Warning
This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.tool_util.linters.inputs
"""This module contains a linting functions for tool inputs."""
import ast
import re
import warnings
from copy import deepcopy
from typing import (
Iterator,
Optional,
Tuple,
TYPE_CHECKING,
)
from packaging.version import Version
from galaxy.tool_util.lint import Linter
from galaxy.util import string_as_bool
from ._util import (
is_datasource,
is_valid_cheetah_placeholder,
)
from ..parser.util import _parse_name
if TYPE_CHECKING:
from galaxy.tool_util.lint import LintContext
from galaxy.tool_util.parser import ToolSource
from galaxy.util.etree import (
Element,
ElementTree,
)
lint_tool_types = ["*"]
ATTRIB_VALIDATOR_COMPATIBILITY = {
"check": ["metadata"],
"expression": ["substitute_value_in_message"],
"table_name": [
"dataset_metadata_in_data_table",
"dataset_metadata_not_in_data_table",
"value_in_data_table",
"value_not_in_data_table",
],
"filename": ["dataset_metadata_in_file"],
"metadata_name": [
"dataset_metadata_equal",
"dataset_metadata_in_data_table",
"dataset_metadata_not_in_data_table",
"dataset_metadata_in_file",
"dataset_metadata_in_range",
],
"metadata_column": [
"dataset_metadata_in_data_table",
"dataset_metadata_not_in_data_table",
"value_in_data_table",
"value_not_in_data_table",
"dataset_metadata_in_file",
],
"line_startswith": ["dataset_metadata_in_file"],
"min": ["in_range", "length", "dataset_metadata_in_range"],
"max": ["in_range", "length", "dataset_metadata_in_range"],
"exclude_min": ["in_range", "dataset_metadata_in_range"],
"exclude_max": ["in_range", "dataset_metadata_in_range"],
"split": ["dataset_metadata_in_file"],
"skip": ["metadata"],
"value": ["dataset_metadata_equal"],
"value_json": ["dataset_metadata_equal"],
}
PARAMETER_VALIDATOR_TYPE_COMPATIBILITY = {
"integer": ["in_range", "expression"],
"float": ["in_range", "expression"],
"data": [
"metadata",
"no_options",
"unspecified_build",
"dataset_ok_validator",
"dataset_metadata_equal",
"dataset_metadata_in_range",
"dataset_metadata_in_file",
"dataset_metadata_in_data_table",
"dataset_metadata_not_in_data_table",
"expression",
],
"data_collection": [
"metadata",
"no_options",
"unspecified_build",
"dataset_ok_validator",
"dataset_metadata_equal",
"dataset_metadata_in_range",
"dataset_metadata_in_file",
"dataset_metadata_in_data_table",
"dataset_metadata_not_in_data_table",
"expression",
],
"text": ["regex", "length", "empty_field", "value_in_data_table", "value_not_in_data_table", "expression"],
"select": [
"in_range",
"no_options",
"regex",
"length",
"empty_field",
"value_in_data_table",
"value_not_in_data_table",
"expression",
],
"drill_down": [
"no_options",
"regex",
"length",
"empty_field",
"value_in_data_table",
"value_not_in_data_table",
"expression",
],
"data_column": [
"no_options",
"regex",
"length",
"empty_field",
"value_in_data_table",
"value_not_in_data_table",
"expression",
],
}
PARAM_TYPE_CHILD_COMBINATIONS = [
("./options", ["data", "select", "drill_down"]),
("./options/option", ["drill_down"]),
("./options/column", ["data", "select"]),
]
# TODO lint for valid param type - attribute combinations
# TODO check if ref input param is present for from_dataset
[docs]
class InputsNum(Linter):
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
tool_node = tool_xml.find("./inputs")
if tool_node is None:
tool_node = tool_xml.getroot()
num_inputs = len(tool_xml.findall("./inputs//param"))
if num_inputs:
lint_ctx.info(f"Found {num_inputs} input parameters.", linter=cls.name(), node=tool_node)
[docs]
class InputsMissing(Linter):
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
tool_node = tool_xml.find("./inputs")
if tool_node is None:
tool_node = tool_xml.getroot()
num_inputs = len(tool_xml.findall("./inputs//param"))
if num_inputs == 0 and not is_datasource(tool_xml):
lint_ctx.warn("Found no input parameters.", linter=cls.name(), node=tool_node)
[docs]
class InputsMissingDataSource(Linter):
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
tool_node = tool_xml.find("./inputs")
if tool_node is None:
tool_node = tool_xml.getroot()
num_inputs = len(tool_xml.findall("./inputs//param"))
if num_inputs == 0 and is_datasource(tool_xml):
lint_ctx.info("No input parameters, OK for data sources", linter=cls.name(), node=tool_node)
[docs]
class InputsDatasourceTags(Linter):
"""
Lint that datasource tools have display and uihints tags
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
tool_node = tool_xml.find("./inputs")
if tool_node is None:
tool_node = tool_xml.getroot()
inputs = tool_xml.findall("./inputs//param")
if is_datasource(tool_xml):
# TODO only display is subtag of inputs, uihints is a separate top level tag (supporting only attrib minwidth)
for datasource_tag in ("display", "uihints"):
