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Source code for galaxy.tools.parameters.validation
"""
Classes related to parameter validation.
"""
import abc
import logging
import os.path
import re
from galaxy import (
model,
util
)
log = logging.getLogger(__name__)
[docs]def get_test_fname(fname):
"""Returns test data filename"""
path, name = os.path.split(__file__)
full_path = os.path.join(path, 'test', fname)
return full_path
[docs]class Validator(abc.ABC):
"""
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 __init__(self, message, negate=False):
self.message = message
self.negate = util.asbool(negate)
super().__init__()
[docs] @abc.abstractmethod
def validate(self, value, trans=None, message=None, value_to_show=None):
"""
validate a value
needs to be implemented in classes derived from validator.
the implementation needs to call `super().validate()`
giving result as a bool (which should be true if the
validation is positive and false otherwise) and the value
that is validated.
the Validator.validate function will then negate the value
depending on `self.negate` and return None if
- value is True and negate is False
- value is False and negate is True
and raise a ValueError otherwise.
return None if positive validation, otherwise a ValueError is raised
"""
assert isinstance(value, bool), 'value must be boolean'
if message is None:
message = self.message
if value_to_show and "%s" in message:
message = message % value_to_show
if (not self.negate and value) or (self.negate and not value):
return
else:
raise ValueError(message)
[docs]class RegexValidator(Validator):
"""
Validator that evaluates a regular expression
>>> from galaxy.util import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" value="10">
... <validator type="regex">[Ff]oo</validator>
... </param>
... '''))
>>> t = p.validate("Foo")
>>> t = p.validate("foo")
>>> t = p.validate("Fop")
Traceback (most recent call last):
...
ValueError: Value 'Fop' does not match regular expression '[Ff]oo'
>>> t = p.validate(["Foo", "foo"])
>>> t = p.validate(["Foo", "Fop"])
Traceback (most recent call last):
...
ValueError: Value 'Fop' does not match regular expression '[Ff]oo'
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" value="10">
... <validator type="regex" negate="true">[Ff]oo</validator>
... </param>
... '''))
>>> t = p.validate("Foo")
Traceback (most recent call last):
...
ValueError: Value 'Foo' does match regular expression '[Ff]oo'
>>> t = p.validate("foo")
Traceback (most recent call last):
...
ValueError: Value 'foo' does match regular expression '[Ff]oo'
>>> t = p.validate("Fop")
>>> t = p.validate(["Fop", "foo"])
Traceback (most recent call last):
...
ValueError: Value 'foo' does match regular expression '[Ff]oo'
>>> t = p.validate(["Fop", "Fop"])
"""
[docs] @classmethod
def from_element(cls, param, elem):
return cls(elem.get('message', None), elem.text, elem.get('negate', 'false'))
[docs] def __init__(self, message, expression, negate):
if message is None:
message = f"Value '%s' does {'not ' if negate == 'false' else ''}match regular expression '{expression}'"
super().__init__(message, negate)
# 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 not isinstance(value, list):
value = [value]
for val in value:
match = re.match(self.expression, val or '')
super().validate(match is not None, value_to_show=val)
[docs]class ExpressionValidator(Validator):
"""
Validator that evaluates a python expression using the value
>>> from galaxy.util 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
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" value="10">
... <validator type="expression" message="Not gonna happen" negate="true">value.lower() == "foo"</validator>
... </param>
... '''))
>>> t = p.validate("Foo")
Traceback (most recent call last):
...
ValueError: Not gonna happen
>>> t = p.validate("foo")
Traceback (most recent call last):
...
ValueError: Not gonna happen
>>> t = p.validate("Fop")
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" value="10">
... <validator type="expression" message="Not gonna happen">value</validator>
... </param>
... '''))
>>> p.validate("Foo")
>>> p.validate("")
Traceback (most recent call last):
...
