def test_tool_with_invalid_priority_destination(self, l):
dt.parse_yaml(path=yt.ivYMLTest147, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority destination 'mine' for rule 1 in 'smalt'. Ignoring..."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_priority_default_destination_without_med_priority_destination(self, l):
dt.parse_yaml(path=yt.ivYMLTest144, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default 'med' priority destination!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_tool_with_invalid_priority_destination(self, l):
dt.parse_yaml(path=yt.ivYMLTest147, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid priority destination 'mine' for rule 1 in 'smalt'. Ignoring..."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_users_with_invalid_priority(self, l):
dt.parse_yaml(path=yt.ivYMLTest148, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "User '*****@*****.**', priority is not valid! Must be either low, med, or high."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_no_default_dest(self, l):
dt.parse_yaml(path=yt.ivYMLTest7, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_priority_default_destination_with_invalid_priority_destination(self, l):
dt.parse_yaml(path=yt.ivYMLTest145, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid default priority destination 'mine' found in config!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_no_default_dest(self, l):
dt.parse_yaml(path=yt.ivYMLTest7, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_priority_default_destination_without_med_priority_destination(self, l):
dt.parse_yaml(path=yt.ivYMLTest144, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No default 'med' priority destination!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_users_with_invalid_priority(self, l):
dt.parse_yaml(path=yt.ivYMLTest148, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "User '*****@*****.**', priority is not valid! Must be either low, med, or high."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_priority_default_destination_with_invalid_priority_destination(self, l):
dt.parse_yaml(path=yt.ivYMLTest145, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Invalid default priority destination 'mine' found in config!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_invalid_category(self, l):
dt.parse_yaml(path=yt.ivYMLTest8, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized category 'ice_cream' found in config file!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_invalid_category(self, l):
dt.parse_yaml(path=yt.ivYMLTest8, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'No global default destination specified in config!'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized category 'ice_cream' found in config file!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_bad_nice(self, l):
dt.parse_yaml(path=yt.ivYMLTest11, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
"Running config validation..."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
"nice_value goes from -20 to 20; rule 1 in 'spades' has a nice_value of '-21'. Setting nice_value to 0."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_bad_nice(self, l):
dt.parse_yaml(path=yt.ivYMLTest11, test=True)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
"Running config validation..."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
"nice_value goes from -20 to 20; rule 1 in 'spades' has a nice_value of '-21'. Setting nice_value to 0."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_blank_tool(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest137, test=True), yt.iv137dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_no_rule_upper_bound(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest52, test=True), yt.ivDict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_reversed_bounds(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest135, test=True), yt.iv135dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'spades'. Reversing bounds."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_worse_num_input_datasets_bound(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest143, test=True), yt.iv143dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_worse_num_input_datasets_bound(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest143, test=True), yt.iv143dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound! Setting lower_bound to 0!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_multiple_jobs(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest133, test=True), yt.iv133dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'. Adding generic fail_message."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_bool_for_empty_users(self, l):
self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest141, test=True, return_bool=True))
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!")
)
def test_return_bool_for_malformed_user_email(self, l):
self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest140, test=True, return_bool=True))
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!")
)
def test_return_bool_for_empty_users(self, l):
self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest141, test=True, return_bool=True))
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!")
)
def test_return_bool_for_malformed_user_email(self, l):
self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest140, test=True, return_bool=True))
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'!")
)
def test_return_rule_for_no_users(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest139, test=True), yt.iv139dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'! Ignoring rule."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_arguments_no_arg(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest132, test=True), yt.iv132dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_no_rule_type(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest4, test=True), yt.ivDict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No rule_type found for rule 1 in 'spades'."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_no_tool_name(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest3, test=True), yt.iv3dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Malformed YML; expected job name, but found a list instead!'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_no_destination(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest134, test=True), yt.iv134dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'. Ignoring..."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_missing_tool_fields(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest136, test=True), yt.iv136dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_bad_rule_type(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest6, test=True), yt.ivDict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized rule_type 'iencs' found in 'spades'. Ignoring..."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_no_users(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest139, test=True), yt.iv139dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'! Ignoring rule."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_no_tool_name(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest3, test=True), yt.iv3dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Malformed YML; expected job name, but found a list instead!'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_bool_for_worse_num_input_datasets_bounds(self, l):
self.assertFalse(
dt.parse_yaml(path=yt.ivYMLTest143, test=True, return_bool=True))
l.check((
'galaxy.jobs.dynamic_tool_destination', 'DEBUG',
"Error: lower_bound is set to Infinity, but must be lower than upper_bound!"
