JAL-2656 JAL-3615 check response headers to test for gzipped url reply

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 68b5d28..167314e 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -35,14 +35,12 @@ 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;
 
 
-import jalview.ws.dbsources.Pfam;
-import jalview.ws.dbsources.Rfam;
-
 /**
  * implements a random access wrapper around a particular datasource, for
  * passing to identifyFile and AlignFile objects.
@@ -53,8 +51,6 @@ public class FileParse
 
   protected static final String TAB = "\t";
 
-  private static final String GZ_EXT = ".gz";
-
   /**
    * text specifying source of data. usually filename or url.
    */
@@ -189,11 +185,11 @@ public class FileParse
     }
     if (!error)
     {
-      if (fileStr.toLowerCase().endsWith(GZ_EXT))
+      if (fileStr.toLowerCase().endsWith(".gz"))
       {
         try
         {
-          dataIn = tryAsGzipSource(new FileInputStream(fileStr));
+          dataIn = getGzipReader(new FileInputStream(fileStr));
           dataName = fileStr;
           return error;
         } catch (Exception x)
@@ -211,7 +207,16 @@ 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(
@@ -222,65 +227,58 @@ public class FileParse
     return inData;
   }
 
-  private boolean checkURLSource(String fileStr)
+  /**
+   * 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 (isGzipped(fileStr))
+    InputStream inputStream = conn.getInputStream();
+    if (isgzipped)
     {
       try
       {
-        InputStream inputStream = url.openStream();
-        dataIn = tryAsGzipSource(inputStream);
-        dataName = fileStr;
-        return false;
-      } catch (Exception ex)
-      {
-        e = ex;
-      }
-    }
-
-    try
-    {
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    } catch (IOException q)
-    {
-      if (e != null)
+        dataIn = getGzipReader(inputStream);
+        dataName = urlStr;
+      } catch (Exception e1)
       {
         throw new IOException(MessageManager
                 .getString("exception.failed_to_resolve_gzip_stream"), e);
       }
-      throw q;
+      return;
     }
-    // record URL as name of datasource.
-    dataName = fileStr;
-    return false;
-  }
 
-  /**
-   * Answers true if the filename (or URL) has a format which Jalview recognises
-   * as denoting gzipped content.
-   * <p>
-   * Currently this means having a ".gz" extension, or ending in "/gzipped" or
-   * "?gz=1" (used to retrieve gzipped from Pfam and Rfam respectively).
-   * 
-   * @param filename
-   * @return
-   */
-  protected static boolean isGzipped(String filename)
-  {
-    if (filename == null)
-    {
-      return false;
-    }
-    String lower = filename.toLowerCase();
-    return lower.endsWith(GZ_EXT) || lower.endsWith(Pfam.GZIPPED)
-            || lower.endsWith(Rfam.GZIPPED);
+    dataIn = new BufferedReader(new InputStreamReader(inputStream));
+    dataName = urlStr;
+    return;
   }
 
   /**

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index de19078..47e66ac 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -38,7 +38,7 @@ abstract public class Pfam extends Xfam
   /*
    * append to URLs to retrieve as a gzipped file
    */
-  public static final String GZIPPED = "/gzipped";
+  protected static final String GZIPPED = "/gzipped";
 
   static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
 

diff --git a/src/jalview/ws/dbsources/Rfam.java b/src/jalview/ws/dbsources/Rfam.java
index dba3e31..c9ee7fc 100644 (file)
--- a/src/jalview/ws/dbsources/Rfam.java
+++ b/src/jalview/ws/dbsources/Rfam.java
@@ -39,7 +39,7 @@ abstract public class Rfam extends Xfam
   /*
    * append to URLs to retrieve as a gzipped file
    */
-  public static final String GZIPPED = "?gz=1&download=1";
+  protected static final String GZIPPED = "?gzip=1&download=1";
 
   @Override
   protected String getURLPrefix()

diff --git a/test/jalview/io/FileParseTest.java b/test/jalview/io/FileParseTest.java
deleted file mode 100644 (file)
index 7eb2c9c..0000000
--- a/test/jalview/io/FileParseTest.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package jalview.io;
-
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertTrue;
-
-import org.testng.annotations.Test;
-
-public class FileParseTest
-{
-  @Test(groups = "Functional")
-  public void setIsGzipped()
-  {
-    assertFalse(FileParse.isGzipped(null));
-    assertFalse(FileParse.isGzipped("foobar"));
-    assertFalse(FileParse.isGzipped(".gz.foobar"));
-
-    assertTrue(FileParse.isGzipped("abc.gz"));
-    assertTrue(FileParse.isGzipped("abc.GZ"));
-    assertTrue(FileParse.isGzipped(".gz"));
-    assertFalse(FileParse.isGzipped("abc/gz"));
-    assertFalse(FileParse.isGzipped("gz"));
-    
-    assertTrue(FileParse.isGzipped("http:/xy.com/abc/gzipped"));
-    assertTrue(FileParse.isGzipped("abc/gzipped"));
-    assertTrue(FileParse.isGzipped("abc/GZIPPED"));
-    assertTrue(FileParse.isGzipped("/gzipped"));
-    assertFalse(FileParse.isGzipped("gzipped"));
-    
-    assertTrue(FileParse.isGzipped("http:/xy.com/abc?gz=1"));
-    assertTrue(FileParse.isGzipped("http:/xy.com/abc?GZ=1"));
-    // currently only recognised if the last token on the URL
-    assertFalse(FileParse.isGzipped("http:/xy.com/abc?gz=1&content-type=text/xml"));
-  }
-}