Mercurial > repos > fubar > tool_factory_2
changeset 36:ce2b1f8ea68d draft
passes flake8 tests finally :)
| author | fubar |
|---|---|
| date | Mon, 10 Aug 2020 23:24:41 -0400 |
| parents | 5d38cb3d9be8 |
| children | 099047ee7094 |
| files | toolfactory/galaxyxml/__init__.py toolfactory/galaxyxml/tool/__init__.py toolfactory/galaxyxml/tool/import_xml.py toolfactory/galaxyxml/tool/parameters/__init__.py toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml toolfactory/sample_toolfactory_tools.ga toolfactory/sample_toolfactory_tools.tgz toolfactory/tf_tests_history.tar.gz toolfactory/tfwfsample.tgz toolfactory/tfworkflowsample.ga |
| diffstat | 11 files changed, 1793 insertions(+), 1077 deletions(-) [+] |
line wrap: on
line diff
--- a/toolfactory/galaxyxml/__init__.py Sat Aug 08 19:55:55 2020 -0400 +++ b/toolfactory/galaxyxml/__init__.py Mon Aug 10 23:24:41 2020 -0400 @@ -4,23 +4,24 @@ class GalaxyXML(object): - def __init__(self): - self.root = etree.Element('root') + self.root = etree.Element("root") def export(self): - return etree.tostring(self.root, pretty_print=True, encoding='unicode') + return etree.tostring(self.root, pretty_print=True, encoding="unicode") class Util(object): - @classmethod def coerce(cls, data, kill_lists=False): """Recursive data sanitisation """ if isinstance(data, dict): - return {k: cls.coerce(v, kill_lists=kill_lists) for k, v in - list(data.items()) if v is not None} + return { + k: cls.coerce(v, kill_lists=kill_lists) + for k, v in list(data.items()) + if v is not None + } elif isinstance(data, list): if kill_lists: return cls.coerce(data[0]) @@ -45,22 +46,22 @@ @classmethod def clean_kwargs(cls, params, final=False): - if 'kwargs' in params: - kwargs = params['kwargs'] + if "kwargs" in params: + kwargs = params["kwargs"] for k in kwargs: params[k] = kwargs[k] - del params['kwargs'] - if 'self' in params: - del params['self'] + del params["kwargs"] + if "self" in params: + del params["self"] - if '__class__' in params: - del params['__class__'] + if "__class__" in params: + del params["__class__"] # There will be more params, it would be NICE to use a whitelist # instead of a blacklist, but until we have more data let's just # blacklist stuff we see commonly. if final: - for blacklist in ('positional',): + for blacklist in ("positional",): if blacklist in params: del params[blacklist] return params
--- a/toolfactory/galaxyxml/tool/__init__.py Sat Aug 08 19:55:55 2020 -0400 +++ b/toolfactory/galaxyxml/tool/__init__.py Mon Aug 10 23:24:41 2020 -0400 @@ -4,56 +4,68 @@ from galaxyxml import Util, GalaxyXML from galaxyxml.tool.parameters import XMLParam -VALID_TOOL_TYPES = ('data_source', 'data_source_async') -VALID_URL_METHODS = ('get', 'post') +VALID_TOOL_TYPES = ("data_source", "data_source_async") +VALID_URL_METHODS = ("get", "post") logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__name__) class Tool(GalaxyXML): - - def __init__(self, name, id, version, description, executable, hidden=False, - tool_type=None, URL_method=None, workflow_compatible=True, - interpreter=None, version_command='interpreter filename.exe --version', - command_line_override=None): + def __init__( + self, + name, + id, + version, + description, + executable, + hidden=False, + tool_type=None, + URL_method=None, + workflow_compatible=True, + interpreter=None, + version_command="interpreter filename.exe --version", + command_line_override=None, + ): self.executable = executable self.interpreter = interpreter self.command_line_override = command_line_override kwargs = { - 'name': name, - 'id': id, - 'version': version, - 'hidden': hidden, - 'workflow_compatible': workflow_compatible, + "name": name, + "id": id, + "version": version, + "hidden": hidden, + "workflow_compatible": workflow_compatible, } self.version_command = version_command # Remove some of the default values to make tools look a bit nicer if not hidden: - del kwargs['hidden'] + del kwargs["hidden"] if workflow_compatible: - del kwargs['workflow_compatible'] + del kwargs["workflow_compatible"] kwargs = Util.coerce(kwargs) - self.root = etree.Element('tool', **kwargs) + self.root = etree.Element("tool", **kwargs) if tool_type is not None: if tool_type not in VALID_TOOL_TYPES: - raise Exception("Tool type must be one of %s" % - ','.join(VALID_TOOL_TYPES)) + raise Exception( + "Tool type must be one of %s" % ",".join(VALID_TOOL_TYPES) + ) else: - kwargs['tool_type'] = tool_type + kwargs["tool_type"] = tool_type if URL_method is not None: if URL_method in VALID_URL_METHODS: - kwargs['URL_method'] = URL_method + kwargs["URL_method"] = URL_method else: - raise Exception("URL_method must be one of %s" % - ','.join(VALID_URL_METHODS)) + raise