Merge pull request #37 from bruceravel/memory

Address memory leaks in libxdifile

Author: newville

baddata/BadFiles.txt

@@ -14,7 +14,7 @@ bad_07.xdi   file read(2)   Y     No Column labels  -
 bad_08.xdi   file read(2)   Y     Too few Column labels
 bad_09.xdi   file read(2)   Y     Too many Column labels
 bad_10.xdi   file read(2)   Y     Column indices not continuous
-bad_11.xdi   error msg      Y     Unsupported comment character
+bad_11.xdi   file read(3)   Y     Unsupported comment character
 bad_12.xdi   file read(1)   Y     angle given without mono.d_spacing
 bad_13.xdi   error msg      Y     inconsistent number of columns in data table -- too few
 bad_14.xdi   error msg      Y     inconsistent number of columns in data table -- too many
@@ -26,17 +26,18 @@ bad_19.xdi   error msg      Y     Header 'Family.Key: Value' -- no ':'
 bad_20.xdi   error msg      Y     Header 'Family.Key: Value' -- two ':'
 bad_21.xdi   error msg      Y     Header 'Family.Key: Value' -- no '.'
 bad_22.xdi   error msg      Y     Header 'Family.Key: Value' -- two '.'
-bad_23.xdi   file read(3)   Y     Header 'Family.Key: Value' -- key starts with number
+bad_23.xdi   file read(4)   Y     Header 'Family.Key: Value' -- key starts with number
 bad_24.xdi   error msg      Y     Header 'Family.Key: Value' -- Family starts with number
-bad_25.xdi   file read(4)   Y     No extra version given
-bad_26.xdi   file read(5)   Y     No user comment
-bad_27.xdi   file read(5)   Y     Line of '////', but no user comment
+bad_25.xdi   file read(5)   Y     No extra version given
+bad_26.xdi   file read(6)   Y     No user comment
+bad_27.xdi   file read(6)   Y     Line of '////', but no user comment
 bad_28.xdi   error msg      Y     incorrectly format date-time
 bad_29.xdi   error msg      Y     date-time has invalid range (month > 12)
 
 Notes:
   1. files read, return value > 0, indicating Warning  
   2. extra column labels ignored, unspecified column labels set to 'colN' (N=1...)
-  3. keys are allowed to start with a number...
-  4. extra version is left as empty string ''
-  5. user comment is left as empty string ''
+  3. lines with unrecognized comment characters ignored
+  4. keys are allowed to start with a number...
+  5. extra version is left as empty string ''
+  6. user comment is left as empty string ''

c/Makefile.in

@@ -20,7 +20,7 @@ includedir = @includedir@
 # you may have to alter these settings
 #---------------------------------
 
-CCOPTS = -fPIC
+CCOPTS = -fPIC -g
 ## CCOPTS =  -arch i386 -arch x86_64
 
 # you shouldn't have to alter anything below this line

c/strutil.c

@@ -33,10 +33,11 @@ int readlines(char *filename, char **textlines) {
       as char *text[MAX] */
 
   FILE *finp;
-  char *thisline ;
-  char *text, *c;
+  char *thisline;
+  char *text;
   long file_length, index, i, ilen;
   int  is_newline;
+  char *orig_text, *orig_thisline;
 
   finp = fopen(filename, "r");
   if (finp == NULL) {
@@ -50,6 +51,9 @@ int readlines(char *filename, char **textlines) {
 
   text = calloc(file_length + 1, sizeof(char));
   thisline = calloc(MAX_LINE_LENGTH, sizeof(char));
+  /* need to save a pointers to the beginning of the original strings so they can be freed at the end of this function */
+  orig_text = text;
+  orig_thisline = thisline;
 
   if (text == NULL ) {
     printf("\nnot enough memory to read file.\n");
@@ -83,6 +87,11 @@ int readlines(char *filename, char **textlines) {
       return -EFBIG;
     }
   }
+  /* free strings */
+  text = orig_text;
+  thisline = orig_thisline;
+  free(text);
+  free(thisline);
   return ilen;
 }
 

c/strutil.h

@@ -1,6 +1,7 @@
 #define CR "\n"
 #define CRLF "\n\r"
 
+#define MAX_WORD_LENGTH 8192 /* Max length of an interpretable word */
 #define MAX_LINE_LENGTH 8192 /* Max chars in a line */
 #define MAX_LINES 16384      /* Max number of lines */
 #define MAX_WORDS 128

c/test_valgrind.pl

@@ -0,0 +1,48 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+use Test::More tests => 90;
+
+## good data
+foreach my $file (qw(co_metal_rt.xdi
+		     cu_metal_10K.xdi
+		     cu_metal_rt.xdi
+		     fe2o3_rt.xdi
+		     fe3c_rt.xdi
+		     fe_metal_rt.xdi
+		     fen_rt.xdi
+		     feo_rt1.xdi
+		     ni_metal_rt.xdi
+		     nonxafs_1d.xdi
+		     nonxafs_2d.xdi
+		     pt_metal_rt.xdi
+		     se_na2so4_rt.xdi
+		     se_znse_rt.xdi
+		     zn_znse_rt.xdi
+		   )) {
+  my $command = "valgrind --track-origins=yes --leak-check=full --show-leak-kinds=all ./xdi_reader ../data/$file 2>&1";
+  my $x = `$command`;
+  ok(($x =~ m{All heap blocks were freed}), $file);
+  ok((not $?), "$file return value is 0");
+};
+
+
+## see baddata/BadFile.txt for explanations of return values
+my %return = ('00' => 0, '01' => 1, '02' => 0, '03' => 0, '04' => 0, '05' => 0,
+	      '06' => 0, '07' => 0, '08' => 0, '09' => 0, '10' => 0, '11' => 0,
+	      '12' => 0, '13' => 1, '14' => 1, '15' => 1, '16' => 1, '17' => 1,
+	      '18' => 1, '19' => 1, '20' => 1, '21' => 1, '22' => 1, '23' => 0,
+	      '24' => 1, '25' => 0, '26' => 0, '27' => 0, '28' => 1, '29' => 1, );
+
+## bad data
+foreach my $i (0 .. 29) {
+  my $n = sprintf("%2.2d", $i);
+  my $command = "valgrind --track-origins=yes --leak-check=full --show-leak-kinds=all ./xdi_reader ../baddata/bad_$n.xdi 2>&1";
+  my $x = `$command`;
+  ok(($x =~ m{All heap blocks were freed}), "bad_$n.xdi");
+  ok((not ($? xor $return{$n})), "bad_$n.xdi return value is $?");
+};
+
+
+

c/xdi_reader.c

@@ -36,6 +36,7 @@ int main(int argc, char **argv) {
   if (ret < 0) {
     printf("Error reading XDI file '%s':\n     %s\t(error code = %ld)\n",
 	   argv[1], XDI_errorstring(ret), ret);
+    XDI_cleanup(xdifile, ret);
     return 1;
   }
 
@@ -82,6 +83,7 @@ int main(int argc, char **argv) {
     }
     printf("\n");
   }
-  free(xdifile);
+  free(tdat);
+  XDI_cleanup(xdifile, 0);
   return 0;
 }