if not any(param.tag == datasource_tag for param in inputs):
lint_ctx.info(
f"{datasource_tag} tag usually present in data sources", linter=cls.name(), node=tool_node
)
def _iter_param(tool_xml: "ElementTree") -> Iterator[Tuple["Element", str]]:
for param in tool_xml.findall("./inputs//param"):
if "name" not in param.attrib and "argument" not in param.attrib:
continue
param_name = _parse_name(param.attrib.get("name"), param.attrib.get("argument"))
yield param, param_name
def _iter_param_type(tool_xml: "ElementTree") -> Iterator[Tuple["Element", str, str]]:
for param, param_name in _iter_param(tool_xml):
if "type" not in param.attrib:
continue
param_type = param.attrib["type"]
if param_type == "":
continue
yield param, param_name, param_type
[docs]
class InputsName(Linter):
"""
Lint params define a name
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param in tool_xml.findall("./inputs//param"):
if "name" not in param.attrib and "argument" not in param.attrib:
lint_ctx.error("Found param input with no name specified.", linter=cls.name(), node=param)
[docs]
class InputsNameRedundantArgument(Linter):
"""
Lint params define a name
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param in tool_xml.findall("./inputs//param"):
if "name" in param.attrib and "argument" in param.attrib:
param_name = _parse_name(param.attrib.get("name"), param.attrib.get("argument"))
if param.attrib.get("name") == _parse_name(None, param.attrib.get("argument")):
lint_ctx.warn(
f"Param input [{param_name}] 'name' attribute is redundant if argument implies the same name.",
linter=cls.name(),
node=param,
)
# TODO redundant with InputsNameValid
[docs]
class InputsNameEmpty(Linter):
"""
Lint params define a non-empty name
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name in _iter_param(tool_xml):
if param_name.strip() == "":
lint_ctx.error("Param input with empty name.", linter=cls.name(), node=param)
[docs]
class InputsNameValid(Linter):
"""
Lint params define valid cheetah placeholder
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name in _iter_param(tool_xml):
if param_name != "" and not is_valid_cheetah_placeholder(param_name):
lint_ctx.warn(
f"Param input [{param_name}] is not a valid Cheetah placeholder.", linter=cls.name(), node=param
)
def _param_path(param: "Element", param_name: str) -> str:
path = [param_name]
parent = param
while True:
parent = parent.getparent()
if parent.tag == "inputs":
break
# parameters of the same name in different when branches are allowed
# just add the value of the when branch to the path (this also allows
# that the conditional select has the same name as params in the whens)
if parent.tag == "when":
path.append(str(parent.attrib.get("value")))
else:
path.append(str(parent.attrib.get("name")))
return ".".join(reversed(path))
[docs]
class InputsNameDuplicate(Linter):
"""
Lint params with duplicate names
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
input_names = set()
for param, param_name in _iter_param(tool_xml):
# check for parameters with duplicate names
path = _param_path(param, param_name)
if path in input_names:
lint_ctx.error(
f"Tool defines multiple parameters with the same name: '{path}'", linter=cls.name(), node=param
)
input_names.add(path)
[docs]
class InputsNameDuplicateOutput(Linter):
"""
Lint params names that are also used in outputs
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
input_names = set()
for param, param_name in _iter_param(tool_xml):
input_names.add(_param_path(param, param_name))
# check if there is an output with the same name as an input
outputs = tool_xml.findall("./outputs/*")
for output in outputs:
if output.get("name") in input_names:
lint_ctx.error(
f'Tool defines an output with a name equal to the name of an input: \'{output.get("name")}\'',
linter=cls.name(),
node=output,
)
[docs]
class InputsTypeChildCombination(Linter):
"""
Lint for invalid parameter type child combinations
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
# lint for valid param type - child node combinations
for ptcc in PARAM_TYPE_CHILD_COMBINATIONS:
if param.find(ptcc[0]) is not None and param_type not in ptcc[1]:
lint_ctx.error(
f"Parameter [{param_name}] '{ptcc[0]}' tags are only allowed for parameters of type {ptcc[1]}",
linter=cls.name(),
node=param,
)
[docs]
class InputsDataFormat(Linter):
"""
Lint for data params wo format
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "data":
continue
if "format" not in param.attrib:
lint_ctx.warn(
f"Param input [{param_name}] with no format specified - 'data' format will be assumed.",
linter=cls.name(),
node=param,
)
[docs]
class InputsDataOptionsMultiple(Linter):
"""
Lint for data params with multiple options tags
