[gnuastro-commits] master 25b5c1a: Library (txt.h): correctly counting existing metadata

[Mohammad Akhlaghi]

branch: master
commit 25b5c1a228cf7eed93e6cdfb4a3aaf8fe7bf7dd1
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>

    Library (txt.h): correctly counting existing metadata
    
    Until now, we were incorrectly counting the number of actual data in a
    plain-text file: the counter was incremented as the plain text file was
    being parsed, so by the end of the line, the counter showed one value
    larger than the actual number of columns. As a result, when there was more
    metadata than actual columns (for example having f '# Column N:'s but only
    three actual data columns), the table-parsing would crash in the sanity
    checks of later phases.
    
    With this commit, after the line of data is parsed, the counter is
    decreased by one, to ensure that it shows the actual number of
    columns. This fixed the problem.
    
    This bug was found thanks to Zohreh Ghaffari.
    
    This fixes bug #61490.
---
 NEWS                         |  2 ++
 doc/announce-acknowledge.txt |  1 +
 lib/txt.c                    | 34 ++++++++++++++++++----------------
 3 files changed, 21 insertions(+), 16 deletions(-)

diff --git a/NEWS b/NEWS
index 167a84d..672f51b 100644
--- a/NEWS
+++ b/NEWS
@@ -82,6 +82,8 @@ See the end of the file for license conditions.
               and fixed with the help of Sebastian Luna-Valero.
   bug #61378: Table crash when input is sexagesimal RA/DEC and no metadata.
   bug #61462: Crash on FITS binary table colums with repeat of 0.
+  bug #61490: Extra columns in the metadata causes crash in plain-text
+              tables, found by Zohre Ghaffari.
 
 
 
diff --git a/doc/announce-acknowledge.txt b/doc/announce-acknowledge.txt
index 1878711..100a1e2 100644
--- a/doc/announce-acknowledge.txt
+++ b/doc/announce-acknowledge.txt
@@ -2,6 +2,7 @@ Alphabetically ordered list to acknowledge in the next release.
 
 Andres Del Pino Molina
 Sepideh Eskandarlou
+Zohreh Ghaffari
 Zahra Hosseini
 Raúl Infante-Sainz
 Sebastian Luna-Valero
diff --git a/lib/txt.c b/lib/txt.c
index b7b252d..f769029 100644
--- a/lib/txt.c
+++ b/lib/txt.c
@@ -318,7 +318,7 @@ txt_info_from_first_row(char *in_line, gal_data_t **datall, 
int format,
   double tmpd;
   void *tmpdptr=&tmpd;
   gal_data_t *col, *prev, *tmp;
-  size_t n=0, maxcnum=0, numtokens;
+  size_t ncol=0, maxcnum=0, numtokens;
   char *line, *token, *end, *aline=NULL;
 
   /* Make a copy of the input line if necessary. */
@@ -350,14 +350,15 @@ txt_info_from_first_row(char *in_line, gal_data_t 
**datall, int format,
     maxcnum = maxcnum>col->status ? maxcnum : col->status;
 
   /* Go over the line check/fill the column information. */
-  while(++n)
+  while(++ncol)
     {
       /* When we are dealing with a text table, check if there is
          information for this column. For a text image, only the number of
          tokens is important (as the second dimension of the image), so
          just assume there no information. */
       if(format==TXT_FORMAT_TABLE)
-        for(col=*datall; col!=NULL; col=col->next) {if(col->status==n) break;}
+        for(col=*datall; col!=NULL; col=col->next)
+          { if(col->status==ncol) break; }
       else
         col=NULL;
 
@@ -392,14 +393,14 @@ txt_info_from_first_row(char *in_line, gal_data_t 
**datall, int format,
             }
           else
             {
-              token=strtok_r(n==1?line:NULL, GAL_TXT_DELIMITERS, &line);
+              token=strtok_r(ncol==1?line:NULL, GAL_TXT_DELIMITERS, &line);
               if(token==NULL) break;
             }
         }
       else
         {
           /* Make sure a token exists in this undefined column. */
-          token=strtok_r(n==1?line:NULL, GAL_TXT_DELIMITERS, &line);
+          token=strtok_r(ncol==1?line:NULL, GAL_TXT_DELIMITERS, &line);
           if(token==NULL) break;
 
           /* A token exists. For a table, define a new element in the
@@ -420,14 +421,14 @@ txt_info_from_first_row(char *in_line, gal_data_t 
**datall, int format,
                   && isnan( gal_units_ra_to_degree(token) )
                   && isnan( gal_units_dec_to_degree(token) ) )
                 error(EXIT_FAILURE, 0, "'%s' couldn't be read as a number "
-                      "(element %zu of first uncommented line) %f ", token, n,
-                      gal_units_ra_to_degree(token));
+                      "(element %zu of first uncommented line) %f ", token,
+                      ncol, gal_units_ra_to_degree(token));
 
               /* Allocate this column's dataset and set it's 'status' to
                  the column number that it corresponds to. */
               gal_list_data_add_alloc(datall, NULL, GAL_TYPE_FLOAT64, 0,
                                       NULL, NULL, 0, -1, 1, NULL, NULL, NULL);
-              (*datall)->status=n;
+              (*datall)->status=ncol;
             }
         }
     }
@@ -443,20 +444,21 @@ txt_info_from_first_row(char *in_line, gal_data_t 
**datall, int format,
 
      Note that 'n' counts from 1, so the total number of tokens is one less
      than 'n'.*/
-  numtokens=n-1;
-  if(format==TXT_FORMAT_IMAGE) n=1;
+  numtokens=ncol-1;
+  if(format==TXT_FORMAT_IMAGE) ncol=1;
 
   /* If the number of columns/images given by the comments is larger than
      the actual number of lines, remove those that have larger numbers from
      the linked list before things get complicated outside of this
      function. */
-  if(maxcnum>n)
+  if(maxcnum>numtokens)
     {
       prev=NULL;
       col=*datall;
       while(col!=NULL)
         {
-          if(col->status > n) /* Column has no data (was only in comments) */
+          /* This column has no data (was only in comments) */
+          if(col->status > numtokens)
             {
               /* This column has to be removed/freed. But we have to make
                  some corrections before freeing it:
@@ -575,12 +577,12 @@ txt_get_info_line(char *line, gal_data_t **datall, char 
*comm_start,
 
   switch( gal_txt_line_stat(line) )
     {
-      /* Line is a comment, see if it has formatted information. */
+    /* Line is a comment, see if it has formatted information. */
     case GAL_TXT_LINESTAT_COMMENT:
       txt_info_from_comment(line, datall, comm_start, inplace);
       break;
 
-      /* Line is actual data, use it to fill in the gaps.  */
+    /* Line is actual data, use it to fill in the gaps.  */
     case GAL_TXT_LINESTAT_DATAROW:
       ++dsize[0];
       if(*firstlinedone==0)
@@ -659,8 +661,8 @@ txt_get_info(char *filename, gal_list_str_t *lines, int 
format,
          lines, but also confirm/complete the info by parsing the first
          uncommented line. */
       while( getline(&line, &linelen, fp) != -1 )
-        txt_get_info_line(line, &datall, comm_start, &firstlinedone, format,
-                          dsize, 1);
+        txt_get_info_line(line, &datall, comm_start, &firstlinedone,
+                          format, dsize, 1);
 
 
       /* Clean up and close the file. */