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.tools.parser.output_actions

"""
Support for dynamically modifying output attributes.
"""

import logging
import os.path
import re

from galaxy import util

log = logging.getLogger(__name__)


class ToolOutputActionGroup(object):
    """
    Manages a set of tool output dataset actions directives
    """
    tag = "group"

    def __init__(self, parent, config_elem):
        self.parent = parent
        self.actions = []
        if config_elem is not None:
            for elem in config_elem:
                if elem.tag == "conditional":
                    self.actions.append(ToolOutputActionConditional(self, elem))
                elif elem.tag == "action":
                    self.actions.append(ToolOutputAction.from_elem(self, elem))
                else:
                    log.debug("Unknown ToolOutputAction tag specified: %s" % elem.tag)

    def apply_action(self, output_dataset, other_values):
        for action in self.actions:
            action.apply_action(output_dataset, other_values)

    @property
    def tool(self):
        return self.parent.tool

    def __len__(self):
        return len(self.actions)


class ToolOutputActionConditionalWhen(ToolOutputActionGroup):
    tag = "when"

    @classmethod
    def from_elem(cls, parent, when_elem):
        """Loads the proper when by attributes of elem"""
        when_value = when_elem.get("value", None)
        if when_value is not None:
            return ValueToolOutputActionConditionalWhen(parent, when_elem, when_value)
        else:
            when_value = when_elem.get("datatype_isinstance", None)
            if when_value is not None:
                return DatatypeIsInstanceToolOutputActionConditionalWhen(parent, when_elem, when_value)
        raise TypeError("When type not implemented")

    def __init__(self, parent, config_elem, value):
        super(ToolOutputActionConditionalWhen, self).__init__(parent, config_elem)
        self.value = value

    def is_case(self, output_dataset, other_values):
        raise TypeError("Not implemented")

    def get_ref(self, output_dataset, other_values):
        ref = other_values
        for ref_name in self.parent.name:
            assert ref_name in ref, "Required dependency '%s' not found in incoming values" % ref_name
            ref = ref.get(ref_name)
        return ref

    def apply_action(self, output_dataset, other_values):
        if self.is_case(output_dataset, other_values):
            return super(ToolOutputActionConditionalWhen, self).apply_action(output_dataset, other_values)


class ValueToolOutputActionConditionalWhen(ToolOutputActionConditionalWhen):
    tag = "when value"

    def is_case(self, output_dataset, other_values):
        ref = self.get_ref(output_dataset, other_values)
        return bool(str(ref) == self.value)


class DatatypeIsInstanceToolOutputActionConditionalWhen(ToolOutputActionConditionalWhen):
    tag = "when datatype_isinstance"

    def __init__(self, parent, config_elem, value):
        super(DatatypeIsInstanceToolOutputActionConditionalWhen, self).__init__(parent, config_elem, value)
        self.value = type(self.tool.app.datatypes_registry.get_datatype_by_extension(value))

    def is_case(self, output_dataset, other_values):
        ref = self.get_ref(output_dataset, other_values)
        return isinstance(ref.datatype, self.value)


class ToolOutputActionConditional(object):
    tag = "conditional"

    def __init__(self, parent, config_elem):
        self.parent = parent
        self.name = config_elem.get('name', None)
        assert self.name is not None, "Required 'name' attribute missing from ToolOutputActionConditional"
        self.name = self.name.split('.')
        self.cases = []
        for when_elem in config_elem.findall('when'):
            self.cases.append(ToolOutputActionConditionalWhen.from_elem(self, when_elem))

    def apply_action(self, output_dataset, other_values):
        for case in self.cases:
            case.apply_action(output_dataset, other_values)

    @property
    def tool(self):
        return self.parent.tool


class ToolOutputAction(object):
    tag = "action"

    @classmethod
    def from_elem(cls, parent, elem):
        """Loads the proper action by the type attribute of elem"""
        action_type = elem.get('type', None)
        assert action_type is not None, "Required 'type' attribute missing from ToolOutputAction"
        return action_types[action_type](parent, elem)

    def __init__(self, parent, elem):
        self.parent = parent
        self.default = elem.get('default', None)
        option_elem = elem.find('option')
        self.option = ToolOutputActionOption.from_elem(self, option_elem)

    def apply_action(self, output_dataset, other_values):
        raise TypeError("Not implemented")

