Warning

This document is for an old release 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."""
from galaxy.util import string_as_bool
from ._util import is_datasource, is_valid_cheetah_placeholder
from ..parser.util import _parse_name


[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") num_inputs = 0 for param in inputs: num_inputs += 1 param_attrib = param.attrib has_errors = False if "type" not in param_attrib: lint_ctx.error("Found param input with no type specified.") has_errors = True if "name" not in param_attrib and "argument" not in param_attrib: lint_ctx.error("Found param input with no name specified.") has_errors = True if has_errors: continue param_type = param_attrib["type"] param_name = _parse_name(param_attrib.get("name"), param_attrib.get("argument")) if not is_valid_cheetah_placeholder(param_name): lint_ctx.warn("Param input [%s] is not a valid Cheetah placeholder.", param_name) if param_type == "data": if "format" not in param_attrib: lint_ctx.warn("Param input [%s] with no format specified - 'data' format will be assumed.", param_name) elif param_type == "select": dynamic_options = param.get("dynamic_options", None) if dynamic_options is None: dynamic_options = param.find("options") select_options = param.findall('./option') if any(['value' not in option.attrib for option in select_options]): lint_ctx.error("Select [%s] has option without value", param_name) if dynamic_options is None and len(select_options) == 0: message = "No options defined for select [%s]" % param_name lint_ctx.warn(message) # TODO: Validate type, much more... 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") 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: lint_ctx.error("Conditional '%s' has no child <param>" % conditional_name) continue first_param_type = first_param.get('type') if first_param_type not in ['select', 'boolean']: lint_ctx.warn("Conditional '%s' first param should have type=\"select\" /> or type=\"boolean\"" % conditional_name) 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') ] if string_as_bool(first_param.get('optional', False)): lint_ctx.warn("Conditional test parameter cannot be optional") whens = conditional.findall('./when') if any('value' not in when.attrib for when in whens): lint_ctx.error("When without value") when_ids = [w.get('value') for w in whens] for option_id in option_ids: if option_id not in when_ids: lint_ctx.warn(f"No <when /> block found for {first_param_type} option '{option_id}' inside conditional '{conditional_name}'") for when_id in when_ids: if when_id not in option_ids: if first_param_type == 'select': lint_ctx.warn(f"No <option /> found for when block '{when_id}' inside conditional '{conditional_name}'") else: lint_ctx.warn(f"No truevalue/falsevalue found for when block '{when_id}' inside conditional '{conditional_name}'") if datasource: for datasource_tag in ('display', 'uihints'): if not any([param.tag == datasource_tag for param in inputs]): lint_ctx.info("%s tag usually present in data sources" % datasource_tag) if num_inputs: lint_ctx.info("Found %d input parameters.", num_inputs) else: if datasource: lint_ctx.info("No input parameters, OK for data sources") else: lint_ctx.warn("Found no input parameters.")
[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.") if "title" not in repeat.attrib: lint_ctx.error("Repeat does not specify title attribute.")
def _find_with_attribute(element, tag, attribute, test_value=None): rval = [] for el in (element.findall('./%s' % 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