ValueError: Not gonna happen
"""
[docs] @classmethod
def from_element(cls, param, elem):
return cls(elem.get('message', None), elem.text, elem.get('negate', 'false'))
[docs] def __init__(self, message, expression, negate):
if message is None:
message = f"Value '%s' does not evaluate to {'True' if negate == 'false' else 'False'} for '{expression}'"
super().__init__(message, negate)
# Save compiled expression, code objects are thread safe (right?)
self.expression = compile(expression, '<string>', 'eval')
[docs] def validate(self, value, trans=None):
try:
evalresult = eval(self.expression, dict(value=value))
except Exception:
super().validate(False, value, f"Validator '{self.expression}' could not be evaluated on '%s'")
super().validate(bool(evalresult), value_to_show=value)
[docs]class InRangeValidator(ExpressionValidator):
"""
Validator that ensures a number is in a specified range
>>> from galaxy.util 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="Doh!! %s not in range" min="10" exclude_min="true" max="20"/>
... </param>
... '''))
>>> t = p.validate(10)
Traceback (most recent call last):
...
ValueError: Doh!! 10 not in range
>>> t = p.validate(15)
>>> t = p.validate(20)
>>> t = p.validate(21)
Traceback (most recent call last):
...
ValueError: Doh!! 21 not in range
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="integer" value="10">
... <validator type="in_range" min="10" exclude_min="true" max="20" negate="true"/>
... </param>
... '''))
>>> t = p.validate(10)
>>> t = p.validate(15)
Traceback (most recent call last):
...
ValueError: Value ('15') must not fulfill float('10') < value <= float('20')
>>> t = p.validate(20)
Traceback (most recent call last):
...
ValueError: Value ('20') must not fulfill float('10') < value <= float('20')
>>> t = p.validate(21)
"""
[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'),
elem.get('negate', 'false'))
[docs] def __init__(self, message, range_min, range_max, exclude_min=False, exclude_max=False, negate=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 = range_min if range_min is not None else '-inf'
self.exclude_min = util.asbool(exclude_min)
self.max = range_max if range_max is not None else 'inf'
self.exclude_max = util.asbool(exclude_max)
assert float(self.min) <= float(self.max), 'min must be less than or equal to max'
# Remove unneeded 0s and decimal from floats to make message pretty.
op1 = '<='
op2 = '<='
if self.exclude_min:
op1 = '<'
if self.exclude_max:
op2 = '<'
expression = f"float('{self.min}') {op1} value {op2} float('{self.max}')"
if message is None:
message = f"Value ('%s') must {'not ' if negate == 'true' else ''}fulfill {expression}"
super().__init__(message, expression, negate)
[docs]class LengthValidator(InRangeValidator):
"""
Validator that ensures the length of the provided string (value) is in a specific range
>>> from galaxy.util 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 and at most 8
>>> t = p.validate("foobarbaz")
Traceback (most recent call last):
...
ValueError: Must have length of at least 2 and at most 8
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" value="foobar">
... <validator type="length" min="2" max="8" negate="true"/>
... </param>
... '''))
>>> t = p.validate("foo")
Traceback (most recent call last):
...
ValueError: Must not have length of at least 2 and at most 8
>>> t = p.validate("bar")
Traceback (most recent call last):
...
ValueError: Must not have length of at least 2 and at most 8
>>> t = p.validate("f")
>>> t = p.validate("foobarbaz")
"""
[docs] @classmethod
def from_element(cls, param, elem):
return cls(elem.get('message', None), elem.get('min', None), elem.get('max', None), elem.get('negate', 'false'))
[docs] def __init__(self, message, length_min, length_max, negate):
if message is None:
message = f"Must {'not ' if negate == 'true' else ''}have length of at least {length_min} and at most {length_max}"
super().__init__(message, range_min=length_min, range_max=length_max, negate=negate)
[docs]class DatasetOkValidator(Validator):
"""
Validator that checks if a dataset is in an 'ok' state
>>> from galaxy.datatypes.registry import example_datatype_registry_for_sample
>>> from galaxy.model import History, HistoryDatasetAssociation, set_datatypes_registry
>>> from galaxy.model.mapping import init
>>> from galaxy.util import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>>
>>> sa_session = init("/tmp", "sqlite:///:memory:", create_tables=True).session
>>> hist = History()
>>> sa_session.add(hist)
>>> sa_session.flush()
>>> set_datatypes_registry(example_datatype_registry_for_sample())
>>> ok_hda = hist.add_dataset(HistoryDatasetAssociation(id=1, extension='interval', create_dataset=True, sa_session=sa_session))
>>> ok_hda.set_dataset_state(model.Dataset.states.OK)
>>> notok_hda = hist.add_dataset(HistoryDatasetAssociation(id=2, extension='interval', create_dataset=True, sa_session=sa_session))
>>> notok_hda.set_dataset_state(model.Dataset.states.EMPTY)
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="data" no_validation="true">
... <validator type="dataset_ok_validator"/>
... </param>
... '''))
>>> t = p.validate(ok_hda)
>>> t = p.validate(notok_hda)
Traceback (most recent call last):
...
