From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 24 May 2018 10:56:32 +0000 (+0100)
Subject: JAL-1460 process .lnk files dragged to Jalview when on Windows using WindowsShortCutH... 
X-Git-Tag: Release_2_10_5~67^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2df0e73f2d10339cd837b0aa3f216ff140cd53e7;p=jalview.git

JAL-1460 process .lnk files dragged to Jalview when on Windows using WindowsShortCutHandler class (thanks to StackOverFlow post..)

---

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index e2baa85..d0d9125 100644
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -9,6 +9,7 @@ ext.edu.ucsf.rbvi.strucviz2 includes sources originally developed by Scooter Mor
  
  jalview.ext.android includes code taken from the Android Open Source Project (https://android.googlesource.com/platform/frameworks/base/+/master/core/java/android/util).
  The Apache 2.0 Licence (http://www.apache.org/licenses/LICENSE-2.0) is acknowledged in the source code.
+ org.stackoverflowusers.file.WindowsShortcuts was downloaded from http://github.com/codebling/WindowsShortcuts via https://stackoverflow.com/questions/309495/windows-shortcut-lnk-parser-in-java 
 
 Licensing information for each library is given below:
 
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 9598f60..e14e991 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -32,6 +32,7 @@ import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -116,6 +117,8 @@ import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import org.stackoverflowusers.file.WindowsShortcut;
+
 /**
  * Jalview Desktop
  * 
@@ -3404,6 +3407,28 @@ public class Desktop extends jalview.jbgui.GDesktop
           files.add(file.toString());
         }
       }
+      if (Platform.isWindows())
+      {
+        Cache.log.debug("Scanning dropped content for Windows Link Files");
+
+         // resolve any .lnk files in the file drop
+        for (int f=0;f<files.size();f++)
+        {
+          if (protocols.get(f).equals(DataSourceType.FILE)) {
+              File lf = new File(files.get(f));
+              if (WindowsShortcut.isPotentialValidLink(lf)) {
+                // process link file to get a URL
+                Cache.log.debug("Found potential link file: "+lf);
+                WindowsShortcut wscfile = new WindowsShortcut(lf);
+                String fullname = wscfile.getRealFilename();
+                protocols.set(f,FormatAdapter.checkProtocol(fullname));
+                files.set(f,fullname);
+                Cache.log.debug("Parsed real filename "+fullname+" to extract protocol: "+protocols.get(f));
+            }
+          }
+        }
+      }
+        
       if (Cache.log.isDebugEnabled())
       {
         if (data == null || !added)
diff --git a/src/org/stackoverflowusers/file/WindowsShortcut.java b/src/org/stackoverflowusers/file/WindowsShortcut.java
new file mode 100644
index 0000000..671e002
--- /dev/null
+++ b/src/org/stackoverflowusers/file/WindowsShortcut.java
@@ -0,0 +1,215 @@
+package org.stackoverflowusers.file;
+
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.text.ParseException;
+
+/**
+ * Represents a Windows shortcut (typically visible to Java only as a '.lnk' file).
+ *
+ * Retrieved 2011-09-23 from http://stackoverflow.com/questions/309495/windows-shortcut-lnk-parser-in-java/672775#672775
+ * Originally called LnkParser
+ *
+ * Written by: (the stack overflow users, obviously!)
+ *   Apache Commons VFS dependency removed by crysxd (why were we using that!?) https://github.com/crysxd
+ *   Headerified, refactored and commented by Code Bling http://stackoverflow.com/users/675721/code-bling
+ *   Network file support added by Stefan Cordes http://stackoverflow.com/users/81330/stefan-cordes
+ *   Adapted by Sam Brightman http://stackoverflow.com/users/2492/sam-brightman
+ *   Based on information in 'The Windows Shortcut File Format' by Jesse Hager &lt;jessehager@iname.com&gt;
+ *   And somewhat based on code from the book 'Swing Hacks: Tips and Tools for Killer GUIs'
+ *     by Joshua Marinacci and Chris Adamson
+ *     ISBN: 0-596-00907-0
+ *     http://www.oreilly.com/catalog/swinghks/
+ */
+public class WindowsShortcut
+{
+    private boolean isDirectory;
+    private boolean isLocal;
+    private String real_file;
+
+    /**
+     * Provides a quick test to see if this could be a valid link !
+     * If you try to instantiate a new WindowShortcut and the link is not valid,
+     * Exceptions may be thrown and Exceptions are extremely slow to generate,
+     * therefore any code needing to loop through several files should first check this.
+     *
+     * @param file the potential link
+     * @return true if may be a link, false otherwise
+     * @throws IOException if an IOException is thrown while reading from the file
+     */
+    public static boolean isPotentialValidLink(File file) throws IOException {
+        final int minimum_length = 0x64;
+        InputStream fis = new FileInputStream(file);
+        boolean isPotentiallyValid = false;
+        try {
+            isPotentiallyValid = file.isFile()
+                && file.getName().toLowerCase().endsWith(".lnk")
+                && fis.available() >= minimum_length
+                && isMagicPresent(getBytes(fis, 32));
+        } finally {
+            fis.close();
+        }
+        return isPotentiallyValid;
+    }
+
+    public WindowsShortcut(File file) throws IOException, ParseException {
+        InputStream in = new FileInputStream(file);
+        try {
+            parseLink(getBytes(in));
+        } finally {
+            in.close();
+        }
+    }
+
+    /**
+     * @return the name of the filesystem object pointed to by this shortcut
+     */
