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Source code for galaxy.tool_util.linters.inputs
"""This module contains a linting functions for tool inputs."""
import ast
import re
from typing import TYPE_CHECKING
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
FILTER_TYPES = [
"data_meta",
"param_value",
"static_value",
"regexp",
"unique_value",
"multiple_splitter",
"attribute_value_splitter",
"add_value",
"remove_value",
"sort_by",
]
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": [
"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"]),
("./column", ["data_column"]),
]
[docs]def lint_inputs(tool_source: "ToolSource", lint_ctx: "LintContext"):
"""Lint parameters in a tool's inputs block."""
tool_xml = getattr(tool_source, "xml_tree", None)
if tool_xml is None:
return
profile = tool_source.parse_profile()
datasource = is_datasource(tool_xml)
input_names = set()
inputs = tool_xml.findall("./inputs//param")
# determine node to report for general problems with outputs
tool_node = tool_xml.find("./inputs")
if tool_node is None:
tool_node = tool_xml.getroot()
num_inputs = 0
for param in inputs:
num_inputs += 1
param_attrib = param.attrib
if "name" not in param_attrib and "argument" not in param_attrib:
lint_ctx.error("Found param input with no name specified.", node=param)
continue
param_name = _parse_name(param_attrib.get("name"), param_attrib.get("argument"))
if "name" in param_attrib and "argument" in param_attrib:
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.",
node=param,
)
if param_name.strip() == "":
lint_ctx.error("Param input with empty name.", node=param)
elif not is_valid_cheetah_placeholder(param_name):
lint_ctx.warn(f"Param input [{param_name}] is not a valid Cheetah placeholder.", node=param)
# check for parameters with duplicate names
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")))
path_str = ".".join(reversed(path))
if path_str in input_names:
lint_ctx.error(f"Tool defines multiple parameters with the same name: '{path_str}'", node=param)
input_names.add(path_str)
if "type" not in param_attrib:
lint_ctx.error(f"Param input [{param_name}] input with no type specified.", node=param)
continue
elif param_attrib["type"].strip() == "":
lint_ctx.error(f"Param input [{param_name}] with empty type specified.", node=param)
continue
param_type = param_attrib["type"]
# TODO lint for valid param type - attribute combinations
# 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]}",
node=param,
)
# param type specific linting
if param_type == "data":
if "format" not in param_attrib:
lint_ctx.warn(
f"Param input [{param_name}] with no format specified - 'data' format will be assumed.", node=param
)
options = param.findall("./options")
has_options_filter_attribute = False
if len(options) == 1:
for oa in options[0].attrib:
if oa == "options_filter_attribute":
has_options_filter_attribute = True
else:
lint_ctx.error(f"Data parameter [{param_name}] uses invalid attribute: {oa}", node=param)
elif len(options) > 1:
lint_ctx.error(f"Data parameter [{param_name}] contains multiple options elements.", node=options[1])
# for data params only filters with key='build' of type='data_meta' are allowed
filters = param.findall("./options/filter")
for f in filters:
if not f.get("ref"):
lint_ctx.error(
f"Data parameter [{param_name}] filter needs to define a ref attribute",
node=f,
)
if has_options_filter_attribute:
if f.get("type") != "data_meta":
lint_ctx.error(
f'Data parameter [{param_name}] for filters only type="data_meta" is allowed, found type="{f.get("type")}"',
node=f,
)
else:
if f.get("key") != "dbkey" or f.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="{f.get("type")}" and key="{f.get("key")}"',
node=f,
)
elif param_type == "select":
# get dynamic/statically defined options
dynamic_options = param.get("dynamic_options", None)
options = param.findall("./options")
filters = param.findall("./options/filter")
select_options = param.findall("./option")
if dynamic_options is not None:
lint_ctx.warn(