ValueError: The selected dataset is still being generated, select another dataset or wait until it is completed
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="data" no_validation="true">
... <validator type="dataset_ok_validator" negate="true"/>
... </param>
... '''))
>>> t = p.validate(ok_hda)
Traceback (most recent call last):
...
ValueError: The selected dataset must not be in state OK
>>> t = p.validate(notok_hda)
"""
[docs] @classmethod
def from_element(cls, param, elem):
negate = elem.get('negate', 'false')
message = elem.get('message', None)
if message is None:
if negate == 'false':
message = "The selected dataset is still being generated, select another dataset or wait until it is completed"
else:
message = "The selected dataset must not be in state OK"
return cls(message, negate)
[docs] def validate(self, value, trans=None):
if value:
super().validate(value.state == model.Dataset.states.OK)
[docs]class DatasetEmptyValidator(Validator):
"""
Validator that checks if a dataset has a positive file size.
>>> from galaxy.datatypes.registry import example_datatype_registry_for_sample
>>> from galaxy.model import Dataset, History, HistoryDatasetAssociation, set_datatypes_registry
>>> from galaxy.model.mapping import init
>>> from galaxy.util import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>>
>>> sa_session = init("/tmp", "sqlite:///:memory:", create_tables=True).session
>>> hist = History()
>>> sa_session.add(hist)
>>> sa_session.flush()
>>> set_datatypes_registry(example_datatype_registry_for_sample())
>>> empty_dataset = Dataset(external_filename=get_test_fname("empty.txt"))
>>> empty_hda = hist.add_dataset(HistoryDatasetAssociation(id=1, extension='interval', dataset=empty_dataset, sa_session=sa_session))
>>> full_dataset = Dataset(external_filename=get_test_fname("1.tabular"))
>>> full_hda = hist.add_dataset(HistoryDatasetAssociation(id=2, extension='interval', dataset=full_dataset, sa_session=sa_session))
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="data">
... <validator type="empty_dataset"/>
... </param>
... '''))
>>> t = p.validate(full_hda)
>>> t = p.validate(empty_hda)
Traceback (most recent call last):
...
ValueError: The selected dataset is empty, this tool expects non-empty files.
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="data">
... <validator type="empty_dataset" negate="true"/>
... </param>
... '''))
>>> t = p.validate(full_hda)
Traceback (most recent call last):
...
ValueError: The selected dataset is non-empty, this tool expects empty files.
>>> t = p.validate(empty_hda)
"""
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get('message', None)
negate = elem.get('negate', 'false')
if not message:
message = f"The selected dataset is {'non-' if negate == 'true' else ''}empty, this tool expects {'non-' if negate=='false' else ''}empty files."
return cls(message, negate)
[docs]class DatasetExtraFilesPathEmptyValidator(Validator):
"""
Validator that checks if a dataset's extra_files_path exists and is not empty.
