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Source code for galaxy.tools.parameters.validation
"""
Classes related to parameter validation.
"""
import abc
import json
import logging
import os.path
import regex
from galaxy import (
model,
util,
)
log = logging.getLogger(__name__)
[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 appropriate 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")
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
"""
[docs] @classmethod
def from_element(cls, param, elem):
return cls(elem.get("message"), 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.replace('%', '%%')}'"
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 = regex.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
"""
[docs] @classmethod
def from_element(cls, param, elem):
return cls(elem.get("message"), 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)
self.expression = expression
# Save compiled expression, code objects are thread safe (right?)
self.compiled_expression = compile(expression, "<string>", "eval")
[docs] def validate(self, value, trans=None):
try:
evalresult = eval(self.compiled_expression, dict(value=value))
except Exception:
super().validate(False, message=f"Validator '{self.expression}' could not be evaluated on '{value}'")
super().validate(bool(evalresult), value_to_show=value)
[docs]class InRangeValidator(ExpressionValidator):
"""
Validator that ensures a number is in a specified range
"""
[docs] @classmethod
def from_element(cls, param, elem):
return cls(
elem.get("message"),
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} float(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
"""
[docs] @classmethod
def from_element(cls, param, elem):
return cls(elem.get("message"), elem.get("min"), elem.get("max"), 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] def validate(self, value, trans=None):
if value is None:
raise ValueError("No value provided")
super().validate(len(value) if value else 0, trans)
[docs]class DatasetOkValidator(Validator):
"""
Validator that checks if a dataset is in an 'ok' state
"""
[docs] @classmethod
def from_element(cls, param, elem):
negate = elem.get("negate", "false")
message = elem.get("message")
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.
"""
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get("message")
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.
"""
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get("message")
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
"""
requires_dataset_metadata = True
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get("message")
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 MetadataEqualValidator(Validator):
"""
Validator that checks for a metadata value for equality
metadata values that are lists are converted as comma separated string
everything else is converted to the string representation
"""
requires_dataset_metadata = True
[docs] def __init__(self, metadata_name=None, value=None, message=None, negate="false"):
if not message:
if not util.asbool(negate):
message = f"Metadata value for '{metadata_name}' must be '{value}', but it is '%s'."
else:
message = f"Metadata value for '{metadata_name}' must not be '{value}' but it is."
super().__init__(message, negate)
self.metadata_name = metadata_name
self.value = value
[docs] @classmethod
def from_element(cls, param, elem):
value = elem.get("value", None) or json.loads(elem.get("value_json", "null"))
return cls(
metadata_name=elem.get("metadata_name", None),
value=value,
message=elem.get("message", None),
negate=elem.get("negate", "false"),
)
[docs] def validate(self, value, trans=None):
if value:
metadata_value = getattr(value.metadata, self.metadata_name)
super().validate(metadata_value == self.value, value_to_show=metadata_value)
[docs]class UnspecifiedBuildValidator(Validator):
"""
Validator that checks for dbkey not equal to '?'
"""
requires_dataset_metadata = True
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get("message")
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
"""
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get("message")
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
"""
[docs] @classmethod
def from_element(cls, param, elem):
message = elem.get("message")
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")
assert filename, f"Required 'filename' attribute missing from {elem.get('type')} validator."
filename = f"{param.tool.app.config.tool_data_path}/{filename.strip()}"
assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found"
metadata_name = elem.get("metadata_name")
assert metadata_name, f"Required 'metadata_name' attribute missing from {elem.get('type')} validator."
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")
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()
with open(filename) as fh:
for line in fh:
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")
assert table_name, f"Required 'table_name' attribute missing from {elem.get('type')} validator."
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")
assert table_name, f"Required 'table_name' attribute missing from {elem.get('type')} validator."
tool_data_table = param.tool.app.tool_data_tables[table_name]
metadata_name = elem.get("metadata_name")
assert metadata_name, f"Required 'metadata_name' attribute missing from {elem.get('type')} validator."
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")
assert metadata_name, f"Required 'metadata_name' attribute missing from {elem.get('type')} validator."
metadata_name = metadata_name.strip()
ret = cls(
metadata_name,
elem.get("message"),
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")
super().validate(value_to_check, trans)
validator_types = dict(
expression=ExpressionValidator,
regex=RegexValidator,
in_range=InRangeValidator,
length=LengthValidator,
metadata=MetadataValidator,
dataset_metadata_equal=MetadataEqualValidator,
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)