Rename traj_2_graph to solutions_2_graph; Update doc; ability to take a...

Rename traj_2_graph to solutions_2_graph; Update doc; ability to take a directory instead of just 1 file

command_line/cadbiom_cmd/cadbiom_cmd.py

@@ -57,19 +57,17 @@ def launch_sort(args):
     solution_sort.sort_solutions(params['path'])
 
 
-def traj_2_graph(args):
+def solutions_2_graph(args):
     """Parse a complete solution file and make a representation of trajectories.
     """
 
     # Module import
     import solution_repr
     params = args_to_param(args)
-    params['output'] = params['output'] if params['output'][-1] == '/' \
-                        else params['output'] + '/'
-    solution_repr.parse_trajectories_main(
+    solution_repr.solutions_2_graph(
         params['output'],
         params['chart_file'],
-        params['sol_file']
+        params['path']
     )
 
 def solutions_2_json(args):
@@ -272,18 +270,18 @@ def main():
     # Model file (xml : cadbiom language)
     # Solution file (cam_complete)
     parser_trajectories = subparsers.add_parser(
-        'traj_2_graph',
-        help=traj_2_graph.__doc__,
+        'solutions_2_graph',
+        help=solutions_2_graph.__doc__,
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser_trajectories.add_argument('chart_file',
         help="bcx model file.")
-    parser_trajectories.add_argument('sol_file',
+    parser_trajectories.add_argument('path',
         help="Complete solution file or directory with MAC solutions files "
         "(*cam_complete.txt files) generated with the 'compute_macs' command.")
     parser_trajectories.add_argument('--output', action=ReadableDir,
         nargs='?', default='graphs/',
         help="Output directory for GraphML files.")
-    parser_trajectories.set_defaults(func=traj_2_graph)
+    parser_trajectories.set_defaults(func=solutions_2_graph)
 
 
     # subparser: Decompilation of trajectories of MACs in a complete file/dir.

command_line/cadbiom_cmd/solution_repr.py

@@ -199,10 +199,45 @@ def draw_graph(output_dir, solution, solution_index, G,
 
 
 def process_solutions(output_dir, sol_steps, transitions):
-    """Build a graph per solution"""
+    """Build a graph based on the given solution
+
+    Each solution is composed of a set of frontier places and steps,
+    themselves composed of events.
+    We construct a graph based on the transitions that occur in the composition
+    of the events of the given solution.
+
+    :param output_dir: Output path.
+    :param sol_steps: A generator of tuples of "frontier places" and a list of
+        events in each step.
+
+        :Example:
+
+            .. code-block:: python
+
+                ("Bx Ax", [['h2', 'h00'], ['h3'], ['h0', 'h1'], ['hlast']])
+
+    :param transitions: A dictionnary of events as keys, and transitions as values.
+        Since many transitions can define an event, values are lists.
+        Each transition is a tuple with: origin node, final node, attributes
+        like label and condition.
+
+        :Example:
+
+            .. code-block:: python
+
+                {'h00': [('Ax', 'n1', {'label': 'h00[]'}),]
+
+    :type output_dir: <str>
+    :type sol_steps: <tuple <str>, <list>>
+    :type transitions: <dict <list <tuple <str>, <str>, <dict <str>: <str>>>>
+    """
 
     for sol_index, (sol, steps) in enumerate(sol_steps):
 
+        # build_graph() returns :
+        # G, transition_nodes, all_nodes, edges_in_cond, edges
+        # sol_index is used to order files according to the order of appearance
+        # in the file
         draw_graph(output_dir, sol, sol_index,
                    *build_graph(sol, steps, transitions)
         )
@@ -282,14 +317,49 @@ def test_main():
 
 
 
-def parse_trajectories_main(output_dir, model_file, solution_file):
-    """Entry point for parse_trajectories"""
+def solutions_2_graph(output_dir, model_file, solution_path):
+    """Entry point for solutions_2_graph
 
-    process_solutions(
-        output_dir,
-        load_solutions(solution_file),
-        get_transitions_from_model_file(model_file)
-    )
+    This functions tests if the given path is a directory or a file.
+
+    :param output_dir: Output path.
+    :param model_file: Filepath of the model.
+    :param solution_path:
+    :type output_dir: <str>
+    :type model_file: <str>
+    :type solution_path: <str>
+    """
+
+    # Check valid input file/directory
+    assert os.path.isfile(solution_path) or os.path.isdir(solution_path)
+
+    # Get transitions from the model
+    model_transitions = get_transitions_from_model_file(model_file)
+
+    if os.path.isfile(solution_path):
+        # The given path is a solution file
+        process_solutions(
+            output_dir,
+            load_solutions(solution_path),
+            model_transitions
+        )
+
+    elif os.path.isdir(solution_path):
+        # The given path is a directory
+        solution_path = solution_path if solution_path[-1] == '/' \
+            else solution_path + '/'
+
+        # Decompilation of all files in the directory
+        for file_number, solution_path in \
+            enumerate(glob.glob(solution_path + '*cam_complete.txt'), 1):
+
+            process_solutions(
+                output_dir,
+                load_solutions(solution_path),
+                model_transitions
+            )
+
+        LOGGER.info("Files processed: " + str(file_number))
 
 
 def graph_isomorph_test(model_file_1, model_file_2, output_dir='graphs/',