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

DMS, and added taxdump import from a compressed file

python/obitools3/apps/optiongroups/__init__.py

@@ -165,9 +165,9 @@ def __addTaxdumpInputOption(optionManager):
     group = optionManager.add_argument_group("Input format options for taxdump")
 
     group.add_argument('--taxdump',
-                     action="store", dest="obi:taxdump",
+                     action="store_true", dest="obi:taxdump",
-                     default=None,
+                     default=False,
-                     help="Taxdump path")
+                     help="Whether the input is a taxdump")
 
 def addMinimalInputOption(optionManager):
     __addInputOption(optionManager)

python/obitools3/dms/capi/obitaxonomy.pxd

@@ -37,7 +37,9 @@ cdef extern from "obidms_taxonomy.h" nogil:
 
     ctypedef OBIDMS_taxonomy_t* OBIDMS_taxonomy_p
     
-
+    
+    int obi_taxonomy_exists(OBIDMS_p dms, const char* taxonomy_name)
+    
     OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const_char_p taxonomy_name, bint read_alternative_names)
 
     OBIDMS_taxonomy_p obi_read_taxdump(const_char_p taxdump)

python/obitools3/dms/taxo/taxo.pyx

@@ -2,7 +2,8 @@
 
 from obitools3.utils cimport str2bytes, bytes2str, tobytes, tostr
 
-from ..capi.obitaxonomy cimport obi_read_taxonomy, \
+from ..capi.obitaxonomy cimport obi_taxonomy_exists, \
+                                obi_read_taxonomy, \
                                 obi_read_taxdump, \
                                 obi_write_taxonomy, \
                                 obi_close_taxonomy, \
@@ -17,6 +18,8 @@ from ..capi.obitaxonomy cimport obi_read_taxonomy, \
                                            
 from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
 
+import tarfile
+
 
 cdef class Taxonomy(OBIWrapper) :
     # TODO function to import taxonomy?
@@ -25,6 +28,16 @@ cdef class Taxonomy(OBIWrapper) :
         return <OBIDMS_taxonomy_p>(self._pointer)        
 
 
+    @staticmethod
+    def exists(DMS dms, object name) :
+        e = obi_taxonomy_exists(dms.pointer(), tobytes(name))
+        if e < 0:
+            raise RuntimeError("Error : Cannot check if taxonomy %s exists" 
+                               % tostr(name))
+        else:
+            return e
+        
+
     @staticmethod
     def open(DMS dms, object name) :
         
@@ -46,27 +59,45 @@ cdef class Taxonomy(OBIWrapper) :
         taxo._ranks = []
         for r in range((<OBIDMS_taxonomy_p>pointer).ranks.count) :
             taxo._ranks.append(obi_taxo_rank_index_to_label(r, (<OBIDMS_taxonomy_p>pointer).ranks))
-                
+
         return taxo
 
 
     @staticmethod
-    def open_taxdump(DMS dms, object name) :
+    def open_taxdump(DMS dms, object path) :
         
         cdef void*    pointer
         cdef Taxonomy taxo
-                
+        cdef bytes    path_b
-        pointer = <void*>obi_read_taxdump(tobytes(name))        
+        cdef int      idx
+        
+        path_b = tobytes(path)
+        folder_path = path_b
+
+        if path_b.endswith(b"tar.gz") or path_b.endswith(b"tar"):
+            idx = path_b.index(b".tar")
+            folder_path = path_b[:idx]
+
+        if path_b.endswith(b"tar.gz"):
+            tar = tarfile.open(path_b, "r:gz")
+            tar.extractall(path=tostr(folder_path))
+            tar.close()
+        elif path_b.endswith(b"tar"):
+            tar = tarfile.open(path_b, "r:")
+            tar.extractall(path=tostr(folder_path))
+            tar.close()
+            
+        pointer = <void*>obi_read_taxdump(folder_path)        
         if pointer == NULL :
             raise RuntimeError("Error : Cannot read taxonomy %s" 
-                               % tostr(name))
+                               % tostr(folder_path))
         
         taxo = OBIWrapper.new_wrapper(Taxonomy, pointer)
 
         dms.register(taxo)
 
         taxo._dms = dms
-        taxo._name = tobytes(name)
+        taxo._name = folder_path
         
         taxo._ranks = []
         for r in range((<OBIDMS_taxonomy_p>pointer).ranks.count) :

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);