+    public String getRealFilename() {
+        return real_file;
+    }
+
+    /**
+     * Tests if the shortcut points to a local resource.
+     * @return true if the 'local' bit is set in this shortcut, false otherwise
+     */
+    public boolean isLocal() {
+        return isLocal;
+    }
+
+    /**
+     * Tests if the shortcut points to a directory.
+     * @return true if the 'directory' bit is set in this shortcut, false otherwise
+     */
+    public boolean isDirectory() {
+        return isDirectory;
+    }
+
+    /**
+     * Gets all the bytes from an InputStream
+     * @param in the InputStream from which to read bytes
+     * @return array of all the bytes contained in 'in'
+     * @throws IOException if an IOException is encountered while reading the data from the InputStream
+     */
+    private static byte[] getBytes(InputStream in) throws IOException {
+        return getBytes(in, null);
+    }
+    
+    /**
+     * Gets up to max bytes from an InputStream
+     * @param in the InputStream from which to read bytes
+     * @param max maximum number of bytes to read
+     * @return array of all the bytes contained in 'in'
+     * @throws IOException if an IOException is encountered while reading the data from the InputStream
+     */
+    private static byte[] getBytes(InputStream in, Integer max) throws IOException {
+        // read the entire file into a byte buffer
+        ByteArrayOutputStream bout = new ByteArrayOutputStream();
+        byte[] buff = new byte[256];
+        while (max == null || max > 0) {
+            int n = in.read(buff);
+            if (n == -1) {
+                break;
+            }
+            bout.write(buff, 0, n);
+            if (max != null)
+                max -= n;
+        }
+        in.close();
+        return bout.toByteArray();
+    }
+
+    private static boolean isMagicPresent(byte[] link) {
+        final int magic = 0x0000004C;
+        final int magic_offset = 0x00;
+        return link.length >= 32 && bytesToDword(link, magic_offset) == magic;
+    }
+
+    /**
+     * Gobbles up link data by parsing it and storing info in member fields
+     * @param link all the bytes from the .lnk file
+     */
+    private void parseLink(byte[] link) throws ParseException {
+        try {
+            if (!isMagicPresent(link))
+                throw new ParseException("Invalid shortcut; magic is missing", 0);
+
+            // get the flags byte
+            byte flags = link[0x14];
+
+            // get the file attributes byte
+            final int file_atts_offset = 0x18;
+            byte file_atts = link[file_atts_offset];
+            byte is_dir_mask = (byte)0x10;
+            if ((file_atts & is_dir_mask) > 0) {
+                isDirectory = true;
+            } else {
+                isDirectory = false;
+            }
+
+            // if the shell settings are present, skip them
+            final int shell_offset = 0x4c;
+            final byte has_shell_mask = (byte)0x01;
+            int shell_len = 0;
+            if ((flags & has_shell_mask) > 0) {
+                // the plus 2 accounts for the length marker itself
+                shell_len = bytesToWord(link, shell_offset) + 2;
+            }
+
+            // get to the file settings
+            int file_start = 0x4c + shell_len;
+
+            final int file_location_info_flag_offset_offset = 0x08;
+            int file_location_info_flag = link[file_start + file_location_info_flag_offset_offset];
+            isLocal = (file_location_info_flag & 2) == 0;
+            // get the local volume and local system values
+            //final int localVolumeTable_offset_offset = 0x0C;
+            final int basename_offset_offset = 0x10;
+            final int networkVolumeTable_offset_offset = 0x14;
+            final int finalname_offset_offset = 0x18;
+            int finalname_offset = link[file_start + finalname_offset_offset] + file_start;
+            String finalname = getNullDelimitedString(link, finalname_offset);
+            if (isLocal) {
+                int basename_offset = link[file_start + basename_offset_offset] + file_start;
+                String basename = getNullDelimitedString(link, basename_offset);
+                real_file = basename + finalname;
+            } else {
+                int networkVolumeTable_offset = link[file_start + networkVolumeTable_offset_offset] + file_start;
+                int shareName_offset_offset = 0x08;
+                int shareName_offset = link[networkVolumeTable_offset + shareName_offset_offset]
+                    + networkVolumeTable_offset;
+                String shareName = getNullDelimitedString(link, shareName_offset);
+                real_file = shareName + "\\" + finalname;
+            }
+        } catch (ArrayIndexOutOfBoundsException e) {
+            throw new ParseException("Could not be parsed, probably not a valid WindowsShortcut", 0);
+        }
+    }
+
+    private static String getNullDelimitedString(byte[] bytes, int off) {
+        int len = 0;
+        // count bytes until the null character (0)
+        while (true) {
+            if (bytes[off + len] == 0) {
+                break;
+            }
+            len++;
+        }
+        return new String(bytes, off, len);
+    }
+
+    /*
+     * convert two bytes into a short note, this is little endian because it's
+     * for an Intel only OS.
+     */
+    private static int bytesToWord(byte[] bytes, int off) {
+        return ((bytes[off + 1] & 0xff) << 8) | (bytes[off] & 0xff);
+    }
+
+    private static int bytesToDword(byte[] bytes, int off) {
+        return (bytesToWord(bytes, off + 2) << 16) | bytesToWord(bytes, off);
+    }
+
+}