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Commit f1f067c5 authored by VIGNET Pierre's avatar VIGNET Pierre
Browse files

[cmd] command line interface: partial black

parent ae6363b8
......@@ -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):
......
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