Add argparse support; full doc; clean code; better logging

Makefile

@@ -19,7 +19,7 @@ run_gui:
 
 unit_test:
 	@echo Unit tests...
-	$(CMD_PYTHON) script_mac.py
+	$(CMD_PYTHON) script_mac.py -vv debug compute_macs bio_models/mini_test_publi.bcx P --steps 10
 	py.test
 
 version:

script_mac.py

@@ -2,16 +2,18 @@
 from __future__ import unicode_literals
 from __future__ import print_function
 
+# Standard imports
+import argparse
+import re
+import os
 
+# Custom imports
 from cadbiom.models.clause_constraints.mcl.MCLAnalyser import MCLAnalyser
 from cadbiom.models.clause_constraints.mcl.MCLQuery import MCLSimpleQuery
-
 import cadbiom.commons as cm
 
 LOGGER = cm.logger()
 
-MODEL_FOLDER="/media/DATA/Projets/dyliss_tgf/cadbiom/bio_models/"
-RESULT_FOLDER="/media/DATA/Projets/dyliss_tgf/cadbiom/result/"
 
 class ErrorRep(object):
     # Cf class CompilReporter(object):
@@ -70,102 +72,133 @@ def make_logical_formula(previous_frontier_places, start_prop):
 
 
 def main2(chart_file, cam_file, cam_step_file, cam_complete_file, cam_strong_file,
-         steps, final_prop, start_prop, inv_prop):
-        """
+          steps, final_prop, start_prop, inv_prop):
+    """
 
-        .. todo: handle these QUERY PARAMETERS... from GUI program
+    .. todo: handle these QUERY PARAMETERS... from GUI program
 
-                #    if self.possible:
-                #        if len(inv_prop) == 0:
-                #            inv_prop = None
-                #        else :
-                #            inv_prop = "not ("+inv_prop+")"
-                #    else:
-                #        if len(inv_prop) != 0:
-                # sert pas:
-                #            final_prop = "not ("+final_prop+" and "+inv_prop+")"
+            #    if self.possible:
+            #        if len(inv_prop) == 0:
+            #            inv_prop = None
+            #        else :
+            #            inv_prop = "not ("+inv_prop+")"
+            #    else:
+            #        if len(inv_prop) != 0:
+            # sert pas:
+            #            final_prop = "not ("+final_prop+" and "+inv_prop+")"
 
-        """
+    """
 
-        # Build MCLA
-        error_reporter = ErrorRep()
-        mcla = MCLAnalyser(error_reporter)
+    # Build MCLA
+    error_reporter = ErrorRep()
+    mcla = MCLAnalyser(error_reporter)
 
-        # Load file
-        mcla.build_from_chart_file(chart_file)
-        if error_reporter.error:
-            raise "Error during loading of file"
+    # Load file
+    detect_model_type(mcla, chart_file)(chart_file)
+    if error_reporter.error:
+        raise "Error during loading of file"
 
-        # Frontier places asked
-        previous_frontier_places = set()
+    # Frontier places asked
+    previous_frontier_places = set()
 
-        while True:
+    while True:
 
-            frontier_places, min_steps = \
-                find_mac(mcla, start_prop, inv_prop, final_prop, steps)
+        frontier_places, min_steps = \
+            find_mac(mcla,
+                     cam_file, cam_step_file, cam_complete_file,
+                     steps, final_prop, start_prop, inv_prop)
 
-            # Add theese frontier places to set of previous ones
-            previous_frontier_places.update(frontier_places)
-            LOGGER.debug("Prev frontier places: " + \
-                         str(previous_frontier_places))
+        # Add theese frontier places to set of previous ones
+        previous_frontier_places.update(frontier_places)
+        LOGGER.debug("Prev frontier places: " + \
+                     str(previous_frontier_places))
 
-            # Compute the formula of the next start_property
-            start_prop = make_logical_formula(previous_frontier_places,
-                                              start_prop)
-            LOGGER.debug("Next start_prop formula: " + str(start_prop))
+        # Compute the formula of the next start_property
+        start_prop = make_logical_formula(previous_frontier_places,
+                                          start_prop)
+        LOGGER.debug("Next start_prop formula: " + str(start_prop))
 
 
-def find_mac(mcla, start_prop, inv_prop, final_prop, steps):
+def find_mac(mcla,
+             cam_file, cam_step_file, cam_complete_file,
+             steps, final_prop, start_prop, inv_prop):
 
-        # Build query
-        query = MCLSimpleQuery(start_prop, inv_prop, final_prop)
+    # Build query
+    query = MCLSimpleQuery(start_prop, inv_prop, final_prop)
 
-        # Is the property reacheable ?
-        reacheable = mcla.sq_is_satisfiable(query, steps)
-        # If yes, in how many steps ?
-        min_step   = mcla.unfolder.get_current_step()
+    # Is the property reacheable ?
+    reacheable = mcla.sq_is_satisfiable(query, steps)
+    # If yes, in how many steps ?
+    min_step   = mcla.unfolder.get_current_step()
 