>>> from galaxy.datatypes.registry import example_datatype_registry_for_sample
>>> from galaxy.model import History, HistoryDatasetAssociation, set_datatypes_registry
>>> from galaxy.model.mapping import init
>>> from galaxy.util import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>>
>>> sa_session = init("/tmp", "sqlite:///:memory:", create_tables=True).session
>>> hist = History()
>>> sa_session.add(hist)
>>> sa_session.flush()
>>> set_datatypes_registry(example_datatype_registry_for_sample())
>>> has_extra_hda = hist.add_dataset(HistoryDatasetAssociation(id=1, extension='interval', create_dataset=True, sa_session=sa_session))
>>> has_extra_hda.dataset.file_size = 10
>>> has_extra_hda.dataset.total_size = 15
>>> has_no_extra_hda = hist.add_dataset(HistoryDatasetAssociation(id=2, extension='interval', create_dataset=True, sa_session=sa_session))
>>> has_no_extra_hda.dataset.file_size = 10
>>> has_no_extra_hda.dataset.total_size = 10
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="data">
... <validator type="empty_extra_files_path"/>
... </param>
... '''))
>>> t = p.validate(has_extra_hda)
>>> t = p.validate(has_no_extra_hda)
Traceback (most recent call last):
...
ValueError: 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.
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="data">
... <validator type="empty_extra_files_path" negate="true"/>
... </param>
... '''))
>>> t = p.validate(has_extra_hda)
Traceback (most recent call last):
...
ValueError: The selected dataset's extra_files_path directory is non-empty or does exist, this tool expects empty extra_files_path directories associated with the selected input.
>>> t = p.validate(has_no_extra_hda)
"""
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get('message', None)
negate = elem.get('negate', 'false')
if not message:
message = f"The selected dataset's extra_files_path directory is {'non-' if negate == 'true' else ''}empty or does {'not ' if negate == 'false' else ''}exist, this tool expects {'non-' if negate == 'false' else ''}empty extra_files_path directories associated with the selected input."
return cls(message, negate)
[docs] def validate(self, value, trans=None):
if value:
super().validate(value.get_total_size() != value.get_size())
[docs]class MetadataValidator(Validator):
"""
Validator that checks for missing metadata
>>> from galaxy.datatypes.registry import example_datatype_registry_for_sample
>>> from galaxy.model import Dataset, History, HistoryDatasetAssociation, set_datatypes_registry
>>> from galaxy.model.mapping import init
>>> from galaxy.util import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>>
>>> sa_session = init("/tmp", "sqlite:///:memory:", create_tables=True).session
>>> hist = History()
>>> sa_session.add(hist)
>>> sa_session.flush()
>>> set_datatypes_registry(example_datatype_registry_for_sample())
>>> fname = get_test_fname('1.bed')
>>> bedds = Dataset(external_filename=fname)
>>> hda = hist.add_dataset(HistoryDatasetAssociation(id=1, extension='bed', create_dataset=True, sa_session=sa_session, dataset=bedds))
>>> hda.set_dataset_state(model.Dataset.states.OK)
>>> hda.set_meta()
>>> hda.metadata.strandCol = hda.metadata.spec["strandCol"].no_value
>>> param_xml = '''<param name="blah" type="data">
... <validator type="metadata" check="{check}" skip="{skip}"/>
... </param>'''
>>> p = ToolParameter.build(None, XML(param_xml.format(check="nameCol", skip="")))
>>> t = p.validate(hda)
>>> p = ToolParameter.build(None, XML(param_xml.format(check="strandCol", skip="")))
>>> t = p.validate(hda)
Traceback (most recent call last):
...
ValueError: Metadata 'strandCol' missing, click the pencil icon in the history item to edit / save the metadata attributes
>>> p = ToolParameter.build(None, XML(param_xml.format(check="", skip="dbkey,comment_lines,column_names,strandCol")))
>>> t = p.validate(hda)
>>> p = ToolParameter.build(None, XML(param_xml.format(check="", skip="dbkey,comment_lines,column_names,nameCol")))
>>> t = p.validate(hda)
Traceback (most recent call last):
...
