annotate toolfactory/galaxyxml/tool/parameters/__init__.py @ 92:6ce360759c28 draft

Uploaded

from builtins import object
from builtins import str

from galaxyxml import Util

from lxml import etree



class XMLParam(object):
    name = "node"

    def __init__(self, *args, **kwargs):
        # http://stackoverflow.com/a/12118700
        self.children = []
        kwargs = {k: v for k, v in list(kwargs.items()) if v is not None}
        kwargs = Util.coerce(kwargs, kill_lists=True)
        kwargs = Util.clean_kwargs(kwargs, final=True)
        self.node = etree.Element(self.name, **kwargs)

    def append(self, sub_node):
        if self.acceptable_child(sub_node):
            # If one of ours, they aren't etree nodes, they're custom objects
            if issubclass(type(sub_node), XMLParam):
                self.node.append(sub_node.node)
                self.children.append(sub_node)
            else:
                raise Exception(
                    "Child was unacceptable to parent (%s is not appropriate for %s)" % (type(self), type(sub_node))
                )
        else:
            raise Exception(
                "Child was unacceptable to parent (%s is not appropriate for %s)" % (type(self), type(sub_node))
            )

    def validate(self):
        # Very few need validation, but some nodes we may want to have
        # validation routines on. Should only be called when DONE.
        for child in self.children:
            # If any child fails to validate return false.
            if not child.validate():
                return False
        return True

    def cli(self):
        lines = []
        for child in self.children:
            lines.append(child.command_line())
            # lines += child.command_line()
        return "\n".join(lines)

    def command_line(self):
        return None


class RequestParamTranslation(XMLParam):
    name = "request_param_translation"

    def __init__(self, **kwargs):
        self.node = etree.Element(self.name)

    def acceptable_child(self, child):
        return isinstance(child, RequestParamTranslation)


class RequestParam(XMLParam):
    name = "request_param"

    def __init__(self, galaxy_name, remote_name, missing, **kwargs):
        # TODO: bulk copy locals into self.attr?
        self.galaxy_name = galaxy_name
        # http://stackoverflow.com/a/1408860
        params = Util.clean_kwargs(locals().copy())
        super(RequestParam, self).__init__(**params)

    def acceptable_child(self, child):
        return isinstance(child, AppendParam) and self.galaxy_name == "URL"


class AppendParam(XMLParam):
    name = "append_param"

    def __init__(self, separator="&", first_separator="?", join="=", **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(AppendParam, self).__init__(**params)

    def acceptable_child(self, child):
        return isinstance(child, AppendParamValue)


class AppendParamValue(XMLParam):
    name = "value"

    def __init__(self, name="_export", missing="1", **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(AppendParamValue, self).__init__(**params)

    def acceptable_child(self, child):
        return False


class EdamOperations(XMLParam):
    name = "edam_operations"

    def acceptable_child(self, child):
        return issubclass(type(child), EdamOperation)

    def has_operation(self, edam_operation):
        """
        Check the presence of a given edam_operation.

        :type edam_operation: STRING
        """
        for operation in self.children:
            if operation.node.text == edam_operation:
                return True
        return False


class EdamOperation(XMLParam):
    name = "edam_operation"

    def __init__(self, value):
        super(EdamOperation, self).__init__()
        self.node.text = str(value)


class EdamTopics(XMLParam):
    name = "edam_topics"

    def acceptable_child(self, child):
        return issubclass(type(child), EdamTopic)

    def has_topic(self, edam_topic):
        """
        Check the presence of a given edam_topic.

        :type edam_topic: STRING
        """
        for topic in self.children:
            if topic.node.text == edam_topic:
                return True
        return False


class EdamTopic(XMLParam):
    name = "edam_topic"

    def __init__(self, value):
        super(EdamTopic, self).__init__()
        self.node.text = str(value)


class Requirements(XMLParam):
    name = "requirements"
    # This bodes to be an issue -__-

    def acceptable_child(self, child):
        return issubclass(type(child), Requirement) or issubclass(type(child), Container)


class Requirement(XMLParam):
    name = "requirement"

    def __init__(self, type, value, version=None, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        passed_kwargs = {}
        passed_kwargs["version"] = params["version"]
        passed_kwargs["type"] = params["type"]
        super(Requirement, self).__init__(**passed_kwargs)
        self.node.text = str(value)


class Container(XMLParam):
    name = "container"

