Taxonomy: adding, writing and reading preferred names, changed some

function names, and fixed a bug with taxa indices not being properly
initialized

python/obitools3/obidms/_obitaxo.pxd

@@ -17,4 +17,5 @@ cdef class OBI_Taxonomy :
  
 cdef class OBI_Taxon :
 
-    cdef ecotx_t* _pointer
+    cdef ecotx_t*      _pointer
+    cdef OBI_Taxonomy  _tax

python/obitools3/obidms/_obitaxo.pyx

@@ -7,10 +7,10 @@ from .capi.obitaxonomy cimport obi_read_taxonomy, \
                                obi_write_taxonomy, \
                                obi_close_taxonomy, \
                                obi_taxo_get_taxon_with_taxid, \
-                               obi_taxonomy_add_local_taxon, \
+                               obi_taxo_add_local_taxon, \
+                               obi_taxo_add_preferred_name_with_taxon, \
                                ecotx_t                            
 
-
 from ._obidms cimport OBIDMS
 
 from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
@@ -42,11 +42,11 @@ cdef class OBI_Taxonomy :
             if taxon_p == NULL :
                 raise Exception("Taxon not found")
             taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
-            return OBI_Taxon(taxon_capsule)
+            return OBI_Taxon(taxon_capsule, self)
         else :
             raise Exception("Not implemented")
-        
-    
+
+
     def __iter__(self):
          
         cdef ecotx_t* taxa
@@ -60,7 +60,7 @@ cdef class OBI_Taxonomy :
         for t in range(self._pointer.taxa.count):
             taxon_p = <ecotx_t*> (taxa+t)
             taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
-            yield OBI_Taxon(taxon_capsule)
+            yield OBI_Taxon(taxon_capsule, self)
 
 
     cpdef write(self, str prefix) :
@@ -70,7 +70,7 @@ cdef class OBI_Taxonomy :
     
     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)
+        taxid = obi_taxo_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 :
@@ -85,10 +85,11 @@ cdef class OBI_Taxonomy :
 
 cdef class OBI_Taxon :    # TODO dict subclass?
 
-    def __init__(self, object taxon_capsule) :
+    def __init__(self, object taxon_capsule, OBI_Taxonomy tax) :
         self._pointer = <ecotx_t*> PyCapsule_GetPointer(taxon_capsule, NULL)
         if self._pointer == NULL :
-            raise Exception("Error reading the taxonomy")
+            raise Exception("Error reading a taxon (NULL pointer)")
+        self._tax = tax
 
     # name property getter
     @property
@@ -115,14 +116,25 @@ cdef class OBI_Taxon :    # TODO dict subclass?
     def parent(self):
         cdef object parent_capsule
         parent_capsule = PyCapsule_New(self._pointer.parent, NULL, NULL)
-        return OBI_Taxon(parent_capsule)
+        return OBI_Taxon(parent_capsule, self._tax)
+
+    # preferred name property getter and setter
+    @property
+    def preferred_name(self):
+        if self._pointer.preferred_name != NULL :
+            return bytes2str(self._pointer.preferred_name)
+    @preferred_name.setter
+    def preferred_name(self, str new_preferred_name) :  # @DuplicatedSignature
+        if (obi_taxo_add_preferred_name_with_taxon(self._tax._pointer, self._pointer, str2bytes(new_preferred_name)) < 0) :
+            raise Exception("Error adding a new preferred name to a taxon")
 
     def __repr__(self):
         d = {}
-        d['taxid']   = self.taxid
-        d['name']    = self.name
-        d['parent']  = self.parent.taxid
-        d['farest']  = self.farest
+        d['taxid']          = self.taxid
+        d['name']           = self.name
+        d['preferred name'] = self.preferred_name
+        d['parent']         = self.parent.taxid
+        d['farest']         = self.farest
         return str(d)
     
     

python/obitools3/obidms/capi/obitaxonomy.pxd

@@ -13,7 +13,8 @@ cdef extern from "obidms_taxonomy.h" nogil:
         int32_t           farest
         ecotxnode*        parent
         char*             name
-    
+        char*             preferred_name
+
     ctypedef ecotxnode ecotx_t
 
 
@@ -56,4 +57,9 @@ 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)
+    int obi_taxo_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid)
+
+    int obi_taxo_add_preferred_name_with_taxid(OBIDMS_taxonomy_p tax, int32_t taxid, const char* preferred_name)
+
+    int obi_taxo_add_preferred_name_with_taxon(OBIDMS_taxonomy_p tax, ecotx_t* taxon, const char* preferred_name)
+

src/obidms_taxonomy.h

@@ -36,7 +36,8 @@ typedef struct ecotxnode {
 	int32_t  		  farest;
 	int32_t			  idx;
 	struct ecotxnode* parent;
-	char*			  name;
+	char*			  name; // scientific name
+	char*			  preferred_name; // preferred name
 	bool			  local;
 } ecotx_t;
 
@@ -98,6 +99,7 @@ typedef struct OBIDMS_taxonomy_t {
 	ecomergedidx_t* merged_idx;
 	ecorankidx_t*   ranks;
 	econameidx_t*   names;
+	econameidx_t*   preferred_names;
 	ecotxidx_t*     taxa;
 } OBIDMS_taxonomy_t, *OBIDMS_taxonomy_p;
 
@@ -127,4 +129,11 @@ 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);
+int obi_taxo_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid);
+
+int obi_taxo_add_preferred_name_with_taxid(OBIDMS_taxonomy_p tax, int32_t taxid, const char* preferred_name);
+
+int obi_taxo_add_preferred_name_with_taxon(OBIDMS_taxonomy_p tax, ecotx_t* taxon, const char* preferred_name);
+
+
+