Mercurial > repos > fubar > tool_factory_2
view toolfactory/galaxyxml/tool/import_xml.py @ 35:5d38cb3d9be8 draft
added patched galaxyxml code temporarily until PR accepted
author | fubar |
---|---|
date | Sat, 08 Aug 2020 19:55:55 -0400 |
parents | |
children | ce2b1f8ea68d |
line wrap: on
line source
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)