annotate toolfactory/galaxyxml/tool/import_xml.py @ 35:5d38cb3d9be8 draft

added patched galaxyxml code temporarily until PR accepted

import logging
import xml.etree.ElementTree as ET
import galaxyxml.tool as gxt
import galaxyxml.tool.parameters as gxtp

logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)


class GalaxyXmlParser(object):
    """
    Class to import content from an existing Galaxy XML wrapper.
    """

    def _init_tool(self, xml_root):
        """
        Init tool from existing xml tool.

        :param xml_root: root of the galaxy xml file.
        :type xml_root: :class:`xml.etree._Element`
        """
        version_cmd = None
        description = None
        for child in xml_root:
            if child.tag == 'description':
                description = child.text
            elif child.tag == 'command':
                executable = child.text.split()[0]
                command = child.text
            elif child.tag == 'version_command':
                version_cmd = child.text

        tool = gxt.Tool(xml_root.attrib['name'],
                        xml_root.attrib['id'],
                        xml_root.attrib.get('version', None),
                        description,
                        executable,
                        hidden=xml_root.attrib.get('hidden', False),
                        tool_type=xml_root.attrib.get('tool_type', None),
                        URL_method=xml_root.attrib.get('URL_method', None),
                        workflow_compatible=xml_root.attrib.get('workflow_compatible', True),
                        version_command=version_cmd)
        tool.command = command
        return tool

    def _load_description(self, tool, desc_root):
        """
        <description> is already loaded during initiation.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param desc_root: root of <description> tag.
        :type desc_root: :class:`xml.etree._Element`
        """
        logger.info("<description> is loaded during initiation of the object.")

    def _load_version_command(self, tool, vers_root):
        """
        <version_command> is already loaded during initiation.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param vers_root: root of <version_command> tag.
        :type vers_root: :class:`xml.etree._Element`
        """
        logger.info("<version_command> is loaded during initiation of the object.")

    def _load_stdio(self, tool, stdio_root):
        """
        So far, <stdio> is automatically generated by galaxyxml.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param desc_root: root of <stdio> tag.
        :type desc_root: :class:`xml.etree._Element`
        """
        logger.info("<stdio> is not loaded but automatically generated by galaxyxml.")

    def _load_command(self, tool, desc_root):
        """
        <command> is already loaded during initiation.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param desc_root: root of <command> tag.
        :type desc_root: :class:`xml.etree._Element`
        """
        logger.info("<command> is loaded during initiation of the object.")

    def _load_help(self, tool, help_root):
        """
        Load the content of the <help> into the tool.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param requirements_root: root of <help> tag.
        :type requirements_root: :class:`xml.etree._Element`
        """
        tool.help = help_root.text

    def _load_requirements(self, tool, requirements_root):
        """
        Add <requirements> to the tool.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param requirements_root: root of <requirements> tag.
        :type requirements_root: :class:`xml.etree._Element`
        """
        tool.requirements = gxtp.Requirements()
        for req in requirements_root:
            req_type = req.attrib['type']
            value = req.text
            if req.tag == 'requirement':
                version = req.attrib.get('version', None)
                tool.requirements.append(gxtp.Requirement(req_type, value, version=version))
            elif req.tag == 'container':
                tool.requirements.append(gxtp.Container(req_type, value))
            else:
                logger.warning(req.tag + ' is not a valid tag for requirements child')

    def _load_edam_topics(self, tool, topics_root):
        """
        Add <edam_topics> to the tool.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param topics_root: root of <edam_topics> tag.
        :type topics_root: :class:`xml.etree._Element`
        """
        tool.edam_topics = gxtp.EdamTopics()
        for edam_topic in topics_root:
            tool.edam_topics.append(gxtp.EdamTopic(edam_topic.text))

    def _load_edam_operations(self, tool, operations_root):
        """
        Add <edam_operations> to the tool.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param operations_root: root of <edam_operations> tag.
        :type operations_root: :class:`xml.etree._Element`
        """
        tool.edam_operations = gxtp.EdamOperations()
        for edam_op in operations_root:
            tool.edam_operations.append(gxtp.EdamOperation(edam_op.text))

    def _load_configfiles(self, tool, configfiles_root):
        """
        Add <configfiles> to the tool.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param configfiles_root: root of <configfiles> tag.
        :type configfiles_root: :class:`xml.etree._Element`
        """
        tool.configfiles = gxtp.Configfiles()
        for conf in configfiles_root:
            name = conf.attrib['name']
            value = conf.text
            tool.configfiles.append(gxtp.Configfile(name, value))