ValueError: Metadata 'strandCol' missing, click the pencil icon in the history item to edit / save the metadata attributes
>>> param_xml_negate = '''<param name="blah" type="data">
... <validator type="metadata" check="{check}" skip="{skip}" negate="true"/>
... </param>'''
>>> p = ToolParameter.build(None, XML(param_xml_negate.format(check="strandCol", skip="")))
>>> t = p.validate(hda)
>>> p = ToolParameter.build(None, XML(param_xml_negate.format(check="nameCol", skip="")))
>>> t = p.validate(hda)
Traceback (most recent call last):
...
ValueError: At least one of the checked metadata 'nameCol' is set, click the pencil icon in the history item to edit / save the metadata attributes
>>> p = ToolParameter.build(None, XML(param_xml_negate.format(check="", skip="dbkey,comment_lines,column_names,nameCol")))
>>> t = p.validate(hda)
>>> p = ToolParameter.build(None, XML(param_xml_negate.format(check="", skip="dbkey,comment_lines,column_names,strandCol")))
>>> t = p.validate(hda)
Traceback (most recent call last):
...
ValueError: At least one of the non skipped metadata 'dbkey,comment_lines,column_names,strandCol' is set, click the pencil icon in the history item to edit / save the metadata attributes
"""
requires_dataset_metadata = True
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get('message', None)
return cls(message=message,
check=elem.get('check', ""),
skip=elem.get('skip', ""),
negate=elem.get('negate', 'false'))
[docs] def __init__(self, message=None, check="", skip="", negate='false'):
if not message:
if not util.asbool(negate):
message = "Metadata '%s' missing, click the pencil icon in the history item to edit / save the metadata attributes"
else:
if check != '':
message = f"At least one of the checked metadata '{check}' is set, click the pencil icon in the history item to edit / save the metadata attributes"
elif skip != '':
message = f"At least one of the non skipped metadata '{skip}' is set, click the pencil icon in the history item to edit / save the metadata attributes"
super().__init__(message, negate)
self.check = check.split(",") if check else None
self.skip = skip.split(",") if skip else None
[docs] def validate(self, value, trans=None):
if value:
# TODO why this validator checks for isinstance(value, model.DatasetInstance)
missing = value.missing_meta(check=self.check, skip=self.skip)
super().validate(isinstance(value, model.DatasetInstance) and not missing, value_to_show=missing)
[docs]class UnspecifiedBuildValidator(Validator):
"""
Validator that checks for dbkey not equal to '?'
>>> from galaxy.datatypes.registry import example_datatype_registry_for_sample
>>> from galaxy.model import History, HistoryDatasetAssociation, set_datatypes_registry
>>> from galaxy.model.mapping import init
>>> from galaxy.util import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>>
>>> sa_session = init("/tmp", "sqlite:///:memory:", create_tables=True).session
>>> hist = History()
>>> sa_session.add(hist)
>>> sa_session.flush()
>>> set_datatypes_registry(example_datatype_registry_for_sample())
>>> has_dbkey_hda = hist.add_dataset(HistoryDatasetAssociation(id=1, extension='interval', create_dataset=True, sa_session=sa_session))
>>> has_dbkey_hda.set_dataset_state(model.Dataset.states.OK)
>>> has_dbkey_hda.metadata.dbkey = 'hg19'
>>> has_no_dbkey_hda = hist.add_dataset(HistoryDatasetAssociation(id=2, extension='interval', create_dataset=True, sa_session=sa_session))
>>> has_no_dbkey_hda.set_dataset_state(model.Dataset.states.OK)
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="data" no_validation="true">
... <validator type="unspecified_build"/>
... </param>
... '''))
>>> t = p.validate(has_dbkey_hda)
>>> t = p.validate(has_no_dbkey_hda)
Traceback (most recent call last):
...
ValueError: Unspecified genome build, click the pencil icon in the history item to set the genome build
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="data" no_validation="true">
... <validator type="unspecified_build" negate="true"/>
... </param>
... '''))
>>> t = p.validate(has_dbkey_hda)
Traceback (most recent call last):
...
