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 (
    is_datasource,
    is_valid_cheetah_placeholder
)
from ..parser.util import _parse_name

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_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"]
}

PARAMETER_VALIDATOR_TYPE_COMPATIBILITY = {
    "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