def run_output(self):
targets = input(
"Search for config files for (a)ll or (s)elect targets:\n")
path = self.get_path()
if targets.lower() == ("a" or "all"):
self.search_configfiles(path)
elif targets.lower() == ("s" or "select"):
targets = Input().targetinput()
while (targets == "help" or targets == "" or targets is None):
targets = Input().helpmessage(targets)
self.targets = Input().parse_targets(targets)
for target in self.targets:
configpath = os.path.join(path, target, "config",
"config.json")
if os.path.isfile(configpath):
self.config_paths.append(configpath)
else:
info = ("No configuration files found for " + target +
" in specified path")
print(info)
G.logger(info)
return self.run_output()
else:
print("no valid input: choose (a)ll or (s)elect")
sys.exit()
for index, target in enumerate(self.targets):
config_path = self.config_paths[index]
self.read_config(target, config_path)
return self.config_dict
def search_configfiles(self, path):
print("Search in " + path)
for root, dirs, files in os.walk(path):
for file_name in files:
if "config.json" == file_name:
file_path = os.path.join(root, file_name)
print("found:", file_path)
G.logger("> Found config file: " + file_path)
target = "/".join(root.split("/")[-2:-1])
abbr = H.abbrev(target, dict_path)
primer_csv = os.path.join(path, "Summary", target,
abbr + "_primer.csv")
if not os.path.isfile(primer_csv):
self.targets.append(target)
self.config_paths.append(file_path)
else:
G.logger("> Skip run found results for " + target)
return self.targets, self.config_paths
def read_config(self, target, config_path):
self.config_dict.update({target: {}})
with open(config_path, "r") as f:
for line in f:
self.config_dict[target] = json.loads(line)
# new 20.11.2018
# make old config files compatible with the updated pipeline
for key in self.default_dict:
try:
self.config_dict[target][key]
except KeyError:
self.config_dict[target].update({key: self.default_dict[key]})
info1 = ("Warning! new option " + str(key) +
" was not found in config file")
info2 = ("Used default value: " + str(key) + " = " +
str(self.default_dict[key]))
print("\n" + info1 + "\n")
print("\n" + info2 + "\n")
G.logger(info1)
G.logger(info2)
def run_gui_output(self, targets, path):
if targets is None:
self.search_configfiles(path)
else:
self.targets = Input().parse_targets(targets)
for target in self.targets:
configpath = os.path.join(path, target, "config",
"config.json")
if os.path.isfile(configpath):
self.config_paths.append(configpath)
else:
self.config_paths.append('None')
info = ("No configuration files found for " + target +
" in specified path")
print(info)
G.logger(info)
for index, target in enumerate(self.targets):
config_path = self.config_paths[index]
if not config_path == 'None':
self.read_config(target, config_path)
return self.config_dict