.ac.uk/Tools... 
X-Git-Tag: Jalview_2_9~268
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0adb44b91b95c023bad382ad414dcb02a24cb890;p=jalview.git

JAL-636 switch to simple REST interface to dbfetch (//ebi.ac.uk/Tools/webservices/services/dbfetch_rest)
---

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