Exception( + "URL_method must be one of %s" % ",".join(VALID_URL_METHODS) + ) - description_node = etree.SubElement(self.root, 'description') + description_node = etree.SubElement(self.root, "description") description_node.text = description def add_comment(self, comment_txt): @@ -61,7 +73,7 @@ self.root.insert(0, comment) def append_version_command(self): - version_command = etree.SubElement(self.root, 'version_command') + version_command = etree.SubElement(self.root, "version_command") try: version_command.text = etree.CDATA(self.version_command) except Exception: @@ -76,10 +88,10 @@ def clean_command_string(self, command_line): clean = [] for x in command_line: - if x is not [] and x is not ['']: + if x is not [] and x is not [""]: clean.append(x) - return '\n'.join(clean) + return "\n".join(clean) def export(self, keep_old_command=False): # noqa @@ -105,7 +117,7 @@ except Exception: pass - if self.command_line_override != None: + if self.command_line_override: command_line = self.command_line_override else: command_line = [] @@ -120,8 +132,8 @@ pass # Add stdio section - stdio = etree.SubElement(export_xml.root, 'stdio') - etree.SubElement(stdio, 'exit_code', range='1:', level='fatal') + stdio = etree.SubElement(export_xml.root, "stdio") + etree.SubElement(stdio, "exit_code", range="1:", level="fatal") # Append version command export_xml.append_version_command() @@ -129,21 +141,25 @@ # Steal interpreter from kwargs command_kwargs = {} if export_xml.interpreter is not None: - command_kwargs['interpreter'] = export_xml.interpreter + command_kwargs["interpreter"] = export_xml.interpreter # Add command section - command_node = etree.SubElement(export_xml.root, 'command', **command_kwargs) + command_node = etree.SubElement(export_xml.root, "command", **command_kwargs) if keep_old_command: - if getattr(self, 'command', None): + if getattr(self, "command", None): command_node.text = etree.CDATA(export_xml.command) else: - logger.warning('The tool does not have any old command stored. ' + - 'Only the command line is written.') + logger.warning( + "The tool does not have any old command stored. " + + "Only the command line is written." + ) command_node.text = export_xml.executable else: actual_cli = "%s %s" % ( - export_xml.executable, export_xml.clean_command_string(command_line)) + export_xml.executable, + export_xml.clean_command_string(command_line), + ) command_node.text = etree.CDATA(actual_cli.strip()) try: @@ -161,7 +177,7 @@ except Exception: pass - help_element = etree.SubElement(export_xml.root, 'help') + help_element = etree.SubElement(export_xml.root, "help") help_element.text = etree.CDATA(export_xml.help) try:
--- a/toolfactory/galaxyxml/tool/import_xml.py Sat Aug 08 19:55:55 2020 -0400 +++ b/toolfactory/galaxyxml/tool/import_xml.py Mon Aug 10 23:24:41 2020 -0400 @@ -22,24 +22,26 @@ version_cmd = None description = None for child in xml_root: - if child.tag == 'description': + if child.tag == "description": description = child.text - elif child.tag == 'command': + elif child.tag == "command": executable = child.text.split()[0] command = child.text - elif child.tag == 'version_command': + 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 = 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 @@ -109,15 +111,17 @@ """ tool.requirements = gxtp.Requirements() for req in requirements_root: - req_type = req.attrib['type'] + 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': + 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') + logger.warning(req.tag + " is not a valid tag for requirements child") def _load_edam_topics(self, tool, topics_root): """ @@ -156,7 +160,7 @@ """ tool.configfiles = gxtp.Configfiles() for conf in configfiles_root: - name = conf.attrib['name'] + name = conf.attrib["name"] value = conf.text tool.configfiles.append(gxtp.Configfile(name, value)) @@ -171,7 +175,7 @@ """ tool.citations = gxtp.Citations() for cit in citations_root: - cit_type = cit.attrib['type'] + cit_type = cit.attrib["type"] value = cit.text tool.citations.append(gxtp.Citation(cit_type, value)) @@ -228,7 +232,7 @@ # Now we import each tag's field for child in xml_root: try: - getattr(self, '_load_{}'.format(child.tag))(tool, child) + getattr(self, "_load_{}".format(child.tag))(tool, child) except AttributeError: logger.warning(child.tag + " tag is not processed.") return tool @@ -247,11 +251,15 @@ :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))) + 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): """ @@ -261,12 +269,16 @@ :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))) + 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): """ @@ -276,13 +288,17 @@ :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))) + 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): """ @@ -292,13 +308,17 @@ :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))) + 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): """ @@ -308,13 +328,17 @@ :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))) + 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): """ @@ -324,9 +348,13 @@ :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))) + root.append( + gxtp.SelectOption( + option.attrib.get("value", None), + option.text, + selected=option.attrib.get("selected", False), + ) + ) def _load_column_options(self, root, column): """ @@ -336,7 +364,7 @@ :param option: root of <column> tag. :type float_param: :class:`xml.etree._Element` """ - root.append(gxtp.Column(column.attrib['name'], column.attrib['index'])) + root.append(gxtp.Column(column.attrib["name"], column.attrib["index"])) def _load_filter_options(self, root, filter): """ @@ -346,17 +374,21 @@ :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))) + 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): """ @@ -366,14 +398,16 @@ :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)) + 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) + 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) @@ -386,19 +420,25 @@ :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)) + 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) + 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'>.") + logger.warning( + sel_child.tag + " tag is not processed for <param type='select'>." + ) root.append(select_param) def _load_param(self, root, param_root): @@ -409,9 +449,9 @@ :param param_root: root of <param> tag. :type param_root: :class:`xml.etree._Element` """ - param_type = param_root.attrib['type'] + param_type = param_root.attrib["type"] try: - getattr(self, '_load_{}_param'.format(param_type))(root, param_root) + getattr(self, "_load_{}_param".format(param_type))(root, param_root) except AttributeError: logger.warning(param_type + " tag is not processed for <param>.") @@ -423,7 +463,7 @@ :param when_root: root of <when> tag. :type when_root: :class:`xml.etree._Element` """ - when = gxtp.When(when_root.attrib['value']) + when = gxtp.When(when_root.attrib["value"]) # Deal with child nodes self.load_inputs(when, when_root) root.append(when) @@ -436,13 +476,15 @@ :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) + 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)) + 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) @@ -455,10 +497,12 @@ :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)) + 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) @@ -471,11 +515,13 @@ :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)) + 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) @@ -491,10 +537,14 @@ """ for inp_child in inputs_root: try: - getattr(self, '_load_{}'.format(inp_child.tag))(root, inp_child) + 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.") + logger.warning( + inp_child.tag + + " tag is not processed for <" + + inputs_root.tag + + "> tag." + ) class OutputsParser(object): @@ -510,17 +560,19 @@ :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)) + 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) + 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) @@ -535,9 +587,13 @@ """ 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'])) + 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): @@ -548,22 +604,23 @@ :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)) + 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) + getattr(self, "_load_{}".format(coll_child.tag))(collection, coll_child) except AttributeError: - logger.warning(coll_child.tag + " tag is not processed for <collection>.") + logger.warning( + coll_child.tag + " tag is not processed for <collection>." + ) outputs_root.append(collection) def _load_discover_datasets(self, root, disc_root): @@ -574,11 +631,15 @@ :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))) + 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): """ @@ -600,7 +661,7 @@ """ for out_child in outputs_root: try: - getattr(self, '_load_{}'.format(out_child.tag))(root, out_child) + getattr(self, "_load_{}".format(out_child.tag))(root, out_child) except AttributeError: logger.warning(out_child.tag + " tag is not processed for <outputs>.") @@ -618,10 +679,14 @@ :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))) + 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): """ @@ -631,16 +696,20 @@ :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))) + 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): """ @@ -654,7 +723,9 @@ test = gxtp.Test() for test_child in test_root: try: - getattr(self, '_load_{}'.format(test_child.tag))(test, test_child) + getattr(self, "_load_{}".format(test_child.tag))(test, test_child) except AttributeError: - logger.warning(test_child.tag + " tag is not processed within <test>.") + logger.warning( + test_child.tag + " tag is not processed within <test>." + ) root.append(test)
