From 60ab503a144d86b07c2ef1e18f4ca2621c1ed657 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Mon, 10 Oct 2016 17:01:17 +0200
Subject: [PATCH] Added properties in the OBI_Taxonomy class

---
 python/obitools3/obidms/_obitaxo.pxd | 21 ++------
 python/obitools3/obidms/_obitaxo.pyx | 80 ++++++++++++++++++----------
 2 files changed, 54 insertions(+), 47 deletions(-)

diff --git a/python/obitools3/obidms/_obitaxo.pxd b/python/obitools3/obidms/_obitaxo.pxd
index 1d42862..7f7ac52 100644
--- a/python/obitools3/obidms/_obitaxo.pxd
+++ b/python/obitools3/obidms/_obitaxo.pxd
@@ -2,30 +2,15 @@
 
 from .capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
 
-from libc.stdint   cimport int32_t
-
 
 cdef class OBI_Taxonomy :
 
-    cdef str name
-    cdef OBIDMS_taxonomy_p pointer
+    cdef str               _name
+    cdef OBIDMS_taxonomy_p _pointer
     
     cpdef close(self)
 
  
 cdef class OBI_Taxon :
 
-    cdef ecotx_t* pointer
-    cdef int32_t  taxid
-    cdef int32_t  rank
-    cdef int32_t  farest
-    cdef ecotx_t* parent
-    cdef str name
-        
-    cpdef int32_t taxid(self)
-    
-    cpdef int32_t rank(self)
-    
-    cpdef int32_t farest(self)
-    
-    cpdef OBI_Taxon parent(self)
+    cdef ecotx_t* _pointer
diff --git a/python/obitools3/obidms/_obitaxo.pyx b/python/obitools3/obidms/_obitaxo.pyx
index feb4a02..2a074d0 100644
--- a/python/obitools3/obidms/_obitaxo.pyx
+++ b/python/obitools3/obidms/_obitaxo.pyx
@@ -9,57 +9,79 @@ from .capi.obitaxonomy cimport obi_read_taxonomy, \
 from ._obidms cimport OBIDMS
 
 from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
+from logging import raiseExceptions
 
 
 cdef class OBI_Taxonomy :
 
+    # TODO function to import taxonomy?
+
     def __init__(self, OBIDMS dms, str name) :
         
-        self.name = name
-        self.pointer = obi_read_taxonomy(dms._pointer, str2bytes(name), True)    # TODO discuss
-    
+        self._name = name
+        self._pointer = obi_read_taxonomy(dms._pointer, str2bytes(name), True)    # TODO discuss
+        # TODO if not found in DMS, try to import?
+        
     
     def __getitem__(self, object ref):
         
         cdef ecotx_t* taxon_p
-        cdef object taxon_capsule
+        cdef object   taxon_capsule
         
         if type(ref) == int :
-            taxon_p = obi_taxo_get_taxon_with_taxid(self.pointer, ref)
+            taxon_p = obi_taxo_get_taxon_with_taxid(self._pointer, ref)
             taxon_capsule = PyCapsule_New(taxon_p, NULL, NULL)
             return OBI_Taxon(taxon_capsule)
+        else :
+            raise Exception("Not implemented")
+        
     
-         
     cpdef close(self) :
-        if (obi_close_taxonomy(self.pointer) < 0) :
+        if (obi_close_taxonomy(self._pointer) < 0) :
             raise Exception("Error closing the taxonomy")
         
 
-cdef class OBI_Taxon :    # dict subclass?
+cdef class OBI_Taxon :    # TODO dict subclass?
 
     def __init__(self, object taxon_capsule) :
-        
-        cdef ecotx_t* taxon
-        
-        taxon = <ecotx_t*> PyCapsule_GetPointer(taxon_capsule, NULL)   
-        self.pointer = taxon
-        self.taxid = taxon.taxid
-        self.rank = taxon.rank
-        self.farest = taxon.farest
-        self.parent = taxon.parent
-        self.name = bytes2str(taxon.name)
-        
-    cpdef int32_t taxid(self):
-        return self.taxid
+        self._pointer = <ecotx_t*> PyCapsule_GetPointer(taxon_capsule, NULL)
+        if self._pointer == NULL :
+            raise Exception("Error reading the taxonomy")
+
+    # name property getter
+    @property
+    def name(self):
+        return bytes2str(self._pointer.name)
     
-    cpdef int32_t rank(self):
-        return self.rank
-    
-    cpdef int32_t farest(self):
-        return self.farest
-    
-    cpdef OBI_Taxon parent(self):
+    # taxid property getter
+    @property
+    def taxid(self):
+        return self._pointer.taxid
+
+    # rank property getter
+    @property
+    def rank(self):
+        return self._pointer.rank
+   
+    # farest property getter
+    @property
+    def farest(self):
+        return self._pointer.farest
+
+    # parent property getter
+    @property
+    def parent(self):
         cdef object parent_capsule
-        parent_capsule = PyCapsule_New(self.parent, NULL, NULL)
+        parent_capsule = PyCapsule_New(self._pointer.parent, NULL, NULL)
         return OBI_Taxon(parent_capsule)
+
+    def __repr__(self):
+        d = {}
+        d['taxid']   = self.taxid
+        d['name']    = self.name
+        d['parent']  = self.parent.taxid
+        d['farest']  = self.farest
+        return str(d)
+        
+