Commit f396625f by Celine Mercier

Taxonomy: function to write *.adx files

parent 89703238
......@@ -996,6 +996,101 @@ int write_nameidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_name
}
int write_mergedidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_name) // TODO prefix in taxonomy struct?
{
int i;
char* file_name;
int file_descriptor;
off_t file_size;
char* taxonomy_path;
// Compute file size
file_size = sizeof(int32_t) + (sizeof(int32_t) * 3 * (tax->merged_idx)->count);
// Build the taxonomy directory path
taxonomy_path = get_taxonomy_path(dms, taxonomy_name);
file_name = (char*) malloc((strlen(taxonomy_path) + strlen(taxonomy_name) + 6)*sizeof(char));
if (file_name == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating the memory for a binary taxonomy file name");
return -1;
}
// Build the file path
if (sprintf(file_name, "%s/%s.adx", taxonomy_path, taxonomy_name) < 0)
{
obi_set_errno(OBI_TAXONOMY_ERROR);
obidebug(1, "\nError building a binary taxonomy file name");
return -1;
}
free(taxonomy_path);
// Create file
file_descriptor = open(file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
if (file_descriptor < 0)
{
obi_set_errno(OBI_TAXONOMY_ERROR);
obidebug(1, "\nError creating a binary taxonomy file %s", file_name);
free(file_name);
return -1;
}
free(file_name);
// Truncate the file to the right size
if (ftruncate(file_descriptor, file_size) < 0)
{
obi_set_errno(OBI_TAXONOMY_ERROR);
obidebug(1, "\nError truncating a binary taxonomy file");
close(file_descriptor);
return -1;
}
// Write merged indices count
if (write(file_descriptor, &((tax->merged_idx)->count), sizeof(int32_t)) < ((ssize_t) sizeof(int32_t)))
{
obi_set_errno(OBI_TAXONOMY_ERROR);
obidebug(1, "\nError writing in a binary taxonomy file");
close(file_descriptor);
return -1;
}
// Write merged indices
for (i=0; i < (tax->merged_idx)->count; i++)
{
// Write taxid
if (write(file_descriptor, &(((tax->merged_idx)->merged)[i].taxid), sizeof(int32_t)) < ((ssize_t) sizeof(int32_t)))
{
obi_set_errno(OBI_TAXONOMY_ERROR);
obidebug(1, "\nError writing in a binary taxonomy file");
close(file_descriptor);
return -1;
}
// Write index corresponding to the taxid in the ecotxidx_t structure
if (write(file_descriptor, &(((tax->merged_idx)->merged)[i].idx), sizeof(int32_t)) < ((ssize_t) sizeof(int32_t)))
{
obi_set_errno(OBI_TAXONOMY_ERROR);
obidebug(1, "\nError writing in a binary taxonomy file");
close(file_descriptor);
return -1;
}
}
// Close file
if (close(file_descriptor) < 0)
{
obi_set_errno(OBI_TAXONOMY_ERROR);
obidebug(1, "\nError closing a taxonomy file file");
return -1;
}
return 0;
}
int obi_write_taxonomy(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* tax_name)
{
......@@ -1024,6 +1119,8 @@ int obi_write_taxonomy(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* tax_name
return -1;
if (write_nameidx(dms, tax, tax_name) < 0)
return -1;
if (write_mergedidx(dms, tax, tax_name) < 0)
return -1;
// Check if there are local taxa (if so last taxon is local)
if ((tax->taxa)->local_count > 0)
if (write_local_taxonomy_idx(dms, tax, tax_name) < 0)
......@@ -1331,7 +1428,7 @@ OBIDMS_taxonomy_p obi_read_taxdump(const char* taxdump)
{
if (strcmp(dp->d_name, "merged.dmp") == 0)
{
merged_found = true; // TODO
merged_found = true;
buffer_size = 10000;
// Initializing the merged structure
......
......@@ -122,11 +122,6 @@ ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
int write_rankidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_name);
int write_taxonomyidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_name);
int write_nameidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_name);
int obi_write_taxonomy(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* tax_name);
OBIDMS_taxonomy_p obi_read_taxdump(const char* taxdump);
......
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