--- a/toolfactory/galaxyxml/tool/parameters/__init__.py Sat Aug 08 19:55:55 2020 -0400 +++ b/toolfactory/galaxyxml/tool/parameters/__init__.py Mon Aug 10 23:24:41 2020 -0400 @@ -5,7 +5,7 @@ class XMLParam(object): - name = 'node' + name = "node" def __init__(self, *args, **kwargs): # http://stackoverflow.com/a/12118700 @@ -22,11 +22,15 @@ self.node.append(sub_node.node) self.children.append(sub_node) else: - raise Exception("Child was unacceptable to parent (%s is not appropriate for %s)" % ( - type(self), type(sub_node))) + raise Exception( + "Child was unacceptable to parent (%s is not appropriate for %s)" + % (type(self), type(sub_node)) + ) else: - raise Exception("Child was unacceptable to parent (%s is not appropriate for %s)" % ( - type(self), type(sub_node))) + raise Exception( + "Child was unacceptable to parent (%s is not appropriate for %s)" + % (type(self), type(sub_node)) + ) def validate(self): # Very few need validation, but some nodes we may want to have @@ -42,14 +46,14 @@ for child in self.children: lines.append(child.command_line()) # lines += child.command_line() - return '\n'.join(lines) + return "\n".join(lines) def command_line(self): return None class RequestParamTranslation(XMLParam): - name = 'request_param_translation' + name = "request_param_translation" def __init__(self, **kwargs): self.node = etree.Element(self.name) @@ -59,7 +63,7 @@ class RequestParam(XMLParam): - name = 'request_param' + name = "request_param" def __init__(self, galaxy_name, remote_name, missing, **kwargs): # TODO: bulk copy locals into self.attr? @@ -73,7 +77,7 @@ class AppendParam(XMLParam): - name = 'append_param' + name = "append_param" def __init__(self, separator="&", first_separator="?", join="=", **kwargs): params = Util.clean_kwargs(locals().copy()) @@ -84,7 +88,7 @@ class AppendParamValue(XMLParam): - name = 'value' + name = "value" def __init__(self, name="_export", missing="1", **kwargs): params = Util.clean_kwargs(locals().copy()) @@ -95,7 +99,7 @@ class EdamOperations(XMLParam): - name = 'edam_operations' + name = "edam_operations" def acceptable_child(self, child): return issubclass(type(child), EdamOperation) @@ -113,7 +117,7 @@ class EdamOperation(XMLParam): - name = 'edam_operation' + name = "edam_operation" def __init__(self, value): super(EdamOperation, self).__init__() @@ -121,7 +125,7 @@ class EdamTopics(XMLParam): - name = 'edam_topics' + name = "edam_topics" def acceptable_child(self, child): return issubclass(type(child), EdamTopic) @@ -139,7 +143,7 @@ class EdamTopic(XMLParam): - name = 'edam_topic' + name = "edam_topic" def __init__(self, value): super(EdamTopic, self).__init__() @@ -147,70 +151,81 @@ class Requirements(XMLParam): - name = 'requirements' + name = "requirements" # This bodes to be an issue -__- def acceptable_child(self, child): - return issubclass(type(child), Requirement) or issubclass(type(child), Container) + return issubclass(type(child), Requirement) or issubclass( + type(child), Container + ) class Requirement(XMLParam): - name = 'requirement' + name = "requirement" def __init__(self, type, value, version=None, **kwargs): params = Util.clean_kwargs(locals().copy()) passed_kwargs = {} - passed_kwargs['version'] = params['version'] - passed_kwargs['type'] = params['type'] + passed_kwargs["version"] = params["version"] + passed_kwargs["type"] = params["type"] super(Requirement, self).__init__(**passed_kwargs) self.node.text = str(value) class Container(XMLParam): - name = 'container' + name = "container" def __init__(self, type, value, **kwargs): params = Util.clean_kwargs(locals().copy()) passed_kwargs = {} - passed_kwargs['type'] = params['type'] + passed_kwargs["type"] = params["type"] super(Container, self).__init__(**passed_kwargs) self.node.text = str(value) class Configfiles(XMLParam): - name = 'configfiles' + name = "configfiles" def acceptable_child(self, child): - return issubclass(type(child), Configfile) or issubclass(type(child), ConfigfileDefaultInputs) + return issubclass(type(child), Configfile) or issubclass( + type(child), ConfigfileDefaultInputs + ) class Configfile(XMLParam): - name = 'configfile' + name = "configfile" def __init__(self, name, text, **kwargs): params = Util.clean_kwargs(locals().copy()) passed_kwargs = {} - passed_kwargs['name'] = params['name'] + passed_kwargs["name"] = params["name"] super(Configfile, self).