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "data":
continue
options = param.findall("./options")
if len(options) > 1:
lint_ctx.error(
f"Data parameter [{param_name}] contains multiple options elements.",
linter=cls.name(),
node=options[1],
)
[docs]
class InputsDataOptionsAttrib(Linter):
"""
Lint for data params with options that have invalid attributes
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "data":
continue
options = param.find("./options")
if options is None:
continue
for oa in options.attrib:
if oa != "options_filter_attribute":
lint_ctx.error(
f"Data parameter [{param_name}] uses invalid attribute: {oa}", linter=cls.name(), node=param
)
[docs]
class InputsDataOptionsFilterAttribFiltersType(Linter):
"""
Lint for valid filter types for data parameters
if options set options_filter_attribute
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "data":
continue
options = param.find("./options")
if options is None:
continue
for filter in param.findall("./options/filter"):
if "options_filter_attribute" in options.attrib:
if filter.get("type") != "data_meta":
lint_ctx.error(
f'Data parameter [{param_name}] for filters only type="data_meta" is allowed, found type="{filter.get("type")}"',
linter=cls.name(),
node=filter,
)
[docs]
class InputsDataOptionsFiltersType(Linter):
"""
Lint for valid filter types for data parameters
if options do not set options_filter_attribute
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "data":
continue
options = param.find("./options")
if options is None:
continue
for filter in param.findall("./options/filter"):
if "options_filter_attribute" not in options.attrib:
if filter.get("key") != "dbkey" or filter.get("type") != "data_meta":
lint_ctx.error(
f'Data parameter [{param_name}] for filters only type="data_meta" and key="dbkey" are allowed, found type="{filter.get("type")}" and key="{filter.get("key")}"',
linter=cls.name(),
node=filter,
)
FILTER_REQUIRED_ATTRIBUTES = {
"data_meta": ["type", "ref", "key"], # column needs special treatment
"param_value": ["type", "ref", "column"],
"static_value": ["type", "column", "value"],
"regexp": ["type", "column", "value"],
"unique_value": ["type", "column"],
"multiple_splitter": ["type", "column"],
"attribute_value_splitter": ["type", "column"],
"add_value": ["type", "value"],
"remove_value": ["type"], # this is handled separately in InputsOptionsRemoveValueFilterRequiredAttributes
"sort_by": ["type", "column"],
"data_table": ["type", "column", "table_name", "data_table_column"],
}
[docs]
class InputsOptionsFiltersRequiredAttributes(Linter):
"""
check required attributes of filters
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name in _iter_param(tool_xml):
options = param.find("./options")
if options is None:
continue
for filter in param.findall("./options/filter"):
filter_type = filter.get("type", None)
if filter_type is None or filter_type not in FILTER_ALLOWED_ATTRIBUTES:
continue
for attrib in FILTER_REQUIRED_ATTRIBUTES[filter_type]:
if attrib not in filter.attrib:
lint_ctx.error(
f"Select parameter [{param_name}] '{filter_type}' filter misses required attribute '{attrib}'",
linter=cls.name(),
node=filter,
)
[docs]
class InputsOptionsRemoveValueFilterRequiredAttributes(Linter):
"""
check required attributes of remove_value filter
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name in _iter_param(tool_xml):
options = param.find("./options")
if options is None:
continue
for filter in param.findall("./options/filter"):
filter_type = filter.get("type", None)
# check for required attributes for filter (remove_value needs a bit more logic here)
if filter_type != "remove_value":
continue
if not (
(
"value" in filter.attrib
and "ref" not in filter.attrib
and "meta_ref" not in filter.attrib
and "key" not in filter.attrib
)
or (
"value" not in filter.attrib
and "ref" in filter.attrib
and "meta_ref" not in filter.attrib
and "key" not in filter.attrib
)
or (
"value" not in filter.attrib
and "ref" not in filter.attrib
and "meta_ref" in filter.attrib
and "key" in filter.attrib
)
):
lint_ctx.error(
f"Select parameter [{param_name}] '{filter_type}'' filter needs either the 'value'; 'ref'; or 'meta' and 'key' attribute(s)",
linter=cls.name(),
node=filter,
)
FILTER_ALLOWED_ATTRIBUTES = deepcopy(FILTER_REQUIRED_ATTRIBUTES)
FILTER_ALLOWED_ATTRIBUTES["static_value"].append("keep")
FILTER_ALLOWED_ATTRIBUTES["regexp"].append("keep")
FILTER_ALLOWED_ATTRIBUTES["data_meta"].extend(["column", "multiple", "separator"])
FILTER_ALLOWED_ATTRIBUTES["param_value"].extend(["keep", "ref_attribute"])
FILTER_ALLOWED_ATTRIBUTES["multiple_splitter"].append("separator")
FILTER_ALLOWED_ATTRIBUTES["attribute_value_splitter"].extend(["pair_separator", "name_val_separator"])
