Mercurial > repos > fubar > tool_factory_2
diff toolfactory/galaxyxml/tool/import_xml.py @ 92:6ce360759c28 draft
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| author | fubar |
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| date | Thu, 19 Nov 2020 23:59:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/galaxyxml/tool/import_xml.py Thu Nov 19 23:59:50 2020 +0000 @@ -0,0 +1,713 @@ +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)