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Create method for verifying destinations
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Now, destinations are validated in a function that returns
both the validity of destination, as well as a suggestion
for typo correction if a typo is suspected. This function
is what does the check for if `app` exists now, making
validating destinations use much less lines of code now,
and also making these sections of code much easier to read.
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Matthew Spelchak committed Mar 1, 2018
1 parent 5d698a6 commit f1f8f69
Showing 1 changed file with 96 additions and 121 deletions.
217 changes: 96 additions & 121 deletions lib/galaxy/jobs/dynamic_tool_destination.py
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Original file line number Diff line number Diff line change
Expand Up @@ -418,7 +418,6 @@ def __validate_destination(cls, valid_rule, return_bool, rule, tool, counter):
rule["destination"] = "fail"

if "destination" in rule:
valid_destination = True
suggestion = None
if isinstance(rule["destination"], str):
if rule["destination"] == "fail" and "fail_message" not in rule:
Expand All @@ -432,27 +431,20 @@ def __validate_destination(cls, valid_rule, return_bool, rule, tool, counter):
if verbose:
log.debug(error)
valid_rule = False
elif app is None:
if (rule["destination"] not in destination_list
and rule["destination"] != "fail"):
valid_destination = False
suggestion = get_typo_correction(rule['destination'],
destination_list, max_edit_dist)
elif not app.job_config.get_destination(rule["destination"]):
valid_destination = False

if not valid_destination:
error = "Destination for '" + str(tool) + "', rule "
error += str(counter) + ": '"
error += str(rule["destination"])
error += "' does not exist in job configuration."
if suggestion:
error += " Did you mean '" + str(suggestion) + "'?"
if not return_bool:
error += " Ignoring..."
if verbose:
log.debug(error)
valid_rule = False
else:
validity = validate_destination(app, rule["destination"])
if not validity[0] and rule["destination"] != "fail":
error = "Destination for '" + str(tool) + "', rule "
error += str(counter) + ": '"
error += str(rule["destination"])
error += "' does not exist in job configuration."
if validity[1]:
error += " Did you mean '" + str(validity[1]) + "'?"
if not return_bool:
error += " Ignoring..."
if verbose:
log.debug(error)
valid_rule = False

elif isinstance(rule["destination"], dict):
if ("priority" in rule["destination"]
Expand Down Expand Up @@ -483,31 +475,21 @@ def __validate_destination(cls, valid_rule, return_bool, rule, tool, counter):
if verbose:
log.debug(error)
valid_rule = False
suggestion = None

elif app is None:
if (rule["destination"]["priority"][priority]
not in destination_list
and rule["destination"]["priority"][priority] != "fail"):
valid_destination = False
suggestion = get_typo_correction(rule['destination']["priority"][priority],
destination_list, max_edit_dist)
elif not app.job_config.get_destination(
rule["destination"]["priority"][priority]):
valid_destination = False

if not valid_destination:
error = "Destination for '" + str(tool) + "', rule "
error += str(counter) + ": '"
error += str(rule["destination"]["priority"][priority])
error += "' does not exist in job configuration."
if suggestion:
error += " Did you mean '" + str(suggestion) + "'?"
if not return_bool:
error += " Ignoring..."
if verbose:
log.debug(error)
valid_rule = False
else:
validity = validate_destination(app,
rule["destination"]["priority"][priority])
if not validity[0]:
error = "Destination for '" + str(tool) + "', rule "
error += str(counter) + ": '"
error += str(rule["destination"]["priority"][priority])
error += "' does not exist in job configuration."
if validity[1]:
error += " Did you mean '" + str(validity[1]) + "'?"
if not return_bool:
error += " Ignoring..."
if verbose:
log.debug(error)
valid_rule = False

else:
error = "No destination specified for rule " + str(counter)
Expand Down Expand Up @@ -730,7 +712,8 @@ def __validate_users(cls, valid_rule, return_bool, rule, tool, counter):


def parse_yaml(path="/config/tool_destinations.yml",
job_conf_path="/config/job_conf.xml", test=False, return_bool=False):
job_conf_path="/config/job_conf.xml", appl=None, test=False,
return_bool=False):
"""
Get a yaml file from path and send it to validate_config for validation.
Expand Down Expand Up @@ -797,6 +780,38 @@ def parse_yaml(path="/config/tool_destinations.yml",
return config


def validate_destination(app, destination):
"""
Validate received destination id.
@type app:
@param app: Current app
@type destination: str
@param destination: string containing the destination id that is being
validated
@rtype: tuple(bool, str/None)
@return: The first item in the tuple is True if the destination is valid
and False otherwise. The second item is a str suggesting the best
typo-correction suggestion, or None if there's no suggestion.
"""

valid_destination = False
suggestion = None

if app is None:
if destination in destination_list:
valid_destination = True
else:
suggestion = get_typo_correction(destination,
destination_list, max_edit_dist)
elif app.job_config.get_destination(destination):
valid_destination = True

return (valid_destination, suggestion)


def validate_config(obj, return_bool=False):
"""
Validate received config.
Expand Down Expand Up @@ -850,27 +865,17 @@ def infinite_defaultdict():
# default_priority, users, and verbose

