obi import: now properly uses macros for column names

python/obitools3/commands/import.pyx

@@ -16,6 +16,14 @@ from obitools3.utils cimport tobytes, \
                              get_obitype, \
                              update_obitype
 
+from obitools3.dms.capi.obiview cimport VIEW_TYPE_NUC_SEQS, \
+                                        NUC_SEQUENCE_COLUMN, \
+                                        ID_COLUMN, \
+                                        DEFINITION_COLUMN, \
+                                        QUALITY_COLUMN, \
+                                        COUNT_COLUMN, \
+                                        TAXID_COLUMN
+                                        
 from obitools3.dms.capi.obitypes cimport obitype_t, \
                                          OBI_VOID, \
                                          OBI_QUAL
@@ -99,7 +107,7 @@ def run(config):
         entry_count = input[4]
         logger("info", "Importing %d entries", entry_count)
         
-        # TODO a bit dirty
+        # TODO a bit dirty?
         if input[2]==Nuc_Seq:
             v = View_NUC_SEQS
         else:
@@ -136,9 +144,9 @@ def run(config):
     
     # Save basic columns in variables for optimization
     if NUC_SEQS_view :
-        id_col = view[b"ID"]            # TODO use macros or globals for column names
-        def_col = view[b"DEFINITION"]
-        seq_col = view[b"NUC_SEQ"]
+        id_col = view[ID_COLUMN]
+        def_col = view[DEFINITION_COLUMN]
+        seq_col = view[NUC_SEQUENCE_COLUMN]
         
     dcols = {}
         
@@ -153,20 +161,22 @@ def run(config):
             seq_col[i] = entry.seq
             # Check if there is a sequencing quality associated by checking the first entry    # TODO haven't found a more robust solution yet
             if i == 0:
-                get_quality = b"QUALITY" in entry
+                get_quality = QUALITY_COLUMN in entry
                 if get_quality:
-                    Column.new_column(view, b"QUALITY", OBI_QUAL)
-                    qual_col = view[b"QUALITY"]
+                    Column.new_column(view, QUALITY_COLUMN, OBI_QUAL)
+                    qual_col = view[QUALITY_COLUMN]
             if get_quality:
                 qual_col[i] = entry.quality
          
         for tag in entry :
             
-            if tag != b"ID" and tag != b"DEFINITION" and tag != b"NUC_SEQ" and tag != b"QUALITY" :  # TODO hmmm... 
+            if tag != ID_COLUMN and tag != DEFINITION_COLUMN and tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN :  # TODO dirty 
                                 
                 value = entry[tag]
                 if tag == b"taxid":
-                    tag = b"TAXID"
+                    tag = TAXID_COLUMN
+                if tag == b"count":
+                    tag = COUNT_COLUMN
                     
                 if tag not in dcols :
                      
@@ -253,7 +263,7 @@ def run(config):
                             # Fill value
                             dcols[tag][0][i] = value
                                     
-        i+=1
+        i+=1  # TODO Not if None sequence
  
     pb(i, force=True)
     print("", file=sys.stderr)