mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge pull request #8203 from martenson/bp-8163
[19.05] backport of "include parameter name in exceptions"
This commit is contained in:
John Chilton
@@ -239,9 +239,9 @@ class ToolParameter(Dictifiable):
|
||||
param_name = cls.parse_name(param)
|
||||
param_type = param.get('type')
|
||||
if not param_type:
|
||||
raise ValueError("Tool parameter '%s' requires a 'type'" % (param_name))
|
||||
raise ValueError("parameter '%s' requires a 'type'" % (param_name))
|
||||
elif param_type not in parameter_types:
|
||||
raise ValueError("Tool parameter '%s' uses an unknown type '%s'" % (param_name, param_type))
|
||||
raise ValueError("parameter '%s' uses an unknown type '%s'" % (param_name, param_type))
|
||||
else:
|
||||
return parameter_types[param_type](tool, param)
|
||||
|
||||
@@ -253,7 +253,7 @@ class ToolParameter(Dictifiable):
|
||||
if argument:
|
||||
name = argument.lstrip('-')
|
||||
else:
|
||||
raise ValueError("Tool parameter must specify a name.")
|
||||
raise ValueError("parameter must specify a name.")
|
||||
return name
|
||||
|
||||
|
||||
@@ -315,7 +315,7 @@ class IntegerToolParameter(TextToolParameter):
|
||||
>>> type(p.from_json("_string", trans))
|
||||
Traceback (most recent call last):
|
||||
...
|
||||
ValueError: An integer or workflow parameter e.g. ${name} is required
|
||||
ValueError: parameter '_name': an integer or workflow parameter is required
|
||||
"""
|
||||
|
||||
dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ['min', 'max']
|
||||
@@ -326,21 +326,21 @@ class IntegerToolParameter(TextToolParameter):
|
||||
try:
|
||||
int(self.value)
|
||||
except ValueError:
|
||||
raise ValueError("An integer is required")
|
||||
raise ValueError("parameter '%s': the attribute 'value' must be an integer" % self.name)
|
||||
elif self.value is None and not self.optional:
|
||||
raise ValueError("The settings for the field named '%s' require a 'value' setting and optionally a default value which must be an integer" % self.name)
|
||||
raise ValueError("parameter '%s': the attribute 'value' must be set for non optional parameters" % self.name)
|
||||
self.min = input_source.get('min')
|
||||
self.max = input_source.get('max')
|
||||
if self.min:
|
||||
try:
|
||||
self.min = int(self.min)
|
||||
except ValueError:
|
||||
raise ValueError("An integer is required")
|
||||
raise ValueError("parameter '%s': attribute 'min' must be an integer" % self.name)
|
||||
if self.max:
|
||||
try:
|
||||
self.max = int(self.max)
|
||||
except ValueError:
|
||||
raise ValueError("An integer is required")
|
||||
raise ValueError("parameter '%s': attribute 'max' must be an integer" % self.name)
|
||||
if self.min is not None or self.max is not None:
|
||||
self.validators.append(validation.InRangeValidator(None, self.min, self.max))
|
||||
|
||||
@@ -353,9 +353,9 @@ class IntegerToolParameter(TextToolParameter):
|
||||
if not value and self.optional:
|
||||
return ""
|
||||
if trans.workflow_building_mode is workflow_building_modes.ENABLED:
|
||||
raise ValueError("An integer or workflow parameter e.g. ${name} is required")
|
||||
raise ValueError("parameter '%s': an integer or workflow parameter is required" % self.name)
|
||||
else:
|
||||
raise ValueError("An integer is required")
|
||||
raise ValueError("parameter '%s': the attribute 'value' must be set for non optional parameters" % self.name)
|
||||
|
||||
def to_python(self, value, app):
|
||||
try:
|
||||
@@ -388,7 +388,7 @@ class FloatToolParameter(TextToolParameter):
|
||||
>>> type(p.from_json("_string", trans))
|
||||
Traceback (most recent call last):
|
||||
...
