JAL-4277 --mkdirs with cautious refusal for paths with ..

[jalview.git] / src / jalview / util / FileUtils.java

diff --git a/src/jalview/util/FileUtils.java b/src/jalview/util/FileUtils.java
index 63af0bc..983ba75 100644 (file)
--- a/src/jalview/util/FileUtils.java
+++ b/src/jalview/util/FileUtils.java
@@ -12,10 +12,13 @@ import java.nio.file.Paths;
 import java.nio.file.SimpleFileVisitor;
 import java.nio.file.attribute.BasicFileAttributes;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.EnumSet;
 import java.util.List;
 import java.util.stream.Collectors;
 
+import jalview.bin.Console;
+
 public class FileUtils
 {
   /*
@@ -33,6 +36,8 @@ public class FileUtils
           boolean allowSingleFilenameThatDoesNotExist)
   {
     pattern = substituteHomeDir(pattern);
+    String relativePattern = pattern.startsWith(File.separator) ? null
+            : pattern;
     List<File> files = new ArrayList<>();
     /*
      * For efficiency of the Files.walkFileTree(), let's find the longest path that doesn't need globbing.
@@ -57,7 +62,11 @@ public class FileUtils
     {
       String pS = pattern.substring(0, lastFS + 1);
       String rest = pattern.substring(lastFS + 1);
-      Path parentDir = Paths.get(pS).toAbsolutePath();
+      if ("".equals(pS))
+      {
+        pS = ".";
+      }
+      Path parentDir = Paths.get(pS);
       if (parentDir.toFile().exists())
       {
         try
@@ -65,10 +74,11 @@ public class FileUtils
           String glob = "glob:" + parentDir.toString() + File.separator
                   + rest;
           PathMatcher pm = FileSystems.getDefault().getPathMatcher(glob);
-          int maxDepth = rest.contains("**") ? Integer.MAX_VALUE
+          int maxDepth = rest.contains("**") ? 1028
                   : (int) (rest.chars()
                           .filter(ch -> ch == File.separatorChar).count())
                           + 1;
+
           Files.walkFileTree(parentDir,
                   EnumSet.of(FileVisitOption.FOLLOW_LINKS), maxDepth,
                   new SimpleFileVisitor<Path>()
@@ -106,6 +116,7 @@ public class FileUtils
         files.add(f);
       }
     }
+    Collections.sort(files);
 
     return files;
   }
@@ -123,4 +134,141 @@ public class FileUtils
             ? System.getProperty("user.home") + path.substring(1)
             : path;
   }
+
+  /*
+   * This method returns the basename of File file
+   */
+  public static String getBasename(File file)
+  {
+    return getBasenameOrExtension(file, false);
+  }
+
+  /*
+   * This method returns the extension of File file.
+   */
+  public static String getExtension(File file)
+  {
+    return getBasenameOrExtension(file, true);
+  }
+
+  public static String getBasenameOrExtension(File file, boolean extension)
+  {
+    if (file == null)
+      return null;
+
+    String value = null;
+    String filename = file.getName();
+    int lastDot = filename.lastIndexOf('.');
+    if (lastDot > 0) // don't truncate if starts with '.'
+    {
+      value = extension ? filename.substring(lastDot + 1)
+              : filename.substring(0, lastDot);
+    }
+    else
+    {
+      value = extension ? "" : filename;
+    }
+    return value;
+  }
+
+  /*
+   * This method returns the dirname of the first --append or --open value. 
+   * Used primarily for substitutions in output filenames.
+   */
+  public static String getDirname(File file)
+  {
+    if (file == null)
+      return null;
+
+    String dirname = null;
+    File p = file.getParentFile();
+    if (p == null)
+    {
+      p = new File(".");
+    }
+    File d = new File(substituteHomeDir(p.getPath()));
+    dirname = d.getPath();
+    return dirname;
+  }
+
+  public static String convertWildcardsToPath(String value, String wildcard,
+          String dirname, String basename)
+  {
+    if (value == null)
+    {
+      return null;
+    }
+    StringBuilder path = new StringBuilder();
+    int lastFileSeparatorIndex = value.lastIndexOf(File.separatorChar);
+    int wildcardBeforeIndex = value.indexOf(wildcard);
+    if (lastFileSeparatorIndex > wildcard.length() - 1
+            && wildcardBeforeIndex < lastFileSeparatorIndex)
+    {
+      path.append(value.substring(0, wildcardBeforeIndex));
+      path.append(dirname);
+      path.append(value.substring(wildcardBeforeIndex + wildcard.length(),
+              lastFileSeparatorIndex + 1));
+    }
+    else
+    {
+      path.append(value.substring(0, lastFileSeparatorIndex + 1));
+    }
+    int wildcardAfterIndex = value.indexOf(wildcard,
+            lastFileSeparatorIndex);
+    if (wildcardAfterIndex > lastFileSeparatorIndex)
+    {
+      path.append(value.substring(lastFileSeparatorIndex + 1,
+              wildcardAfterIndex));
+      path.append(basename);
+      path.append(value.substring(wildcardAfterIndex + wildcard.length()));
+    }
+    else
+    {
+      path.append(value.substring(lastFileSeparatorIndex + 1));
+    }
+    return path.toString();
+  }
+
+  public static File getParentDir(File file)
+  {
+    if (file == null)
+    {
+      return null;
+    }
+    File parentDir = file.getAbsoluteFile().getParentFile();
+    return parentDir;
+  }
+
+  public static boolean checkParentDir(File file, boolean mkdirs)
+  {
+    if (file == null)
+    {
+      return false;
+    }
+    File parentDir = getParentDir(file);
+    if (parentDir.exists())
+    {
+      // already exists, nothing to do so nothing to worry about!
+      return true;
+    }
+
+    if (!mkdirs)
+    {
+      return false;
+    }
+
+    Path path = file.toPath();
+    for (int i = 0; i < path.getNameCount(); i++)
+    {
+      Path p = path.getName(i);
+      if ("..".equals(p.toString()))
+      {
+        Console.warn("Cautiously not running mkdirs on " + file.toString()
+                + " because the path to be made contains '..'");
+        return false;
+      }
+    }
+
+    return parentDir.mkdirs();
+  }
 }