    def _load_citations(self, tool, citations_root):
        """
        Add <citations> to the tool.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param citations_root: root of <citations> tag.
        :type citations_root: :class:`xml.etree._Element`
        """
        tool.citations = gxtp.Citations()
        for cit in citations_root:
            cit_type = cit.attrib['type']
            value = cit.text
            tool.citations.append(gxtp.Citation(cit_type, value))

    def _load_inputs(self, tool, inputs_root):
        """
        Add <inputs> to the tool using the :class:`galaxyxml.tool.import_xml.InputsParser` object.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param inputs_root: root of <inputs> tag.
        :type inputs_root: :class:`xml.etree._Element`
        """
        tool.inputs = gxtp.Inputs()
        inp_parser = InputsParser()
        inp_parser.load_inputs(tool.inputs, inputs_root)

    def _load_outputs(self, tool, outputs_root):
        """
        Add <outputs> to the tool using the :class:`galaxyxml.tool.import_xml.OutputsParser` object.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param outputs_root: root of <outputs> tag.
        :type outputs_root: :class:`xml.etree._Element`
        """
        tool.outputs = gxtp.Outputs()
        out_parser = OutputsParser()
        out_parser.load_outputs(tool.outputs, outputs_root)

    def _load_tests(self, tool, tests_root):
        """
        Add <tests> to the tool using the :class:`galaxyxml.tool.import_xml.TestsParser` object.

        :param tool: Tool object from galaxyxml.
        :type tool: :class:`galaxyxml.tool.Tool`
        :param tests_root: root of <tests> tag.
        :type tests_root: :class:`xml.etree._Element`
        """
        tool.tests = gxtp.Tests()
        tests_parser = TestsParser()
        tests_parser.load_tests(tool.tests, tests_root)

    def import_xml(self, xml_path):
        """
        Load existing xml into the :class:`galaxyxml.tool.Tool` object.

        :param xml_path: Path of the XML to be loaded.
        :type xml_path: STRING
        :return: XML content in the galaxyxml model.
        :rtype: :class:`galaxyxml.tool.Tool`
        """
        xml_root = ET.parse(xml_path).getroot()
        tool = self._init_tool(xml_root)
        # Now we import each tag's field
        for child in xml_root:
            try:
                getattr(self, '_load_{}'.format(child.tag))(tool, child)
            except AttributeError:
                logger.warning(child.tag + " tag is not processed.")
        return tool


class InputsParser(object):
    """
    Class to parse content of the <inputs> tag from a Galaxy XML wrapper.
    """

    def _load_text_param(self, root, text_param):
        """
        Add <param type="text" /> to the root.

        :param root: root to append the param to.
        :param text_param: root of <param> tag.
        :type text_param: :class:`xml.etree._Element`
        """
        root.append(gxtp.TextParam(text_param.attrib['name'],
                                   optional=text_param.get('optional', None),
                                   label=text_param.get('label', None),
                                   help=text_param.get('help', None),
                                   value=text_param.get('value', None)))

    def _load_data_param(self, root, data_param):
        """
        Add <param type="data" /> to the root.

        :param root: root to append the param to.
        :param data_param: root of <param> tag.
        :type data_param: :class:`xml.etree._Element`
        """
        root.append(gxtp.DataParam(data_param.attrib['name'],
                                   optional=data_param.attrib.get('optional', None),
                                   label=data_param.attrib.get('label', None),
                                   help=data_param.attrib.get('help', None),
                                   format=data_param.attrib.get('format', None),
                                   multiple=data_param.attrib.get('multiple', None)))

    def _load_boolean_param(self, root, bool_param):
        """
        Add <param type="boolean" /> to the root.

        :param root: root to append the param to.
        :param bool_param: root of <param> tag.
        :type bool_param: :class:`xml.etree._Element`
        """
        root.append(gxtp.BooleanParam(bool_param.attrib['name'],
                                      optional=bool_param.attrib.get('optional', None),
                                      label=bool_param.attrib.get('label', None),
                                      help=bool_param.attrib.get('help', None),
                                      checked=bool_param.attrib.get('checked', False),
                                      truevalue=bool_param.attrib.get('truevalue', None),
                                      falsevalue=bool_param.attrib.get('falsevalue', None)))

    def _load_integer_param(self, root, int_param):
        """
        Add <param type="integer" /> to the root.