if 'default_destination' in obj:
valid_destination = False
suggestion = None
if isinstance(obj['default_destination'], str):
if app is None:
if obj['default_destination'] in destination_list:
new_config["default_destination"] = obj['default_destination']
valid_destination = True
else:
suggestion = get_typo_correction(obj['default_destination'],
destination_list, max_edit_dist)
elif app.job_config.get_destination(
obj['default_destination']):
validity = validate_destination(app, obj['default_destination'])
if validity[0]:
new_config["default_destination"] = obj['default_destination']
valid_destination = True

if not valid_destination:
else:
error = ("Default destination '"
+ obj['default_destination']
+ "' does not appear in the job configuration.")
if suggestion:
error += " Did you mean '" + str(suggestion) + "'?"
if validity[1]:
error += " Did you mean '" + str(validity[1]) + "'?"
if verbose:
log.debug(error)
valid_config = False
Expand All @@ -884,29 +889,20 @@ def infinite_defaultdict():
if isinstance(obj['default_destination']['priority'][priority],
str):
priority_list.add(priority)

if app is None:
if obj['default_destination']['priority'][priority] in destination_list:
new_config["default_destination"]['priority'][priority] = obj['default_destination']['priority'][priority]
valid_destination = True
else:
suggestion = get_typo_correction(obj['default_destination']['priority'][priority],
destination_list, max_edit_dist)
elif app.job_config.get_destination(
obj['default_destination']['priority'][priority]):
new_config["default_destination"]['priority'][priority] = obj['default_destination']['priority'][priority]
valid_destination = True

if not valid_destination:
validity = validate_destination(app,
obj['default_destination']['priority'][priority])
if validity[0]:
new_config["default_destination"]['priority'][priority] = (
obj['default_destination']['priority'][priority])
else:
error = ("Default destination '"
+ obj['default_destination']['priority'][priority]
+ "' does not appear in the job configuration.")
if suggestion:
error += " Did you mean '" + str(suggestion) + "'?"
if validity[1]:
error += " Did you mean '" + str(validity[1]) + "'?"
if verbose:
log.debug(error)
valid_config = False

else:
error = ("Invalid default priority destination '"
+ str(priority) + "' found in config!")
Expand Down Expand Up @@ -1019,34 +1015,24 @@ def infinite_defaultdict():
# in each tool, there should always be only 2 sub-categories:
# default_destination (not mandatory) and rules (mandatory)
if "default_destination" in curr:
valid_destination = False
suggestion = None
if isinstance(curr['default_destination'], str):
if app is None:
if curr['default_destination'] in destination_list:
new_config['tools'][tool]['default_destination'] = (curr['default_destination'])
tool_has_default = True
valid_destination = True
else:
suggestion = get_typo_correction(curr['default_destination'],
destination_list, max_edit_dist)
elif app.job_config.get_destination(
curr['default_destination']):
new_config['tools'][tool]['default_destination'] = (curr['default_destination'])
validity = validate_destination(app,
curr['default_destination'])
if validity[0]:
new_config['tools'][tool]['default_destination'] = (
(curr['default_destination']))
tool_has_default = True
valid_destination = True

if not valid_destination:
else:
error = ("Default destination for '"
+ str(tool) + "': '"
+ curr['default_destination']
+ "' does not appear in the job configuration.")
if suggestion:
error += " Did you mean '" + str(suggestion) + "'?"
if validity[1]:
error += " Did you mean '" + validity[1] + "'?"
if verbose:
log.debug(error)
valid_config = False

elif isinstance(curr['default_destination'], dict):

if ('priority' in curr['default_destination']
Expand All @@ -1056,33 +1042,22 @@ def infinite_defaultdict():
destination = curr['default_destination']['priority'][priority]
if priority in priority_list:
if isinstance(destination, str):
if app is None:
if destination in destination_list:
new_config['tools'][tool]['default_destination'][
'priority'][priority] = destination
tool_has_default = True
valid_destination = True
else:
suggestion = get_typo_correction(destination,
destination_list, max_edit_dist)
elif app.job_config.get_destination(
destination):
new_config['tools'][tool]['default_destination'][
'priority'][priority] = destination
validity = validate_destination(
app, destination)
if validity[0]:
new_config['tools'][tool]['default_destination']['priority'][priority] = destination
tool_has_default = True
valid_destination = True

if not valid_destination:
else:
error = ("Default destination for '"
+ str(tool) + "': '"
+ destination + "' does not appear "
+ "in the job configuration.")
if suggestion:
error += " Did you mean '" + str(suggestion) + "'?"
+ str(tool) + "': '"
+ destination + "' does not appear "
+ "in the job configuration.")
if validity[1]:
error += " Did you mean '"
error += str(validity[1]) + "'?"
if verbose:
log.debug(error)
valid_config = False

else:
error = ("No default '" + str(priority)
+ "' priority destination for tool "
Expand Down Expand Up @@ -1662,7 +1637,7 @@ def map_tool_to_destination(
output += destination + "'."
log.debug(output)

#unset app so that it doesn't mess with future runs.
# unset app so that it doesn't mess with future runs.
app = None

return destination
Expand Down

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