ValueError: Specified genome build, click the pencil icon in the history item to remove the genome build
>>> t = p.validate(has_no_dbkey_hda)
"""
requires_dataset_metadata = True
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get('message', None)
negate = elem.get('negate', 'false')
if not message:
message = f"{'Unspecified' if negate == 'false' else 'Specified'} genome build, click the pencil icon in the history item to {'set' if negate == 'false' else 'remove'} the genome build"
return cls(message, negate)
[docs] def validate(self, value, trans=None):
# if value is None, we cannot validate
if value:
dbkey = value.metadata.dbkey
# TODO can dbkey really be a list?
if isinstance(dbkey, list):
dbkey = dbkey[0]
super().validate(dbkey != '?')
[docs]class NoOptionsValidator(Validator):
"""
Validator that checks for empty select list
>>> from galaxy.util import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>> p = ToolParameter.build(None, XML('''
... <param name="index" type="select" label="Select reference genome">
... <validator type="no_options" message="No options available for selection"/>
... </param>
... '''))
>>> t = p.validate('foo')
>>> t = p.validate(None)
Traceback (most recent call last):
...
ValueError: No options available for selection
>>>
>>> p = ToolParameter.build(None, XML('''
... <param name="index" type="select" label="Select reference genome">
... <options from_data_table="bowtie2_indexes"/>
... <validator type="no_options" negate="true"/>
... </param>
... '''))
>>> t = p.validate('foo')
Traceback (most recent call last):
...
ValueError: Options available for selection
>>> t = p.validate(None)
"""
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get('message', None)
negate = elem.get('negate', 'false')
if not message:
message = f"{'No options' if negate == 'false' else 'Options'} available for selection"
return cls(message, negate)
[docs]class EmptyTextfieldValidator(Validator):
"""
Validator that checks for empty text field
>>> from galaxy.util import XML
>>> from galaxy.tools.parameters.basic import ToolParameter
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" value="">
... <validator type="empty_field"/>
... </param>
... '''))
>>> t = p.validate("")
Traceback (most recent call last):
...
ValueError: Field requires a value
>>> p = ToolParameter.build(None, XML('''
... <param name="blah" type="text" value="">
... <validator type="empty_field" negate="true"/>
... </param>
... '''))
>>> t = p.validate("foo")
Traceback (most recent call last):
...
ValueError: Field must not set a value
>>> t = p.validate("")
"""
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get('message', None)
negate = elem.get('negate', 'false')
if not message:
if negate == 'false':
message = elem.get('message', "Field requires a value")
else:
message = elem.get('message', "Field must not set a value")
return cls(message, negate)
[docs]class MetadataInFileColumnValidator(Validator):
"""
Validator that checks if the value for a dataset's metadata item exists in a file.
Deprecated: DataTables are now the preferred way.
note: this is covered in a framework test (validation_dataset_metadata_in_file)
"""
requires_dataset_metadata = True
[docs] @classmethod
def from_element(cls, param, elem):
filename = elem.get("filename", None)
if filename:
filename = f"{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", f"Value for metadata {metadata_name} was not found in {filename}.")
line_startswith = elem.get("line_startswith", None)
if line_startswith:
line_startswith = line_startswith.strip()
negate = elem.get('negate', 'false')
return cls(filename, metadata_name, metadata_column, message, line_startswith, split, negate)
[docs] def __init__(self, filename, metadata_name, metadata_column, message="Value for metadata not found.", line_startswith=None, split="\t", negate="false"):
super().__init__(message, negate)
self.metadata_name = metadata_name
self.valid_values = set()
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.add(fields[metadata_column].strip())
[docs] def validate(self, value, trans=None):
if not value:
return
super().validate(value.metadata.spec[self.metadata_name].param.to_string(value.metadata.get(self.metadata_name)) in self.valid_values)
[docs]class ValueInDataTableColumnValidator(Validator):
"""
Validator that checks if a value is in a tool data table column.
note: this is covered in a framework test (validation_value_in_datatable)
"""
[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", f"Value was not found in {table_name}.")
