X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=167314eee2dae90118035a57b15feb649e5729e0;hb=9e338a58713e1f3a451aa34c5e6c488bdd6d8cab;hp=dc0418fb04d6cae7571d730d65864baeca4ded64;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index dc0418f..167314e 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -35,16 +35,22 @@ import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.Reader;
 import java.io.StringReader;
+import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.zip.GZIPInputStream;
 
+
 /**
  * implements a random access wrapper around a particular datasource, for
  * passing to identifyFile and AlignFile objects.
  */
 public class FileParse
 {
+  protected static final String SPACE = " ";
+
+  protected static final String TAB = "\t";
+
   /**
    * text specifying source of data. usually filename or url.
    */
@@ -52,6 +58,7 @@ public class FileParse
 
   public File inFile = null;
 
+
   /**
    * a viewport associated with the current file operation. May be null. May
    * move to different object.
@@ -125,9 +132,8 @@ public class FileParse
   {
     if (from == null)
     {
-      throw new Error(
-              MessageManager
-                      .getString("error.implementation_error_null_fileparse"));
+      throw new Error(MessageManager
+              .getString("error.implementation_error_null_fileparse"));
     }
     if (from == this)
     {
@@ -183,7 +189,7 @@ public class FileParse
       {
         try
         {
-          dataIn = tryAsGzipSource(new FileInputStream(fileStr));
+          dataIn = getGzipReader(new FileInputStream(fileStr));
           dataName = fileStr;
           return error;
         } catch (Exception x)
@@ -201,57 +207,78 @@ public class FileParse
     return error;
   }
 
-  private BufferedReader tryAsGzipSource(InputStream inputStream)
+  /**
+   * Returns a {@code BufferedReader} which wraps the input stream with a
+   * GZIPInputStream. Throws a {@code ZipException} if a GZIP format error
+   * occurs or the compression method used is unsupported.
+   * 
+   * @param inputStream
+   * @return
+   * @throws Exception
+   */
+  private BufferedReader getGzipReader(InputStream inputStream)
           throws Exception
   {
-    BufferedReader inData = new BufferedReader(new InputStreamReader(
-            new GZIPInputStream(inputStream)));
+    BufferedReader inData = new BufferedReader(
+            new InputStreamReader(new GZIPInputStream(inputStream)));
     inData.mark(2048);
     inData.read();
     inData.reset();
     return inData;
   }
 
-  private boolean checkURLSource(String fileStr) throws IOException,
-          MalformedURLException
+  /**
+   * Tries to read from the given URL. If successful, saves a reader to the
+   * response in field {@code dataIn}, otherwise (on exception, or HTTP response
+   * status not 200), throws an exception.
+   * <p>
+   * If the response status includes
+   * 
+   * <pre>
+   * Content-Type : application/x-gzip
+   * </pre>
+   * 
+   * then tries to read as gzipped content.
+   * 
+   * @param urlStr
+   * @throws IOException
+   * @throws MalformedURLException
+   */
+  private void checkURLSource(String urlStr)
+          throws IOException, MalformedURLException
   {
     errormessage = "URL NOT FOUND";
-    URL url = new URL(fileStr);
-    //
-    // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via
-    // Kenny Sabir
+    URL url = new URL(urlStr);
+    HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+    int rc = conn.getResponseCode();
+    if (rc != HttpURLConnection.HTTP_OK)
+    {
+      throw new IOException(
+              "Response status from " + urlStr + " was " + rc);
+    }
+    String encoding = conn.getContentEncoding();
+    String contentType = conn.getContentType();
+    boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType)
+            || "gzip".equals(encoding);
     Exception e = null;
-    if (fileStr.toLowerCase().endsWith(".gz"))
+    InputStream inputStream = conn.getInputStream();
+    if (isgzipped)
     {
       try
       {
-        InputStream inputStream = url.openStream();
-        dataIn = tryAsGzipSource(inputStream);
-        dataName = fileStr;
-        return false;
-      } catch (Exception ex)
+        dataIn = getGzipReader(inputStream);
+        dataName = urlStr;
+      } catch (Exception e1)
       {
-        e = ex;
+        throw new IOException(MessageManager
+                .getString("exception.failed_to_resolve_gzip_stream"), e);
       }
+      return;
     }
 
-    try
-    {
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    } catch (IOException q)
-    {
-      if (e != null)
-      {
-        throw new IOException(
-                MessageManager
-                        .getString("exception.failed_to_resolve_gzip_stream"),
-                e);
-      }
-      throw q;
-    }
-    // record URL as name of datasource.
-    dataName = fileStr;
-    return false;
+    dataIn = new BufferedReader(new InputStreamReader(inputStream));
+    dataName = urlStr;
+    return;
   }
 
   /**
@@ -326,15 +353,15 @@ public class FileParse
           {
             throw new IOException(MessageManager.formatMessage(
                     "exception.problem_opening_file_also_tried",
-                    new String[] { inFile.getName(), suffixLess,
-                        errormessage }));
+                    new String[]
+                    { inFile.getName(), suffixLess, errormessage }));
           }
         }
         else
         {
           throw new IOException(MessageManager.formatMessage(
-                  "exception.problem_opening_file",
-                  new String[] { inFile.getName(), errormessage }));
+                  "exception.problem_opening_file", new String[]
+                  { inFile.getName(), errormessage }));
         }
       }
     }
@@ -414,8 +441,8 @@ public class FileParse
     {
       // pass up the reason why we have no source to read from
       throw new IOException(MessageManager.formatMessage(
-              "exception.failed_to_read_data_from_source",
-              new String[] { errormessage }));
+              "exception.failed_to_read_data_from_source", new String[]
+              { errormessage }));
     }
     error = false;
     dataIn.mark(READAHEAD_LIMIT);
@@ -446,9 +473,9 @@ public class FileParse
     {
       return dataIn.readLine();
     }
-    throw new IOException(MessageManager.formatMessage(
-            "exception.invalid_source_stream",
-            new String[] { errormessage }));
+    throw new IOException(MessageManager
+            .formatMessage("exception.invalid_source_stream", new String[]
+            { errormessage }));
   }
 
   /**
@@ -501,9 +528,8 @@ public class FileParse
     }
     else
     {
-      throw new IOException(
-              MessageManager
-                      .getString("error.implementation_error_reset_called_for_invalid_source"));
+      throw new IOException(MessageManager.getString(
+              "error.implementation_error_reset_called_for_invalid_source"));
     }
   }