    def __init__(self, type, value, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        passed_kwargs = {}
        passed_kwargs["type"] = params["type"]
        super(Container, self).__init__(**passed_kwargs)
        self.node.text = str(value)


class Configfiles(XMLParam):
    name = "configfiles"

    def acceptable_child(self, child):
        return issubclass(type(child), Configfile) or issubclass(type(child), ConfigfileDefaultInputs)


class Configfile(XMLParam):
    name = "configfile"

    def __init__(self, name, text, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        passed_kwargs = {}
        passed_kwargs["name"] = params["name"]
        super(Configfile, self).__init__(**passed_kwargs)
        self.node.text = etree.CDATA(str(text))


class ConfigfileDefaultInputs(XMLParam):
    name = "inputs"

    def __init__(self, name, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        passed_kwargs = {}
        passed_kwargs["name"] = params["name"]
        super(ConfigfileDefaultInputs, self).__init__(**passed_kwargs)


class Inputs(XMLParam):
    name = "inputs"
    # This bodes to be an issue -__-

    def __init__(self, action=None, check_value=None, method=None, target=None, nginx_upload=None, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(Inputs, self).__init__(**params)

    def acceptable_child(self, child):
        return issubclass(type(child), InputParameter)


class InputParameter(XMLParam):
    def __init__(self, name, **kwargs):
        # TODO: look at
        self.mako_identifier = name
        # We use kwargs instead of the usual locals(), so manually copy the
        # name to kwargs
        if name is not None:
            kwargs["name"] = name

        # Handle positional parameters
        if "positional" in kwargs and kwargs["positional"]:
            self.positional = True
        else:
            self.positional = False

        if "num_dashes" in kwargs:
            self.num_dashes = kwargs["num_dashes"]
            del kwargs["num_dashes"]
        else:
            self.num_dashes = 0

        self.space_between_arg = " "

        # Not sure about this :(
        # https://wiki.galaxyproject.org/Tools/BestPractices#Parameter_help
        if "label" in kwargs:
            # TODO: replace with positional attribute
            if len(self.flag()) > 0:
                if kwargs["label"] is None:
                    kwargs["label"] = "Author did not provide help for this parameter... "
                if not self.positional:
                    kwargs["argument"] = self.flag()

        super(InputParameter, self).__init__(**kwargs)

    def command_line(self):
        before = self.command_line_before()
        cli = self.command_line_actual()
        after = self.command_line_after()

        complete = [x for x in (before, cli, after) if x is not None]
        return "\n".join(complete)

    def command_line_before(self):
        try:
            return self.command_line_before_override
        except Exception:
            return None

    def command_line_after(self):
        try:
            return self.command_line_after_override
        except Exception:
            return None

    def command_line_actual(self):
        try:
            return self.command_line_override
        except Exception:
            if self.positional:
                return self.mako_name()
            else:
                return "%s%s%s" % (self.flag(), self.space_between_arg, self.mako_name())

    def mako_name(self):
        # TODO: enhance logic to check up parents for things like
        # repeat>condotion>param
        return "$" + self.mako_identifier

    def flag(self):
        flag = "-" * self.num_dashes
        return flag + self.mako_identifier


class Section(InputParameter):
    name = "section"

    def __init__(self, name, title, expanded=None, help=None, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(Section, self).__init__(**params)

    def acceptable_child(self, child):
        return issubclass(type(child), InputParameter)


class Repeat(InputParameter):
    name = "repeat"

    def __init__(self, name, title, min=None, max=None, default=None, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        # Allow overriding
        self.command_line_before_override = "#for $i in $%s:" % name
        self.command_line_after_override = "#end for"
        # self.command_line_override
        super(Repeat, self).__init__(**params)

    def acceptable_child(self, child):
        return issubclass(type(child), InputParameter)

    def command_line_actual(self):
        if hasattr(self, "command_line_override"):
            return self.command_line_override
        else:
            return "%s" % self.mako_name()


class Conditional(InputParameter):
    name = "conditional"

    def __init__(self, name, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(Conditional, self).__init__(**params)

    def acceptable_child(self, child):
        return issubclass(type(child), InputParameter) and not isinstance(child, Conditional)

    def validate(self):
        # Find a way to check if one of the kids is a WHEN
        pass


class When(InputParameter):
    name = "when"

    def __init__(self, value):
        params = Util.clean_kwargs(locals().copy())
        super(When, self).__init__(None, **params)

    def acceptable_child(self, child):
        return issubclass(type(child), InputParameter)


class Param(InputParameter):
    name = "param"

