Proper script before refactoring and suppression of files

Makefile

@@ -23,7 +23,7 @@ run_gui:
 
 unit_test:
 	@echo Unit tests...
-	./mac.sh
+	$(CMD_PYTHON) script_mac.py
 	py.test
 
 version:

script_mac.py

@@ -6,7 +6,12 @@ from __future__ import print_function
 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):
@@ -26,118 +31,75 @@ class ErrorRep(object):
     def set_context(self, cont):
         self.context = cont
 
-def logical_or(list):
+def logical_or(elements):
     """
     @return logical_formula: str - OR of the input list
     """
-    if len(list)==0 :
+    if len(elements) == 0:
         return
-    elif len(list)==1 :
-        return list[0]
-    else :
-        logical_formula = ''
-        for elemnt in list :
-            logical_formula +=elemnt+' or '
-        logical_formula = logical_formula[:-4]
-#        print logical_formula
-        return '('+logical_formula+')'
-
-def logical_and(list):
+    elif len(elements) == 1:
+        return elements[0]
+    else:
+        return '(' + " or ".join(elements) + ')'
+
+
+def logical_and(elements):
     """
     @return logical_formula: str - AND of the input list
     """
-    if len(list)==0 :
+    print("elements:", elements)
+    if len(elements) == 0:
         return
-    elif len(list)==1 :
-        return list[0]
-    else :
-        logical_formula = ''
-        for elemnt in list :
-            logical_formula +=elemnt+' and '
-        logical_formula = logical_formula[:-5]
-        return '('+logical_formula+')'
+    elif len(elements) == 1:
+        return elements[0]
+    else:
+        return '(' + " and ".join(elements) + ')'
+
 
 def camFile2notOr(camFile):
     """
     translate a cam file into a logical formula to forbid previous cam
     """
-    cam_list = []
-    f=open(camFile,'r')
-    for line in f :
-        place_list =[]
-        new_line = line.split('\t')
-        place_and = logical_and(new_line[:-1])
-        cam_list.append(place_and)
-    f.close()
+
+    with open(camFile, 'r') as file:
+        cam_list = [logical_and(line.rstrip('\n').split('\t'))
+                        for line in file]
+
     if len(cam_list) != 0:
-        cam_or = logical_or(cam_list)
-        return 'not('+cam_or+')'
+        return 'not(' + logical_or(cam_list) + ')'
     else :
         return ''
 
+
 def write_list(input_list, output_file) :
     """
     write input_list in output_file, tabular form
     """
-    f=open(output_file,'a')
-    for elemt in input_list :
-        f.write(elemt+'\t')
-    f.write('\n')
-    f.close()
-
-def get_last_line(input_file):
-    list_of_line = []
-    f=open(input_file,'r')
-    for line in f :
-        line = line.split()
-        list_of_line.append(line[0])#remove \n
-    f.close()
-    return list_of_line[-1]
-
-if __name__ == "__main__":
-    import sys
-    import os.path
-    sys.setrecursionlimit(10000)
-    sys.path.append('~/cadbiom/solver') # SOLVER FOLDER
-    #AFFECT ARGUMENTS
-
-    print("APPEL !")
 
-    # FILES
-    chart_file = sys.argv[1]
-    cam_file = sys.argv[2]
-    cam_step_file = cam_file[:-4] + '_step.txt'
-    cam_complete_file = cam_file[:-4] + '_complete.txt'
-    cam_strong_file = cam_file[:-4] + '_strongA.txt'
+    with open(output_file, 'a') as file:
+        file.write('\t'.join(input_list) + '\n')
 
-    # QUERY PARAMETERS
-    if sys.argv[3] == 'n':
-        inv_p = None
-    else :
-        inv_p = sys.argv[3]
 
-#    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+")"
+def get_last_line(input_file):
 
+    with open(input_file, "rb") as f:
+        first = f.readline()                     # Read the first line.
+        f.seek(-2, 2)                            # Jump to the second last byte.
+        try:
+            while f.read(1) != b"\n":            # Until EOL is found...
+                # Raises an IOError if the file contains only 1 line
+                f.seek(-2, 1) # ...jump back the read byte plus one more.
+                return f.readline().rstrip('\n') # Read last line.
+        except IOError:
+            return first.rstrip('\n')
 
-    if sys.argv[4] == 'n':
-        start_p = None
-    else :
-        start_p = sys.argv[4]
 
-    if sys.argv[5] == 'n':
-        prop = None
-    else :
-        prop = sys.argv[5]
+def main(chart_file, cam_file, cam_step_file, cam_complete_file, cam_strong_file,
+         steps, final_prop, start_prop, inv_prop):
 
