Rename sol_digging to get_json_solutions; improve arguments readability

command_line/cadbiom_cmd/cadbiom_cmd.py

@@ -73,8 +73,9 @@ def traj_2_graph(args):
     )
 
 def traj_2_json(args):
-    """Convert all events for all solutions in a complete MAC file
-    and write them in a separate file in the JSON format.
+    """Create a JSON formated file containing all data from complete MAC files
+    (frontier places/boundaries and decompiled steps with their respective
+    events).
 
     This is a function to quickly search all transition attributes involved
     in a solution.
@@ -85,10 +86,10 @@ def traj_2_json(args):
     params = args_to_param(args)
     params['output'] = params['output'] if params['output'][-1] == '/' \
                         else params['output'] + '/'
-    solution_repr.sol_digging_main(
+    solution_repr.traj_2_json(
         params['output'],
         params['chart_file'],
-        params['sol_file'],
+        params['path'],
         conditions=not params['no_conditions'], # Inv the param...
     )
 
@@ -287,23 +288,23 @@ def main():
     # subparser: Decompilation of trajectories of MACs in a complete file/dir.
     # Model file (xml : cadbiom language)
     # Solution file (cam_complete)
-    parser_sol_digging = subparsers.add_parser(
+    parser_traj_2_json = subparsers.add_parser(
         'traj_2_json',
         help=traj_2_json.__doc__,
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser_sol_digging.add_argument('chart_file',
+    parser_traj_2_json.add_argument('chart_file',
         help="bcx model file.")
-    parser_sol_digging.add_argument('sol_file',
+    parser_traj_2_json.add_argument('path',
         help="Complete solution file or directory with solution files " + \
-        "(output of 'compute_macs' command).")
-    parser_sol_digging.add_argument('--output', action=ReadableDir,
+        "(*cam_complete.txt files) generated with the 'compute_macs' command.")
+    parser_traj_2_json.add_argument('--output', action=ReadableDir,
         nargs='?', default='decompiled_solutions/',
-        help="Output directory for decompiled solutions files.")
-    parser_sol_digging.add_argument('--no_conditions', action='store_true',
+        help="Directory for newly created files.")
+    parser_traj_2_json.add_argument('--no_conditions', action='store_true',
         help="Don't export conditions of transitions. This allows " + \
         "to have only places/entities that are used inside trajectories; " + \
         "thus, inhibitors nodes are not present in the json file")
-    parser_sol_digging.set_defaults(func=traj_2_json)
+    parser_traj_2_json.set_defaults(func=traj_2_json)
 
 
     # subparser: Merge solutions to a csv file

command_line/cadbiom_cmd/solution_repr.py

@@ -489,8 +489,8 @@ def test_main():
     print(transitions)
 
 
-def sol_digging_main(output_dir, model_file, solution_path, conditions=True):
-    """Entry point for sol_digging
+def traj_2_json(output_dir, model_file, solution_path, conditions=True):
+    """Entry point for traj_2_json
 
     .. note:: This functions tests if the solution_path is a directory
         or just a file.
@@ -501,6 +501,7 @@ def sol_digging_main(output_dir, model_file, solution_path, conditions=True):
         with open(decompiled_filename, 'w') as f_d:
             json.dump(decomp_solutions, f_d, sort_keys=True, indent=4)
 
+
     # Get transitions from the model
     model_transitions = get_transitions_from_model_file(model_file)
 
@@ -509,7 +510,7 @@ def sol_digging_main(output_dir, model_file, solution_path, conditions=True):
         # Add _decomp to the solution filename
         filename = os.path.basename(os.path.splitext(solution_path)[0])
         decompiled_filename = output_dir + filename + '_decomp.txt'
-        decomp_solutions = sol_digging(
+        decomp_solutions = get_json_solutions(
             load_solutions(solution_path),
             model_transitions,
             conditions=conditions,
@@ -528,7 +529,7 @@ def sol_digging_main(output_dir, model_file, solution_path, conditions=True):
             # Add _decomp to the solution filename
             filename = os.path.basename(os.path.splitext(solution_file)[0])
             decompiled_filename = output_dir + filename + '_decomp.txt'
-            decomp_solutions = sol_digging(
+            decomp_solutions = get_json_solutions(
                 load_solutions(solution_file),
                 model_transitions,
                 conditions=conditions,
@@ -1026,11 +1027,11 @@ if __name__ == "__main__":
 #    print(g)
 #    exit()
 
-    sol_digging(load_solutions(LOG_DIR + "../run/pid_and_clock_no_perm_p21corrected_start_SRP9_complete.txt"),
+    get_json_solutions(load_solutions(LOG_DIR + "../run/pid_and_clock_no_perm_p21corrected_start_SRP9_complete.txt"),
              get_transitions_from_model_file(BIO_MOLDELS_DIR + "Whole NCI-PID database translated into CADBIOM formalism(and).bcx"))
     exit()
 
-    sol_digging(load_solutions(LOG_DIR + "sols_new_solver.txt"),
+    get_json_solutions(load_solutions(LOG_DIR + "sols_new_solver.txt"),
              get_transitions_from_model_file(BIO_MOLDELS_DIR + "mini_test_publi.bcx"))
     exit()
     process_solutions(load_solutions(LOG_DIR + "sols_new_solver.txt"),

command_line/cadbiom_cmd/tools/solutions.py

@@ -36,8 +36,11 @@ import cadbiom.commons as cm
 LOGGER = cm.logger()
 
 
+## Handle *cam_complete.txt files ##############################################
+
 def load_solutions(file):
-    """Open a file with many solution/MACs and yield them.
+    """Open a file with many solution/MACs (*cam_complete.txt files)
+    and yield them.
 
     :Example:
 
@@ -104,7 +107,7 @@ def load_solutions(file):
         yield sol, sol_steps[sol]
 
 
-def sol_digging(sol_steps, transitions, conditions=True):
+def get_json_solutions(sol_steps, transitions, conditions=True):
     """Convert all events for all solutions in a complete MAC file
     and write them in a separate file in the JSON format.
 
@@ -118,7 +121,7 @@ def sol_digging(sol_steps, transitions, conditions=True):
             >>> from tools.models import get_transitions
             >>> # Get transitions from the model
             >>> model_transitions = get_transitions('model.bcx')
-            >>> decomp_solutions = sol_digging(
+            >>> decomp_solutions = get_json_solutions(
             ...     load_solutions('./solution_cam_complete.txt'),
             ...     model_transitions,
             ...     conditions=True,