__init__(**passed_kwargs) self.node.text = etree.CDATA(str(text)) class ConfigfileDefaultInputs(XMLParam): - name = 'inputs' + name = "inputs" def __init__(self, name, **kwargs): params = Util.clean_kwargs(locals().copy()) passed_kwargs = {} - passed_kwargs['name'] = params['name'] + passed_kwargs["name"] = params["name"] super(ConfigfileDefaultInputs, self).__init__(**passed_kwargs) class Inputs(XMLParam): - name = 'inputs' + name = "inputs" # This bodes to be an issue -__- - def __init__(self, action=None, check_value=None, method=None, - target=None, nginx_upload=None, **kwargs): + def __init__( + self, + action=None, + check_value=None, + method=None, + target=None, + nginx_upload=None, + **kwargs, + ): params = Util.clean_kwargs(locals().copy()) super(Inputs, self).__init__(**params) @@ -219,24 +234,23 @@ class InputParameter(XMLParam): - def __init__(self, name, **kwargs): # TODO: look at self.mako_identifier = name # We use kwargs instead of the usual locals(), so manually copy the # name to kwargs if name is not None: - kwargs['name'] = name + kwargs["name"] = name # Handle positional parameters - if 'positional' in kwargs and kwargs['positional']: + if "positional" in kwargs and kwargs["positional"]: self.positional = True else: self.positional = False - if 'num_dashes' in kwargs: - self.num_dashes = kwargs['num_dashes'] - del kwargs['num_dashes'] + if "num_dashes" in kwargs: + self.num_dashes = kwargs["num_dashes"] + del kwargs["num_dashes"] else: self.num_dashes = 0 @@ -244,14 +258,15 @@ # Not sure about this :( # https://wiki.galaxyproject.org/Tools/BestPractices#Parameter_help - if 'label' in kwargs: + if "label" in kwargs: # TODO: replace with positional attribute if len(self.flag()) > 0: - if kwargs['label'] is None: + if kwargs["label"] is None: kwargs[ - 'label'] = 'Author did not provide help for this parameter... ' + "label" + ] = "Author did not provide help for this parameter... " if not self.positional: - kwargs['argument'] = self.flag() + kwargs["argument"] = self.flag() super(InputParameter, self).__init__(**kwargs) @@ -261,7 +276,7 @@ after = self.command_line_after() complete = [x for x in (before, cli, after) if x is not None] - return '\n'.join(complete) + return "\n".join(complete) def command_line_before(self): try: @@ -282,20 +297,24 @@ if self.positional: return self.mako_name() else: - return "%s%s%s" % (self.flag(), self.space_between_arg, self.mako_name()) + return "%s%s%s" % ( + self.flag(), + self.space_between_arg, + self.mako_name(), + ) def mako_name(self): # TODO: enhance logic to check up parents for things like # repeat>condotion>param - return '$' + self.mako_identifier + return "$" + self.mako_identifier def flag(self): - flag = '-' * self.num_dashes + flag = "-" * self.num_dashes return flag + self.mako_identifier class Section(InputParameter): - name = 'section' + name = "section" def __init__(self, name, title, expanded=None, help=None, **kwargs): params = Util.clean_kwargs(locals().copy()) @@ -306,14 +325,13 @@ class Repeat(InputParameter): - name = 'repeat' + name = "repeat" - def __init__(self, name, title, min=None, max=None, default=None, - **kwargs): + def __init__(self, name, title, min=None, max=None, default=None, **kwargs): params = Util.clean_kwargs(locals().copy()) # Allow overriding - self.command_line_before_override = '#for $i in $%s:' % name - self.command_line_after_override = '#end for' + self.command_line_before_override = "#for $i in $%s:" % name + self.command_line_after_override = "#end for" # self.command_line_override super(Repeat, self).__init__(**params) @@ -321,22 +339,23 @@ return issubclass(type(child), InputParameter) def command_line_actual(self): - if hasattr(self, 'command_line_override'): + if hasattr(self, "command_line_override"): return self.command_line_override else: return "%s" % self.mako_name() class Conditional(InputParameter): - name = 'conditional' + name = "conditional" def __init__(self, name, **kwargs): params = Util.clean_kwargs(locals().copy()) super(Conditional, self).__init__(**params) def acceptable_child(self, child): - return issubclass(type(child), InputParameter) \ - and not isinstance(child, Conditional) + return issubclass(type(child), InputParameter) and not isinstance( + child, Conditional + ) def validate(self): # Find a way to check if one of the kids is a WHEN @@ -344,7 +363,7 @@ class When(InputParameter): - name = 'when' + name = "when" def __init__(self, value): params = Util.clean_kwargs(locals().copy()) @@ -355,27 +374,31 @@ class Param(InputParameter): - name = 'param' + name = "param" # This...isn't really valid as-is, and shouldn't be used. def __init__(self, name, optional=None, label=None, help=None, **kwargs): params = Util.clean_kwargs(locals().copy()) - params['type'] = self.type + params["type"] = self.type super(Param, self).