        :param root: root to append the param to.
        :param int_param: root of <param> tag.
        :type int_param: :class:`xml.etree._Element`
        """
        root.append(gxtp.IntegerParam(int_param.attrib['name'],
                                      int_param.attrib.get('value', None),
                                      optional=int_param.attrib.get('optional', None),
                                      label=int_param.attrib.get('label', None),
                                      help=int_param.attrib.get('help', None),
                                      min=int_param.attrib.get('min', None),
                                      max=int_param.attrib.get('max', None)))

    def _load_float_param(self, root, float_param):
        """
        Add <param type="float" /> to the root.

        :param root: root to append the param to.
        :param float_param: root of <param> tag.
        :type float_param: :class:`xml.etree._Element`
        """
        root.append(gxtp.FloatParam(float_param.attrib['name'],
                                    float_param.attrib.get('value', None),
                                    optional=float_param.attrib.get('optional', None),
                                    label=float_param.attrib.get('label', None),
                                    help=float_param.attrib.get('help', None),
                                    min=float_param.attrib.get('min', None),
                                    max=float_param.attrib.get('max', None)))

    def _load_option_select(self, root, option):
        """
        Add <option> to the root (usually <param type="select" />).

        :param root: root to append the param to.
        :param option: root of <option> tag.
        :type float_param: :class:`xml.etree._Element`
        """
        root.append(gxtp.SelectOption(option.attrib.get('value', None),
                                      option.text,
                                      selected=option.attrib.get('selected', False)))

    def _load_column_options(self, root, column):
        """
        Add <column> to the root (usually <options>).

        :param root: root to append the param to.
        :param option: root of <column> tag.
        :type float_param: :class:`xml.etree._Element`
        """
        root.append(gxtp.Column(column.attrib['name'], column.attrib['index']))

    def _load_filter_options(self, root, filter):
        """
        Add <filter> to the root (usually <options>).

        :param root: root to append the param to.
        :param option: root of <filter> tag.
        :type float_param: :class:`xml.etree._Element`
        """
        root.append(gxtp.Filter(filter.attrib['type'],
                                column=filter.attrib.get('column', None),
                                name=filter.attrib.get('name', None),
                                ref=filter.attrib.get('ref', None),
                                key=filter.attrib.get('key', None),
                                multiple=filter.attrib.get('multiple', None),
                                separator=filter.attrib.get('separator', None),
                                keep=filter.attrib.get('keep', None),
                                value=filter.attrib.get('value', None),
                                ref_attribute=filter.attrib.get('ref_attribute', None),
                                index=filter.attrib.get('index', None)))

    def _load_options_select(self, root, options):
        """
        Add <options> to the root (usually <param type="select" />).

        :param root: root to append the param to.
        :param option: root of <options> tag.
        :type float_param: :class:`xml.etree._Element`
        """
        opts = gxtp.Options(from_dataset=options.attrib.get('from_dataset', None),
                            from_file=options.attrib.get('from_file', None),
                            from_data_table=options.attrib.get('from_data_table', None),
                            from_parameter=options.attrib.get('from_parameter', None))
        # Deal with child nodes (usually filter and column)
        for opt_child in options:
            try:
                getattr(self, '_load_{}_options'.format(opt_child.tag))(opts, opt_child)
            except AttributeError:
                logger.warning(opt_child.tag + " tag is not processed for <options>.")
        root.append(opts)

    def _load_select_param(self, root, sel_param):
        """
        Add <param type="select" /> to the root.

        :param root: root to append the param to.
        :param sel_param: root of <param> tag.
        :type sel_param: :class:`xml.etree._Element`
        """
        select_param = gxtp.SelectParam(sel_param.attrib['name'],
                                        optional=sel_param.attrib.get('optional', None),
                                        label=sel_param.attrib.get('label', None),
                                        help=sel_param.attrib.get('help', None),
                                        data_ref=sel_param.attrib.get('data_ref', None),
                                        display=sel_param.attrib.get('display', None),
                                        multiple=sel_param.attrib.get('multiple', None))
        # Deal with child nodes (usually option and options)
        for sel_child in sel_param:
            try:
                getattr(self, '_load_{}_select'.format(sel_child.tag))(select_param, sel_child)
            except AttributeError:
                logger.warning(sel_child.tag + " tag is not processed for <param type='select'>.")
        root.append(select_param)

    def _load_param(self, root, param_root):
        """
        Method to select which type of <param> is being added to the root.

        :param root: root to attach param to.
        :param param_root: root of <param> tag.
        :type param_root: :class:`xml.etree._Element`
        """
        param_type = param_root.attrib['type']
        try:
            getattr(self, '_load_{}_param'.format(param_type))(root, param_root)
        except AttributeError:
            logger.warning(param_type + " tag is not processed for <param>.")

    def _load_when(self, root, when_root):
        """
        Add <when> to the root (usually <conditional>).

