Taxonomy: function to write *.adx files

src/obidms_taxonomy.c

@@ -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

src/obidms_taxonomy.h

@@ -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);