[model_info] Ability to extract smallmolecules; json files carry the type of...

[model_info] Ability to extract smallmolecules; json files carry the type of entities queried; fix typos

command_line/cadbiom_cmd/cadbiom_cmd.py

@@ -509,6 +509,8 @@ def main():
         help="Retrieve data only for the frontier places/boundaries of the model.")
     group.add_argument('--genes', action='store_true',
         help="Retrieve data only for the genes in the model.")
+    group.add_argument('--smallmolecules', action='store_true',
+        help="Retrieve data only for the smallmolecules in the model.")
     # Outputs
     parser_model_info.add_argument('--csv', action='store_true',
         help="Create a CSV file containing data about previously filtered "

command_line/cadbiom_cmd/solution_repr.py

@@ -447,22 +447,25 @@ def low_graph_info(model_file, centralities):
 
 
 def low_model_info(model_file,
-                    all_entities=False, boundaries=False, genes=False):
+                   all_entities=False, boundaries=False, genes=False, smallmolecules=False):
     """Low level function for :meth:`~cadbiom_cmd.solution_repr.model_info`.
 
     Get JSON data with information about the model and its entities.
 
-    :param arg1: File for the model.
-    :param arg2: If True, data for all places of the model are returned
+    :param model_file: File for the model.
+    :key all_entities: If True, data for all places of the model are returned
         (optional).
-    :param arg3: If True, only data for the frontier places of the model
+    :key boundaries: If True, only data for the frontier places of the model
         are returned (optional).
-    :param arg4: If True, only data for the genes of the model are returned
+    :key genes: If True, only data for the genes of the model are returned
         (optional).
-    :type arg1: <str>
-    :type arg2: <boolean>
-    :type arg3: <boolean>
-    :type arg4: <boolean>
+    :key smallmolecules: If True, only data for the smallmolecules of the model
+        are returned (optional).
+    :type model_file: <str>
+    :type all_entities: <boolean>
+    :type boundaries: <boolean>
+    :type genes: <boolean>
+    :type smallmolecules: <boolean>
     :return: Dictionary with informations about the model and the queried nodes.
 
         :Example:
@@ -538,7 +541,7 @@ def low_model_info(model_file,
     # from cadbiom_gui.gt_gui.utils.reporter import CompilReporter
     static_analyser = StaticAnalyzer(Reporter())
     static_analyser.build_from_chart_model(model)
-    info['entitiesLocations'], info['entitesTypes'] = \
+    info['entitiesLocations'], info['entitiesTypes'] = \
         static_analyser.get_stats_entities_data()
 
     # Filter places
@@ -552,6 +555,12 @@ def low_model_info(model_file,
         g = (place_name for place_name in all_places_1 if '_gene' in place_name)
         info['entitiesData'] = get_places_data(g, model)
 
+    if smallmolecules:
+        # Filter on entityTypes
+        info['entitiesData'] = \
+            [data for data in get_places_data(all_places_1, model)
+             if data["entityType"] == "SmallMolecule"]
+
     return info
 
 
@@ -641,28 +650,31 @@ def model_graph(model_file, output_dir='./graphs/',
 
 def model_info(model_file, output_dir='./',
                all_entities=False, boundaries=False,
-               genes=False, default=True, **kwargs):
+               genes=False, smallmolecules=False, default=True, **kwargs):
     """Get quick and full informations about the model structure and places.
 
     :param model_file: File for the '.bcx' model.
-    :param output_dir: Output directory.
-    :param all_entities: If True, data for all places of the model are returned
+    :key output_dir: Output directory.
+    :key all_entities: If True, data for all places of the model are returned
         (optional).
-    :param boundaries: If True, only data for the frontier places of the model
+    :key boundaries: If True, only data for the frontier places of the model
         are returned (optional).
-    :param genes: If True, only data for the genes of the model are returned
+    :key genes: If True, only data for the genes of the model are returned
         (optional).
-    :param default: Display quick description of the model
+    :key smallmolecules: If True, only data for the smallmolecules of the model
+        are returned (optional).
+    :key default: Display quick description of the model
         (Number of places, transitions, entities types, entities locations).
 
-    :keyword json: If True, make a JSON dump of results in output path(optional).
-    :keyword csv: If True, make a csv dump of informations about filtered places.
+    :key json: If True, make a JSON dump of results in output path(optional).
+    :key csv: If True, make a csv dump of informations about filtered places.
 
     :type model_file: <str>
     :type output_dir: <str>
     :type all_entities: <boolean>
     :type boundaries: <boolean>
     :type genes: <boolean>
+    :type smallmolecules: <boolean>
     :type default: <boolean>
     :type json: <boolean>
     :type csv: <boolean>
@@ -704,14 +716,16 @@ def model_info(model_file, output_dir='./',
                 writer.writerow(temp_place)
 
 
-    def get_csv_filename():
-        """Return the csv filename according to the given filters."""
+    def get_output_filename(filetype="csv"):
+        """Return the filename according to the given filters and filetype."""
         if all_entities:
-            return output_dir + "all_entities.csv"
+            return "all_entities." + filetype
         if boundaries:
-            return output_dir + "boundaries.csv"
+            return "boundaries." + filetype
         if genes:
-            return output_dir + "genes.csv"
+            return "genes." + filetype
+        if smallmolecules:
+            return "smallmolecules." + filetype
 
 
     if default:
@@ -724,16 +738,16 @@ def model_info(model_file, output_dir='./',
 
     model_info = low_model_info(
         model_file,
-        all_entities, boundaries, genes
+        all_entities, boundaries, genes, smallmolecules
     )
 
     # Export to csv file
     if make_csv:
-        dump_places_to_csv(model_info['entitiesData'], get_csv_filename())
+        dump_places_to_csv(model_info['entitiesData'], output_dir + get_output_filename())
 
     # Export to json file
     if make_json:
-        with open(output_dir + "model_summary.json", 'w') as f_d:
+        with open(output_dir + "model_summary_" + get_output_filename("json"), 'w') as f_d:
             # Handle escaped unicode characters in model
             # Ex: \u03b2-catenin => β-Catenin
             f_d.write(