    @property
    def tool(self):
        return self.parent.tool


class ToolOutputActionOption(object):
    tag = "object"

    @classmethod
    def from_elem(cls, parent, elem):
        """Loads the proper action by the type attribute of elem"""
        if elem is None:
            option_type = NullToolOutputActionOption.tag  # no ToolOutputActionOption's have been defined, use implicit NullToolOutputActionOption
        else:
            option_type = elem.get('type', None)
        assert option_type is not None, "Required 'type' attribute missing from ToolOutputActionOption"
        return option_types[option_type](parent, elem)

    def __init__(self, parent, elem):
        self.parent = parent
        self.filters = []
        if elem is not None:
            for filter_elem in elem.findall('filter'):
                self.filters.append(ToolOutputActionOptionFilter.from_elem(self, filter_elem))

    def get_value(self, other_values):
        raise TypeError("Not implemented")

    @property
    def tool(self):
        return self.parent.tool


class NullToolOutputActionOption(ToolOutputActionOption):
    tag = "null_option"

    def get_value(self, other_values):
        return None


class FromFileToolOutputActionOption(ToolOutputActionOption):
    tag = "from_file"

    def __init__(self, parent, elem):
        super(FromFileToolOutputActionOption, self).__init__(parent, elem)
        self.name = elem.get('name', None)
        assert self.name is not None, "Required 'name' attribute missing from FromFileToolOutputActionOption"
        self.column = elem.get('column', None)
        assert self.column is not None, "Required 'column' attribute missing from FromFileToolOutputActionOption"
        self.column = int(self.column)
        self.offset = elem.get('offset', -1)
        self.offset = int(self.offset)
        self.separator = elem.get('separator', '\t')
        self.options = []
        data_file = self.name
        if not os.path.isabs(data_file):
            data_file = os.path.join(self.tool.app.config.tool_data_path, data_file)
        for line in open(data_file):
            self.options.append(line.rstrip('\n\r').split(self.separator))

    def get_value(self, other_values):
        options = self.options
        for filter in self.filters:
            options = filter.filter_options(options, other_values)
        try:
            if options:
                return str(options[self.offset][self.column])
        except Exception as e:
            log.debug("Error in FromFileToolOutputActionOption get_value: %s" % e)
        return None


class FromParamToolOutputActionOption(ToolOutputActionOption):
    tag = "from_param"

    def __init__(self, parent, elem):
        super(FromParamToolOutputActionOption, self).__init__(parent, elem)
        self.name = elem.get('name', None)
        assert self.name is not None, "Required 'name' attribute missing from FromFileToolOutputActionOption"
        self.name = self.name.split('.')
        self.column = elem.get('column', 0)
        self.column = int(self.column)
        self.offset = elem.get('offset', -1)
        self.offset = int(self.offset)
        self.param_attribute = elem.get('param_attribute', [])
        if self.param_attribute:
            self.param_attribute = self.param_attribute.split('.')

    def get_value(self, other_values):
        value = other_values
        for ref_name in self.name:
            assert ref_name in value, "Required dependency '%s' not found in incoming values" % ref_name
            value = value.get(ref_name)
        for attr_name in self.param_attribute:
            # if the value is a list from a repeat tag you can access the first element of the repeat with
            # artifical 'first' attribute_name. For example: .. param_attribute="first.input_mate1.ext"
            if isinstance(value, list) and attr_name == 'first':
                value = value[0]
            elif isinstance(value, dict):
                value = value[attr_name]
            elif hasattr(value, "collection"):
                # if this is an HDCA for instance let reverse.ext grab
                # the reverse element and then continue for loop to grab
                # dataset extension
                try:
                    value = value.collection[attr_name].element_object
                except KeyError:
                    value = value.child_collection[attr_name].element_object
            else:
                value = getattr(value, attr_name)
        options = [[str(value)]]
        for filter in self.filters:
            options = filter.filter_options(options, other_values)
        try:
            if options:
                return str(options[self.offset][self.column])
        except Exception as e:
            log.debug("Error in FromParamToolOutputActionOption get_value: %s" % e)
        return None


class FromDataTableOutputActionOption(ToolOutputActionOption):
    tag = "from_data_table"