__init__(**params) if type(self) == Param: raise Exception( - "Param class is not an actual parameter type, use a subclass of Param") + "Param class is not an actual parameter type, use a subclass of Param" + ) def acceptable_child(self, child): - return issubclass(type(child, InputParameter) or isinstance(child), ValidatorParam) + return issubclass( + type(child, InputParameter) or isinstance(child), ValidatorParam + ) class TextParam(Param): - type = 'text' + type = "text" - def __init__(self, name, optional=None, label=None, help=None, - value=None, **kwargs): + def __init__( + self, name, optional=None, label=None, help=None, value=None, **kwargs + ): params = Util.clean_kwargs(locals().copy()) super(TextParam, self).__init__(**params) @@ -390,26 +413,43 @@ class _NumericParam(Param): - - def __init__(self, name, value, optional=None, label=None, help=None, - min=None, max=None, **kwargs): + def __init__( + self, + name, + value, + optional=None, + label=None, + help=None, + min=None, + max=None, + **kwargs, + ): params = Util.clean_kwargs(locals().copy()) super(_NumericParam, self).__init__(**params) class IntegerParam(_NumericParam): - type = 'integer' + type = "integer" class FloatParam(_NumericParam): - type = 'float' + type = "float" class BooleanParam(Param): - type = 'boolean' + type = "boolean" - def __init__(self, name, optional=None, label=None, help=None, - checked=False, truevalue=None, falsevalue=None, **kwargs): + def __init__( + self, + name, + optional=None, + label=None, + help=None, + checked=False, + truevalue=None, + falsevalue=None, + **kwargs, + ): params = Util.clean_kwargs(locals().copy()) super(BooleanParam, self).__init__(**params) @@ -422,36 +462,54 @@ # Unfortunately, mako_identifier is set as a result of the super # call, which we shouldn't call TWICE, so we'll just hack around this :( # params['truevalue'] = '%s%s' % (self.) - self.node.attrib['truevalue'] = self.flag() + self.node.attrib["truevalue"] = self.flag() if falsevalue is None: - self.node.attrib['falsevalue'] = "" + self.node.attrib["falsevalue"] = "" def command_line_actual(self): - if hasattr(self, 'command_line_override'): + if hasattr(self, "command_line_override"): return self.command_line_override else: return "%s" % self.mako_name() class DataParam(Param): - type = 'data' + type = "data" - def __init__(self, name, optional=None, label=None, help=None, format=None, - multiple=None, **kwargs): + def __init__( + self, + name, + optional=None, + label=None, + help=None, + format=None, + multiple=None, + **kwargs, + ): params = Util.clean_kwargs(locals().copy()) super(DataParam, self).__init__(**params) class SelectParam(Param): - type = 'select' + type = "select" - def __init__(self, name, optional=None, label=None, help=None, - data_ref=None, display=None, multiple=None, options=None, - default=None, **kwargs): + def __init__( + self, + name, + optional=None, + label=None, + help=None, + data_ref=None, + display=None, + multiple=None, + options=None, + default=None, + **kwargs, + ): params = Util.clean_kwargs(locals().copy()) - del params['options'] - del params['default'] + del params["options"] + del params["default"] super(SelectParam, self).__init__(**params) @@ -461,34 +519,39 @@ if options: for k, v in list(sorted(options.items())): - selected = (k == default) + selected = k == default self.append(SelectOption(k, v, selected=selected)) def acceptable_child(self, child): - return issubclass(type(child), SelectOption) \ - or issubclass(type(child), Options) + return issubclass(type(child), SelectOption) or issubclass(type(child), Options) class SelectOption(InputParameter): - name = 'option' + name = "option" def __init__(self, value, text, selected=False, **kwargs): params = Util.clean_kwargs(locals().copy()) passed_kwargs = {} if selected: - passed_kwargs['selected'] = "true" - passed_kwargs['value'] = params['value'] + passed_kwargs["selected"] = "true" + passed_kwargs["value"] = params["value"] super(SelectOption, self).__init__(None, **passed_kwargs) self.node.text = str(text) class Options(InputParameter): - name = 'options' + name = "options" - def __init__(self, from_dataset=None, from_file=None, from_data_table=None, - from_parameter=None, **kwargs): + def __init__( + self, + from_dataset=None, + from_file=None, + from_data_table=None, + from_parameter=None, + **kwargs, + ): params = Util.clean_kwargs(locals().copy()) super(Options, self).