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Alter validate_destination to also print error messages
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Now, `validate_destination` is also passed an error message to
format, and a tuple of values to be be used in the formatted
message. All code that calls validate_destination has been updated
to acknowledge this new functionality.
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Matthew Spelchak committed Mar 2, 2018
1 parent 2d18f16 commit ead6dbf
Showing 1 changed file with 68 additions and 91 deletions.
159 changes: 68 additions & 91 deletions lib/galaxy/jobs/dynamic_tool_destination.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,11 @@
valid_categories = ['verbose', 'tools', 'default_destination',
'users', 'default_priority']

# --- destination validation error messages --- #
dest_err_default_dest = "Default destination '%s' does not appear in the job configuration." # destination
dest_err_tool_default_dest = "Default destination for '%s': '%s' does not appear in the job configuration." # tool, destination
dest_err_tool_rule_dest = "Destination for '%s', rule %s: '%s' does not exist in job configuration." # tool, counter, destination


class MalformedYMLException(Exception):
pass
Expand Down Expand Up @@ -427,20 +432,11 @@ def __validate_destination(cls, valid_rule, app, return_bool, rule, tool, counte
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)
is_valid = validate_destination(app, rule["destination"],
dest_err_tool_rule_dest, (tool, counter, rule["destination"]),
return_bool)
if not is_valid:
valid_rule = False

elif isinstance(rule["destination"], dict):
if ("priority" in rule["destination"]
and isinstance(rule["destination"]["priority"], dict)):
Expand Down Expand Up @@ -471,21 +467,13 @@ def __validate_destination(cls, valid_rule, app, return_bool, rule, tool, counte
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)
is_valid = validate_destination(app,
rule["destination"]["priority"][priority],
dest_err_tool_rule_dest,
(tool, counter, rule["destination"]["priority"][priority]),
return_bool)
if not is_valid:
valid_rule = False

else:
error = "No destination specified for rule " + str(counter)
error += " in '" + str(tool) + "'."
Expand Down Expand Up @@ -775,7 +763,8 @@ def parse_yaml(path="/config/tool_destinations.yml",
return config


def validate_destination(app, destination):
def validate_destination(app, destination, err_message, err_message_contents,
return_bool=True):
"""
Validate received destination id.
Expand All @@ -786,16 +775,30 @@ def validate_destination(app, destination):
@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.
@type err_message: str
@param err_message: Error message to be formatted with the contents of
`err_message_contents` upon the event of invalid
destination
@type err_message_contents: tuple
@param err_message_contents: A tuple of strings to be placed in
`err_message`
@type return_bool: bool
@param return_bool: Whether or not the calling function has been told to
return a boolean value or not. Determines whether or
not to print 'Ignoring...' after error messages.
@rtype: bool
@return: True if the destination is valid and False otherwise.
"""

valid_destination = False
suggestion = None

if app is None:
if destination is 'fail' and err_message is dest_err_tool_rule_dest: # It's a tool rule that is set to fail. It's valid
valid_destination = True
elif app is None:
if destination in destination_list:
valid_destination = True
else:
Expand All @@ -804,7 +807,16 @@ def validate_destination(app, destination):
elif app.job_config.get_destination(destination):
valid_destination = True

return (valid_destination, suggestion)
if not valid_destination:
error = err_message % err_message_contents
if suggestion:
error += " Did you mean '" + suggestion + "'?"
if not return_bool:
error += " Ignoring..."
if verbose:
log.debug(error)

return valid_destination


def validate_config(obj, app=None, return_bool=False,):
Expand Down Expand Up @@ -862,18 +874,11 @@ def infinite_defaultdict():
if 'default_destination' in obj:
suggestion = None
if isinstance(obj['default_destination'], str):
validity = validate_destination(app, obj['default_destination'])
if validity[0]:
valid_config = validate_destination(app, obj['default_destination'],
dest_err_default_dest,
(obj['default_destination']))
if valid_config:
new_config["default_destination"] = obj['default_destination']
else:
error = ("Default destination '"
+ obj['default_destination']
+ "' does not appear in the job configuration.")
if validity[1]:
error += " Did you mean '" + str(validity[1]) + "'?"
if verbose:
log.debug(error)
valid_config = False

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

Expand All @@ -884,27 +889,14 @@ def infinite_defaultdict():
if isinstance(obj['default_destination']['priority'][priority],
str):
priority_list.add(priority)
validity = validate_destination(app,
obj['default_destination']['priority'][priority])
if validity[0]:
valid_config = validate_destination(
app, obj['default_destination']['priority'][priority],
dest_err_default_dest,
(obj['default_destination']['priority'][priority]))

if valid_config:
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 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!")
if verbose:
log.debug(error)
valid_config = False

if len(priority_list) < 1:
error = ("No valid priorities found!")
if verbose:
Expand Down Expand Up @@ -1012,22 +1004,14 @@ def infinite_defaultdict():
if "default_destination" in curr:
suggestion = None
if isinstance(curr['default_destination'], str):
validity = validate_destination(app,
curr['default_destination'])
if validity[0]:
valid_config = validate_destination(app,
curr['default_destination'],
dest_err_tool_default_dest,
(tool, curr['default_destination']))
if valid_config:
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.")
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 @@ -1037,22 +1021,15 @@ def infinite_defaultdict():
destination = curr['default_destination']['priority'][priority]
if priority in priority_list:
if isinstance(destination, str):
validity = validate_destination(
app, destination)
if validity[0]:

valid_config = validate_destination(
app, destination,
dest_err_tool_default_dest,
(tool, curr['default_destination']['priority'][priority]))
if valid_config:
new_config['tools'][tool]['default_destination']['priority'][priority] = destination
tool_has_default = True
else:
error = ("Default destination for '"
+ 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

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