From 2df5932b6731bc85d00a032a9960c8b8000b495e Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 13 Dec 2017 22:27:36 +0100
Subject: [PATCH] Cython column API: fixed a memory leak, optimized the reading
 of elements names, added a __len__ method to Column_line, and the API for
 columns with character strings to evaluate

---
 python/obitools3/dms/column/column.pxd |  1 +
 python/obitools3/dms/column/column.pyx | 32 +++++++++++++++++++++++---
 2 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/python/obitools3/dms/column/column.pxd b/python/obitools3/dms/column/column.pxd
index 0e1e0b3..6af1f84 100644
--- a/python/obitools3/dms/column/column.pxd
+++ b/python/obitools3/dms/column/column.pxd
@@ -18,6 +18,7 @@ cdef class Column(OBIWrapper) :
  
     cdef View  _view
     cdef bytes _alias
+    cdef list  elements_names
     
     cdef inline OBIDMS_column_p pointer(self)
  
diff --git a/python/obitools3/dms/column/column.pyx b/python/obitools3/dms/column/column.pyx
index 62bd6df..2f80863 100644
--- a/python/obitools3/dms/column/column.pyx
+++ b/python/obitools3/dms/column/column.pyx
@@ -28,6 +28,8 @@ from obitools3.utils cimport tobytes, \
  
 from obitools3.dms.column import typed_column
  
+from libc.stdlib  cimport free
+ 
 import importlib
 import inspect
 import pkgutil
@@ -75,6 +77,7 @@ cdef class Column(OBIWrapper) :
                    index_t   nb_elements_per_line=1,
                    list      elements_names=None,
                    bint      tuples=False,
+                   bint      to_eval=False,
                    object    comments=b"",
                    object    alias=b""):
         # TODO indexer_name?
@@ -114,7 +117,9 @@ cdef class Column(OBIWrapper) :
                                 nb_lines                  = len(view),
                                 nb_elements_per_line      = nb_elements_per_line,
                                 elements_names            = elements_names_p,
+                                elt_names_formatted       = False,
                                 tuples                    = tuples,
+                                to_eval                   = to_eval,
                                 indexer_name              = NULL,
                                 associated_column_name    = NULL,
                                 associated_column_version = -1,
@@ -155,6 +160,7 @@ cdef class Column(OBIWrapper) :
         
         column._view = view
         column._alias = column_name_b
+        column.elements_names = column._elements_names
         view.register(column)
 
         return column
@@ -184,7 +190,9 @@ cdef class Column(OBIWrapper) :
                                 nb_lines                  = -1,
                                 nb_elements_per_line      = -1,
                                 elements_names            = NULL,
+                                elt_names_formatted       = False,
                                 tuples                    = False,
+                                to_eval                   = False,
                                 indexer_name              = NULL,
                                 associated_column_name    = NULL,
                                 associated_column_version = -1,
@@ -280,10 +288,17 @@ cdef class Column(OBIWrapper) :
  
     # elements_names property getter
     @property
-    def elements_names(self):
+    def _elements_names(self):
+        cdef char* elts_names_b
+        cdef list  elts_names_list
         if not self.active() :
             raise OBIDeactivatedInstanceError()
-        return obi_get_elements_names(self.pointer()).split(b';')
+        elts_names_b = obi_get_elements_names(self.pointer())
+        if elts_names_b == NULL:
+            raise Exception("Error reading the elements names of a column")
+        elts_names_list = elts_names_b.split(b';')
+        free(elts_names_b)
+        return elts_names_list
  
     # nb_elements_per_line property getter
     @property
@@ -334,6 +349,13 @@ cdef class Column(OBIWrapper) :
             raise OBIDeactivatedInstanceError()
         return self.pointer().header.tuples
 
+    # to_eval property getter
+    @property
+    def to_eval(self):
+        if not self.active() :
+            raise OBIDeactivatedInstanceError()
+        return self.pointer().header.to_eval
+
     # comments property getter
     @property
     def comments(self):
@@ -395,7 +417,11 @@ cdef class Column_line :
             return self._column.get_item(self._index, elt_id)
         else:
             return default
-        
+    
+    
+    def __len__(self):
+        return self._column.nb_elements_per_line
+         
         
     def __contains__(self, object elt_id):
         if type(elt_id) == int: