create temporary files in a different directorytest2

5 files changed, 87 insertions, 50 deletions

diff --git a/README.TXT b/README.TXT
index 71d8bd3..bdf5a6f 100644
--- a/README.TXT
+++ b/README.TXT
@@ -27,6 +27,13 @@ http://turingmachine.org/~dmg/papers/dmg2010ninka.pdf
 If you use Ninka for research purposes, we would appreciate you cite
 the above paper.
 
+* Mailing list
+
+Ninka has a mailing list located at sourceforge:
+
+https://sourceforge.net/p/ninka/mailman/
+
+
 * Contributors
 
 - Paul Clough for his code to split sentences
diff --git a/extComments/extComments.pl b/extComments/extComments.pl
index 0509012..39dbeb5 100755
--- a/extComments/extComments.pl
+++ b/extComments/extComments.pl
@@ -30,8 +30,8 @@ if ($path eq '') {
 
 # set parameters
 my %opts = ();
-if (!getopts ('vc:p:',\%opts)) {
-print STDERR "Usage $0 -v
+if (!getopts ('vc:p:',\%opts) or scalar(@ARGV) != 1 ) {
+print STDERR "Usage $0 -v <filename>
 
   -v verbose
   -c count of comment blocks
@@ -50,7 +50,6 @@ $f =~ s/\$/\\\$/g;
 $f =~ s/;/\\;/g;
 $f =~ s/ /\\ /g;
 
-
 #die "illegal file [$f]"  if $f =~ m@/\.@;
 
 my $numberComments = 1;
@@ -69,12 +68,7 @@ if (get_size($original) == 0) {
 
 my $commentsCmd = Determine_Comments_Extractor($f);
 
-execute("$commentsCmd");
-
-if ($commentsCmd =~ /^comments/ and
-    get_size("${f}.comments") == 0){
-    `cat $f | head -700  > ${f}.comments`;
-}
+print execute("$commentsCmd");
 
 exit 0;
 
@@ -91,33 +85,31 @@ sub Determine_Comments_Extractor
 ########################
 # for the time being, let us just extract the top 400 lines
 
-            return "cat '$f' | head -400  > '${f}.comments'";
+            return "cat $f | head -400";
 #            return "$path/hashComments.pl -p '#' '$f'";
         } elsif ($ext eq 'jl' or
                  $ext eq 'el'
             ) {
-            return "cat $f | head -400  > ${f}.comments";
+            return "cat $f | head -400";
 #            return "$path/hashComments.pl -p ';' $f";;
         } elsif ($ext =~ /^(java|c|cpp|h|cxx|c\+\+|cc)$/ ) {
             my $comm = `which comments`;
             if ($comm ne '') {
-                return "comments -c1 '$f' 2> /dev/null";
+                return "comments -o -c1 $f 2> /dev/null";
             } else {
-                return "cat $f | head -400  > ${f}.comments";
+                return "head -400 $f";
             }
         } else {
-            return "cat $f | head -700  > ${f}.comments";
+            return "head -700 $f";
         }
     } else {
-        print "\n>>>>>>>>>>>>>>>>>>>>>\n";
-        return "cat $f | head -700  > ${f}.comments";
+        return "head -700 $f";
     }
 }
 
 sub execute
 {
     my ($c) = @_;
-#    print "\nTo execute [$c]\n";
     my $r = `$c`;
     my $status = ($? >> 8);
     die "execution of program [$c] failed: status [$status]" if ($status != 0);
diff --git a/ninka-excel.pl b/ninka-excel.pl
index 71adddf..9f95dc9 100755
--- a/ninka-excel.pl
+++ b/ninka-excel.pl
@@ -62,8 +62,7 @@ $worksheet->write(0, 7, 'TokensUnmatched', $format);
 $worksheet->write(0, 8, 'TokensUnknown', $format);
 $worksheet->write(0, 9, 'Tokens', $format);
 
-my $tempdir = File::Temp->newdir();
-my $dirname = $tempdir->dirname;
+my $dirname = File::Temp->newdir()->dirname;
 
 print "***** Extracting file [$pack] to temporary directory [$dirname] *****\n";
 my $packext = getExtension($pack);
@@ -85,7 +84,7 @@ print "***** Beginning Execution of Ninka *****\n";
 foreach my $file (@files) {
     if (-T $file) {
 	print "Running ninka on file [$file]\n";
-	execute("perl ${path}/ninka.pl '$file'");
+	execute("perl ${path}/ninka.pl -h '$file' /");
     }
 }
 
diff --git a/ninka-sqlite.pl b/ninka-sqlite.pl
index d53f60f..214d000 100755
--- a/ninka-sqlite.pl
+++ b/ninka-sqlite.pl
@@ -66,8 +66,7 @@ $dbh->do("CREATE TABLE IF NOT EXISTS
           toks_unknown INT, tokens TEXT,
           PRIMARY KEY(filename, path, container))");
 
-my $tempdir = File::Temp->newdir();
-my $dirname = $tempdir->dirname;
+my $dirname = File::Temp->newdir()->dirname;
 
 print "***** Extracting file [$pack] to temporary directory [$dirname] *****\n";
 my $packext = getExtension($pack);
@@ -88,7 +87,7 @@ find(
 print "***** Beginning Execution of Ninka *****\n";
 foreach my $file (@files) {
     print "Running ninka on file [$file]\n";
-    execute("perl ${path}/ninka.pl '$file'");
+    execute("perl ${path}/ninka.pl -h '$file' /");
 }
 
 my @ninkafiles;
@@ -116,6 +115,7 @@ foreach my $file (@ninkafiles) {
     my $filedata = do { local $/; <$fh> };
 
     my $sth;
+    next if ($basefile =~ /comments$/);
     switch (getExtension($basefile)){
 