FILTER_ALLOWED_ATTRIBUTES["add_value"].extend(["name", "index"])
FILTER_ALLOWED_ATTRIBUTES["remove_value"].extend(["value", "ref", "meta_ref", "key"])
FILTER_ALLOWED_ATTRIBUTES["data_table"].append("keep")
[docs]
class InputsOptionsFiltersAllowedAttributes(Linter):
"""
check allowed attributes of filters
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name in _iter_param(tool_xml):
options = param.find("./options")
if options is None:
continue
for filter in param.findall("./options/filter"):
filter_type = filter.get("type", None)
if filter_type is None or filter_type not in FILTER_ALLOWED_ATTRIBUTES:
continue
for attrib in filter.attrib:
if attrib not in FILTER_ALLOWED_ATTRIBUTES[filter_type]:
lint_ctx.warn(
f"Select parameter [{param_name}] '{filter_type}' filter specifies unnecessary attribute '{attrib}'",
linter=cls.name(),
node=filter,
)
[docs]
class InputsOptionsRegexFilterExpression(Linter):
"""
Check the regular expression of regexp filters
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name in _iter_param(tool_xml):
options = param.find("./options")
if options is None:
continue
for filter in param.findall("./options/filter"):
filter_type = filter.get("type", None)
if filter_type == "regexp" and "value" in filter.attrib:
try:
re.compile(filter.attrib["value"])
except re.error as re_error:
lint_ctx.error(
f"Select parameter [{param_name}] '{filter_type}'' filter 'value' is not a valid regular expression ({re_error})'",
linter=cls.name(),
node=filter,
)
[docs]
class InputsOptionsFiltersCheckReferences(Linter):
"""
Check the references used in filters
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
# get the set of param names
param_names = {param_name for _, param_name in _iter_param(tool_xml)}
for param, param_name in _iter_param(tool_xml):
options = param.find("./options")
if options is None:
continue
for filter in param.findall("./options/filter"):
filter_type = filter.get("type", None)
if filter_type is not None:
# check for references to other inputs
# TODO: currently ref and metaref seem only to work for top level params,
# once this is fixed the linter needs to be extended, e.g. `f.attrib[ref_attrib].split('|')[-1]`
for ref_attrib in ["meta_ref", "ref"]:
if ref_attrib in filter.attrib and filter.attrib[ref_attrib] not in param_names:
lint_ctx.error(
f"Select parameter [{param_name}] '{filter_type}'' filter attribute '{ref_attrib}' refers to non existing parameter '{filter.attrib[ref_attrib]}'",
linter=cls.name(),
node=filter,
)
[docs]
class InputsDataOptionsFiltersRef(Linter):
"""
Lint for set ref for filters of data parameters
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "data":
continue
options = param.find("./options")
if options is None:
continue
for filter in param.findall("./options/filter"):
if not filter.get("ref"):
lint_ctx.error(
f"Data parameter [{param_name}] filter needs to define a ref attribute",
linter=cls.name(),
node=filter,
)
[docs]
class InputsSelectDynamicOptions(Linter):
"""
Lint for select with deprecated dynamic_options attribute
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "select":
continue
dynamic_options = param.get("dynamic_options", None)
if dynamic_options is not None:
lint_ctx.warn(
f"Select parameter [{param_name}] uses deprecated 'dynamic_options' attribute.",
linter=cls.name(),
node=param,
)
[docs]
class InputsSelectOptionsDef(Linter):
"""
Lint for valid ways to define select options
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "select":
continue
dynamic_options = param.get("dynamic_options", None)
options = param.findall("./options")
select_options = param.findall("./option")
if param.getparent().tag != "conditional":
if (dynamic_options is not None) + (len(options) > 0) + (len(select_options) > 0) != 1:
lint_ctx.error(
f"Select parameter [{param_name}] options have to be defined by either 'option' children elements, a 'options' element or the 'dynamic_options' attribute.",
linter=cls.name(),
node=param,
)
[docs]
class InputsSelectOptionsDefConditional(Linter):
"""
Lint for valid ways to define select options
(for a select in a conditional)
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "select":
continue
dynamic_options = param.get("dynamic_options", None)
options = param.findall("./options")
select_options = param.findall("./option")
if param.getparent().tag == "conditional":
if len(select_options) == 0 or dynamic_options is not None or len(options) > 0:
lint_ctx.error(
f"Select parameter of a conditional [{param_name}] options have to be defined by 'option' children elements.",
linter=cls.name(),
node=param,
)
# TODO xsd
[docs]
class InputsSelectOptionValueMissing(Linter):
"""
Lint for select option tags without value
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "select":
