Taxonomy: added functions to check if a taxonomy already exists in a

DMS, and added taxdump import from a compressed file

src/obidms_taxonomy.c

@@ -2740,6 +2740,35 @@ int read_names_dmp(const char* taxdump, OBIDMS_taxonomy_p tax)
  **********************************************************************/
 
 
+int obi_taxonomy_exists(OBIDMS_p dms, const char* taxonomy_name)
+{
+	char* taxonomy_path;
+	DIR* dir;
+
+	taxonomy_path = get_taxonomy_path(dms, taxonomy_name);
+	if (taxonomy_path == NULL)
+		return -1;
+
+	dir = opendir(taxonomy_path);
+	if (dir)
+	{
+	    /* Directory exists. */
+	    closedir(dir);
+	    return 1;
+	}
+	else if (ENOENT == errno)
+	{
+	    /* Directory does not exist. */
+		return 0;
+	}
+	else
+	{
+	    /* opendir() failed for some other reason. */
+		return -1;
+	}
+}
+
+
 OBIDMS_taxonomy_p obi_read_taxdump(const char* taxdump)
 {
 	OBIDMS_taxonomy_p tax;
@@ -3705,7 +3734,7 @@ 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)
 {
-	static int32_t		     rankindex = -1;
+	static int32_t rankindex = -1;
 
 	if (taxonomy == NULL)
 	{
@@ -3738,3 +3767,23 @@ const char* obi_taxo_rank_index_to_label(int32_t rank_idx, ecorankidx_t* ranks)
 	return (ranks->label)[rank_idx];
 }
 
+
+int obi_taxo_is_taxid_included(OBIDMS_taxonomy_p taxonomy,
+			     			   int32_t* restrict_to_taxids,
+				    		   int32_t count,
+					    	   int32_t taxid)
+{
+	int i;
+	ecotx_t* taxon;
+
+	taxon = obi_taxo_get_taxon_with_taxid(taxonomy, taxid);
+
+	if (taxon)
+		for (i=0; i < count; i++)
+			if ((taxon->taxid == restrict_to_taxids[i]) ||
+				 (obi_taxo_is_taxon_under_taxid(taxon, restrict_to_taxids[i])))
+				return 1;
+
+	return 0;
+}
+

src/obidms_taxonomy.h

@@ -183,6 +183,25 @@ typedef struct OBIDMS_taxonomy_t {
 } OBIDMS_taxonomy_t, *OBIDMS_taxonomy_p;
 
 
+
+/**
+ * @brief Function checking whether a taxonomy is already registered in a DMS using its name.
+ *
+ * @param dms The path to the taxdump directory.
+ *
+ * @param dms A pointer on the DMS.
+ * @param taxonomy_name The name (prefix) of the taxonomy.
+ *
+ * @retval 1 if the taxonomy exists.
+ * @retval 0 if the taxonomy does not exist
+ * @retval -1 if an error occurred.
+ *
+ * @since June 2018
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_taxonomy_exists(OBIDMS_p dms, const char* taxonomy_name);
+
+
 /**
  * @brief Function reading an NCBI taxdump and loading its information into a taxonomy structure.
  *
@@ -414,3 +433,10 @@ ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
  * @see rank_label_to_index()
  */
 const char* obi_taxo_rank_index_to_label(int32_t rank_idx, ecorankidx_t* ranks);
+
+
+// TODO
+int obi_taxo_is_taxid_included(OBIDMS_taxonomy_p taxonomy,
+			     			   int32_t* restrict_to_taxids,
+				    		   int32_t count,
+					    	   int32_t taxid);