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Source code for galaxy.tools.parameters.validation
"""
Classes related to parameter validation.
"""
import logging
import re
from six import string_types
from galaxy import (
model,
util
)
log = logging.getLogger(__name__)
[docs]class Validator(object):
"""
A validator checks that a value meets some conditions OR raises ValueError
"""
requires_dataset_metadata = False
[docs] @classmethod
def from_element(cls, param, elem):
"""
Initialize the appropiate Validator class
example call `validation.Validator.from_element(ToolParameter_object, Validator_object)`
needs to be implemented in the subclasses and should return the
corresponding Validator object by a call to `cls( ... )` which calls the
`__init__` method of the corresponding validator
param cls the Validator class
param param the element to be evaluated (which contains the validator)
param elem the validator element
return an object of a Validator subclass that corresponds to the type attribute of the validator element
"""
type = elem.get('type', None)
assert type is not None, "Required 'type' attribute missing from validator"
return validator_types[type].from_element(param, elem)
[docs] def validate(self, value, trans=None):
"""
validate a value
return None if positive validation, otherwise a ValueError is raised
"""
raise TypeError("Abstract Method")
[docs]class RegexValidator(Validator):
"""
Validator that evaluates a regular expression
>>> from xml.etree.ElementTree import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" value="10">
... <validator type="regex" message="Not gonna happen">[Ff]oo</validator>
... </param>
... '''))
>>> t = p.validate("Foo")
>>> t = p.validate("foo")
>>> t = p.validate("Fop")
Traceback (most recent call last):
...
ValueError: Not gonna happen
"""
[docs] def __init__(self, message, expression):
self.message = message
# Compile later. RE objects used to not be thread safe. Not sure about
# the sre module.
self.expression = expression
[docs] def validate(self, value, trans=None):
if re.match(self.expression, value or '') is None:
raise ValueError(self.message)
[docs]class ExpressionValidator(Validator):
"""
Validator that evaluates a python expression using the value
>>> from xml.etree.ElementTree import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" value="10">
... <validator type="expression" message="Not gonna happen">value.lower() == "foo"</validator>
... </param>
... '''))
>>> t = p.validate("Foo")
>>> t = p.validate("foo")
>>> t = p.validate("Fop")
Traceback (most recent call last):
...
ValueError: Not gonna happen
"""
[docs] @classmethod
def from_element(cls, param, elem):
return cls(elem.get('message'), elem.text, elem.get('substitute_value_in_message'))
[docs] def __init__(self, message, expression, substitute_value_in_message):
self.message = message
self.substitute_value_in_message = substitute_value_in_message
# Save compiled expression, code objects are thread safe (right?)
self.expression = compile(expression, '<string>', 'eval')
[docs] def validate(self, value, trans=None):
message = self.message
if self.substitute_value_in_message:
message = message % value
try:
evalresult = eval(self.expression, dict(value=value))
except Exception:
log.debug("Validator %s could not be evaluated on %s" % (self.expression, str(value)), exc_info=True)
raise ValueError(message)
if not(evalresult):
raise ValueError(message)
[docs]class InRangeValidator(Validator):
"""
Validator that ensures a number is in a specified range
>>> from xml.etree.ElementTree import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="integer" value="10">
... <validator type="in_range" message="Not gonna happen" min="10" exclude_min="true" max="20"/>
... </param>
... '''))
>>> t = p.validate(10)
Traceback (most recent call last):
...
ValueError: Not gonna happen
>>> t = p.validate(15)
>>> t = p.validate(20)
>>> t = p.validate(21)
Traceback (most recent call last):
...
ValueError: Not gonna happen
"""
[docs] @classmethod
def from_element(cls, param, elem):
return cls(elem.get('message', None), elem.get('min'),
elem.get('max'), elem.get('exclude_min', 'false'),
elem.get('exclude_max', 'false'))
[docs] def __init__(self, message, range_min, range_max, exclude_min=False, exclude_max=False):
"""
When the optional exclude_min and exclude_max attributes are set
to true, the range excludes the end points (i.e., min < value < max),
while if set to False (the default), then range includes the end points
(1.e., min <= value <= max). Combinations of exclude_min and exclude_max
values are allowed.