 #	case ".comments" {
diff --git a/ninka.pl b/ninka.pl
index 3987a41..4ce644e 100755
--- a/ninka.pl
+++ b/ninka.pl
@@ -19,12 +19,14 @@
 use strict;
 use Getopt::Std;
 use File::Basename;
+use File::Path qw(make_path);
+
 
 my %opts = ();
-if (!getopts ("vfCcSsGgTtLd",\%opts) or scalar(@ARGV) == 0) {
+if (!getopts ("vfCcSsGgTtLdDh",\%opts) or scalar(@ARGV) != 2) {
 print STDERR "Ninka version 1.3
 
-Usage $0 -fCtTvcgsGd <filename>
+Usage $0 -fCtTvcgsGd <filename> <outputDir>
 
   -v verbose
   -f force all processing
@@ -44,6 +46,9 @@ Usage $0 -fCtTvcgsGd <filename>
   -L force creation of matching
 
   -d delete intermediate files
+  -D delete license output file
+
+  -h re-create directory structure of original filename in output files under output dir. For the sake of security, no .. directory is allowed in the path name. Starting /s are removed.
 
 \n";
 
@@ -54,6 +59,8 @@ Usage $0 -fCtTvcgsGd <filename>
 
 my $verbose = exists $opts{v};
 my $delete = exists $opts{d};
+my $deleteLic = exists $opts{D};
+my $createDirsHier = exists $opts{h};
 #$delete = 1;
 
 my $path = dirname($0);
@@ -71,35 +78,54 @@ my $forceLicense = exists $opts{L};
 
 #die "Usage $0 <filename>" unless $ARGV[0] =~ /\.(c|cpp|java|cc|cxx|h|jl|py|pm|el|pl)$/;
 
-my $f = $ARGV[0];
-
-
-my $original = $f;
-
-$f =~ s/'/\\'/g;
-$f =~ s/\$/\\\$/g;
-$f =~ s/;/\\;/g;
-$f =~ s/ /\\ /g;
+my $original = $ARGV[0];
+my $escapedOriginal = escape_filename($original);
+my $dirOriginal = $ARGV[1];
+my $f = basename($escapedOriginal);
 
 print "Starting: $original;\n" if ($verbose);
 
 print "$original;";
 
-my $commentsFile = "${f}.comments";
-my $sentencesFile = "${f}.sentences";
-my $goodsentFile = "${f}.goodsent";
-my $sentokFile = "${f}.senttok";
-
 if (not (-f $original)) {
     print "ERROR;[${original}] is not a file\n" ;
     exit 0;
 }
+if (not (-d $dirOriginal)) {
+    print "ERROR;[${dirOriginal}] is not a directory\n" ;
+    exit 0;
+} 
+$dirOriginal =~ s@/$@@;
+
+my $dir;
+my $hier = "";
+if ($createDirsHier) {
+    $hier = dirname($original);
+    # make sure it does not start with /
+    $hier =~ s@^/+@@;
+    # abort if relative... 
+    if ($hier =~ m@/\.\./@ or $hier =~ m@^\.\.@ or $hier =~ m@\.\.$@) {
+        die "directory name [$hier] of input file contains .. aborting\n";
+    }
+    $dir = "$dirOriginal/$hier";
+    make_path($dir) unless -d $dir;
+    $dir = escape_filename($dir);
+}
+
+my $commentsFile = "$dir/${f}.comments";
+my $sentencesFile = "$dir/${f}.sentences";
+my $goodsentFile = "$dir/${f}.goodsent";
+my $badsentFile = "$dir/${f}.badsent";
+my $sentokFile = "$dir/${f}.senttok";
+my $licenseFile = "$dir/${f}.license";
+my $codeFile = "$dir/${f}.code";
 
 
 Do_File_Process($original, $commentsFile, ($force or $forceComments),
-                "$path/extComments/extComments.pl -c1 ${f}",
+                "$path/extComments/extComments.pl -c1 ${escapedOriginal} > $commentsFile",
                 "Creating comments file",
-                exists $opts{c});
+                exists $opts{c}
+    );
 
 
 Do_File_Process($commentsFile, $sentencesFile, ($force or $forceSentences),
@@ -119,18 +145,21 @@ Do_File_Process($goodsentFile, $sentokFile, ($force or $forceSentok),
 
 
 print "Matching ${f}.senttok against rules" if ($verbose);
-execute("$path/matcher/matcher.pl ${f}.senttok > ${f}.license");
+execute("$path/matcher/matcher.pl ${sentokFile} > ${licenseFile}");
 
-print `cat ${f}.license`;
-
-unlink("${f}.code");
+print `cat ${licenseFile}`;
 
 if ($delete) {
-    unlink("${f}.badsent");
-    unlink("${f}.comments");
-    unlink("${f}.goodsent");
-    unlink("${f}.sentences");
-    unlink("${f}.senttok");
+    unlink($commentsFile);
+    unlink($sentencesFile);
+    unlink($goodsentFile);
+    unlink($badsentFile);
+    unlink($sentokFile);
+    unlink($codeFile) if -f $codeFile;
+}
+
+if ($deleteLic) {
+    unlink($licenseFile);
 }
 
 exit 0;
@@ -179,3 +208,13 @@ sub newer
         return 1;
     }
 }
+
+sub escape_filename
+{
+    my ($f) = @_;
+    $f =~ s/'/\\'/g;
+    $f =~ s/\$/\\\$/g;
+    $f =~ s/;/\\;/g;
+    $f =~ s/ /\\ /g;
+    return $f;
+}