From 8a9ba8b0a85c1d55cf28e48e3b28b30061cd3115 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 17 Oct 2018 11:23:07 +0200
Subject: [PATCH] Cython: Added Column line methods to get a Column line as a
 str or bytes, and elements (keys, values) with None values are not returned
 anymore

---
 python/obitools3/dms/column/column.pxd |  6 +++-
 python/obitools3/dms/column/column.pyx | 44 +++++++++++++++++++++++---
 2 files changed, 45 insertions(+), 5 deletions(-)

diff --git a/python/obitools3/dms/column/column.pxd b/python/obitools3/dms/column/column.pxd
index d182f55..7e68906 100644
--- a/python/obitools3/dms/column/column.pxd
+++ b/python/obitools3/dms/column/column.pxd
@@ -43,7 +43,11 @@ cdef class Column_line:
  
     cdef Column    _column
     cdef index_t   _index
-
+    
+    cpdef list keys(self)
+    cpdef list items(self)
+    cpdef dict dict(self)
+    cpdef bytes bytes(self)  
     cpdef update(self, object data)
      
     
diff --git a/python/obitools3/dms/column/column.pyx b/python/obitools3/dms/column/column.pyx
index 175616b..aae7f71 100644
--- a/python/obitools3/dms/column/column.pyx
+++ b/python/obitools3/dms/column/column.pyx
@@ -543,15 +543,51 @@ cdef class Column_line :
     def __iter__(self) :
         cdef list  elements_names
         cdef bytes element_name
-        elements_names = self._column._elements_names
-        for element_name in elements_names :
+        for element_name in self._column.get_line(self._index) :
             yield element_name
     
     
-    def keys(self):    # TODO Discuss if keys with None values should be returned too
-        return self._column._elements_names
+    cpdef list keys(self):    
+    # TODO just returning all element names of the column would be faster but 
+    # potentially lots of keys associated with None values on that given line.
+    # get_line() methods don't return None values
+        return [element_name for element_name in self._column.get_line(self._index)]
     
 
+    cpdef list items(self):
+        return [(k, self[k]) for k in self.keys()]
+    
+    
+    cpdef dict dict(self):
+        cdef dict d
+        d = {}
+        for k,v in self.items():
+            d[k] = v
+        return d
+    
+    
+    def __str__(self):
+        cdef dict d
+        cdef str  s
+        d = {}
+        for k,v in self.items():
+            if type(v) == bytes:
+                value = bytes2str(v)
+            else:
+                value = v
+            d[bytes2str(k)] = value
+        s = str(d)
+        return s
+
+
+    cpdef bytes bytes(self):
+        cdef str   s
+        cdef bytes b
+        s = self.__str__()
+        b = str2bytes(s)
+        return b
+        
+        
     # column property getter
     @property
     def column(self):