    # TODO: allow accessing by column 'name' not just index
    def __init__(self, parent, elem):
        super(FromDataTableOutputActionOption, self).__init__(parent, elem)
        self.name = elem.get('name', None)
        assert self.name is not None, "Required 'name' attribute missing from FromDataTableOutputActionOption"
        self.missing_tool_data_table_name = None
        if self.name in self.tool.app.tool_data_tables:
            self.options = self.tool.app.tool_data_tables[self.name].get_fields()
            self.column = elem.get('column', None)
            assert self.column is not None, "Required 'column' attribute missing from FromDataTableOutputActionOption"
            self.column = int(self.column)
            self.offset = elem.get('offset', -1)
            self.offset = int(self.offset)
        else:
            self.options = []
            self.missing_tool_data_table_name = self.name

    def get_value(self, other_values):
        if self.options:
            options = self.options
        else:
            options = []
        for filter in self.filters:
            options = filter.filter_options(options, other_values)
        try:
            if options:
                return str(options[self.offset][self.column])
        except Exception as e:
            log.debug("Error in FromDataTableOutputActionOption get_value: %s" % e)
        return None


class MetadataToolOutputAction(ToolOutputAction):
    tag = "metadata"

    def __init__(self, parent, elem):
        super(MetadataToolOutputAction, self).__init__(parent, elem)
        self.name = elem.get('name', None)
        assert self.name is not None, "Required 'name' attribute missing from MetadataToolOutputAction"

    def apply_action(self, output_dataset, other_values):
        value = self.option.get_value(other_values)
        if value is None and self.default is not None:
            value = self.default
        if value is not None:
            setattr(output_dataset.metadata, self.name, value)


class FormatToolOutputAction(ToolOutputAction):
    tag = "format"

    def __init__(self, parent, elem):
        super(FormatToolOutputAction, self).__init__(parent, elem)
        self.default = elem.get('default', None)

    def apply_action(self, output_dataset, other_values):
        value = self.option.get_value(other_values)
        if value is None and self.default is not None:
            value = self.default
        if value is not None:
            output_dataset.extension = value


class ToolOutputActionOptionFilter(object):
    tag = "filter"

    @classmethod
    def from_elem(cls, parent, elem):
        """Loads the proper action by the type attribute of elem"""
        filter_type = elem.get('type', None)
        assert filter_type is not None, "Required 'type' attribute missing from ToolOutputActionOptionFilter"
        return filter_types[filter_type](parent, elem)

    def __init__(self, parent, elem):
        self.parent = parent

    def filter_options(self, options, other_values):
        raise TypeError("Not implemented")

    @property
    def tool(self):
        return self.parent.tool


class ParamValueToolOutputActionOptionFilter(ToolOutputActionOptionFilter):
    tag = "param_value"

    def __init__(self, parent, elem):
        super(ParamValueToolOutputActionOptionFilter, self).__init__(parent, elem)
        self.ref = elem.get('ref', None)
        if self.ref:
            self.ref = self.ref.split('.')
        self.value = elem.get('value', None)
        assert self.ref != self.value, "Required 'ref' or 'value' attribute missing from ParamValueToolOutputActionOptionFilter"
        self.column = elem.get('column', None)
        assert self.column is not None, "Required 'column' attribute missing from ParamValueToolOutputActionOptionFilter"
        self.column = int(self.column)
        self.keep = util.string_as_bool(elem.get("keep", 'True'))
        self.compare = parse_compare_type(elem.get('compare', None))
        self.cast = parse_cast_attribute(elem.get("cast", None))
        self.param_attribute = elem.get('param_attribute', [])
        if self.param_attribute:
            self.param_attribute = self.param_attribute.split('.')

    def filter_options(self, options, other_values):
        if self.ref:
            # find ref value
            value = other_values
            for ref_name in self.ref:
                assert ref_name in value, "Required dependency '%s' not found in incoming values" % ref_name
                value = value.get(ref_name)
            for attr_name in self.param_attribute:
                value = getattr(value, attr_name)
            value = str(value)
        else:
            value = self.value
        value = self.cast(value)
        rval = []
        for fields in options:
            try:
                if self.keep == (self.compare(self.cast(fields[self.column]), value)):
                    rval.append(fields)
            except Exception as e:
                log.debug(e)
                continue  # likely a bad cast or column out of range
        return rval


class InsertColumnToolOutputActionOptionFilter(ToolOutputActionOptionFilter):
    tag = "insert_column"