        :param root: root to append when to.
        :param when_root: root of <when> tag.
        :type when_root: :class:`xml.etree._Element`
        """
        when = gxtp.When(when_root.attrib['value'])
        # Deal with child nodes
        self.load_inputs(when, when_root)
        root.append(when)

    def _load_conditional(self, root, conditional_root):
        """
        Add <conditional> to the root.

        :param root: root to append conditional to.
        :param conditional_root: root of <conditional> tag.
        :type conditional_root: :class:`xml.etree._Element`
        """
        value_ref_in_group = conditional_root.attrib.get('value_ref_in_group', None)
        # Other optional parameters need to be added to conditional object
        conditional = gxtp.Conditional(conditional_root.attrib['name'],
                                       value_from=conditional_root.attrib.get('value_from', None),
                                       value_ref=conditional_root.attrib.get('value_ref', None),
                                       value_ref_in_group=value_ref_in_group,
                                       label=conditional_root.attrib.get('label', None))
        # Deal with child nodes
        self.load_inputs(conditional, conditional_root)
        root.append(conditional)

    def _load_section(self, root, section_root):
        """
        Add <section> to the root.

        :param root: root to append conditional to.
        :param section_root: root of <section> tag.
        :type section_root: :class:`xml.etree._Element`
        """
        section = gxtp.Section(section_root.attrib['name'],
                               section_root.attrib['title'],
                               expanded=section_root.attrib.get('expanded', None),
                               help=section_root.attrib.get('help', None))
        # Deal with child nodes
        self.load_inputs(section, section_root)
        root.append(section)

    def _load_repeat(self, root, repeat_root):
        """
        Add <repeat> to the root.

        :param root: root to append repeat to.
        :param repeat_root: root of <repeat> tag.
        :param repeat_root: :class:`xml.etree._Element`
        """
        repeat = gxtp.Repeat(repeat_root.attrib['name'],
                             repeat_root.attrib['title'],
                             min=repeat_root.attrib.get('min', None),
                             max=repeat_root.attrib.get('max', None),
                             default=repeat_root.attrib.get('default', None))
        # Deal with child nodes
        self.load_inputs(repeat, repeat_root)
        root.append(repeat)

    def load_inputs(self, root, inputs_root):
        """
        Add <inputs.tag> to the root (it can be any tags with children such as
        <inputs>, <repeat>, <section> ...)

        :param root: root to attach inputs to (either <inputs> or <when>).
        :param inputs_root: root of <inputs> tag.
        :type inputs_root: :class:`xml.etree._Element`
        """
        for inp_child in inputs_root:
            try:
                getattr(self, '_load_{}'.format(inp_child.tag))(root, inp_child)
            except AttributeError:
                logger.warning(inp_child.tag + " tag is not processed for <" +
                               inputs_root.tag + "> tag.")


class OutputsParser(object):
    """
    Class to parse content of the <outputs> tag from a Galaxy XML wrapper.
    """

    def _load_data(self, outputs_root, data_root):
        """
        Add <data> to <outputs>.

        :param outputs_root: <outputs> root to append <data> to.
        :param data_root: root of <data> tag.
        :param data_root: :class:`xml.etree._Element`
        """
        data = gxtp.OutputData(data_root.attrib.get('name', None),
                               data_root.attrib.get('format', None),
                               format_source=data_root.attrib.get('format_source', None),
                               metadata_source=data_root.attrib.get('metadata_source', None),
                               label=data_root.attrib.get('label', None),
                               from_work_dir=data_root.attrib.get('from_work_dir', None),
                               hidden=data_root.attrib.get('hidden', False))
        # Deal with child nodes
        for data_child in data_root:
            try:
                getattr(self, '_load_{}'.format(data_child.tag))(data, data_child)
            except AttributeError:
                logger.warning(data_child.tag + " tag is not processed for <data>.")
        outputs_root.append(data)

    def _load_change_format(self, root, chfmt_root):
        """
        Add <change_format> to root (<data>).

        :param root: root to append <change_format> to.
        :param chfm_root: root of <change_format> tag.
        :param chfm_root: :class:`xml.etree._Element`
        """
        change_format = gxtp.ChangeFormat()
        for chfmt_child in chfmt_root:
            change_format.append(gxtp.ChangeFormatWhen(chfmt_child.attrib['input'],
                                                       chfmt_child.attrib['format'],
                                                       chfmt_child.attrib['value']))
        root.append(change_format)

    def _load_collection(self, outputs_root, coll_root):
        """
        Add <collection> to <outputs>.

