Commands: updated for JSON formatted comments with history

python/obitools3/commands/grep.pyx

@@ -12,7 +12,8 @@ from obitools3.utils cimport tobytes
 from functools import reduce
 import time
 import re
- 
+import sys
+
  
 __title__="Grep view lines that match the given predicates"
 
@@ -29,7 +30,7 @@ def addOptions(parser):
     group=parser.add_argument_group("obi grep specific options")
  
     group.add_argument("--predicate", "-p",
-                       action="append", dest="grep:predicates",
+                       action="append", dest="grep:grep_predicates",
                        metavar="<PREDICATE>",
                        default=None,
                        type=str,
@@ -306,12 +307,22 @@ def run(config):
 
     # Create output view with the line selection
     try:
-        o_view = selection.materialize(output_view_name, comments="obi grep: "+str(config["grep"])+"\n")
+        o_view = selection.materialize(output_view_name)
     except Exception, e:
         raise RollbackException("obi grep error, rollbacking view: "+str(e), o_view)
 
     # TODO DISCUSS if output URI to different DMS, copy 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, "grep", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    input[0].record_command_line(command_line)  # TODO assuming input and output dms are the same
+
     print("\n")
     print(repr(o_view))