    def __init__(self, parent, elem):
        super(InsertColumnToolOutputActionOptionFilter, self).__init__(parent, elem)
        self.ref = elem.get('ref', None)
        if self.ref:
            self.ref = self.ref.split('.')
        self.value = elem.get('value', None)
        assert self.ref != self.value, "Required 'ref' or 'value' attribute missing from InsertColumnToolOutputActionOptionFilter"
        self.column = elem.get('column', None)  # None is append
        if self.column:
            self.column = int(self.column)
        self.iterate = util.string_as_bool(elem.get("iterate", 'False'))

    def filter_options(self, options, other_values):
        if self.ref:
            # find ref value
            value = other_values
            for ref_name in self.ref:
                assert ref_name in value, "Required dependency '%s' not found in incoming values" % ref_name
                value = value.get(ref_name)
            value = str(value)
        else:
            value = self.value
        if self.iterate:
            value = int(value)
        rval = []
        for fields in options:
            if self.column is None:
                rval.append(fields + [str(value)])
            else:
                fields = list(fields)
                fields.insert(self.column, str(value))
                rval.append(fields)
            if self.iterate:
                value += 1
        return rval


class MultipleSplitterFilter(ToolOutputActionOptionFilter):
    tag = "multiple_splitter"

    def __init__(self, parent, elem):
        super(MultipleSplitterFilter, self).__init__(parent, elem)
        self.column = elem.get('column', None)
        assert self.column is not None, "Required 'column' attribute missing from MultipleSplitterFilter"
        self.column = int(self.column)
        self.separator = elem.get("separator", ",")

    def filter_options(self, options, other_values):
        rval = []
        for fields in options:
            for field in fields[self.column].split(self.separator):
                rval.append(fields[0:self.column] + [field] + fields[self.column + 1:])
        return rval


class ColumnStripFilter(ToolOutputActionOptionFilter):
    tag = "column_strip"

    def __init__(self, parent, elem):
        super(ColumnStripFilter, self).__init__(parent, elem)
        self.column = elem.get('column', None)
        assert self.column is not None, "Required 'column' attribute missing from ColumnStripFilter"
        self.column = int(self.column)
        self.strip = elem.get("strip", None)

    def filter_options(self, options, other_values):
        rval = []
        for fields in options:
            rval.append(fields[0:self.column] + [fields[self.column].strip(self.strip)] + fields[self.column + 1:])
        return rval


class ColumnReplaceFilter(ToolOutputActionOptionFilter):
    tag = "column_replace"

    def __init__(self, parent, elem):
        super(ColumnReplaceFilter, self).__init__(parent, elem)
        self.old_column = elem.get('old_column', None)
        self.old_value = elem.get("old_value", None)
        self.new_value = elem.get("new_value", None)
        self.new_column = elem.get('new_column', None)
        assert (bool(self.old_column) ^ bool(self.old_value) and bool(self.new_column) ^ bool(self.new_value)), "Required 'old_column' or 'old_value' and 'new_column' or 'new_value' attribute missing from ColumnReplaceFilter"
        self.column = elem.get('column', None)
        assert self.column is not None, "Required 'column' attribute missing from ColumnReplaceFilter"
        self.column = int(self.column)
        if self.old_column is not None:
            self.old_column = int(self.old_column)
        if self.new_column is not None:
            self.new_column = int(self.new_column)

    def filter_options(self, options, other_values):
        rval = []
        for fields in options:
            if self.old_column:
                old_value = fields[self.old_column]
            else:
                old_value = self.old_value
            if self.new_column:
                new_value = fields[self.new_column]
            else:
                new_value = self.new_value
            rval.append(fields[0:self.column] + [fields[self.column].replace(old_value, new_value)] + fields[self.column + 1:])
        return rval


class MetadataValueFilter(ToolOutputActionOptionFilter):
    tag = "metadata_value"

    def __init__(self, parent, elem):
        super(MetadataValueFilter, self).__init__(parent, elem)
        self.ref = elem.get('ref', None)
        assert self.ref is not None, "Required 'ref' attribute missing from MetadataValueFilter"
        self.ref = self.ref.split('.')
        self.name = elem.get('name', None)
        assert self.name is not None, "Required 'name' attribute missing from MetadataValueFilter"
        self.column = elem.get('column', None)
        assert self.column is not None, "Required 'column' attribute missing from MetadataValueFilter"
        self.column = int(self.column)
        self.keep = util.string_as_bool(elem.get("keep", 'True'))
        self.compare = parse_compare_type(elem.get('compare', None))