|
||||
ValueError: A real number or workflow parameter e.g. ${name} is required
|
||||
ValueError: parameter '_name': an integer or workflow parameter is required
|
||||
"""
|
||||
|
||||
dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ['min', 'max']
|
||||
@@ -401,19 +401,19 @@ class FloatToolParameter(TextToolParameter):
|
||||
try:
|
||||
float(self.value)
|
||||
except ValueError:
|
||||
raise ValueError("A real number is required")
|
||||
raise ValueError("parameter '%s': the attribute 'value' must be a real number" % self.name)
|
||||
elif self.value is None and not self.optional:
|
||||
raise ValueError("The settings for this field require a 'value' setting and optionally a default value which must be a real number")
|
||||
raise ValueError("parameter '%s': the attribute 'value' must be set for non optional parameters" % self.name)
|
||||
if self.min:
|
||||
try:
|
||||
self.min = float(self.min)
|
||||
except ValueError:
|
||||
raise ValueError("A real number is required")
|
||||
raise ValueError("parameter '%s': attribute 'min' must be a real number" % self.name)
|
||||
if self.max:
|
||||
try:
|
||||
self.max = float(self.max)
|
||||
except ValueError:
|
||||
raise ValueError("A real number is required")
|
||||
raise ValueError("parameter '%s': attribute 'max' must be a real number" % self.name)
|
||||
if self.min is not None or self.max is not None:
|
||||
self.validators.append(validation.InRangeValidator(None, self.min, self.max))
|
||||
|
||||
@@ -425,10 +425,10 @@ class FloatToolParameter(TextToolParameter):
|
||||
return value
|
||||
if not value and self.optional:
|
||||
return ""
|
||||
if trans and trans.workflow_building_mode is workflow_building_modes.ENABLED:
|
||||
raise ValueError("A real number or workflow parameter e.g. ${name} is required")
|
||||
if trans.workflow_building_mode is workflow_building_modes.ENABLED:
|
||||
raise ValueError("parameter '%s': an integer or workflow parameter is required" % self.name)
|
||||
else:
|
||||
raise ValueError("A real number is required")
|
||||
raise ValueError("parameter '%s': the attribute 'value' must be set for non optional parameters" % self.name)
|
||||
|
||||
def to_python(self, value, app):
|
||||
try:
|
||||
@@ -867,20 +867,20 @@ class SelectToolParameter(ToolParameter):
|
||||
elif value is None:
|
||||
if self.optional:
|
||||
return None
|
||||
raise ValueError("An invalid option was selected for %s, please verify." % (self.name))
|
||||
raise ValueError("parameter '%s': an invalid option (None) was selected, please verify" % self.name)
|
||||
elif not legal_values:
|
||||
if self.optional and self.tool.profile < 18.09:
|
||||
# Covers optional parameters with default values that reference other optional parameters.
|
||||
# These will have a value but no legal_values.
|
||||
return None
|
||||
raise ValueError("Parameter %s requires a value, but has no legal values defined." % self.name)
|
||||
raise ValueError("parameter '%s': requires a value, but no legal values defined" % self.name)
|
||||
if isinstance(value, list):
|
||||
if not self.multiple:
|
||||
raise ValueError("Multiple values provided but parameter %s is not expecting multiple values." % self.name)
|
||||
raise ValueError("parameter '%s': multiple values provided but parameter is not expecting multiple values" % (self.name))
|
||||
rval = []
|
||||
for v in value:
|
||||
if v not in legal_values:
|
||||
raise ValueError("An invalid option was selected for %s, %r, please verify." % (self.name, v))
|
||||
raise ValueError("parameter '%s': an invalid option (%r) was selected (valid options: %s)" % (self.name, v, ",".join(legal_values)))
|
||||
rval.append(v)
|
||||
return rval
|
||||
else:
|
||||
@@ -890,9 +890,9 @@ class SelectToolParameter(ToolParameter):
|
||||
if self.optional:
|
||||
return []
|
||||
else:
|
||||
raise ValueError("No option was selected for %s but input is not optional." % self.name)
|
||||
raise ValueError("parameter '%s': no option was selected for non optional parameter" % (self.name))
|
||||
if value not in legal_values and require_legal_value:
|
||||
raise ValueError("An invalid option was selected for %s, %r, please verify." % (self.name, value))
|
||||
raise ValueError("parameter '%s': an invalid option (%r) was selected (valid options: %s)" % (self.name, value, ",".join(legal_values)))
|
||||
return value
|
||||
|
||||
def to_param_dict_string(self, value, other_values={}):
|
||||
@@ -900,7 +900,7 @@ class SelectToolParameter(ToolParameter):
|
||||
return "None"
|
||||
if isinstance(value, list):
|
||||
if not self.multiple:
|
||||
raise ValueError("Multiple values provided but parameter %s is not expecting multiple values." % self.name)
|
||||
raise ValueError("parameter '%s': multiple values provided but parameter is not expecting multiple values" % (self.name))
|
||||
value = list(map(str, value))
|
||||
else:
|
||||
value = str(value)
|
||||
@@ -1427,17 +1427,17 @@ class DrillDownSelectToolParameter(SelectToolParameter):
|
||||
elif value is None:
|
||||
if self.optional:
|
||||
return None
|
||||
raise ValueError("An invalid option was selected for %s, please verify." % (self.name))
|
||||
raise ValueError("parameter '%s': an invalid option (%r) was selected" % (self.name, value))
|
||||
elif not legal_values:
|
||||
raise ValueError("Parameter %s requires a value, but has no legal values defined." % self.name)
|
||||
raise ValueError("parameter '%s': requires a value, but no legal values defined" % (self.name))
|
||||
if not isinstance(value, list):
|
||||
value = [value]
|
||||
if len(value) > 1 and not self.multiple:
|
||||
raise ValueError("Multiple values provided but parameter %s is not expecting multiple values." % self.name)
|
||||
raise ValueError("parameter '%s': multiple values provided but parameter is not expecting multiple values" % (self.name))
|
||||
rval = []
|
||||
for val in value:
|
||||
if val not in legal_values:
|
||||
raise ValueError("An invalid option was selected for %s, %r, please verify" % (self.name, val))
|
||||
raise ValueError("parameter '%s': an invalid option (%r) was selected (valid options: %s)" % (self.name, val, ",".join(legal_values)))
|
||||
rval.append(val)
|
||||
return rval
|
||||
|
||||
@@ -1472,7 +1472,7 @@ class DrillDownSelectToolParameter(SelectToolParameter):
|
||||
options = get_options_list(val)
|
||||
rval.extend(options)
|
||||
if len(rval) > 1 and not self.multiple:
|
||||
raise ValueError("Multiple values provided but parameter %s is not expecting multiple values." % self.name)
|
||||
raise ValueError("parameter '%s': multiple values provided but parameter is not expecting multiple values" % (self.name))
|
||||
rval = self.separator.join(rval)
|
||||
if self.tool is None or self.tool.options.sanitize:
|
||||
if self.sanitizer:
|
||||
@@ -1704,16 +1704,16 @@ class DataToolParameter(BaseDataToolParameter):
|
||||
try:
|
||||
self.min = int(self.min)
|
||||
except ValueError:
|
||||
raise ValueError("An integer is required for min property.")
|
||||
raise ValueError("parameter '%s': attribute 'min' must be an integer" % self.name)
|
||||
if self.max:
|
||||
try:
|
||||
self.max = int(self.max)
|
||||
except ValueError:
|
||||
raise ValueError("An integer is required for max property.")