continue
select_options = param.findall("./option")
if any("value" not in option.attrib for option in select_options):
lint_ctx.error(
f"Select parameter [{param_name}] has option without value", linter=cls.name(), node=param
)
[docs]
class InputsSelectOptionDuplicateValue(Linter):
"""
Lint for select option with same value
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "select":
continue
select_options = param.findall("./option")
select_options_values = []
for option in select_options:
value = option.attrib.get("value", "")
select_options_values.append((value, option.attrib.get("selected", "false")))
if len(set(select_options_values)) != len(select_options_values):
lint_ctx.error(
f"Select parameter [{param_name}] has multiple options with the same value",
linter=cls.name(),
node=param,
)
[docs]
class InputsSelectOptionDuplicateText(Linter):
"""
Lint for select option with same text
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "select":
continue
select_options = param.findall("./option")
select_options_texts = []
for option in select_options:
if option.text is None:
text = option.attrib.get("value", "").capitalize()
else:
text = option.text
select_options_texts.append((text, option.attrib.get("selected", "false")))
if len(set(select_options_texts)) != len(select_options_texts):
lint_ctx.error(
f"Select parameter [{param_name}] has multiple options with the same text content",
linter=cls.name(),
node=param,
)
[docs]
class InputsSelectOptionsMultiple(Linter):
"""
Lint dynamic options select for multiple options tags
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "select":
continue
options = param.findall("./options")
if len(options) > 1:
lint_ctx.error(
f"Select parameter [{param_name}] contains multiple options elements.",
linter=cls.name(),
node=options[1],
)
[docs]
class InputsSelectOptionsDefinesOptions(Linter):
"""
Lint dynamic options select for the potential to define options
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "select":
continue
options = param.find("./options")
if options is None:
continue
filter_adds_options = any(
f.get("type", None) in ["add_value", "data_meta"] for f in param.findall("./options/filter")
)
from_file = options.get("from_file", None)
from_parameter = options.get("from_parameter", None)
# TODO check if input param is present for from_dataset
from_dataset = options.get("from_dataset", None)
from_data_table = options.get("from_data_table", None)
from_url = options.get("from_url", None)
if (
from_file is None
and from_parameter is None
and from_dataset is None
and from_data_table is None
and from_url is None
and not filter_adds_options
):
lint_ctx.error(
f"Select parameter [{param_name}] options tag defines no options. Use 'from_dataset', 'from_data_table', or a filter that adds values.",
linter=cls.name(),
node=options,
)
[docs]
class InputsSelectOptionsDeprecatedAttr(Linter):
"""
Lint dynamic options select deprecated attributes
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "select":
continue
options = param.find("./options")
if options is None:
continue
for deprecated_attr in ["from_file", "from_parameter", "options_filter_attribute", "transform_lines"]:
if options.get(deprecated_attr) is not None:
lint_ctx.warn(
f"Select parameter [{param_name}] options uses deprecated '{deprecated_attr}' attribute.",
linter=cls.name(),
node=options,
)
[docs]
class InputsSelectOptionsFromDatasetAndDatatable(Linter):
"""
Lint dynamic options select for from_dataset and from_data_table
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "select":
continue
options = param.find("./options")
if options is None:
continue
from_dataset = options.get("from_dataset", None)
from_data_table = options.get("from_data_table", None)
if from_dataset is not None and from_data_table is not None:
lint_ctx.error(
f"Select parameter [{param_name}] options uses 'from_dataset' and 'from_data_table' attribute.",
linter=cls.name(),
node=options,
)
[docs]
class InputsSelectOptionsMetaFileKey(Linter):
"""
Lint dynamic options select: meta_file_key attribute can only be used with from_dataset
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "select":
continue
options = param.find("./options")
if options is None:
continue
from_dataset = options.get("from_dataset", None)
if options.get("meta_file_key", None) is not None and from_dataset is None:
lint_ctx.error(
f"Select parameter [{param_name}] 'meta_file_key' is only compatible with 'from_dataset'.",
linter=cls.name(),
node=options,
)
[docs]
class InputsBoolDistinctValues(Linter):
"""
Lint booleans for distinct true/false value
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "boolean":
continue
profile = tool_source.parse_profile()