-        if reacheable:
-            LOGGER.info(
-                "Property {} is reacheable in {} steps".format(
-                    final_prop, min_step
-                )
+    if reacheable:
+        LOGGER.info(
+            "Property {} is reacheable in {} steps".format(
+                final_prop, min_step
             )
-        else:
-            LOGGER.info(
-                "Property {} is NOT reacheable in {} steps".format(
-                    final_prop, min_step
-                )
+        )
+    else:
+        LOGGER.info(
+            "Property {} is NOT reacheable in {} steps".format(
+                final_prop, min_step
             )
-            LOGGER.info("STOP the search!")
-            exit()
-
-        # Find next MAC
-        next_mac_object = mcla.next_mac(query, min_step)
-        if next_mac_object:
-            LOGGER.debug("Next MAC object:\n{}".format(next_mac_object))
-
-            # Save MAC and timings
-            LOGGER.debug("Save MAC and timings...")
-            with open(cam_complete_file, 'a') as file:
-                next_mac_object.save(file)
-
-            # Save MAC
-            next_mac = next_mac_object.activated_frontier
-            LOGGER.debug("Save next MAC: {}".format(next_mac))
-            with open(cam_file, 'a') as file:
-                file.write('\t'.join(next_mac) + '\n')
-
-            # Save min steps
-            min_step = mcla.unfolder.get_current_step()
-            LOGGER.debug("Save minimal steps: {}".format(min_step))
-            with open(cam_step_file, 'a') as file:
-                file.write(str(min_step)+'\n')
-
-            return next_mac, min_step
-        else:
-            LOGGER.info("STOP the search! No more MAC.")
-            exit()
+        )
+        LOGGER.info("STOP the search!")
+        exit()
+
+    # Find next MAC
+    next_mac_object = mcla.next_mac(query, min_step)
+    if next_mac_object:
+        LOGGER.debug("Next MAC object:\n{}".format(next_mac_object))
+
+        # Save MAC and timings
+        LOGGER.debug("Save MAC and timings...")
+        with open(cam_complete_file, 'a') as file:
+            next_mac_object.save(file)
+
+        # Save MAC
+        next_mac = next_mac_object.activated_frontier
+        LOGGER.debug("Save next MAC: {}".format(next_mac))
+        with open(cam_file, 'a') as file:
+            file.write('\t'.join(next_mac) + '\n')
+
+        # Save min steps
+        min_step = mcla.unfolder.get_current_step()
+        LOGGER.debug("Save minimal steps: {}".format(min_step))
+        with open(cam_step_file, 'a') as file:
+            file.write(str(min_step)+'\n')
+
+        return next_mac, min_step
+    else:
+        LOGGER.info("STOP the search! No more MAC.")
+        exit()
+
+
+def detect_model_type(mclanalyser, filepath):
+    """Return the function to use to load the model.
+
+    bcx file: Build an MCLAnalyser from a .bcx file:
+        build_from_chart_file()
+    cal file: Build an MCLAnalyser from a .cal file of PID database
+        build_from_cadlang()
+    xml file: Build an MCLAnalyser from a .xml file of PID database:
+        build_from_pid_file()
+
+    """
+
+    build_func = {".bcx": mclanalyser.build_from_chart_file,
+                  ".cal": mclanalyser.build_from_cadlang,
+                  ".xml": mclanalyser.build_from_pid_file,
+                 }
+    try:
+        extension = re.search('^.*(\.[bcx|xml|cal]{3})', filepath).group(1)
+        LOGGER.debug("Find '" + extension + "' extension")
+    except:
+        LOGGER.error("Unauthorized file")
+        exit()
+
+    return build_func[extension]
+
 
 def main(chart_file, cam_file, cam_step_file, cam_complete_file, cam_strong_file,
          steps, final_prop, start_prop, inv_prop):
@@ -190,19 +223,6 @@ def main(chart_file, cam_file, cam_step_file, cam_complete_file, cam_strong_file
     # BUILD MCLA
     error_reporter = ErrorRep()
     mcla = MCLAnalyser(error_reporter)
-    # build_from_chart_model
-    # Build an MCLAnalyser from a chartmodel object
-    #    @param model: object - ChartModel
-    # = représentation interne...
-    # build_from_chart_file
-    # Build an MCLAnalyser from a .bcx file
-    #    @param file_name: str - path of the .bcx file
-    # build_from_pid_file
-    # Build an MCLAnalyser from a .xml file of PID database
-    #    @param file_name: str - path of .xml file
-    # build_from_cadlang
-    # Build an MCLAnalyser from a .cal file of PID database
-    #    @param file_name: str - path of .cal file
     mcla.build_from_chart_file(chart_file)
 
     if error_reporter.error:
@@ -211,14 +231,6 @@ def main(chart_file, cam_file, cam_step_file, cam_complete_file, cam_strong_file
         #return
         print("ERROR:: " + error_reporter.error)
         raise
-#
-#    if len(inv_prop) == 0:
-#                inv_prop = None
-#            else :
-#                inv_prop = "not ("+inv_prop+")"
-#
-#            if len(start_prop) == 0:
-#                start_prop = None
 #
     # BUILD QUERY
     query = MCLSimpleQuery(start_prop, inv_prop, final_prop)
@@ -233,7 +245,7 @@ def main(chart_file, cam_file, cam_step_file, cam_complete_file, cam_strong_file
 #    print("DEBUG:: " + str(lsol))
 #    print("DEBUG:: ", len( lsol))
 
