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Source code for galaxy.tool_util.linters.inputs

"""This module contains a linting functions for tool inputs."""
import re

from galaxy.util import string_as_bool
from ._util import (
from ..parser.util import _parse_name


    "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_in_data_table", "dataset_metadata_not_in_data_table", "dataset_metadata_in_file"],
    "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"]

    "integer": ["in_range", "expression"],
    "float": ["in_range", "expression"],
    "data": ["metadata", "unspecified_build", "dataset_ok_validator", "dataset_metadata_in_range", "dataset_metadata_in_file", "dataset_metadata_in_data_table", "dataset_metadata_not_in_data_table", "expression"],
    "data_collection": ["metadata", "unspecified_build", "dataset_ok_validator", "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"]

[docs]def lint_inputs(tool_xml, lint_ctx): """Lint parameters in a tool's inputs block.""" datasource = is_datasource(tool_xml) 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) # TODO lint for params with duplicated name (in inputs & outputs) 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 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) 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) 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 == "expression": if validator.text is None: lint_ctx.error(f"Parameter [{param_name}]: expression validators are expected to contain text", node=validator) else: try: re.compile(validator.text) 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 ["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) 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)
[docs]def lint_repeats(tool_xml, lint_ctx): """Lint repeat blocks in tool inputs.""" 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