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Adhering (better) to Galaxy style guidelines
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Matthew Spelchak committed Feb 8, 2018
1 parent 76b771d commit f619906
Showing 1 changed file with 40 additions and 41 deletions.
81 changes: 40 additions & 41 deletions lib/galaxy/jobs/dynamic_tool_destination.py
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Original file line number Diff line number Diff line change
Expand Up @@ -670,7 +670,7 @@ 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 Down Expand Up @@ -791,9 +791,9 @@ def infinite_defaultdict():
if obj['default_destination'] in destination_list:
new_config["default_destination"] = obj['default_destination']
else:
error = ("Default destination '" +
obj['default_destination'] +
"' does not appear in the job configuration.")
error = ("Default destination '"
+ obj['default_destination']
+ "' does not appear in the job configuration.")
if verbose:
log.debug(error)
valid_config = False
Expand All @@ -809,18 +809,18 @@ def infinite_defaultdict():

if obj['default_destination']['priority'][priority] in destination_list:
new_config['default_destination']['priority'][priority] = obj[
'default_destination']['priority'][priority]
'default_destination']['priority'][priority]
else:
error = ("Default destination '" +
obj['default_destination']['priority'][priority] +
"' does not appear in the job configuration.")
error = ("Default destination '"
+ obj['default_destination']['priority'][priority]
+ "' does not appear in the job configuration.")
if verbose:
log.debug(error)
valid_config = False

else:
error = ("Invalid default priority destination '" +
str(priority) + "' found in config!")
error = ("Invalid default priority destination '"
+ str(priority) + "' found in config!")
if verbose:
log.debug(error)
valid_config = False
Expand Down Expand Up @@ -858,9 +858,9 @@ def infinite_defaultdict():
if curr['priority'] in priority_list:
new_config['users'][user]['priority'] = curr['priority']
else:
error = ("User '" + user + "', priority '" +
str(curr['priority']) + "' is not defined " +
"in the global default_destination section")
error = ("User '" + user + "', priority '"
+ str(curr['priority']) + "' is not defined "
+ "in the global default_destination section")
if verbose:
log.debug(error)
valid_config = False
Expand Down Expand Up @@ -899,10 +899,10 @@ def infinite_defaultdict():
new_config['tools'][tool]['default_destination'] = (curr['default_destination'])
tool_has_default = True
else:
error = ("Default destination for '" +
str(tool) + "': '" +
curr['default_destination'] +
"' does not appear in the job configuration.")
error = ("Default destination for '"
+ str(tool) + "': '"
+ curr['default_destination']
+ "' does not appear in the job configuration.")
if verbose:
log.debug(error)
valid_config = False
Expand All @@ -913,8 +913,8 @@ def infinite_defaultdict():
### May not be necessary check if something has all priorities specified as default
for priority in priority_list:
if priority not in curr['default_destination']['priority']:
error = ("No default for destination for priority '" +
str(priority) + "' in '" + str(tool)) + "'."
error = ("No default for destination for priority '"
+ str(priority) + "' in '" + str(tool)) + "'."
if verbose:
log.debug(error)
valid_config = False
Expand All @@ -928,25 +928,25 @@ def infinite_defaultdict():
'priority'][priority] = destination
tool_has_default = True
else:
error = ("Default destination for '" +
str(tool) + "': '" +
destination + "' does not appear " +
"in the job configuration.")
error = ("Default destination for '"
+ str(tool) + "': '"
+ destination + "' does not appear "
+ "in the job configuration.")
if verbose:
log.debug(error)
valid_config = False
else:
error = ("No default '" + str(priority) +
"' priority destination for tool " +
str(tool) + " in config!")
error = ("No default '" + str(priority)
+ "' priority destination for tool "
+ str(tool) + " in config!")
if verbose:
log.debug(error)
valid_config = False

else:
error = ("Invalid default destination priority '" +
str(priority) + "' for '" + str(tool) +
"'.")
error = ("Invalid default destination priority '"
+ str(priority) + "' for '" + str(tool)
+ "'.")
if verbose:
log.debug(error)
valid_config = False
Expand Down Expand Up @@ -1307,16 +1307,15 @@ def map_tool_to_destination(
# making default destinations a mandatory field for all tools
if len(priority_list) > 0:
default_priority = next(iter(priority_list))
priority = default_priority ###FIXME: this is sometimes a value that isn't in the tool's default destinations field.
priority = default_priority ###FIXME: this is sometimes a value that isn't in the tool's default destinations field
else:
fail_message = ("No priorities declared in config file!" +
"cannot map " + str(tool.old_id) + " to destination" +
"using priorities")
error = ("No priorities found so no default priorty set! " +
"Things may behave unexpectedly.")
fail_message = ("No priorities declared in config file!"
+ "cannot map " + str(tool.old_id) + " to destination"
+ "using priorities")
error = ("No priorities found so no default priorty set! "
+ "Things may behave unexpectedly.")
if verbose:
log.debug(error)
valid_config = False

if config is not None:
# get the users priority
Expand Down Expand Up @@ -1531,11 +1530,11 @@ def get_destination_list_from_job_config(job_config_location='/config/job_conf.x

parser.add_argument(
'-c', '--check-config', dest='check_config', nargs='?',
help='Use this option to validate tool_destinations.yml.' +
' Optionally, provide the path to the tool_destinations.yml' +
' that you would like to check, and/or the path to the related' +
' job_conf.xml. Default: galaxy/config/tool_destinations.yml and' +
' galaxy/config/job_conf.xml')
help='Use this option to validate tool_destinations.yml.'
+ ' Optionally, provide the path to the tool_destinations.yml'
+ ' that you would like to check, and/or the path to the related'
+ ' job_conf.xml. Default: galaxy/config/tool_destinations.yml and'
+ ' galaxy/config/job_conf.xml')

parser.add_argument(
'-j', '--job-config', dest='job_config')
Expand Down

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