Added functions to add new taxa to a taxonomy with handling of

associated *.ldx files

python/obitools3/obidms/_obitaxo.pxd

@@ -10,8 +10,9 @@ cdef class OBI_Taxonomy :
     cdef OBIDMS_taxonomy_p _pointer
     cdef OBIDMS            _dms
     
-    cpdef close(self)
     cpdef write(self, str prefix)
+    cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=*)
+    cpdef close(self)
 
  
 cdef class OBI_Taxon :

python/obitools3/obidms/_obitaxo.pyx

@@ -7,6 +7,7 @@ from .capi.obitaxonomy cimport obi_read_taxonomy, \
                                obi_write_taxonomy, \
                                obi_close_taxonomy, \
                                obi_taxo_get_taxon_with_taxid, \
+                               obi_taxonomy_add_local_taxon, \
                                ecotx_t                            
 
 
@@ -38,6 +39,8 @@ cdef class OBI_Taxonomy :
         
         if type(ref) == int :
             taxon_p = obi_taxo_get_taxon_with_taxid(self._pointer, ref)
+            if taxon_p == NULL :
+                raise Exception("Taxon not found")
             taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
             return OBI_Taxon(taxon_capsule)
         else :
@@ -55,7 +58,7 @@ cdef class OBI_Taxonomy :
  
         # Yield each taxid
         for t in range(self._pointer.taxa.count):
-            taxon_p = <ecotx_t*> (taxa+t)    # TODO not compiling for mysterious cython reasons
+            taxon_p = <ecotx_t*> (taxa+t)
             taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
             yield OBI_Taxon(taxon_capsule)
 
@@ -64,6 +67,15 @@ cdef class OBI_Taxonomy :
         if obi_write_taxonomy(self._dms._pointer, self._pointer, str2bytes(prefix)) < 0 :
             raise Exception("Error writing the taxonomy to binary files")
 
+    
+    cpdef int add_taxon(self, str name, str rank_name, int parent_taxid, int min_taxid=10000000) :
+        cdef int taxid
+        taxid = obi_taxonomy_add_local_taxon(self._pointer, str2bytes(name), str2bytes(rank_name), parent_taxid, min_taxid)
+        if taxid < 0 :
+            raise Exception("Error adding a new taxon to the taxonomy")
+        else :
+            return taxid
+        
 
     cpdef close(self) :
         if (obi_close_taxonomy(self._pointer) < 0) :

python/obitools3/obidms/capi/obitaxonomy.pxd

@@ -56,3 +56,4 @@ cdef extern from "obidms_taxonomy.h" nogil:
     
     ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
     
+    int obi_taxonomy_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid)