Move solutions_2_json to solution_sort module

command_line/cadbiom_cmd/cadbiom_cmd.py

@@ -82,11 +82,11 @@ def solutions_2_json(args):
     """
 
     # Module import
-    import solution_repr
+    import solution_sort
     params = args_to_param(args)
     params['output'] = params['output'] if params['output'][-1] == '/' \
                         else params['output'] + '/'
-    solution_repr.solutions_2_json(
+    solution_sort.solutions_2_json(
         params['output'],
         params['chart_file'],
         params['path'],

command_line/cadbiom_cmd/solution_repr.py

@@ -63,8 +63,6 @@ import datetime as dt
 import networkx as nx
 import networkx.algorithms.isomorphism as iso
 import json
-import os
-import glob
 import csv
 from urllib import quote as urllib_quote
 # Remove matplotlib dependency
@@ -281,64 +279,7 @@ def test_main():
     print(transitions)
 
 
-def solutions_2_json(output_dir, model_file, solution_path, conditions=True):
-    """Entry point for solutions_2_json
 
-    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: Filepath/directory of a complete solution file.
-    :param conditions: (Optional) If False, conditions of transitions will not
-        be present in the JSON file. This allows to have only places/entities
-        used inside trajectories; thus, inhibitors are avoided.
-    :type output_dir: <str>
-    :type model_file: <str>
-    :type solution_path: <str>
-    :type conditions: <boolean>
-    """
-
-    def write_json_file(decompiled_filename, decomp_solutions):
-        # Write file
-        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)
-
-    if os.path.isfile(solution_path):
-        # The given path is a solution file
-        # 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 = get_json_solutions(
-            load_solutions(solution_path),
-            model_transitions,
-            conditions=conditions,
-        )
-        write_json_file(decompiled_filename, decomp_solutions)
-
-    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_file in \
-            enumerate(glob.glob(solution_path + '*cam_complete.txt'), 1):
-
-            # 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 = get_json_solutions(
-                load_solutions(solution_file),
-                model_transitions,
-                conditions=conditions,
-            )
-            write_json_file(decompiled_filename, decomp_solutions)
-
-        LOGGER.info("Files processed: " + str(file_number))
 
 
 def parse_trajectories_main(output_dir, model_file, solution_file):

command_line/cadbiom_cmd/solution_sort.py

@@ -27,10 +27,20 @@ files of Cadbiom.
 from __future__ import unicode_literals
 from __future__ import print_function
 
+# Standard imports
+import json
 import os
 import glob
 
+# Library imports
+
 from tools.solutions import get_solutions
+from tools.models import get_transitions_from_model_file
+from tools.solutions import load_solutions, get_json_solutions
+
+import cadbiom.commons as cm
+
+LOGGER = cm.logger()
 
 ## Sort functions ##############################################################
 
@@ -93,3 +103,64 @@ def sort_solutions(path):
         [sort_solutions_in_file(file) for file in glob.glob(path + '*cam*')]
     else:
         sort_solutions_in_file(path)
+
+## Conversion functions ########################################################
+
+def solutions_2_json(output_dir, model_file, solution_path, conditions=True):
+    """Entry point for solutions_2_json
+
+    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: Filepath/directory of a complete solution file.
+    :param conditions: (Optional) If False, conditions of transitions will not
+        be present in the JSON file. This allows to have only places/entities
+        used inside trajectories; thus, inhibitors are avoided.
+    :type output_dir: <str>
+    :type model_file: <str>
+    :type solution_path: <str>
+    :type conditions: <boolean>
+    """
+
+    def write_json_file(decompiled_filename, decomp_solutions):
+        # Write file
+        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)
+
+    if os.path.isfile(solution_path):
+        # The given path is a solution file
+        # 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 = get_json_solutions(
+            load_solutions(solution_path),
+            model_transitions,
+            conditions=conditions,
+        )
+        write_json_file(decompiled_filename, decomp_solutions)
+
+    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_file in \
+            enumerate(glob.glob(solution_path + '*cam_complete.txt'), 1):
+
+            # 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 = get_json_solutions(
+                load_solutions(solution_file),
+                model_transitions,
+                conditions=conditions,
+            )
+            write_json_file(decompiled_filename, decomp_solutions)
+
+        LOGGER.info("Files processed: " + str(file_number))