Commands: updated for JSON formatted comments with history

python/obitools3/commands/uniq.pyx

@@ -14,6 +14,8 @@ from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes
 
+import sys
+
 
 __title__="Group sequence records together"
  
@@ -214,8 +216,6 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
     cdef object         mcol
     cdef object         to_merge
 
-    #print(categories)
-
     uniques = {}
     
     mergedKeys_list_b = []
@@ -521,7 +521,17 @@ def run(config):
         uniq_sequences(entries, o_view, pb, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'], max_elts=config['obi']['maxelts'])       
     except Exception, e:
         raise RollbackException("obi uniq error, rollbacking view: "+str(e), o_view)
-        
+    
+    # Save command config in View and DMS comments
+    command_line = " ".join(sys.argv[1:])
+    input_dms_name=[input[0].name]
+    input_view_name=[input[1].name]
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
+        input_dms_name.append(config['obi']['taxoURI'].split("/", 1)[0])
+        input_view_name.append(config['obi']['taxoURI'].split("/", 1)[1])
+    o_view.write_config(config, "uniq", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    output[0].record_command_line(command_line)
+
     print("\n")
     print(repr(o_view))