truevalue = param.attrib.get("truevalue", "true")
falsevalue = param.attrib.get("falsevalue", "false")
problematic_booleans_allowed = Version(profile) < Version("23.1")
lint_level = lint_ctx.warn if problematic_booleans_allowed else lint_ctx.error
if truevalue == falsevalue:
lint_level(
f"Boolean parameter [{param_name}] needs distinct 'truevalue' and 'falsevalue' values.",
linter=cls.name(),
node=param,
)
[docs]
class InputsBoolProblematic(Linter):
"""
Lint booleans for problematic values, i.e. truevalue being false and vice versa
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type != "boolean":
continue
profile = tool_source.parse_profile()
truevalue = param.attrib.get("truevalue", "true")
falsevalue = param.attrib.get("falsevalue", "false")
problematic_booleans_allowed = Version(profile) < Version("23.1")
lint_level = lint_ctx.warn if problematic_booleans_allowed else lint_ctx.error
if truevalue.lower() == "false":
lint_level(
f"Boolean parameter [{param_name}] has invalid truevalue [{truevalue}].",
linter=cls.name(),
node=param,
)
if falsevalue.lower() == "true":
lint_level(
f"Boolean parameter [{param_name}] has invalid falsevalue [{falsevalue}].",
linter=cls.name(),
node=param,
)
[docs]
class InputsSelectSingleCheckboxes(Linter):
"""
Lint selects that allow only a single selection but display as checkboxes
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type not in ["select", "data_column", "drill_down"]:
continue
multiple = string_as_bool(param.attrib.get("multiple", "false"))
if param.attrib.get("display") == "checkboxes":
if not multiple:
lint_ctx.error(
f'Select [{param_name}] `display="checkboxes"` is incompatible with `multiple="false"`, remove the `display` attribute',
linter=cls.name(),
node=param,
)
[docs]
class InputsSelectMandatoryCheckboxes(Linter):
"""
Lint selects that are mandatory but display as checkboxes
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type not in ["select", "data_column", "drill_down"]:
continue
multiple = string_as_bool(param.attrib.get("multiple", "false"))
optional = string_as_bool(param.attrib.get("optional", multiple))
if param.attrib.get("display") == "checkboxes":
if not optional:
lint_ctx.error(
f'Select [{param_name}] `display="checkboxes"` is incompatible with `optional="false"`, remove the `display` attribute',
linter=cls.name(),
node=param,
)
[docs]
class InputsSelectMultipleRadio(Linter):
"""
Lint selects that allow only multiple selections but display as radio
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type not in ["select", "data_column", "drill_down"]:
continue
multiple = string_as_bool(param.attrib.get("multiple", "false"))
if param.attrib.get("display") == "radio":
if multiple:
lint_ctx.error(
f'Select [{param_name}] display="radio" is incompatible with multiple="true"',
linter=cls.name(),
node=param,
)
[docs]
class InputsSelectOptionalRadio(Linter):
"""
Lint selects that are optional but display as radio
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param, param_name, param_type in _iter_param_type(tool_xml):
if param_type not in ["select", "data_column", "drill_down"]:
continue
multiple = string_as_bool(param.attrib.get("multiple", "false"))
optional = string_as_bool(param.attrib.get("optional", multiple))
if param.attrib.get("display") == "radio":
if optional:
lint_ctx.error(
f'Select [{param_name}] display="radio" is incompatible with optional="true"',
linter=cls.name(),
node=param,
)
def _iter_param_validator(tool_xml: "ElementTree") -> Iterator[Tuple[str, str, "Element", str]]:
input_params = tool_xml.findall("./inputs//param[@type]")
for param in input_params:
try:
param_name = _parse_name(param.attrib.get("name"), param.attrib.get("argument"))
except ValueError:
continue
param_type = param.attrib["type"]
validators = param.findall("./validator[@type]")
for validator in validators:
vtype = validator.attrib["type"]
yield (param_name, param_type, validator, vtype)
[docs]
class ValidatorParamIncompatible(Linter):
"""
Lint for validator type - parameter type incompatibilities
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param_name, param_type, validator, vtype in _iter_param_validator(tool_xml):
if param_type in PARAMETER_VALIDATOR_TYPE_COMPATIBILITY:
if vtype not in PARAMETER_VALIDATOR_TYPE_COMPATIBILITY[param_type]:
lint_ctx.error(
f"Parameter [{param_name}]: validator with an incompatible type '{vtype}'",
linter=cls.name(),
node=validator,
)
[docs]
class ValidatorAttribIncompatible(Linter):
"""
Lint for incompatibilities between validator type and given attributes
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param_name, _, validator, vtype in _iter_param_validator(tool_xml):
for attrib in ATTRIB_VALIDATOR_COMPATIBILITY:
