Remove the shell usage of bz2, which could be a security problem if s…

…omeone else hijacks the system's bz2 installation. Addresses https://nvd.nist.gov/vuln/detail/CVE-2023-39020

src/edu/stanford/nlp/ie/crf/CRFFeatureExporter.java

@@ -18,8 +18,7 @@
 /**
  * Exports CRF features for use with other programs.
  * Usage: CRFFeatureExporter -prop crfClassifierPropFile -trainFile inputFile -exportFeatures outputFile
- * - Output file is automatically gzipped/b2zipped if ending in gz/bz2
- * - bzip2 requires that bzip2 is available via command line
+ * - Output file is automatically gzipped/b2zipped if ending in gz
  * - Currently exports features in a format that can be read by a modified crfsgd
  *   (crfsgd assumes features are gzipped)
  * TODO: Support other formats (like crfsuite)

src/edu/stanford/nlp/io/IOUtils.java

@@ -1488,7 +1488,7 @@ public static LinkedList<String[]> readCSVStrictly(String filename, int numColum
   }
 
   /**
-   * Get a input file stream (automatically gunzip/bunzip2 depending on file extension)
+   * Get a input file stream (automatically gunzip depending on file extension)
    * @param filename Name of file to open
    * @return Input stream that can be used to read from the file
    * @throws IOException if there are exceptions opening the file
@@ -1497,15 +1497,12 @@ public static InputStream getFileInputStream(String filename) throws IOException
     InputStream in = new FileInputStream(filename);
     if (filename.endsWith(".gz")) {
       in = new GZIPInputStream(in);
-    } else if (filename.endsWith(".bz2")) {
-      //in = new CBZip2InputStream(in);
-      in = getBZip2PipedInputStream(filename);
     }
     return in;
   }
 
   /**
-   * Get a output file stream (automatically gzip/bzip2 depending on file extension)
+   * Get a output file stream (automatically gzip depending on file extension)
    * @param filename Name of file to open
    * @return Output stream that can be used to write to the file
    * @throws IOException if there are exceptions opening the file
@@ -1514,9 +1511,6 @@ public static OutputStream getFileOutputStream(String filename) throws IOExcepti
     OutputStream out = new FileOutputStream(filename);
     if (filename.endsWith(".gz")) {
       out = new GZIPOutputStream(out);
-    } else if (filename.endsWith(".bz2")) {
-      //out = new CBZip2OutputStream(out);
-      out = getBZip2PipedOutputStream(filename);
     }
     return out;
   }
@@ -1525,9 +1519,6 @@ public static OutputStream getFileOutputStream(String filename, boolean append)
     OutputStream out = new FileOutputStream(filename, append);
     if (filename.endsWith(".gz")) {
       out = new GZIPOutputStream(out);
-    } else if (filename.endsWith(".bz2")) {
-      //out = new CBZip2OutputStream(out);
-      out = getBZip2PipedOutputStream(filename);
     }
     return out;
   }
@@ -1584,22 +1575,6 @@ public static PrintWriter getPrintWriter(String filename, String encoding) throw
     return new PrintWriter(new BufferedWriter(new OutputStreamWriter(out, encoding)), true);
   }
 
-  public static InputStream getBZip2PipedInputStream(String filename) throws IOException {
-    String bzcat = System.getProperty("bzcat", "bzcat");
-    Runtime rt = Runtime.getRuntime();
-    String cmd = bzcat + " " + filename;
-    //log.info("getBZip2PipedInputStream: Running command: "+cmd);
-    Process p = rt.exec(cmd);
-    Writer errWriter = new BufferedWriter(new OutputStreamWriter(System.err));
-    StreamGobbler errGobbler = new StreamGobbler(p.getErrorStream(), errWriter);
-    errGobbler.start();
-    return p.getInputStream();
-  }
-
-  public static OutputStream getBZip2PipedOutputStream(String filename) throws IOException {
-    return new BZip2PipedOutputStream(filename);
-  }
-
   private static final Pattern tab = Pattern.compile("\t");
 
   /**