"""
self.min = float(range_min if range_min is not None else '-inf')
self.exclude_min = util.asbool(exclude_min)
self.max = float(range_max if range_max is not None else 'inf')
self.exclude_max = util.asbool(exclude_max)
assert self.min <= self.max, 'min must be less than or equal to max'
# Remove unneeded 0s and decimal from floats to make message pretty.
self_min_str = str(self.min).rstrip('0').rstrip('.')
self_max_str = str(self.max).rstrip('0').rstrip('.')
op1 = '>='
op2 = '<='
if self.exclude_min:
op1 = '>'
if self.exclude_max:
op2 = '<'
self.message = message or "Value must be %s %s and %s %s" % (op1, self_min_str, op2, self_max_str)
[docs] def validate(self, value, trans=None):
if self.exclude_min:
if not self.min < float(value):
raise ValueError(self.message)
else:
if not self.min <= float(value):
raise ValueError(self.message)
if self.exclude_max:
if not float(value) < self.max:
raise ValueError(self.message)
else:
if not float(value) <= self.max:
raise ValueError(self.message)
[docs]class LengthValidator(Validator):
"""
Validator that ensures the length of the provided string (value) is in a specific range
>>> from xml.etree.ElementTree import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" value="foobar">
... <validator type="length" min="2" max="8"/>
... </param>
... '''))
>>> t = p.validate("foo")
>>> t = p.validate("bar")
>>> t = p.validate("f")
Traceback (most recent call last):
...
ValueError: Must have length of at least 2
>>> t = p.validate("foobarbaz")
Traceback (most recent call last):
...
ValueError: Must have length no more than 8
"""
[docs] @classmethod
def from_element(cls, param, elem):
return cls(elem.get('message', None), elem.get('min', None), elem.get('max', None))
[docs] def __init__(self, message, length_min, length_max):
self.message = message
if length_min is not None:
length_min = int(length_min)
if length_max is not None:
length_max = int(length_max)
self.min = length_min
self.max = length_max
[docs] def validate(self, value, trans=None):
if self.min is not None and len(value) < self.min:
raise ValueError(self.message or ("Must have length of at least %d" % self.min))
if self.max is not None and len(value) > self.max:
raise ValueError(self.message or ("Must have length no more than %d" % self.max))
[docs]class DatasetOkValidator(Validator):
"""
Validator that checks if a dataset is in an 'ok' state
"""
[docs] def validate(self, value, trans=None):
if value and value.state != model.Dataset.states.OK:
if self.message is None:
self.message = "The selected dataset is still being generated, select another dataset or wait until it is completed"
raise ValueError(self.message)
[docs]class DatasetEmptyValidator(Validator):
"""Validator that checks if a dataset has a positive file size."""
[docs] def validate(self, value, trans=None):
if value:
if value.get_size() == 0:
if self.message is None:
self.message = "The selected dataset is empty, this tool expects non-empty files."
raise ValueError(self.message)
[docs]class DatasetExtraFilesPathEmptyValidator(Validator):
"""Validator that checks if a dataset's extra_files_path exists and is not empty."""
[docs] def validate(self, value, trans=None):
if value:
if value.get_total_size() == value.get_size():
if self.message is None:
self.message = "The selected dataset's extra_files_path directory is empty or does not exist, this tool expects non-empty extra_files_path directories associated with the selected input."
raise ValueError(self.message)
[docs]class MetadataValidator(Validator):
"""
Validator that checks for missing metadata
"""
requires_dataset_metadata = True
[docs] def __init__(self, message=None, check="", skip=""):
self.message = message
self.check = check.split(",")
self.skip = skip.split(",")
[docs] @classmethod
def from_element(cls, param, elem):
return cls(message=elem.get('message', None), check=elem.get('check', ""), skip=elem.get('skip', ""))
[docs] def validate(self, value, trans=None):
if value:
if not isinstance(value, model.DatasetInstance):
raise ValueError('A non-dataset value was provided.')
if value.missing_meta(check=self.check, skip=self.skip):
if self.message is None:
self.message = "Metadata missing, click the pencil icon in the history item to edit / save the metadata attributes"
raise ValueError(self.message)
[docs]class UnspecifiedBuildValidator(Validator):
"""
Validator that checks for dbkey not equal to '?'
"""
requires_dataset_metadata = True
[docs] def __init__(self, message=None):
if message is None:
self.message = "Unspecified genome build, click the pencil icon in the history item to set the genome build"
else:
self.message = message
[docs] def validate(self, value, trans=None):
# if value is None, we cannot validate
if value:
dbkey = value.metadata.dbkey
if isinstance(dbkey, list):
dbkey = dbkey[0]
if dbkey == '?':
raise ValueError(self.message)
[docs]class NoOptionsValidator(Validator):
"""Validator that checks for empty select list"""
[docs] def validate(self, value, trans=None):
if value is None:
if self.message is None:
self.message = "No options available for selection"
raise ValueError(self.message)
[docs]class EmptyTextfieldValidator(Validator):
"""Validator that checks for empty text field"""
[docs] def validate(self, value, trans=None):
if value == '':
if self.message is None:
self.message = "Field requires a value"
raise ValueError(self.message)
[docs]class MetadataInFileColumnValidator(Validator):
"""
Validator that checks if the value for a dataset's metadata item exists in a file.
