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Shorten logical lines over 79 characters where it makes sense
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Matthew Spelchak committed Feb 8, 2018
1 parent d41df08 commit cc98baf
Showing 1 changed file with 31 additions and 21 deletions.
52 changes: 31 additions & 21 deletions lib/galaxy/jobs/dynamic_tool_destination.py
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Original file line number Diff line number Diff line change
Expand Up @@ -345,8 +345,8 @@ def __validate_nice_value(cls, valid_rule, return_bool, rule, tool, counter):
valid_rule = False

else:
error = "No nice_value found for rule " + str(counter) + " in '" + str(tool)
error += "'."
error = "No nice_value found for rule " + str(counter) + " in '"
error += str(tool) + "'."
if not return_bool:
error += " Setting nice_value to 0."
rule["nice_value"] = 0
Expand Down Expand Up @@ -409,7 +409,8 @@ def __validate_destination(cls, valid_rule, return_bool, rule, tool, counter):
if verbose:
log.debug(error)
valid_rule = False
elif rule["destination"] not in destination_list and rule["destination"] != "fail":
elif (rule["destination"] not in destination_list
and rule["destination"] != "fail"):
error = "Destination for '" + str(tool) + "', rule "
error += str(counter) + ": '"
error += str(rule["destination"])
Expand All @@ -421,7 +422,8 @@ def __validate_destination(cls, valid_rule, return_bool, rule, tool, counter):
valid_rule = False

elif isinstance(rule["destination"], dict):
if ("priority" in rule["destination"] and isinstance(rule["destination"]["priority"], dict)):
if ("priority" in rule["destination"]
and isinstance(rule["destination"]["priority"], dict)):

for priority in rule["destination"]["priority"]:
if priority not in priority_list:
Expand Down Expand Up @@ -519,8 +521,8 @@ def __validate_bounds(cls, valid_rule, return_bool, rule, tool, counter):
lower_bound = rule["lower_bound"]

if lower_bound == "Infinity":
error = "Error: lower_bound is set to Infinity, but must be lower than "
error += "upper_bound!"
error = "Error: lower_bound is set to Infinity, but must be "
error += "lower than upper_bound!"
if not return_bool:
error += " Setting lower_bound to 0!"
lower_bound = 0
Expand Down Expand Up @@ -631,8 +633,8 @@ def __validate_users(cls, valid_rule, return_bool, rule, tool, counter):
for user in reversed(rule["users"]):
if not isinstance(user, str):
error = "Entry '" + str(user) + "' in users for rule "
error += str(counter) + " in tool '" + str(tool) + "' is in an "
error += "invalid format!"
error += str(counter) + " in tool '" + str(tool)
error += "' is in an " + "invalid format!"
if not return_bool:
error += " Ignoring entry."
if verbose:
Expand All @@ -642,9 +644,9 @@ def __validate_users(cls, valid_rule, return_bool, rule, tool, counter):

else:
if re.match(emailregex, user) is None:
error = "Supplied email '" + str(user) + "' for rule "
error += str(counter) + " in tool '" + str(tool) + "' is in "
error += "an invalid format!"
error = "Supplied email '" + str(user)
error += "' for rule " + str(counter) + " in tool '"
error += str(tool) + "' is in " + "an invalid format!"
if not return_bool:
error += " Ignoring email."
if verbose:
Expand Down Expand Up @@ -676,7 +678,8 @@ def __validate_users(cls, valid_rule, return_bool, rule, tool, counter):
return valid_rule, rule


def parse_yaml(path="/config/tool_destinations.yml", job_conf_path="/config/job_conf.xml", test=False, return_bool=False):
def parse_yaml(path="/config/tool_destinations.yml",
job_conf_path="/config/job_conf.xml", test=False, return_bool=False):
"""
Get a yaml file from path and send it to validate_config for validation.
Expand All @@ -699,7 +702,8 @@ def parse_yaml(path="/config/tool_destinations.yml", job_conf_path="/config/job_
"""

global destination_list
destination_list = get_destination_list_from_job_config(job_config_location=job_conf_path)
destination_list = get_destination_list_from_job_config(
job_config_location=job_conf_path)

# Import file from path
try:
Expand Down Expand Up @@ -917,7 +921,8 @@ def infinite_defaultdict():
valid_config = False
elif isinstance(curr['default_destination'], dict):

if ('priority' in curr['default_destination'] and isinstance(curr['default_destination']['priority'], dict)):
if ('priority' in curr['default_destination']
and isinstance(curr['default_destination']['priority'], dict)):

### May not be necessary check if something has all priorities specified as default
for priority in priority_list:
Expand Down Expand Up @@ -1030,8 +1035,8 @@ def infinite_defaultdict():
# if "rules" in curr and isinstance(curr['rules'], list):
elif not tool_has_default:
valid_config = False
error = "Tool '" + str(tool) + "' does not have rules nor a"
error += " default_destination!"
error = "Tool '" + str(tool) + "' does not have"
error += " rules nor a default_destination!"
if verbose:
log.debug(error)

Expand Down Expand Up @@ -1420,7 +1425,8 @@ def map_tool_to_destination(

# if we matched a rule
if matched:
if (matched_rule is None or rule["nice_value"] < matched_rule["nice_value"]):
if (matched_rule is None or rule["nice_value"]
< matched_rule["nice_value"]):
matched_rule = rule
# if user_authorized
else:
Expand Down Expand Up @@ -1563,16 +1569,20 @@ def get_destination_list_from_job_config(job_config_location='/config/job_conf.x
sys.exit(1)

if args.check_config and args.job_config:
valid_config = parse_yaml(path=args.check_config, job_conf_path=args.job_config, return_bool=True)
valid_config = parse_yaml(path=args.check_config,
job_conf_path=args.job_config, return_bool=True)

elif args.check_config:
valid_config = parse_yaml(path=args.check_config, job_conf_path="/config/job_conf.xml", return_bool=True)
valid_config = parse_yaml(path=args.check_config,
job_conf_path="/config/job_conf.xml", return_bool=True)

elif args.job_config:
valid_config = parse_yaml(path="/config/tool_destinations.yml", job_conf_path=args.job_config, return_bool=True)
valid_config = parse_yaml(path="/config/tool_destinations.yml",
job_conf_path=args.job_config, return_bool=True)

else:
valid_config = parse_yaml(path="/config/tool_destinations.yml", job_conf_path="/config/job_conf.xml", return_bool=True)
valid_config = parse_yaml(path="/config/tool_destinations.yml",
job_conf_path="/config/job_conf.xml", return_bool=True)

if valid_config:
print("Configuration is valid!")
Expand Down

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