    def filter_options(self, options, other_values):
        ref = other_values
        for ref_name in self.ref:
            assert ref_name in ref, "Required dependency '%s' not found in incoming values" % ref_name
            ref = ref.get(ref_name)
        value = str(getattr(ref.metadata, self.name))
        rval = []
        for fields in options:
            if self.keep == (self.compare(fields[self.column], value)):
                rval.append(fields)
        return rval


class BooleanFilter(ToolOutputActionOptionFilter):
    tag = "boolean"

    def __init__(self, parent, elem):
        super(BooleanFilter, self).__init__(parent, elem)
        self.column = elem.get('column', None)
        assert self.column is not None, "Required 'column' attribute missing from BooleanFilter"
        self.column = int(self.column)
        self.keep = util.string_as_bool(elem.get("keep", 'True'))
        self.cast = parse_cast_attribute(elem.get("cast", None))

    def filter_options(self, options, other_values):
        rval = []
        for fields in options:
            try:
                value = fields[self.column]
                value = self.cast(value)
            except Exception:
                value = False  # unable to cast or access value; treat as false
            if self.keep == bool(value):
                rval.append(fields)
        return rval


class StringFunctionFilter(ToolOutputActionOptionFilter):
    tag = "string_function"

    def __init__(self, parent, elem):
        super(StringFunctionFilter, self).__init__(parent, elem)
        self.column = elem.get('column', None)
        assert self.column is not None, "Required 'column' attribute missing from StringFunctionFilter"
        self.column = int(self.column)
        self.function = elem.get("name", None)
        assert self.function in ['lower', 'upper'], "Required function 'name' missing or invalid from StringFunctionFilter"  # add function names as needed
        self.function = getattr(str, self.function)

    def filter_options(self, options, other_values):
        rval = []
        for fields in options:
            rval.append(fields[0:self.column] + [self.function(fields[self.column])] + fields[self.column + 1:])
        return rval


# tag to class lookups
action_types = {}
for action_type in [MetadataToolOutputAction, FormatToolOutputAction]:
    action_types[action_type.tag] = action_type

option_types = {}
for option_type in [NullToolOutputActionOption, FromFileToolOutputActionOption, FromParamToolOutputActionOption, FromDataTableOutputActionOption]:
    option_types[option_type.tag] = option_type

filter_types = {}
for filter_type in [ParamValueToolOutputActionOptionFilter, InsertColumnToolOutputActionOptionFilter, MultipleSplitterFilter, ColumnStripFilter, MetadataValueFilter, BooleanFilter, StringFunctionFilter, ColumnReplaceFilter]:
    filter_types[filter_type.tag] = filter_type


# helper classes
# determine cast function
def parse_cast_attribute(cast):
    if cast == 'string_as_bool':
        cast = util.string_as_bool
    elif cast == 'int':
        cast = int
    elif cast == 'str':
        cast = str
    else:
        # return value as-is
        def cast(x):
            return x
    return cast


# comparison
def parse_compare_type(compare):
    if compare is None:
        compare = 'eq'
    assert compare in compare_types, "Invalid compare type specified: %s" % compare
    return compare_types[compare]


def compare_eq(value1, value2):
    return value1 == value2


def compare_neq(value1, value2):
    return value1 != value2


def compare_gt(value1, value2):
    return value1 > value2


def compare_gte(value1, value2):
    return value1 >= value2


def compare_lt(value1, value2):
    return value1 < value2


def compare_lte(value1, value2):
    return value1 <= value2


def compare_in(value1, value2):
    return value1 in value2


def compare_startswith(value1, value2):
    return value1.startswith(value2)


def compare_endswith(value1, value2):
    return value1.endswith(value2)


def compare_re_search(value1, value2):
    # checks pattern=value2 in value1
    return bool(re.search(value2, value1))


compare_types = {
    'eq': compare_eq,
    'neq': compare_neq,
    'gt': compare_gt,
    'gte': compare_gte,
    'lt': compare_lt,
    'lte': compare_lte,
    'in': compare_in,
    'startswith': compare_startswith,
    'endswith': compare_endswith,
    "re_search": compare_re_search
}