    # This...isn't really valid as-is, and shouldn't be used.
    def __init__(self, name, optional=None, label=None, help=None, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        params["type"] = self.type
        super(Param, self).__init__(**params)

        if type(self) == Param:
            raise Exception("Param class is not an actual parameter type, use a subclass of Param")

    def acceptable_child(self, child):
        return issubclass(type(child, InputParameter) or isinstance(child), ValidatorParam)


class TextParam(Param):
    type = "text"

    def __init__(self, name, optional=None, label=None, help=None, value=None, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(TextParam, self).__init__(**params)

    def command_line_actual(self):
        try:
            return self.command_line_override
        except Exception:
            if self.positional:
                return self.mako_name()
            else:
                return f"{self.flag}{self.space_between_arg}'{self.mako_name()}'"


class _NumericParam(Param):
    def __init__(self, name, value, optional=None, label=None, help=None, min=None, max=None, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(_NumericParam, self).__init__(**params)


class IntegerParam(_NumericParam):
    type = "integer"


class FloatParam(_NumericParam):
    type = "float"


class BooleanParam(Param):
    type = "boolean"

    def __init__(
        self, name, optional=None, label=None, help=None, checked=False, truevalue=None, falsevalue=None, **kwargs
    ):
        params = Util.clean_kwargs(locals().copy())

        super(BooleanParam, self).__init__(**params)
        if truevalue is None:
            # If truevalue and falsevalue are None, then we use "auto", the IUC
            # recommended default.
            #
            # truevalue is set to the parameter's value, and falsevalue is not.
            #
            # Unfortunately, mako_identifier is set as a result of the super
            # call, which we shouldn't call TWICE, so we'll just hack around this :(
            # params['truevalue'] = '%s%s' % (self.)
            self.node.attrib["truevalue"] = self.flag()

        if falsevalue is None:
            self.node.attrib["falsevalue"] = ""

    def command_line_actual(self):
        if hasattr(self, "command_line_override"):
            return self.command_line_override
        else:
            return "%s" % self.mako_name()


class DataParam(Param):
    type = "data"

    def __init__(self, name, optional=None, label=None, help=None, format=None, multiple=None, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(DataParam, self).__init__(**params)


class SelectParam(Param):
    type = "select"

    def __init__(
        self,
        name,
        optional=None,
        label=None,
        help=None,
        data_ref=None,
        display=None,
        multiple=None,
        options=None,
        default=None,
        **kwargs
    ):
        params = Util.clean_kwargs(locals().copy())
        del params["options"]
        del params["default"]

        super(SelectParam, self).__init__(**params)

        if options is not None and default is not None:
            if default not in options:
                raise Exception("Specified a default that isn't in options")

        if options:
            for k, v in list(sorted(options.items())):
                selected = k == default
                self.append(SelectOption(k, v, selected=selected))

    def acceptable_child(self, child):
        return issubclass(type(child), SelectOption) or issubclass(type(child), Options)


class SelectOption(InputParameter):
    name = "option"

    def __init__(self, value, text, selected=False, **kwargs):
        params = Util.clean_kwargs(locals().copy())

        passed_kwargs = {}
        if selected:
            passed_kwargs["selected"] = "true"
        passed_kwargs["value"] = params["value"]

        super(SelectOption, self).__init__(None, **passed_kwargs)
        self.node.text = str(text)


class Options(InputParameter):
    name = "options"

    def __init__(self, from_dataset=None, from_file=None, from_data_table=None, from_parameter=None, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(Options, self).__init__(None, **params)

    def acceptable_child(self, child):
        return issubclass(type(child), Column) or issubclass(type(child), Filter)


class Column(InputParameter):
    name = "column"

    def __init__(self, name, index, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(Column, self).__init__(**params)


class Filter(InputParameter):
    name = "filter"

    def __init__(
        self,
        type,
        column=None,
        name=None,
        ref=None,
        key=None,
        multiple=None,
        separator=None,
        keep=None,
        value=None,
        ref_attribute=None,
        index=None,
        **kwargs
    ):
        params = Util.clean_kwargs(locals().copy())
        super(Filter, self).__init__(**params)


class ValidatorParam(InputParameter):
    name = "validator"