"""
requires_dataset_metadata = True
[docs] @classmethod
def from_element(cls, param, elem):
filename = elem.get("filename", None)
if filename:
filename = "%s/%s" % (param.tool.app.config.tool_data_path, filename.strip())
metadata_name = elem.get("metadata_name", None)
if metadata_name:
metadata_name = metadata_name.strip()
metadata_column = int(elem.get("metadata_column", 0))
split = elem.get("split", "\t")
message = elem.get("message", "Value for metadata %s was not found in %s." % (metadata_name, filename))
line_startswith = elem.get("line_startswith", None)
if line_startswith:
line_startswith = line_startswith.strip()
return cls(filename, metadata_name, metadata_column, message, line_startswith, split)
[docs] def __init__(self, filename, metadata_name, metadata_column, message="Value for metadata not found.", line_startswith=None, split="\t"):
self.metadata_name = metadata_name
self.message = message
self.valid_values = []
for line in open(filename):
if line_startswith is None or line.startswith(line_startswith):
fields = line.split(split)
if metadata_column < len(fields):
self.valid_values.append(fields[metadata_column].strip())
[docs] def validate(self, value, trans=None):
if not value:
return
if hasattr(value, "metadata"):
if value.metadata.spec[self.metadata_name].param.to_string(value.metadata.get(self.metadata_name)) in self.valid_values:
return
raise ValueError(self.message)
[docs]class ValueInDataTableColumnValidator(Validator):
"""
Validator that checks if a value is in a tool data table column.
"""
[docs] @classmethod
def from_element(cls, param, elem):
table_name = elem.get("table_name", None)
assert table_name, 'You must specify a table_name.'
tool_data_table = param.tool.app.tool_data_tables[table_name]
column = elem.get("metadata_column", 0)
try:
column = int(column)
except ValueError:
pass
message = elem.get("message", "Value was not found in %s." % (table_name))
line_startswith = elem.get("line_startswith", None)
if line_startswith:
line_startswith = line_startswith.strip()
return cls(tool_data_table, column, message, line_startswith)
[docs] def __init__(self, tool_data_table, column, message="Value not found.", line_startswith=None):
self.message = message
self.valid_values = []
self._data_table_content_version = None
self._tool_data_table = tool_data_table
if isinstance(column, string_types):
column = tool_data_table.columns[column]
self._column = column
self._load_values()
def _load_values(self):
self._data_table_content_version, data_fields = self._tool_data_table.get_version_fields()
self.valid_values = []
for fields in data_fields:
if self._column < len(fields):
self.valid_values.append(fields[self._metadata_column])
[docs] def validate(self, value, trans=None):
if not value:
return
if not self._tool_data_table.is_current_version(self._data_table_content_version):
log.debug('MetadataInDataTableColumnValidator values are out of sync with data table (%s), updating validator.', self._tool_data_table.name)
self._load_values()
if value in self.valid_values:
return
raise ValueError(self.message)
[docs]class ValueNotInDataTableColumnValidator(ValueInDataTableColumnValidator):
"""
Validator that checks if a value is NOT in a tool data table column.
"""
[docs] def __init__(self, tool_data_table, metadata_column, message="Value already present.", line_startswith=None):
super(ValueNotInDataTableColumnValidator, self).__init__(tool_data_table, metadata_column, message, line_startswith)
[docs] def validate(self, value, trans=None):
try:
super(ValueInDataTableColumnValidator, self).validate(value, trans)
except ValueError:
return
else:
raise ValueError(self.message)
[docs]class MetadataInDataTableColumnValidator(Validator):
"""
Validator that checks if the value for a dataset's metadata item exists in a file.