        :param outputs_root: <outputs> root to append <collection> to.
        :param coll_root: root of <collection> tag.
        :param coll_root: :class:`xml.etree._Element`
        """
        collection = gxtp.OutputCollection(coll_root.attrib['name'],
                                           type=coll_root.attrib.get('type', None),
                                           label=coll_root.attrib.get('label', None),
                                           format_source=coll_root.attrib.get('format_source',
                                                                              None),
                                           type_source=coll_root.attrib.get('type_source', None),
                                           structured_like=coll_root.attrib.get('structured_like',
                                                                                None),
                                           inherit_format=coll_root.attrib.get('inherit_format',
                                                                               None))
        # Deal with child nodes
        for coll_child in coll_root:
            try:
                getattr(self, '_load_{}'.format(coll_child.tag))(collection, coll_child)
            except AttributeError:
                logger.warning(coll_child.tag + " tag is not processed for <collection>.")
        outputs_root.append(collection)

    def _load_discover_datasets(self, root, disc_root):
        """
        Add <discover_datasets> to root (<collection>).

        :param root: root to append <collection> to.
        :param disc_root: root of <discover_datasets> tag.
        :param disc_root: :class:`xml.etree._Element`
        """
        root.append(gxtp.DiscoverDatasets(disc_root.attrib['pattern'],
                                          directory=disc_root.attrib.get('directory', None),
                                          format=disc_root.attrib.get('format', None),
                                          ext=disc_root.attrib.get('ext', None),
                                          visible=disc_root.attrib.get('visible', None)))

    def _load_filter(self, root, filter_root):
        """
        Add <filter> to root (<collection> or <data>).

        :param root: root to append <collection> to.
        :param coll_root: root of <filter> tag.
        :param coll_root: :class:`xml.etree._Element`
        """
        root.append(gxtp.OutputFilter(filter_root.text))

    def load_outputs(self, root, outputs_root):
        """
        Add <outputs> to the root.

        :param root: root to attach <outputs> to (<tool>).
        :param tests_root: root of <outputs> tag.
        :type tests_root: :class:`xml.etree._Element`
        """
        for out_child in outputs_root:
            try:
                getattr(self, '_load_{}'.format(out_child.tag))(root, out_child)
            except AttributeError:
                logger.warning(out_child.tag + " tag is not processed for <outputs>.")


class TestsParser(object):
    """
    Class to parse content of the <tests> tag from a Galaxy XML wrapper.
    """

    def _load_param(self, test_root, param_root):
        """
        Add <param> to the <test>.

        :param root: <test> root to append <param> to.
        :param repeat_root: root of <param> tag.
        :param repeat_root: :class:`xml.etree._Element`
        """
        test_root.append(gxtp.TestParam(param_root.attrib['name'],
                                        value=param_root.attrib.get('value', None),
                                        ftype=param_root.attrib.get('ftype', None),
                                        dbkey=param_root.attrib.get('dbkey', None)))

    def _load_output(self, test_root, output_root):
        """
        Add <output> to the <test>.

        :param root: <test> root to append <output> to.
        :param repeat_root: root of <output> tag.
        :param repeat_root: :class:`xml.etree._Element`
        """
        test_root.append(gxtp.TestOutput(name=output_root.attrib.get('name', None),
                                         file=output_root.attrib.get('file', None),
                                         ftype=output_root.attrib.get('ftype', None),
                                         sort=output_root.attrib.get('sort', None),
                                         value=output_root.attrib.get('value', None),
                                         md5=output_root.attrib.get('md5', None),
                                         checksum=output_root.attrib.get('checksum', None),
                                         compare=output_root.attrib.get('compare', None),
                                         lines_diff=output_root.attrib.get('lines_diff', None),
                                         delta=output_root.attrib.get('delta', None)))

    def load_tests(self, root, tests_root):
        """
        Add <tests> to the root.

        :param root: root to attach <tests> to (<tool>).
        :param tests_root: root of <tests> tag.
        :type tests_root: :class:`xml.etree._Element`
        """
        for test_root in tests_root:
            test = gxtp.Test()
            for test_child in test_root:
                try:
                    getattr(self, '_load_{}'.format(test_child.tag))(test, test_child)
                except AttributeError:
                    logger.warning(test_child.tag + " tag is not processed within <test>.")
            root.append(test)