f"Select parameter [{param_name}] uses deprecated 'dynamic_options' attribute.", node=param
)
# check if options are defined by exactly one possibility
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.",
node=param,
)
else:
if len(select_options) == 0:
lint_ctx.error(
f"Select parameter of a conditional [{param_name}] options have to be defined by 'option' children elements.",
node=param,
)
# lint dynamic options
if len(options) == 1:
filters = options[0].findall("./filter")
# lint filters
# TODO check if dataset is available for filters referring other datasets
filter_adds_options = False
for f in filters:
ftype = f.get("type", None)
if ftype is None:
lint_ctx.error(f"Select parameter [{param_name}] contains filter without type.", node=f)
continue
if ftype not in FILTER_TYPES:
lint_ctx.error(
f"Select parameter [{param_name}] contains filter with unknown type '{ftype}'.", node=f
)
continue
if ftype in ["add_value", "data_meta"]:
filter_adds_options = True
# TODO more linting of filters
from_file = options[0].get("from_file", None)
from_parameter = options[0].get("from_parameter", None)
from_dataset = options[0].get("from_dataset", None)
from_data_table = options[0].get("from_data_table", None)
# TODO check if input param is present for from_dataset
if (
from_file is None
and from_parameter is None
and from_dataset is None
and from_data_table 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.",
node=options[0],
)
for deprecated_attr in ["from_file", "from_parameter", "options_filter_attribute", "transform_lines"]:
if options[0].get(deprecated_attr) is not None:
lint_ctx.warn(
f"Select parameter [{param_name}] options uses deprecated '{deprecated_attr}' attribute.",
node=options[0],
)
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.",
node=options[0],
)
if options[0].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'.",
node=options[0],
)
elif len(options) > 1:
lint_ctx.error(f"Select parameter [{param_name}] contains multiple options elements.", node=options[1])
# lint statically defined options
if any("value" not in option.attrib for option in select_options):
lint_ctx.error(f"Select parameter [{param_name}] has option without value", node=param)
if any(option.text is None for option in select_options):
lint_ctx.warn(f"Select parameter [{param_name}] has option without text", node=param)
select_options_texts = list()
select_options_values = list()
for option in select_options:
value = option.attrib.get("value", "")
if option.text is None:
text = value.capitalize()
else:
text = option.text
select_options_texts.append((text, option.attrib.get("selected", "false")))
select_options_values.append((value, 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", node=param
)
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", node=param)
if param_type == "boolean":
truevalue = param_attrib.get("truevalue", "true")
falsevalue = param_attrib.get("falsevalue", "false")
problematic_booleans_allowed = profile < "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.", node=param
)
if truevalue.lower() == "false":
lint_level(f"Boolean parameter [{param_name}] has invalid truevalue [{truevalue}].", node=param)
if falsevalue.lower() == "true":
lint_level(f"Boolean parameter [{param_name}] has invalid falsevalue [{falsevalue}].", node=param)
if param_type in ["select", "data_column", "drill_down"]:
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 multiple:
lint_ctx.error(
f'Select [{param_name}] `display="checkboxes"` is incompatible with `multiple="false"`, remove the `display` attribute',
node=param,
)
if not optional:
lint_ctx.error(
f'Select [{param_name}] `display="checkboxes"` is incompatible with `optional="false"`, remove the `display` attribute',
node=param,
)
if param_attrib.get("display") == "radio":
if multiple:
lint_ctx.error(
f'Select [{param_name}] display="radio" is incompatible with multiple="true"', node=param
)
if optional:
lint_ctx.error(
f'Select [{param_name}] display="radio" is incompatible with optional="true"', node=param
)
