From 1a5b499b5c9fbe1b05ad1aa2dea48dfcabb808d5 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Tue, 19 Dec 2017 11:06:24 +0100
Subject: [PATCH] Cython API to add an OBI_QUAL column after creating a view

---
 python/obitools3/dms/column/column.pyx | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/python/obitools3/dms/column/column.pyx b/python/obitools3/dms/column/column.pyx
index d867f41..8ffc562 100644
--- a/python/obitools3/dms/column/column.pyx
+++ b/python/obitools3/dms/column/column.pyx
@@ -6,8 +6,9 @@ __OBIDMS_COLUMN_CLASS__ = {}
 
 from ..capi.obitypes cimport name_data_type, \
                              obitype_t, \
-                             obiversion_t
- 
+                             obiversion_t, \
+                             OBI_QUAL
+
 from ..capi.obidms cimport obi_import_column
 
 from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \
@@ -18,7 +19,8 @@ from ..capi.obiutils cimport obi_format_date
  
 from ..capi.obiview cimport obi_view_add_column, \
                             obi_view_get_pointer_on_column_in_view, \
-                            Obiview_p
+                            Obiview_p, \
+                            NUC_SEQUENCE_COLUMN
 
 from ..object cimport OBIDeactivatedInstanceError
 
@@ -85,6 +87,8 @@ cdef class Column(OBIWrapper) :
         cdef bytes  column_name_b = tobytes(column_name)
         cdef bytes  alias_b = tobytes(alias)
         cdef bytes  comments_b = tobytes(comments)
+        cdef char*  associated_column_name
+        cdef int    associated_column_version
         cdef list   elements_names_s
         cdef bytes  elements_names_b
         cdef char*  elements_names_p
@@ -109,6 +113,17 @@ cdef class Column(OBIWrapper) :
         else:
             elements_names_p = NULL
         
+        # TODO discuss
+        if data_type == OBI_QUAL:
+            if NUC_SEQUENCE_COLUMN not in view:
+                 raise RuntimeError("Cannot create column %s in view %s: trying to create quality column but no NUC_SEQ column to associate it with in the view" % (bytes2str(column_name_b),
+                                                                       bytes2str(view.name)))
+            associated_column_name = NUC_SEQUENCE_COLUMN
+            associated_column_version = view[NUC_SEQUENCE_COLUMN].version
+        else:
+            associated_column_name = NULL
+            associated_column_version = -1
+        
         if (obi_view_add_column(view                      = view.pointer(),
                                 column_name               = column_name_b,
                                 version_number            = -1,
@@ -121,8 +136,8 @@ cdef class Column(OBIWrapper) :
                                 tuples                    = tuples,
                                 to_eval                   = to_eval,
                                 indexer_name              = NULL,
-                                associated_column_name    = NULL,
-                                associated_column_version = -1,
+                                associated_column_name    = associated_column_name,
+                                associated_column_version = associated_column_version,
                                 comments                  = comments_b,
                                 create                    = True)<0):
             raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name_b),