    def __init__(
        self,
        type,
        message=None,
        filename=None,
        metadata_name=None,
        metadata_column=None,
        line_startswith=None,
        min=None,
        max=None,
        **kwargs
    ):
        params = Util.clean_kwargs(locals().copy())
        super(ValidatorParam, self).__init__(**params)


class Outputs(XMLParam):
    name = "outputs"

    def acceptable_child(self, child):
        return isinstance(child, OutputData) or isinstance(child, OutputCollection)


class OutputData(XMLParam):
    """Copypasta of InputParameter, needs work
    """

    name = "data"

    def __init__(
        self,
        name,
        format,
        format_source=None,
        metadata_source=None,
        label=None,
        from_work_dir=None,
        hidden=False,
        **kwargs
    ):
        # TODO: validate format_source&metadata_source against something in the
        # XMLParam children tree.
        self.mako_identifier = name
        if "num_dashes" in kwargs:
            self.num_dashes = kwargs["num_dashes"]
            del kwargs["num_dashes"]
        else:
            self.num_dashes = 0
        self.space_between_arg = " "
        params = Util.clean_kwargs(locals().copy())

        super(OutputData, self).__init__(**params)

    def command_line(self):
        if hasattr(self, "command_line_override"):
            return self.command_line_override
        else:
            return "%s%s%s" % (self.flag(), self.space_between_arg, self.mako_name())

    def mako_name(self):
        return "$" + self.mako_identifier

    def flag(self):
        flag = "-" * self.num_dashes
        return flag + self.mako_identifier

    def acceptable_child(self, child):
        return isinstance(child, OutputFilter) or isinstance(child, ChangeFormat) or isinstance(child, DiscoverDatasets)


class OutputFilter(XMLParam):
    name = "filter"

    def __init__(self, text, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        del params["text"]
        super(OutputFilter, self).__init__(**params)
        self.node.text = text

    def acceptable_child(self, child):
        return False


class ChangeFormat(XMLParam):
    name = "change_format"

    def __init__(self, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(ChangeFormat, self).__init__(**params)

    def acceptable_child(self, child):
        return isinstance(child, ChangeFormatWhen)


class ChangeFormatWhen(XMLParam):
    name = "when"

    def __init__(self, input, format, value, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(ChangeFormatWhen, self).__init__(**params)

    def acceptable_child(self, child):
        return False


class OutputCollection(XMLParam):
    name = "collection"

    def __init__(
        self,
        name,
        type=None,
        label=None,
        format_source=None,
        type_source=None,
        structured_like=None,
        inherit_format=None,
        **kwargs
    ):
        params = Util.clean_kwargs(locals().copy())
        super(OutputCollection, self).__init__(**params)

    def acceptable_child(self, child):
        return isinstance(child, OutputData) or isinstance(child, OutputFilter) or isinstance(child, DiscoverDatasets)


class DiscoverDatasets(XMLParam):
    name = "discover_datasets"

    def __init__(self, pattern, directory=None, format=None, ext=None, visible=None, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(DiscoverDatasets, self).__init__(**params)


class Tests(XMLParam):
    name = "tests"

    def acceptable_child(self, child):
        return issubclass(type(child), Test)


class Test(XMLParam):
    name = "test"

    def acceptable_child(self, child):
        return isinstance(child, TestParam) or isinstance(child, TestOutput)


class TestParam(XMLParam):
    name = "param"

    def __init__(self, name, value=None, ftype=None, dbkey=None, **kwargs):
        params = Util.clean_kwargs(locals().copy())
        super(TestParam, self).__init__(**params)


class TestOutput(XMLParam):
    name = "output"

    def __init__(
        self,
        name=None,
        file=None,
        ftype=None,
        sort=None,
        value=None,
        md5=None,
        checksum=None,
        compare=None,
        lines_diff=None,
        delta=None,
        **kwargs
    ):
        params = Util.clean_kwargs(locals().copy())
        super(TestOutput, self).__init__(**params)


class Citations(XMLParam):
    name = "citations"

    def acceptable_child(self, child):
        return issubclass(type(child), Citation)

    def has_citation(self, type, value):
        """
        Check the presence of a given citation.

        :type type: STRING
        :type value: STRING
        """
        for citation in self.children:
            if citation.node.attrib["type"] == type and citation.node.text == value:
                return True
        return False


class Citation(XMLParam):
    name = "citation"

    def __init__(self, type, value):
        passed_kwargs = {}
        passed_kwargs["type"] = type
        super(Citation, self).__init__(**passed_kwargs)
        self.node.text = str(value)