X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FEBIFetchClient.java;h=b71e1521828444bcd08d3f7af469fb39c0d39710;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=008094cf0a5454b21592293a5f8c4484a53a55b7;hpb=9ad5f37d63398fd6633bc33e3c46f4974d76af32;p=jalview.git

diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java
index 008094c..b71e152 100755
--- a/src/jalview/io/EBIFetchClient.java
+++ b/src/jalview/io/EBIFetchClient.java
@@ -1,203 +1,259 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* 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 java.io.*;
-
-import org.apache.axis.client.*;
-import org.apache.axis.encoding.XMLType;
-
-import javax.xml.namespace.QName;
-import javax.xml.rpc.ParameterMode;
-
-
-/**
- * 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)
-        {
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    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;
-        }
-    }
-
-    /**
-     * 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[] {  });
-        }
-        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 static void main (String [] args)
-    {
-      EBIFetchClient ebi = new EBIFetchClient();
-      String[] result = ebi.fetchData("uniprot:25KD_SARPE;G6PD_HUMAN",
-                           "xml", null);
-
-     try{
-       java.io.PrintWriter out = new java.io.PrintWriter(
-      new java.io.FileWriter("out.xml"));
-
-
-       for(int i=0; i<result.length; i++)
-       {
-         out.println(result[i]);
-       }
-       out.close();
-     }catch(Exception ex){ex.printStackTrace();}
-
-    }
-
-
-    public File fetchDataAsFile(String ids, String f, String s)
-    {
-      String [] data = fetchData(ids, f, s);
-      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 )
-        {
-          out.println(data[index]);
-          index++;
-        }
-        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
-        {
-            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;
-            }
-
-            try{
-              return (String[]) call.invoke(new Object[]
-                                            {ids, format, style});
-            }catch(OutOfMemoryError er)
-            {
-              System.out.println("OUT OF MEMORY LOADING PDB FILE!!");
-            }
-            return null;
-        }
-        catch (Exception ex)
-        {
-            return null;
-        }
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * 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 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.*;
+
+/**
+ * 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)
+    {
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  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;
+    }
+  }
+
+  /**
+   * 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[]
+                                    {});
+    }
+    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 static void main(String[] args)
+  {
+    EBIFetchClient ebi = new EBIFetchClient();
+    String[] result = ebi.fetchData("uniprot:25KD_SARPE;G6PD_HUMAN",
+                                    "xml", null);
+
+    try
+    {
+      java.io.PrintWriter out = new java.io.PrintWriter(
+          new java.io.FileWriter("out.xml"));
+
+      for (int i = 0; i < result.length; i++)
+      {
+        out.println(result[i]);
+      }
+      out.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+  }
+
+  public File fetchDataAsFile(String ids, String f, String s)
+  {
+    String[] data = fetchData(ids, f, s);
+    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)
+      {
+        out.println(data[index]);
+        index++;
+      }
+      out.close();
+    }
+    catch (Exception ex)
+    {}
+    return outFile;
+  }
+
+  /**
+   * Single DB multiple record retrieval
+   *
+   * @param ids db:query1;query2;query3
+   * @param f raw/xml
+   * @param s ?
+   *
+   * @return Raw string array result of query set
+   */
+  public String[] fetchData(String ids, String f, String s)
+  {
+    // Need to split
+    // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
+
+    StringTokenizer queries = new StringTokenizer(ids, ";");
+    String db = null;
+    StringBuffer querystring = null;
+    while (queries.hasMoreTokens())
+    {
+      String query = queries.nextToken();
+      int p;
+      if ( (p = query.indexOf(':')) > -1 && (p + 3 < query.length()))
+      {
+        db = query.substring(0, p);
+        query = query.substring(p + 1);
+      }
+      if (querystring == null)
+      {
+        querystring = new StringBuffer(query);
+      }
+      else
+      {
+        querystring.append("," + query);
+      }
+    }
+    if (db == null)
+    {
+      System.err.println("Invalid Query string : '" + ids +
+                         "'\nShould be of form 'dbname:q1;q2;q3;q4'");
+    }
+    return fetchBatch(querystring.toString(), db, f, s);
+  }
+
+  public String[] fetchBatch(String ids, String db, String f, String s)
+  {
+    // max 50 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);
+
+      if (f != null)
+      {
+        format = f;
+      }
+
+      if (s != null)
+      {
+        style = s;
+      }
+
+      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);
+      }
+      return null;
+    }
+    catch (Exception ex)
+    {
+      if (ex.getMessage().startsWith(
+          "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
+      {
+        return null;
+      }
+      System.err.println("Unexpected exception when retrieving from " + db +
+                         "\nQuery was : '" + ids + "'");
+      ex.printStackTrace(System.err);
+      return null;
+    }
+  }
+}