__init__(None, **params) @@ -497,7 +560,7 @@ class Column(InputParameter): - name = 'column' + name = "column" def __init__(self, name, index, **kwargs): params = Util.clean_kwargs(locals().copy()) @@ -505,27 +568,48 @@ class Filter(InputParameter): - name = 'filter' + name = "filter" - def __init__(self, type, column=None, name=None, ref=None, key=None, - multiple=None, separator=None, keep=None, value=None, - ref_attribute=None, index=None, **kwargs): + def __init__( + self, + type, + column=None, + name=None, + ref=None, + key=None, + multiple=None, + separator=None, + keep=None, + value=None, + ref_attribute=None, + index=None, + **kwargs, + ): params = Util.clean_kwargs(locals().copy()) super(Filter, self).__init__(**params) class ValidatorParam(InputParameter): - name = 'validator' + name = "validator" - def __init__(self, type, message=None, filename=None, metadata_name=None, - metadata_column=None, line_startswith=None, min=None, - max=None, **kwargs): + def __init__( + self, + type, + message=None, + filename=None, + metadata_name=None, + metadata_column=None, + line_startswith=None, + min=None, + max=None, + **kwargs, + ): params = Util.clean_kwargs(locals().copy()) super(ValidatorParam, self).__init__(**params) class Outputs(XMLParam): - name = 'outputs' + name = "outputs" def acceptable_child(self, child): return isinstance(child, OutputData) or isinstance(child, OutputCollection) @@ -534,16 +618,26 @@ class OutputData(XMLParam): """Copypasta of InputParameter, needs work """ - name = 'data' + + name = "data" - def __init__(self, name, format, format_source=None, metadata_source=None, - label=None, from_work_dir=None, hidden=False, **kwargs): + def __init__( + self, + name, + format, + format_source=None, + metadata_source=None, + label=None, + from_work_dir=None, + hidden=False, + **kwargs, + ): # TODO: validate format_source&metadata_source against something in the # XMLParam children tree. self.mako_identifier = name - if 'num_dashes' in kwargs: - self.num_dashes = kwargs['num_dashes'] - del kwargs['num_dashes'] + if "num_dashes" in kwargs: + self.num_dashes = kwargs["num_dashes"] + del kwargs["num_dashes"] else: self.num_dashes = 0 self.space_between_arg = " " @@ -552,30 +646,32 @@ super(OutputData, self).__init__(**params) def command_line(self): - if hasattr(self, 'command_line_override'): + if hasattr(self, "command_line_override"): return self.command_line_override else: return "%s%s%s" % (self.flag(), self.space_between_arg, self.mako_name()) def mako_name(self): - return '$' + self.mako_identifier + return "$" + self.mako_identifier def flag(self): - flag = '-' * self.num_dashes + flag = "-" * self.num_dashes return flag + self.mako_identifier def acceptable_child(self, child): - return isinstance(child, OutputFilter) or \ - isinstance(child, ChangeFormat) or \ - isinstance(child, DiscoverDatasets) + return ( + isinstance(child, OutputFilter) + or isinstance(child, ChangeFormat) + or isinstance(child, DiscoverDatasets) + ) class OutputFilter(XMLParam): - name = 'filter' + name = "filter" def __init__(self, text, **kwargs): params = Util.clean_kwargs(locals().copy()) - del params['text'] + del params["text"] super(OutputFilter, self).__init__(**params) self.node.text = text @@ -584,7 +680,7 @@ class ChangeFormat(XMLParam): - name = 'change_format' + name = "change_format" def __init__(self, **kwargs): params = Util.clean_kwargs(locals().copy()) @@ -595,7 +691,7 @@ class ChangeFormatWhen(XMLParam): - name = 'when' + name = "when" def __init__(self, input, format, value, **kwargs): params = Util.clean_kwargs(locals().copy()) @@ -606,43 +702,56 @@ class OutputCollection(XMLParam): - name = 'collection' + name = "collection" - def __init__(self, name, type=None, label=None, format_source=None, - type_source=None, structured_like=None, inherit_format=None, **kwargs): + def __init__( + self, + name, + type=None, + label=None, + format_source=None, + type_source=None, + structured_like=None, + inherit_format=None, + **kwargs, + ): params = Util.clean_kwargs(locals().copy()) super(OutputCollection, self).__init__(**params) def acceptable_child(self, child): - return isinstance(child, OutputData) or isinstance(child, OutputFilter) \ + return ( + isinstance(child, OutputData) + or isinstance(child, OutputFilter) or isinstance(child, DiscoverDatasets) + ) class DiscoverDatasets(XMLParam): - name = 'discover_datasets' + name = "discover_datasets" - def __init__(self, pattern, directory=None, format=None, ext=None, - visible=None, **kwargs): + def __init__( + self, pattern, directory=None, format=None, ext=None, visible=None, **kwargs + ): params = Util.clean_kwargs(locals().copy()) super(DiscoverDatasets, self).