negate = elem.get('negate', 'false')
return cls(tool_data_table, column, message, negate)
[docs] def __init__(self, tool_data_table, column, message="Value not found.", negate='false'):
super().__init__(message, negate)
self.valid_values = []
self._data_table_content_version = None
self._tool_data_table = tool_data_table
if isinstance(column, str):
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._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('ValueInDataTableColumnValidator: values are out of sync with data table (%s), updating validator.', self._tool_data_table.name)
self._load_values()
super().validate(value in self.valid_values)
[docs]class ValueNotInDataTableColumnValidator(ValueInDataTableColumnValidator):
"""
Validator that checks if a value is NOT in a tool data table column.
Equivalent to ValueInDataTableColumnValidator with `negate="true"`.
note: this is covered in a framework test (validation_value_in_datatable)
"""
[docs] def __init__(self, tool_data_table, metadata_column, message="Value already present.", negate='false'):
super().__init__(tool_data_table, metadata_column, message, negate)
[docs] def validate(self, value, trans=None):
try:
super().validate(value)
except ValueError:
return
else:
raise ValueError(self.message)
[docs]class MetadataInDataTableColumnValidator(ValueInDataTableColumnValidator):
"""
Validator that checks if the value for a dataset's metadata item exists in a file.
note: this is covered in a framework test (validation_metadata_in_datatable)
"""
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()
# TODO rename to column?
metadata_column = elem.get("metadata_column", 0)
try:
metadata_column = int(metadata_column)
except ValueError:
pass
message = elem.get("message", f"Value for metadata {metadata_name} was not found in {table_name}.")
negate = elem.get('negate', 'false')
return cls(tool_data_table, metadata_name, metadata_column, message, negate)
[docs] def __init__(self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", negate="false"):
super().__init__(tool_data_table, metadata_column, message, negate)
self.metadata_name = metadata_name
[docs] def validate(self, value, trans=None):
super().validate(value.metadata.spec[self.metadata_name].param.to_string(value.metadata.get(self.metadata_name)), trans)
[docs]class MetadataNotInDataTableColumnValidator(MetadataInDataTableColumnValidator):
"""
Validator that checks if the value for a dataset's metadata item doesn't exists in a file.
Equivalent to MetadataInDataTableColumnValidator with `negate="true"`.
note: this is covered in a framework test (validation_metadata_in_datatable)
"""
requires_dataset_metadata = True
[docs] def __init__(self, tool_data_table, metadata_name, metadata_column, message="Value for metadata not found.", negate="false"):
super().__init__(tool_data_table, metadata_name, metadata_column, message, negate)
[docs] def validate(self, value, trans=None):
try:
super().validate(value, trans)
except ValueError:
return
else:
raise ValueError(self.message)
[docs]class MetadataInRangeValidator(InRangeValidator):
"""
validator that ensures metadata is in a specified range
note: this is covered in a framework test (validation_metadata_in_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()
ret = cls(metadata_name, elem.get('message', None),
elem.get('min'), elem.get('max'),
elem.get('exclude_min', 'false'), elem.get('exclude_max', 'false'),
elem.get('negate', 'false'))
ret.message = "Metadata: " + ret.message
return ret
[docs] def __init__(self, metadata_name, message, range_min, range_max, exclude_min, exclude_max, negate):
self.metadata_name = metadata_name
super().__init__(message, range_min, range_max, exclude_min, exclude_max, negate)
[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(f'{self.metadata_name} Metadata missing')
except ValueError:
raise ValueError(f'{self.metadata_name} must be a float or an integer')
log.error(f"MetadataInRangeValidato.validate value_to_check {value_to_check}")
super().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_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=ValueNotInDataTableColumnValidator,
dataset_ok_validator=DatasetOkValidator,
)
deprecated_validator_types = dict(
dataset_metadata_in_file=MetadataInFileColumnValidator
)
validator_types.update(deprecated_validator_types)
[docs]def get_suite():
"""Get unittest suite for this module"""
import doctest
import sys
return doctest.DocTestSuite(sys.modules[__name__])