if attrib in validator.attrib and vtype not in ATTRIB_VALIDATOR_COMPATIBILITY[attrib]:
lint_ctx.error(
f"Parameter [{param_name}]: attribute '{attrib}' is incompatible with validator of type '{vtype}'",
linter=cls.name(),
node=validator,
)
[docs]
class ValidatorHasText(Linter):
"""
Lint that parameters that need text have text
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param_name, _, validator, vtype in _iter_param_validator(tool_xml):
if vtype in ["expression", "regex"]:
if validator.text is None:
lint_ctx.error(
f"Parameter [{param_name}]: {vtype} validators are expected to contain text",
linter=cls.name(),
node=validator,
)
[docs]
class ValidatorHasNoText(Linter):
"""
Lint that parameters that need no text have no text
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param_name, _, validator, vtype in _iter_param_validator(tool_xml):
if vtype not in ["expression", "regex"] and validator.text is not None:
lint_ctx.warn(
f"Parameter [{param_name}]: '{vtype}' validators are not expected to contain text (found '{validator.text}')",
linter=cls.name(),
node=validator,
)
[docs]
class ValidatorExpression(Linter):
"""
Lint that checks expressions / regexp (ignoring FutureWarning)
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
with warnings.catch_warnings():
warnings.simplefilter("error", FutureWarning)
for param_name, _, validator, vtype in _iter_param_validator(tool_xml):
if vtype in ["expression", "regex"] and validator.text is not None:
try:
if vtype == "regex":
re.compile(validator.text)
else:
ast.parse(validator.text, mode="eval")
except FutureWarning:
pass
except Exception as e:
lint_ctx.error(
f"Parameter [{param_name}]: '{validator.text}' is no valid {vtype}: {str(e)}",
linter=cls.name(),
node=validator,
)
[docs]
class ValidatorExpressionFuture(Linter):
"""
Lint that checks expressions / regexp FutureWarnings
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
with warnings.catch_warnings():
warnings.simplefilter("error", FutureWarning)
for param_name, _, validator, vtype in _iter_param_validator(tool_xml):
if vtype in ["expression", "regex"] and validator.text is not None:
try:
if vtype == "regex":
re.compile(validator.text)
else:
ast.parse(validator.text, mode="eval")
except FutureWarning as e:
lint_ctx.warn(
f"Parameter [{param_name}]: '{validator.text}' is marked as deprecated {vtype}: {str(e)}",
linter=cls.name(),
node=validator,
)
except Exception:
pass
[docs]
class ValidatorMinMax(Linter):
"""
Lint for min/max for validator that need it
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param_name, _, validator, vtype in _iter_param_validator(tool_xml):
if vtype in ["in_range", "length", "dataset_metadata_in_range"] and (
"min" not in validator.attrib and "max" not in validator.attrib
):
lint_ctx.error(
f"Parameter [{param_name}]: '{vtype}' validators need to define the 'min' or 'max' attribute(s)",
linter=cls.name(),
node=validator,
)
[docs]
class ValidatorDatasetMetadataEqualValue(Linter):
"""
Lint dataset_metadata_equal needs value or value_json
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param_name, _, validator, vtype in _iter_param_validator(tool_xml):
if vtype in ["dataset_metadata_equal"]:
if (
not ("value" in validator.attrib or "value_json" in validator.attrib)
or "metadata_name" not in validator.attrib
):
lint_ctx.error(
f"Parameter [{param_name}]: '{vtype}' validators need to define the 'value'/'value_json' and 'metadata_name' attributes",
linter=cls.name(),
node=validator,
)
[docs]
class ValidatorDatasetMetadataEqualValueOrJson(Linter):
"""
Lint dataset_metadata_equal needs either value or value_json
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param_name, _, validator, vtype in _iter_param_validator(tool_xml):
if vtype in ["dataset_metadata_equal"]:
if "value" in validator.attrib and "value_json" in validator.attrib:
lint_ctx.error(
f"Parameter [{param_name}]: '{vtype}' validators must not define the 'value' and the 'value_json' attributes",
linter=cls.name(),
node=validator,
)
[docs]
class ValidatorMetadataCheckSkip(Linter):
"""
Lint metadata needs check or skip
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param_name, _, validator, vtype in _iter_param_validator(tool_xml):
if vtype in ["metadata"] and ("check" not in validator.attrib and "skip" not in validator.attrib):
lint_ctx.error(
f"Parameter [{param_name}]: '{vtype}' validators need to define the 'check' or 'skip' attribute(s)",
linter=cls.name(),
node=validator,
)
[docs]
class ValidatorTableName(Linter):
"""
Lint table_name is present if needed
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param_name, _, validator, vtype in _iter_param_validator(tool_xml):
if (
vtype
in [
"value_in_data_table",
"value_not_in_data_table",
"dataset_metadata_in_data_table",
