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Taxonomy: fixed a critical memory bug when building the list of merged

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taxids
This commit is contained in:
Celine Mercier
2020-04-15 17:46:13 +02:00
parent e9a40630e9
commit 343999a627
1 changed files with 6 additions and 5 deletions
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11
src/obidms_taxonomy.c
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@ -2376,9 +2376,10 @@ int read_merged_dmp(const char* taxdump, OBIDMS_taxonomy_p tax, int32_t* delnode
// and the deleted taxids with no current reference. An element of the list is composed of the taxid, and the index // and the deleted taxids with no current reference. An element of the list is composed of the taxid, and the index
// of the taxon in the taxa structure, or -1 for deleted taxids. // of the taxon in the taxa structure, or -1 for deleted taxids.
// Creating the merged list requires to merge the 3 ordered lists into one. // Creating the merged list requires to merge the 3 ordered lists into one.
while (((nT < (tax->taxa)->count) && ((tax->taxa)->taxon[nT].taxid < old_taxid)) || ((nD >= 0) && (delnodes[nD] < old_taxid))) while (((nT < (tax->taxa)->count) && ((tax->taxa)->taxon[nT].taxid < old_taxid)) ||
((nD >= 0) && (delnodes[nD] < old_taxid)))
{ {
if ((tax->taxa)->taxon[nT].taxid < delnodes[nD]) if ((nT < (tax->taxa)->count) && (tax->taxa)->taxon[nT].taxid < delnodes[nD])
{ // Add element from taxa list { // Add element from taxa list
// Enlarge structure if needed // Enlarge structure if needed
if (n == buffer_size) if (n == buffer_size)
@ -2401,7 +2402,7 @@ int read_merged_dmp(const char* taxdump, OBIDMS_taxonomy_p tax, int32_t* delnode
nT++; nT++;
n++; n++;
} }
else if (delnodes[nD] < (tax->taxa)->taxon[nT].taxid) else
{ // Add element from deleted taxids list { // Add element from deleted taxids list
// Enlarge structure if needed // Enlarge structure if needed
if (n == buffer_size) if (n == buffer_size)
@ -3036,12 +3037,12 @@ OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, boo
strcpy(tax->tax_name, taxonomy_name); strcpy(tax->tax_name, taxonomy_name);
buffer_size = 2048;
taxonomy_path = get_taxonomy_path(dms, taxonomy_name); taxonomy_path = get_taxonomy_path(dms, taxonomy_name);
if (taxonomy_path == NULL) if (taxonomy_path == NULL)
return NULL; return NULL;
buffer_size = strlen(taxonomy_path) + strlen(taxonomy_name) + 6;
// Read ranks // Read ranks
ranks_file_name = (char*) malloc(buffer_size*sizeof(char)); ranks_file_name = (char*) malloc(buffer_size*sizeof(char));
if (ranks_file_name == NULL) if (ranks_file_name == NULL)