|
||||
raise ValueError("parameter '%s': attribute 'max' must be an integer" % self.name)
|
||||
if not self.multiple and (self.min is not None):
|
||||
raise ValueError("Cannot specify min property on single data parameter '%s'. Set multiple=\"true\" to enable this option." % self.name)
|
||||
raise ValueError("parameter '%s': cannot specify 'min' property on single data parameter '%s'. Set multiple=\"true\" to enable this option" % self.name)
|
||||
if not self.multiple and (self.max is not None):
|
||||
raise ValueError("Cannot specify max property on single data parameter '%s'. Set multiple=\"true\" to enable this option." % self.name)
|
||||
raise ValueError("parameter '%s': cannot specify 'max' property on single data parameter '%s'. Set multiple=\"true\" to enable this option" % self.name)
|
||||
self.is_dynamic = True
|
||||
self._parse_options(input_source)
|
||||
# Load conversions required for the dataset input
|
||||
@@ -1723,14 +1723,14 @@ class DataToolParameter(BaseDataToolParameter):
|
||||
if self.datatypes_registry:
|
||||
conv_type = self.datatypes_registry.get_datatype_by_extension(conv_extension.lower())
|
||||
if conv_type is None:
|
||||
raise ValueError("Datatype class not found for extension '%s', which is used as 'type' attribute in conversion of data parameter '%s'" % (conv_type, self.name))
|
||||
raise ValueError("parameter '%s': datatype class not found for extension '%s', which is used as 'type' attribute in conversion of data parameter" % (self.name, conv_type))
|
||||
self.conversions.append((name, conv_extension, [conv_type]))
|
||||
|
||||
def from_json(self, value, trans, other_values={}):
|
||||
if trans.workflow_building_mode is workflow_building_modes.ENABLED or is_runtime_value(value):
|
||||
return None
|
||||
if not value and not self.optional:
|
||||
raise ValueError("Specify a dataset of the required format / build for parameter %s." % self.name)
|
||||
raise ValueError("parameter '%s': specify a dataset of the required format / build for parameter" % self.name)
|
||||
if value in [None, "None", '']:
|
||||
return None
|
||||
if isinstance(value, dict) and 'values' in value:
|
||||
@@ -1772,7 +1772,7 @@ class DataToolParameter(BaseDataToolParameter):
|
||||
if found_hdca:
|
||||
for val in rval:
|
||||
if not isinstance(val, trans.app.model.HistoryDatasetCollectionAssociation):
|
||||
raise ValueError("If collections are supplied to multiple data input parameter, only collections may be used.")
|
||||
raise ValueError("parameter '%s': if collections are supplied to multiple data input parameter, only collections may be used" % self.name)
|
||||
elif isinstance(value, trans.app.model.HistoryDatasetAssociation):
|
||||
rval = value
|
||||
elif isinstance(value, dict) and 'src' in value and 'id' in value:
|
||||
@@ -1801,20 +1801,20 @@ class DataToolParameter(BaseDataToolParameter):
|
||||
for v in values:
|
||||
if v:
|
||||
if hasattr(v, "deleted") and v.deleted:
|
||||
raise ValueError("The previously selected dataset has been deleted.")
|
||||
raise ValueError("parameter '%s': the previously selected dataset has been deleted." % self.name)
|
||||
elif hasattr(v, "dataset") and v.dataset.state in [galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED]:
|
||||
raise ValueError("The previously selected dataset has entered an unusable state")
|
||||
raise ValueError("parameter '%s': the previously selected dataset has entered an unusable state" % self.name)
|
||||
elif hasattr(v, "dataset"):
|
||||
match = dataset_matcher.hda_match(v)
|
||||
if match and match.implicit_conversion:
|
||||
v.implicit_conversion = True
|
||||
if not self.multiple:
|
||||
if len(values) > 1:
|
||||
raise ValueError("More than one dataset supplied to single input dataset parameter.")
|
||||
raise ValueError("parameter '%s': more than one dataset supplied to single input dataset parameter" % self.name)
|
||||
if len(values) > 0:
|
||||
rval = values[0]
|
||||
else:
|
||||
raise ValueError("Invalid dataset supplied to single input dataset parameter.")