"dataset_metadata_not_in_data_table",
]
and "table_name" not in validator.attrib
):
lint_ctx.error(
f"Parameter [{param_name}]: '{vtype}' validators need to define the 'table_name' attribute",
linter=cls.name(),
node=validator,
)
[docs]
class ValidatorMetadataName(Linter):
"""
Lint metadata_name is present if needed
"""
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for param_name, _, validator, vtype in _iter_param_validator(tool_xml):
if (
vtype
in [
"dataset_metadata_in_data_table",
"dataset_metadata_not_in_data_table",
"dataset_metadata_in_file",
"dataset_metadata_in_range",
]
and "metadata_name" not in validator.attrib
):
lint_ctx.error(
f"Parameter [{param_name}]: '{vtype}' validators need to define the 'metadata_name' attribute",
linter=cls.name(),
node=validator,
)
def _iter_conditional(tool_xml: "ElementTree") -> Iterator[Tuple["Element", Optional[str], "Element", Optional[str]]]:
conditionals = tool_xml.findall("./inputs//conditional")
for conditional in conditionals:
conditional_name = conditional.get("name")
if conditional.get("value_from"): # Probably only the upload tool use this, no children elements
continue
first_param = conditional.find("param")
if first_param is None:
continue
first_param_type = first_param.get("type")
yield conditional, conditional_name, first_param, first_param_type
[docs]
class ConditionalParamTypeBool(Linter):
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for _, conditional_name, first_param, first_param_type in _iter_conditional(tool_xml):
if first_param_type == "boolean":
lint_ctx.warn(
f'Conditional [{conditional_name}] first param of type="boolean" is discouraged, use a select',
linter=cls.name(),
node=first_param,
)
[docs]
class ConditionalParamType(Linter):
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for _, conditional_name, first_param, first_param_type in _iter_conditional(tool_xml):
if first_param_type not in ["boolean", "select"]:
lint_ctx.error(
f'Conditional [{conditional_name}] first param should have type="select"',
linter=cls.name(),
node=first_param,
)
[docs]
class ConditionalParamIncompatibleAttributes(Linter):
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for _, conditional_name, first_param, first_param_type in _iter_conditional(tool_xml):
if first_param_type not in ["boolean", "select"]:
continue
for incomp in ["optional", "multiple"]:
if string_as_bool(first_param.get(incomp, False)):
lint_ctx.warn(
f'Conditional [{conditional_name}] test parameter cannot be {incomp}="true"',
linter=cls.name(),
node=first_param,
)
[docs]
class ConditionalWhenMissing(Linter):
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for conditional, conditional_name, first_param, first_param_type in _iter_conditional(tool_xml):
if first_param_type not in ["boolean", "select"]:
continue
if first_param_type == "select":
options = first_param.findall("./option[@value]")
option_ids = {option.get("value") for option in options}
else: # boolean
option_ids = {first_param.get("truevalue", "true"), first_param.get("falsevalue", "false")}
whens = conditional.findall("./when[@value]")
when_ids = {w.get("value") for w in whens if w.get("value") is not None}
for option_id in option_ids - when_ids:
lint_ctx.warn(
f"Conditional [{conditional_name}] no <when /> block found for {first_param_type} option '{option_id}'",
linter=cls.name(),
node=conditional,
)
[docs]
class ConditionalOptionMissing(Linter):
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for conditional, conditional_name, first_param, first_param_type in _iter_conditional(tool_xml):
if first_param_type != "select":
continue
options = first_param.findall("./option[@value]")
option_ids = {option.get("value") for option in options}
whens = conditional.findall("./when[@value]")
when_ids = {w.get("value") for w in whens if w.get("value") is not None}
for when_id in when_ids - option_ids:
lint_ctx.warn(
f"Conditional [{conditional_name}] no <option /> found for when block '{when_id}'",
linter=cls.name(),
node=conditional,
)
[docs]
class ConditionalOptionMissingBoolean(Linter):
[docs]
@classmethod
def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
tool_xml = getattr(tool_source, "xml_tree", None)
if not tool_xml:
return
for conditional, conditional_name, first_param, first_param_type in _iter_conditional(tool_xml):
if first_param_type != "boolean":
continue
option_ids = {first_param.get("truevalue", "true"), first_param.get("falsevalue", "false")}
whens = conditional.findall("./when[@value]")
when_ids = {w.get("value") for w in whens if w.get("value")}
for when_id in when_ids - option_ids:
lint_ctx.warn(
f"Conditional [{conditional_name}] no truevalue/falsevalue found for when block '{when_id}'",
linter=cls.name(),
node=conditional,
)