[cmd] command line interface: partial black

command_line/cadbiom_cmd/cadbiom_cmd.py

@@ -43,12 +43,12 @@ def check_output_dir(function):
     @wraps(function)
     def modified_func(*args, **kwargs):
         """Fix paths in arguments (add trailing '/')"""
-        output_dir = args[0]['output']
-        output_dir = output_dir if output_dir[-1] == '/' else output_dir + '/'
+        output_dir = args[0]["output"]
+        output_dir = output_dir if output_dir[-1] == "/" else output_dir + "/"
 
         # Compatibility for output and output_dir
-        args[0]['output'] = output_dir
-        args[0]['output_dir'] = output_dir
+        args[0]["output"] = output_dir
+        args[0]["output_dir"] = output_dir
 
         return function(*args, **kwargs)
 
@@ -63,9 +63,10 @@ def solutions_search(args):
 
     # Module import
     import solution_search
+
     # Temporary fix: all_macs is always activated in the new API
     args["all_macs"] = True
-    solution_search.solutions_search(args) # !
+    solution_search.solutions_search(args)  # !
 
 
 def solutions_sort(args):
@@ -75,7 +76,8 @@ def solutions_sort(args):
 
     # Module import
     import solution_sort
-    solution_sort.solutions_sort(args['path'])
+
+    solution_sort.solutions_sort(args["path"])
 
 
 @check_output_dir
@@ -89,11 +91,8 @@ def solutions_2_graphs(args):
 
     # Module import
     import solution_sort
-    solution_sort.solutions_2_graphs(
-        args['output'],
-        args['model_file'],
-        args['path']
-    )
+
+    solution_sort.solutions_2_graphs(args["output"], args["model_file"], args["path"])
 
 
 @check_output_dir
@@ -108,11 +107,12 @@ def queries_2_json(args):
 
     # Module import
     import solution_sort
+
     solution_sort.queries_2_json(
-        args['output'],
-        args['model_file'],
-        args['path'],
-        conditions=not args['no_conditions'], # Reverse the param...
+        args["output"],
+        args["model_file"],
+        args["path"],
+        conditions=not args["no_conditions"],  # Reverse the param...
     )
 
 
@@ -128,10 +128,9 @@ def json_2_interaction_graph(args):
 
     # Module import
     import interaction_graph
+
     interaction_graph.json_2_interaction_graph(
-        args['output'],
-        args['molecules_of_interest'],
-        args['path'],
+        args["output"], args["molecules_of_interest"], args["path"]
     )
 
 
@@ -147,6 +146,7 @@ def queries_2_common_graph(args):
 
     # Module import
     import solution_sort
+
     if not any((args["graphs"], args["csv"], args["json"])):
         parser.error("at least one flag is required")
     solution_sort.queries_2_common_graph(**args)
@@ -160,11 +160,12 @@ def queries_2_occcurrence_matrix(args):
 
     # Module import
     import solution_sort
+
     solution_sort.queries_2_occcurrence_matrix(
-        args['output'],
-        args['model_file'],
-        args['path'],
-        transposed=args['transpose_csv']
+        args["output"],
+        args["model_file"],
+        args["path"],
+        transposed=args["transpose_csv"],
     )
 
 
@@ -177,6 +178,7 @@ def model_identifier_mapping(args):
 
     # Module import
     import models
+
     models.model_identifier_mapping(**args)
 
 
@@ -190,12 +192,13 @@ def model_comparison(args):
 
     # Module import
     import models
+
     models.graph_isomorph_test(
-        args['model_file_1'],
-        args['model_file_2'],
-        args['output'],
-        args['graphs'],
-        args['json'],
+        args["model_file_1"],
+        args["model_file_2"],
+        args["output"],
+        args["graphs"],
+        args["json"],
     )
 
 
@@ -207,6 +210,7 @@ def model_info(args):
 
     # Module import
     import models
+
     models.model_info(**args)
 
 
@@ -220,6 +224,7 @@ def model_graph(args):
 
     # Module import
     import models
+
     models.model_graph(**args)
 
 
@@ -229,8 +234,8 @@ def merge_macs(args):
 
     # Module import
     import solution_merge
-    solution_merge.merge_macs_to_csv(args['solutions_directory'],
-                                     args['output'])
+
+    solution_merge.merge_macs_to_csv(args["solutions_directory"], args["output"])
 
 
 def analytics(params):
@@ -250,8 +255,11 @@ def analytics(params):
     )
 
     # {"1":["key","val"],}
-    cvar = {str(i): [key, val] for i, (key, val) in enumerate(params.items(), 1)
-            if val is not None and key in white_list}
+    cvar = {
+        str(i): [key, val]
+        for i, (key, val) in enumerate(params.items(), 1)
+        if val is not None and key in white_list
+    }
     data = {
         "url": "http://cadbiom.genouest.org/",
         "_rcn": "cadbiom",
@@ -260,20 +268,20 @@ def analytics(params):
         "apiv": 1,
         "send_image": 0,
         "rec": 1,
-        "_id": "0000" + ''.join(re.findall('..', '%0012x' % getnode()))[:16],
+        "_id": "0000" + "".join(re.findall("..", "%0012x" % getnode()))[:16],
         "_cvar": json.dumps(cvar).encode("utf8"),
         "ua": platform,
     }
     data = urlencode(data).encode("ascii")
     page = urlopen("http://cadbiom.genouest.org/lytic.html", data=data).read()
-    m = re.search(".*URL=(.*)\">", page)
+    m = re.search('.*URL=(.*)">', page)
     if m:
         urlopen(m.group(1), data=data)
 
 
 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'}
+    return {k: v for k, v in vars(args).items() if k != "func"}
 
 
 def ensure_dir_presence(path):