))
def test_no_rule_upper_bound(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest52, test=True), yt.ivDict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing bounds for rule 1 in 'spades'. Ignoring rule."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_no_rule_type(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest4, test=True), yt.ivDict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No rule_type found for rule 1 in 'spades'."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_bad_rule_type(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest6, test=True), yt.ivDict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Unrecognized rule_type 'iencs' found in 'spades'. Ignoring..."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_blank_tool(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest137, test=True), yt.iv137dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Config section for tool 'spades' is blank!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_reversed_bounds(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest135, test=True), yt.iv135dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "lower_bound exceeds upper_bound for rule 1 in 'spades'. Reversing bounds."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_missing_tool_fields(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest136, test=True), yt.iv136dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Tool 'spades' does not have rules nor a default_destination!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_no_destination(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest134, test=True), yt.iv134dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No destination specified for rule 1 in 'spades'. Ignoring..."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_multiple_jobs(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest133, test=True), yt.iv133dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Missing a fail_message for rule 1 in 'smalt'. Adding generic fail_message."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_arguments_no_arg(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest132, test=True), yt.iv132dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Found a fail_message for rule 1 in 'spades', but destination is not 'fail'! Setting destination to 'fail'."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_arguments_no_err_msg(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest12, test=True), yt.iv12dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
"Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_arguments_no_err_msg(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest12, test=True), yt.iv12dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
"Missing a fail_message for rule 1 in 'spades'. Adding generic fail_message."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_malformed_users(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest138, test=True), yt.iv138dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format! Ignoring entry."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format! Ignoring email."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_arguments_no_args(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest131, test=True), yt.iv131dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
"No arguments found for rule 1 in 'spades' despite being of type arguments. Ignoring rule."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_arguments_no_args(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest131, test=True), yt.iv131dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
"No arguments found for rule 1 in 'spades' despite being of type arguments. Ignoring rule."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_malformed_users(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest138, test=True), yt.iv138dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format! Ignoring entry."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format! Ignoring email."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_empty_users(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest141, test=True), yt.iv141dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_malformed_user_email(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest140, test=True), yt.iv140dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_malformed_user_email(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest140, test=True), yt.iv140dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user2@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invalid.user1@com' for rule 2 in tool 'spades' is in an invalid format! Ignoring email."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_rule_for_empty_users(self, l):
self.assertEquals(dt.parse_yaml(path=yt.ivYMLTest141, test=True), yt.iv141dict)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry 'None' in users for rule 2 in tool 'spades' is in an invalid format! Ignoring entry."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "No valid user emails were specified for rule 2 in tool 'spades'! Ignoring rule."),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.')
)
def test_return_bool_for_malformed_users(self, l):
self.assertFalse(
dt.parse_yaml(path=yt.ivYMLTest138, test=True, return_bool=True))
l.check((
'galaxy.jobs.dynamic_tool_destination', 'DEBUG',
"Entry '123' in users for rule 1 in tool 'spades' is in an invalid format!"
), ('galaxy.jobs.dynamic_tool_destination', 'DEBUG',
"Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format!"
))
def test_parse_valid_yml(self, l):
self.assertEqual(dt.parse_yaml(yt.vYMLTest1, test=True), yt.vdictTest1_yml)
self.assertEqual(dt.parse_yaml(yt.vYMLTest2, test=True), yt.vdictTest2_yml)
self.assertEqual(dt.parse_yaml(yt.vYMLTest3, test=True), yt.vdictTest3_yml)
self.assertTrue(dt.parse_yaml(yt.vYMLTest4, test=True, return_bool=True))
self.assertEqual(dt.parse_yaml(yt.vYMLTest4, test=True), yt.vdictTest4_yml)
self.assertTrue(dt.parse_yaml(yt.vYMLTest5, test=True, return_bool=True))
self.assertEqual(dt.parse_yaml(yt.vYMLTest5, test=True), yt.vdictTest5_yml)
self.assertTrue(dt.parse_yaml(yt.vYMLTest6, test=True, return_bool=True))
self.assertEqual(dt.parse_yaml(yt.vYMLTest6, test=True), yt.vdictTest6_yml)
self.assertTrue(dt.parse_yaml(yt.vYMLTest7, test=True, return_bool=True))
self.assertEqual(dt.parse_yaml(yt.vYMLTest7, test=True), yt.vdictTest7_yml)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
)
def test_return_bool_for_no_users(self, l):
self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest139, test=True, return_bool=True))
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'!")
)
def test_parse_valid_yml(self, l):
self.assertEqual(dt.parse_yaml(yt.vYMLTest1, test=True), yt.vdictTest1_yml)
self.assertEqual(dt.parse_yaml(yt.vYMLTest2, test=True), yt.vdictTest2_yml)
self.assertEqual(dt.parse_yaml(yt.vYMLTest3, test=True), yt.vdictTest3_yml)
self.assertTrue(dt.parse_yaml(yt.vYMLTest4, test=True, return_bool=True))
self.assertEqual(dt.parse_yaml(yt.vYMLTest4, test=True), yt.vdictTest4_yml)
self.assertTrue(dt.parse_yaml(yt.vYMLTest5, test=True, return_bool=True))
self.assertEqual(dt.parse_yaml(yt.vYMLTest5, test=True), yt.vdictTest5_yml)
self.assertTrue(dt.parse_yaml(yt.vYMLTest6, test=True, return_bool=True))
self.assertEqual(dt.parse_yaml(yt.vYMLTest6, test=True), yt.vdictTest6_yml)
self.assertTrue(dt.parse_yaml(yt.vYMLTest7, test=True, return_bool=True))
self.assertEqual(dt.parse_yaml(yt.vYMLTest7, test=True), yt.vdictTest7_yml)
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Running config validation...'),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', 'Finished config validation.'),
)
def test_return_bool_for_malformed_users(self, l):
self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest138, test=True, return_bool=True))
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Entry '123' in users for rule 1 in tool 'spades' is in an invalid format!"),
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Supplied email 'invaliduser.email@com' for rule 1 in tool 'spades' is in an invalid format!")
)
def test_return_bool_for_no_users(self, l):
self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest139, test=True, return_bool=True))
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Couldn't find a list under 'users:'!")
)
def test_return_bool_for_worse_num_input_datasets_bounds(self, l):
self.assertFalse(dt.parse_yaml(path=yt.ivYMLTest143, test=True, return_bool=True))
l.check(
('galaxy.jobs.dynamic_tool_destination', 'DEBUG', "Error: lower_bound is set to Infinity, but must be lower than upper_bound!")
)
