From 6f780148e2aa032ff6051fe2a00e2d9a74b8a5cd Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Fri, 14 Apr 2017 16:20:30 +0200
Subject: [PATCH] Cython API: added taxonomy API

---
 python/obitools3/dms/taxo/taxo.pxd |  19 ++++
 python/obitools3/dms/taxo/taxo.pyx | 136 +++++++++++++++++++++++++++++
 2 files changed, 155 insertions(+)
 create mode 100644 python/obitools3/dms/taxo/taxo.pxd
 create mode 100644 python/obitools3/dms/taxo/taxo.pyx

diff --git a/python/obitools3/dms/taxo/taxo.pxd b/python/obitools3/dms/taxo/taxo.pxd
new file mode 100644
index 0000000..45ae0ed
--- /dev/null
+++ b/python/obitools3/dms/taxo/taxo.pxd
@@ -0,0 +1,19 @@
+#cython: language_level=3
+
+from ..capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
+
+from ..dms cimport DMS
+
+
+cdef class OBI_Taxonomy :
+    cdef str               _name
+    cdef OBIDMS_taxonomy_p _pointer
+    cdef OBIDMS            _dms
+    
+    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 :
+    cdef ecotx_t*      _pointer
+    cdef OBI_Taxonomy  _tax
\ No newline at end of file
diff --git a/python/obitools3/dms/taxo/taxo.pyx b/python/obitools3/dms/taxo/taxo.pyx
new file mode 100644
index 0000000..d11711b
--- /dev/null
+++ b/python/obitools3/dms/taxo/taxo.pyx
@@ -0,0 +1,136 @@
+#cython: language_level=3
+
+from obitools3.utils cimport str2bytes, bytes2str, tobytes
+
+from ..capi.obitaxonomy cimport obi_read_taxonomy, \
+                                obi_read_taxdump, \
+                                obi_write_taxonomy, \
+                                obi_close_taxonomy, \
+                                obi_taxo_get_taxon_with_taxid, \
+                                obi_taxo_add_local_taxon, \
+                                obi_taxo_add_preferred_name_with_taxon, \
+                                ecotx_t                
+                                           
+from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
+
+
+cdef class OBI_Taxonomy :
+    # TODO function to import taxonomy?
+    def __init__(self, OBIDMS dms, str name, bint taxdump=False) :
+        
+        self._dms = dms
+        self._name = name
+        if taxdump :
+            self._pointer = obi_read_taxdump(tobytes(name))
+        else :
+            self._pointer = obi_read_taxonomy(dms._pointer, tobytes(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
+        
+        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, self)
+        else :
+            raise Exception("Not implemented")
+        
+        
+    def __iter__(self):
+         
+        cdef ecotx_t* taxa
+        cdef ecotx_t* taxon_p
+        cdef object   taxon_capsule
+        cdef int      t
+ 
+        taxa = self._pointer.taxa.taxon
+ 
+        # Yield each taxid
+        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, self)
+            
+            
+    cpdef write(self, str prefix) :
+        if obi_write_taxonomy(self._dms._pointer, self._pointer, tobytes(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_taxo_add_local_taxon(self._pointer, tobytes(name), tobytes(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) :
+            raise Exception("Error closing the taxonomy")
+    
+    
+cdef class OBI_Taxon :    # TODO dict subclass?
+    
+    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 a taxon (NULL pointer)")
+        self._tax = tax
+    
+    
+    # name property getter
+    @property
+    def name(self):
+        return bytes2str(self._pointer.name)
+    
+    # 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._pointer.parent, NULL, NULL)
+        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, tobytes(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['preferred name'] = self.preferred_name
+        d['parent']         = self.parent.taxid
+        d['farest']         = self.farest
+        return str(d)
+    
+    
\ No newline at end of file