"""
requires_dataset_metadata = True
[docs] @classmethod
def from_element(cls, param, elem):
table_name = elem.get("table_name", None)
assert table_name, 'You must specify a table_name.'
tool_data_table = param.tool.app.tool_data_tables[table_name]
metadata_name = elem.get("metadata_name", None)
if metadata_name:
metadata_name = metadata_name.strip()
metadata_column = elem.get("metadata_column", 0)
try:
metadata_column = int(metadata_column)
except ValueError:
pass
message = elem.get("message", "Value for metadata %s was not found in %s." % (metadata_name, table_name))
line_startswith = elem.get("line_startswith", None)
if line_startswith:
line_startswith = line_startswith.strip()
return cls(tool_data_table, metadata_name, metadata_column, message, line_startswith)
[docs] def __init__(self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", line_startswith=None):
self.metadata_name = metadata_name
self.message = message
self.valid_values = []
self._data_table_content_version = None
self._tool_data_table = tool_data_table
if isinstance(metadata_column, string_types):
metadata_column = tool_data_table.columns[metadata_column]
self._metadata_column = metadata_column
self._load_values()
def _load_values(self):
self._data_table_content_version, data_fields = self._tool_data_table.get_version_fields()
self.valid_values = []
for fields in data_fields:
if self._metadata_column < len(fields):
self.valid_values.append(fields[self._metadata_column])
[docs] def validate(self, value, trans=None):
if not value:
return
if hasattr(value, "metadata"):
if not self._tool_data_table.is_current_version(self._data_table_content_version):
log.debug('MetadataInDataTableColumnValidator values are out of sync with data table (%s), updating validator.', self._tool_data_table.name)
self._load_values()
if value.metadata.spec[self.metadata_name].param.to_string(value.metadata.get(self.metadata_name)) in self.valid_values:
return
raise ValueError(self.message)
[docs]class MetadataNotInDataTableColumnValidator(MetadataInDataTableColumnValidator):
"""
Validator that checks if the value for a dataset's metadata item doesn't exists in a file.
"""
requires_dataset_metadata = True
[docs] def __init__(self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", line_startswith=None):
super(MetadataInDataTableColumnValidator, self).__init__(tool_data_table, metadata_name, metadata_column, message, line_startswith)
[docs] def validate(self, value, trans=None):
try:
super(MetadataInDataTableColumnValidator, self).validate(value, trans)
except ValueError:
return
else:
raise ValueError(self.message)
[docs]class MetadataInRangeValidator(InRangeValidator):
"""
Validator that ensures metadata is in a specified range
"""
requires_dataset_metadata = True
[docs] @classmethod
def from_element(cls, param, elem):
metadata_name = elem.get('metadata_name', None)
assert metadata_name, "dataset_metadata_in_range validator requires metadata_name attribute."
metadata_name = metadata_name.strip()
return cls(metadata_name,
elem.get('message', None), elem.get('min'),
elem.get('max'), elem.get('exclude_min', 'false'),
elem.get('exclude_max', 'false'))
[docs] def __init__(self, metadata_name, message, range_min, range_max, exclude_min=False, exclude_max=False):
self.metadata_name = metadata_name
super(MetadataInRangeValidator, self).__init__(message, range_min, range_max, exclude_min, exclude_max)
[docs] def validate(self, value, trans=None):
if value:
if not isinstance(value, model.DatasetInstance):
raise ValueError('A non-dataset value was provided.')
try:
value_to_check = float(value.metadata.spec[self.metadata_name].param.to_string(value.metadata.get(self.metadata_name)))
except KeyError:
raise ValueError('{} Metadata missing'.format(self.metadata_name))
except ValueError:
raise ValueError('{} must be a float or an integer'.format(self.metadata_name))
super(MetadataInRangeValidator, self).validate(value_to_check, trans)
validator_types = dict(
expression=ExpressionValidator,
regex=RegexValidator,
in_range=InRangeValidator,
length=LengthValidator,
metadata=MetadataValidator,
unspecified_build=UnspecifiedBuildValidator,
no_options=NoOptionsValidator,
empty_field=EmptyTextfieldValidator,
empty_dataset=DatasetEmptyValidator,
empty_extra_files_path=DatasetExtraFilesPathEmptyValidator,
dataset_metadata_in_file=MetadataInFileColumnValidator,
dataset_metadata_in_data_table=MetadataInDataTableColumnValidator,
dataset_metadata_not_in_data_table=MetadataNotInDataTableColumnValidator,
dataset_metadata_in_range=MetadataInRangeValidator,
value_in_data_table=ValueInDataTableColumnValidator,
value_not_in_data_table=ValueInDataTableColumnValidator,
dataset_ok_validator=DatasetOkValidator,
)
[docs]def get_suite():
"""Get unittest suite for this module"""
import doctest
import sys
return doctest.DocTestSuite(sys.modules[__name__])