-    step = int(sys.argv[6])
+    LOGGER.debug("Params: start: {}, inv: {}, final: {}".format(start_prop,
+                                                                inv_prop,
+                                                                final_prop))
 
     cam_p = None
     # forbid previous cam
@@ -147,15 +109,10 @@ if __name__ == "__main__":
     except :
         print('error in camFile2notOr')
 
-    if start_p and cam_p :
-        start_p += ' and ('+cam_p+')'
+    if start_prop and cam_p :
+        start_prop += ' and ('+cam_p+')'
     elif cam_p :
-        start_p = cam_p
-
-    print('start p : ', start_p)
-    print('inv p : ', inv_p)
-    print('final_p : ', prop)
-
+        start_prop = cam_p
 
     # BUILD MCLA
     error_reporter = ErrorRep()
@@ -191,8 +148,11 @@ if __name__ == "__main__":
 #                start_prop = None
 #
     # BUILD QUERY
-    # final_prop
-    query = MCLSimpleQuery(start_p, inv_p, prop)
+    query = MCLSimpleQuery(start_prop, inv_prop, final_prop)
+
+#    lsol = mcla.sq_frontier_solutions(query, step, 10)
+#    print("DEBUG:: " + str(lsol))
+#    print("DEBUG:: ", len( lsol))
 
     # OPTIMIZE STEP RESEARCH
     if os.path.isfile(cam_step_file):
@@ -201,7 +161,7 @@ if __name__ == "__main__":
         query.set_steps_before_reach(min_step-1)
 
 
-    reacheable = mcla.sq_is_satisfiable(query, step)
+    reacheable = mcla.sq_is_satisfiable(query, steps) #important step
     print("reacheable:", reacheable)
     min_step = mcla.unfolder.get_current_step()
     print("min_step:", min_step)
@@ -209,29 +169,108 @@ if __name__ == "__main__":
     query.set_steps_before_reach(min_step-1)
 
     # FIND NEXT MAC
-    next_mac_object = mcla.next_mac(query, min_step)
+    next_mac_object = mcla.next_mac(query, min_step) #important step
     print("next_mac_object:", next_mac_object)
-    if next_mac_object :
+    if next_mac_object:
 
         # SAVE MAC AND TIMING
-        cam_complete_file = open(cam_complete_file,'a')
-        next_mac_object.save(cam_complete_file)
+        with open(cam_complete_file, 'a') as file:
+            next_mac_object.save(file)
 
         # SAVE MAC
         next_mac = next_mac_object.activated_frontier
         print("save next mac:", next_mac)
-        write_list(next_mac,cam_file)
+        write_list(next_mac, cam_file)
 
         # SAVE STEP
         min_step = mcla.unfolder.get_current_step()
         print("save min step:", min_step)
-        step_file = open(cam_step_file,'a')
-        step_file.write(str(min_step)+'\n')
-        step_file.close()
+        with open(cam_step_file, 'a') as file:
+            file.write(str(min_step)+'\n')
+
+        return 0
+    else:
+        print("stop")
+        return 1
+
+
+
+if __name__ == "__main__":
+
+
+    import sys
+    import os.path
+    sys.setrecursionlimit(10000)
+
+    #print(os.listdir(os.getcwd()))
+
+    # EXPERIMENT PARAMS
+    MODEL_NAME = "mini_test_publi"
+#    MODEL_NAME = "pid_or_clock"
+
+    # QUERY PARAMETERS
+    steps      = 10
+#    final_prop = "CCR5"
+    final_prop = "P"
+    start_prop = None
+    inv_prop   = None
+
+    # FILES
+    CAM_FILE_PREFIX = RESULT_FOLDER + MODEL_NAME
+    # chart_file
+    chart_file        = MODEL_FOLDER + MODEL_NAME + ".bcx"
+    # cam_file
+    cam_file          = CAM_FILE_PREFIX + "_P_cam.txt"
+    # cam_step_file
+    cam_step_file     = CAM_FILE_PREFIX + "_P_cam_step.txt"
+    # cam_complete_file
+    cam_complete_file =  CAM_FILE_PREFIX + "_P_cam_complete.txt"
+    # cam_strong_file
+    cam_strong_file   = CAM_FILE_PREFIX + "_P_cam_strongA.txt"
+
+
+    # Reset files
+    def remove_file(file):
+        try:
+            os.remove(file)
+        except:
+            pass
+
+    remove_file(cam_file)
+    remove_file(cam_step_file)
+    remove_file(cam_complete_file)
+    remove_file(cam_strong_file)
+
+    # MAC research
+    status = 0
+    while status == 0:
+
+        print("NEW LOOP !")
+
+        status = \
+            main(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
+            )
+
+
+    # QUERY PARAMETERS
+
+#    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+")"
+
+
 
-        sys.exit(0)
-    else :
-        sys.exit(1)