-    # Dans le programme: minimal activation conditions
+    # minimal activation conditions
     # on_cam function:
 #    cam_list = self.mcla.mac_search(query, self.max_step)
 #            if len(cam_list)==0 :
@@ -280,37 +292,30 @@ def main(chart_file, cam_file, cam_step_file, cam_complete_file, cam_strong_file
         return 1
 
 
+def compute_macs(args):
+    """Launch Cadbiom search of MACs (Minimal Activation Conditions)"""
 
-if __name__ == "__main__":
-
+    # Limit recursion
     import sys
-    import os.path
     sys.setrecursionlimit(10000)
 
-    # EXPERIMENT PARAMS
-    MODEL_NAME = "mini_test_publi"
-#    MODEL_NAME = "pid_or_clock"
+    params = args_to_param(args)
 
     # QUERY PARAMETERS
-    steps      = 10
-#    final_prop = "CCR5"
-    final_prop = "P"
-    start_prop = None
-    inv_prop   = None
+    # Todo beware with type of separators in path..
+    MODEL_NAME = params['chart_file'].split('/')[-1][:-4]
 
     # FILES
-    CAM_FILE_PREFIX = RESULT_FOLDER + MODEL_NAME
-    # chart_file
-    chart_file        = MODEL_FOLDER + MODEL_NAME + ".bcx"
+    CAM_FILE_PREFIX   = params['output'] + MODEL_NAME + \
+                        '_' + params['final_prop'] + '_cam'
     # cam_file
-    cam_file          = CAM_FILE_PREFIX + "_P_cam.txt"
+    cam_file          = CAM_FILE_PREFIX + ".txt"
     # cam_step_file
-    cam_step_file     = CAM_FILE_PREFIX + "_P_cam_step.txt"
+    cam_step_file     = CAM_FILE_PREFIX + "_step.txt"
     # cam_complete_file
-    cam_complete_file =  CAM_FILE_PREFIX + "_P_cam_complete.txt"
+    cam_complete_file =  CAM_FILE_PREFIX + "_complete.txt"
     # cam_strong_file
-    cam_strong_file   = CAM_FILE_PREFIX + "_P_cam_strongA.txt"
-
+    cam_strong_file   = CAM_FILE_PREFIX + "_strongA.txt"
 
     # Reset files
     def remove_file(file):
@@ -326,11 +331,49 @@ if __name__ == "__main__":
 
     # MAC research
     main2(
-        chart_file,        # chart_file
-        cam_file,          # cam_file
-        cam_step_file,     # cam_step_file
-        cam_complete_file, # cam_complete_file
-        cam_strong_file,   # cam_strong_file
-        steps, final_prop, start_prop, inv_prop
+        params['chart_file'],   # chart_file
+        cam_file,               # cam_file
+        cam_step_file,          # cam_step_file
+        cam_complete_file,      # cam_complete_file
+        cam_strong_file,        # cam_strong_file
+        params['steps'], params['final_prop'],
+        params['start_prop'], params['inv_prop']
     )
 
+def args_to_param(args):
+    """Return argparse namespace as a dict {variable name: value}"""
+    return {k: v for k, v in vars(args).items() if k != 'func'}
+
+
+if __name__ == "__main__":
+
+    # parser configuration
+    parser = argparse.ArgumentParser(description=__doc__)
+    # Default log level: debug
+    parser.add_argument('-vv', '--verbose', nargs='?', default='debug')
+    # Subparsers
+    subparsers = parser.add_subparsers(title='subcommands')
+
+
+    # subparser: Compute macs
+    #    steps      = 10
+    #    final_prop = "P"
+    #    start_prop = None
+    #    inv_prop   = None
+    parser_input_file = subparsers.add_parser('compute_macs',
+                                              help=compute_macs.__doc__)
+    parser_input_file.add_argument('chart_file')
+    parser_input_file.add_argument('final_prop')
+    parser_input_file.add_argument('--steps', type=int, nargs='?', default=10)
+    parser_input_file.add_argument('--start_prop', nargs='?', default=None)
+    parser_input_file.add_argument('--inv_prop', nargs='?', default=None)
+    parser_input_file.add_argument('--output', nargs='?', default='result/')
+    parser_input_file.set_defaults(func=compute_macs)
+
+
+    # get program args and launch associated command
+    args = parser.parse_args()
+    # Set log level
+    cm._logger.setLevel(cm.LOG_LEVELS[vars(args)['verbose']])
+    # launch associated command
+    args.func(args)