# TODO: Validate type, much more...
# lint validators
# TODO check if dataset is available for validators referring other datasets
validators = param.findall("./validator")
for validator in validators:
vtype = validator.attrib["type"]
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}'", node=validator
)
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}'",
node=validator,
)
if vtype in ["expression", "regex"]:
if validator.text is None:
lint_ctx.error(
f"Parameter [{param_name}]: {vtype} validators are expected to contain text", node=validator
)
else:
try:
if vtype == "regex":
re.compile(validator.text)
else:
ast.parse(validator.text, mode="eval")
except Exception as e:
lint_ctx.error(
f"Parameter [{param_name}]: '{validator.text}' is no valid regular expression: {str(e)}",
node=validator,
)
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}')",
node=validator,
)
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)",
node=validator,
)
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",
node=validator,
)
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",
node=validator,
)
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)",
node=validator,
)
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",
node=validator,
)
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",
node=validator,
)
conditional_selects = tool_xml.findall("./inputs//conditional")
for conditional in conditional_selects:
conditional_name = conditional.get("name")
if not conditional_name:
lint_ctx.error("Conditional without a name", node=conditional)
if conditional.get("value_from"):
# Probably only the upload tool use this, no children elements
continue
first_param = conditional.findall("param")
if len(first_param) != 1:
lint_ctx.error(
f"Conditional [{conditional_name}] needs exactly one child <param> found {len(first_param)}",
node=conditional,
)
continue
first_param = first_param[0]
first_param_type = first_param.get("type")
if first_param_type == "boolean":
lint_ctx.warn(
f'Conditional [{conditional_name}] first param of type="boolean" is discouraged, use a select',
node=first_param,
)
elif first_param_type != "select":
lint_ctx.error(f'Conditional [{conditional_name}] first param should have type="select"', node=first_param)
continue
if first_param_type == "select":
select_options = _find_with_attribute(first_param, "option", "value")
option_ids = [option.get("value") for option in select_options]
else: # boolean
option_ids = [first_param.get("truevalue", "true"), first_param.get("falsevalue", "false")]
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"', node=first_param
)
whens = conditional.findall("./when")
if any("value" not in when.attrib for when in whens):
lint_ctx.error(f"Conditional [{conditional_name}] when without value", node=conditional)
when_ids = [w.get("value") for w in whens if w.get("value") is not None]
for option_id in option_ids:
if option_id not in when_ids:
lint_ctx.warn(
f"Conditional [{conditional_name}] no <when /> block found for {first_param_type} option '{option_id}'",
node=conditional,
)
for when_id in when_ids:
if when_id not in option_ids:
if first_param_type == "select":
lint_ctx.warn(
f"Conditional [{conditional_name}] no <option /> found for when block '{when_id}'",
node=conditional,
)
else:
lint_ctx.warn(
f"Conditional [{conditional_name}] no truevalue/falsevalue found for when block '{when_id}'",
node=conditional,
)
if datasource:
# 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", node=tool_node)
if num_inputs:
lint_ctx.info(f"Found {num_inputs} input parameters.", node=tool_node)
else:
if datasource:
lint_ctx.info("No input parameters, OK for data sources", node=tool_node)
else:
lint_ctx.warn("Found no input parameters.", node=tool_node)
# check if there is an output with the same name as an input
outputs = tool_xml.find("./outputs")
if outputs is not None:
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")}\'',
node=output,
)
[docs]def lint_repeats(tool_source: "ToolSource", lint_ctx):
"""Lint repeat blocks in tool inputs."""
tool_xml = getattr(tool_source, "xml_tree", None)
if tool_xml is None:
return
repeats = tool_xml.findall("./inputs//repeat")
for repeat in repeats:
if "name" not in repeat.attrib:
lint_ctx.error("Repeat does not specify name attribute.", node=repeat)
if "title" not in repeat.attrib:
lint_ctx.error("Repeat does not specify title attribute.", node=repeat)
def _find_with_attribute(element, tag, attribute, test_value=None):
rval = []
for el in element.findall(f"./{tag}") or []:
if attribute not in el.attrib:
continue
value = el.attrib[attribute]
if test_value is not None:
if value == test_value:
rval.append(el)
else:
rval.append(el)
return rval