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)

src/obidms_taxonomy.h

@@ -17,6 +17,10 @@
 #include "obidms.h"
 
 
+#define MIN_LOCAL_TAXID (10000000)
+#define TAX_NAME_LEN (1024)
+
+
 typedef struct {
 	int32_t  taxid;
 	int32_t  rank;
@@ -33,11 +37,14 @@ typedef struct ecotxnode {
 	int32_t			  idx;
 	struct ecotxnode* parent;
 	char*			  name;
+	bool			  local;
 } ecotx_t;
 
 
 typedef struct {
 	int32_t count;
+	int32_t ncbi_count;
+	int32_t local_count;
 	int32_t max_taxid;
 	int32_t buffer_size;
 	ecotx_t taxon[1];
@@ -74,6 +81,8 @@ typedef struct {
 
 
 typedef struct OBIDMS_taxonomy_t {
+	char          tax_name[TAX_NAME_LEN];
+	OBIDMS_p      dms;
 	ecorankidx_t* ranks;
 	econameidx_t* names;
 	ecotxidx_t*   taxa;
@@ -109,3 +118,4 @@ int obi_write_taxonomy(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* tax_name
 
 OBIDMS_taxonomy_p obi_read_taxdump(const char* taxdump);
 
+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);