comparison toolfactory/galaxyxml/tool/parameters/__init__.py @ 38:a30536c100bf draft

Updated history outputs

37:099047ee7094

from builtins import str
from builtins import object
from lxml import etree
from galaxyxml import Util


class XMLParam(object):
    name = "node"

            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.

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"

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"

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)

        # 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)

            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 __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

        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:

            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):

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:

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):

        data_ref=None,
        display=None,
        multiple=None,
        options=None,
        default=None,
        **kwargs,
    ):
        params = Util.clean_kwargs(locals().copy())
        del params["options"]
        del params["default"]

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)

        separator=None,
        keep=None,
        value=None,
        ref_attribute=None,
        index=None,
        **kwargs,
    ):
        params = Util.clean_kwargs(locals().copy())
        super(Filter, self).__init__(**params)

        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)

        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:

    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"

        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):

        md5=None,
        checksum=None,
        compare=None,
        lines_diff=None,
        delta=None,
        **kwargs,
    ):
        params = Util.clean_kwargs(locals().copy())
        super(TestOutput, self).__init__(**params)

38:a30536c100bf

from builtins import object
from builtins import str

from galaxyxml import Util

from lxml import etree



class XMLParam(object):
    name = "node"

            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.

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"

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"

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)

        # 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)

            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 __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

        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:

            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):

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:

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):

        data_ref=None,
        display=None,
        multiple=None,
        options=None,
        default=None,
        **kwargs
    ):
        params = Util.clean_kwargs(locals().copy())
        del params["options"]
        del params["default"]

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)

        separator=None,
        keep=None,
        value=None,
        ref_attribute=None,
        index=None,
        **kwargs
    ):
        params = Util.clean_kwargs(locals().copy())
        super(Filter, self).__init__(**params)

        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)

        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:

    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"

        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):

        md5=None,
        checksum=None,
        compare=None,
        lines_diff=None,
        delta=None,
        **kwargs
    ):
        params = Util.clean_kwargs(locals().copy())
        super(TestOutput, self).__init__(**params)