|
||||
raise ValueError("parameter '%s': invalid dataset supplied to single input dataset parameter" % self.name)
|
||||
return rval
|
||||
|
||||
def to_param_dict_string(self, value, other_values={}):
|
||||
@@ -1863,10 +1863,10 @@ class DataToolParameter(BaseDataToolParameter):
|
||||
|
||||
if self.min is not None:
|
||||
if self.min > dataset_count:
|
||||
raise ValueError("At least %d datasets are required." % self.min)
|
||||
raise ValueError("At least %d datasets are required for %s" % (self.min, self.name))
|
||||
if self.max is not None:
|
||||
if self.max < dataset_count:
|
||||
raise ValueError("At most %d datasets are required." % self.max)
|
||||
raise ValueError("At most %d datasets are required for %s" % (self.max, self.name))
|
||||
|
||||
def get_dependencies(self):
|
||||
"""
|
||||
@@ -2052,7 +2052,7 @@ class DataCollectionToolParameter(BaseDataToolParameter):
|
||||
if trans.workflow_building_mode is workflow_building_modes.ENABLED:
|
||||
return None
|
||||
if not value and not self.optional:
|
||||
raise ValueError("Specify a dataset collection of the correct type.")
|
||||
raise ValueError("parameter '%s': specify a dataset collection of the correct type" % self.name)
|
||||
if value in [None, "None"]:
|
||||
return None
|
||||
if isinstance(value, dict) and 'values' in value:
|
||||
@@ -2084,7 +2084,7 @@ class DataCollectionToolParameter(BaseDataToolParameter):
|
||||
rval = trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get(value)
|
||||
if rval and isinstance(rval, trans.app.model.HistoryDatasetCollectionAssociation):
|
||||
if rval.deleted:
|
||||
raise ValueError("The previously selected dataset collection has been deleted")
|
||||
raise ValueError("parameter '%s': the previously selected dataset collection has been deleted" % self.name)
|
||||
# TODO: Handle error states, implement error states ...
|
||||
return rval
|
||||
|
||||
@@ -2242,10 +2242,10 @@ class LibraryDatasetToolParameter(ToolParameter):
|
||||
if lda is not None:
|
||||
lst.append(lda)
|
||||
elif validate:
|
||||
raise ValueError("One of the selected library datasets is invalid or not available anymore.")
|
||||
raise ValueError("parameter '%s': one of the selected library datasets is invalid or not available anymore" % self.name)
|
||||
if len(lst) == 0:
|
||||
if not self.optional and validate:
|
||||
raise ValueError("Please select a valid library dataset.")
|
||||
raise ValueError("parameter '%s': invalid library dataset selected" % self.name)
|
||||
return None
|
||||
else:
|
||||
return lst
|
||||
|
||||
@@ -11,7 +11,7 @@ class SelectToolParameterTestCase(BaseParameterTestCase):
|
||||
try:
|
||||
self.param.from_json("42", self.trans, {"input_bam": model.HistoryDatasetAssociation()})
|
||||
except ValueError as err:
|
||||
assert str(err) == "An invalid option was selected for my_name, '42', please verify."
|
||||
assert str(err) == "parameter 'my_name': an invalid option ('42') was selected (valid options: ?)"
|
||||
return
|
||||
assert False
|
||||
|
||||
@@ -20,7 +20,7 @@ class SelectToolParameterTestCase(BaseParameterTestCase):
|
||||
try:
|
||||
self.param.from_json("42", self.trans)
|
||||
except ValueError as err:
|
||||
assert str(err) == "Parameter my_name requires a value, but has no legal values defined."
|
||||
assert str(err) == "parameter 'my_name': requires a value, but no legal values defined"
|
||||
return
|
||||
assert False
|
||||
|
||||
@@ -34,7 +34,7 @@ class SelectToolParameterTestCase(BaseParameterTestCase):
|
||||
try:
|
||||
self.param.from_json(model.HistoryDatasetAssociation(), self.trans, {"input_bam": None})
|
||||
except ValueError as err:
|
||||
assert str(err) == "Parameter my_name requires a value, but has no legal values defined."
|
||||
assert str(err) == "parameter 'my_name': requires a value, but no legal values defined"
|
||||
return
|
||||
assert False
|
||||
|
||||
|
||||
Reference in New Issue
Block a user