X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Febi%2FEBIFetchClient.java;h=3e8c55ed621b8f9d3a60c1d3f81911122211b139;hb=a862a922bf20918fc3f5066ac92e4c69da07e105;hp=dd3cc16222324f50c9d4e5949161639d7b5a2a2f;hpb=65d7b70ce9788fd1680a5e81b1eaae30126b8ed2;p=jalview.git

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index dd3cc16..3e8c55e 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -91,7 +91,7 @@ public class EBIFetchClient
    * @param format
    *          the format wanted
    * @param extension
-   *          for the temporary file to hold response
+   *          for the temporary file to hold response (without separator)
    * @return the file holding the response
    * @throws OutOfMemoryError
    */
@@ -102,7 +102,7 @@ public class EBIFetchClient
     File outFile = null;
     try
     {
-      outFile = File.createTempFile("jalview", ext);
+      outFile = File.createTempFile("jalview", "." + ext);
       outFile.deleteOnExit();
       fetchData(ids, format, outFile);
       if (outFile.length() == 0)
@@ -116,28 +116,33 @@ public class EBIFetchClient
     return outFile;
   }
 
-  String[] fetchData(String ids, String f, File outFile)
+  /**
+   * Fetches queries and either saves the response to a file or returns as
+   * string data
+   * 
+   * @param ids
+   * @param format
+   * @param outFile
+   * @return
+   * @throws OutOfMemoryError
+   */
+  String[] fetchData(String ids, String format, File outFile)
           throws OutOfMemoryError
   {
-    String[] rslts = new String[0];
     StringBuilder querystring = new StringBuilder(ids.length());
-    String db = parseIds(ids, querystring);
-    if (db == null)
+    String database = parseIds(ids, querystring);
+    if (database == null)
     {
       System.err.println("Invalid Query string : '" + ids + "'");
       System.err.println("Should be of form 'dbname:q1;q2;q3;q4'");
       return null;
     }
-    String[] rslt = fetchBatch(querystring.toString(), db, f, 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);
+    // note: outFile is currently always specified, so return value is null
+    String[] rslt = fetchBatch(querystring.toString(), database, format,
+            outFile);
+
+    return (rslt != null && rslt.length > 0 ? rslt : null);
   }
 
   /**
@@ -179,11 +184,22 @@ public class EBIFetchClient
     return database;
   }
 
-  String[] fetchBatch(String ids, String dbPath, String format,
+  /**
+   * Fetches queries and either saves the response to a file or (if no file
+   * specified) returns as string data
+   * 
+   * @param ids
+   * @param database
+   * @param format
+   * @param outFile
+   * @return
+   * @throws OutOfMemoryError
+   */
+  String[] fetchBatch(String ids, String database, String format,
           File outFile) throws OutOfMemoryError
   {
     // long time = System.currentTimeMillis();
-    String url = buildUrl(ids, dbPath, format);
+    String url = buildUrl(ids, database, format);
 
     try
     {
@@ -215,8 +231,7 @@ public class EBIFetchClient
       }
     } catch (OutOfMemoryError er)
     {
-
-      System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + dbPath
+      System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + database
               + ":\n" + ids);
       throw er;
     } catch (Exception ex)
@@ -227,8 +242,7 @@ public class EBIFetchClient
         return null;
       }
       System.err.println("Unexpected exception when retrieving from "
-              + dbPath
-              + "\nQuery was : '" + ids + "'");
+              + database + "\nQuery was : '" + ids + "'");
       ex.printStackTrace(System.err);
       return null;
     } finally