__init__(**params) class Tests(XMLParam): - name = 'tests' + name = "tests" def acceptable_child(self, child): return issubclass(type(child), Test) class Test(XMLParam): - name = 'test' + name = "test" def acceptable_child(self, child): return isinstance(child, TestParam) or isinstance(child, TestOutput) class TestParam(XMLParam): - name = 'param' + name = "param" def __init__(self, name, value=None, ftype=None, dbkey=None, **kwargs): params = Util.clean_kwargs(locals().copy()) @@ -650,17 +759,28 @@ class TestOutput(XMLParam): - name = 'output' + name = "output" - def __init__(self, name=None, file=None, ftype=None, sort=None, value=None, - md5=None, checksum=None, compare=None, lines_diff=None, - delta=None, **kwargs): + def __init__( + self, + name=None, + file=None, + ftype=None, + sort=None, + value=None, + md5=None, + checksum=None, + compare=None, + lines_diff=None, + delta=None, + **kwargs, + ): params = Util.clean_kwargs(locals().copy()) super(TestOutput, self).__init__(**params) class Citations(XMLParam): - name = 'citations' + name = "citations" def acceptable_child(self, child): return issubclass(type(child), Citation) @@ -673,16 +793,16 @@ :type value: STRING """ for citation in self.children: - if citation.node.attrib['type'] == type and citation.node.text == value: + if citation.node.attrib["type"] == type and citation.node.text == value: return True return False class Citation(XMLParam): - name = 'citation' + name = "citation" def __init__(self, type, value): passed_kwargs = {} - passed_kwargs['type'] = type + passed_kwargs["type"] = type super(Citation, self).__init__(**passed_kwargs) self.node.text = str(value)
--- a/toolfactory/rgToolFactory2.py Sat Aug 08 19:55:55 2020 -0400 +++ b/toolfactory/rgToolFactory2.py Mon Aug 10 23:24:41 2020 -0400 @@ -19,27 +19,30 @@ # TODO: add option to run that code as a post execution hook # TODO: add additional history input parameters - currently only one -import sys + +import argparse +import logging +import os +import re +import shutil import subprocess -import shutil -import os +import sys +import tarfile +import tempfile import time -import tempfile -import argparse -import tarfile -import re + import galaxyxml.tool as gxt import galaxyxml.tool.parameters as gxtp -import logging +import lxml - +foo = lxml.__name__ # fug you, flake8. Say my name! Please accept the PR, Helena! progname = os.path.split(sys.argv[0])[1] -myversion = 'V2.1 July 2020' +myversion = "V2.1 July 2020" verbose = True debug = True -toolFactoryURL = 'https://github.com/fubar2/toolfactory' -ourdelim = '~~~' +toolFactoryURL = "https://github.com/fubar2/toolfactory" +ourdelim = "~~~" # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label~~~$input_help" IPATHPOS = 0 @@ -54,7 +57,7 @@ OCLPOS = 2 OOCLPOS = 3 -#--additional_parameters="$i.param_name~~~$i.param_value~~~$i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL" +# --additional_parameters="$i.param_name~~~$i.param_value~~~$i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL" ANAMEPOS = 0 AVALPOS = 1 ALABPOS = 2 @@ -63,10 +66,11 @@ ACLPOS = 5 AOCLPOS = 6 + def timenow(): """return current time as a string """ - return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) + return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time())) def quote_non_numeric(s): @@ -80,12 +84,7 @@ return '"%s"' % s -html_escape_table = { - "&": "&", - ">": ">", - "<": "<", - "$": r"\$" -} +html_escape_table = {"&": "&", ">": ">", "<": "<", "$": r"\$"} def html_escape(text): @@ -95,10 +94,10 @@ def html_unescape(text): """Revert entities within text. Multiple character targets so use replace""" - t = text.replace('&', '&') - t = t.replace('>', '>') - t = t.replace('<', '<') - t = t.replace('\\$', '$') + t = text.replace("&", "&") + t = t.replace(">", ">") + t = t.replace("<", "<") + t = t.replace("\\$", "$") return t @@ -111,8 +110,7 @@ if citation.startswith("doi"): citation_tuples.append(("doi", citation[len("doi"):].strip())) else: - citation_tuples.append( - ("bibtex", citation[len("bibtex"):].strip())) + citation_tuples.append(("bibtex", citation[len("bibtex"):].strip())) return citation_tuples @@ -121,8 +119,7 @@ uses galaxyxml """ - - + def __init__(self, args=None): """ prepare command line cl for running the tool here @@ -138,38 +135,43 @@ self.lastxclredirect = None self.cl = [] self.xmlcl = [] + self.is_positional = self.args.parampass == "positional" aCL = self.cl.append - assert args.parampass in ['0','argparse','positional'],'Parameter passing in args.parampass must be "0","positional" or "argparse"' - self.tool_name = re.sub('[^a-zA-Z0-9_]+', '', args.tool_name) + assert args.parampass in [ + "0", + "argparse", + "positional", + ], 'Parameter passing in args.parampass must be "0","positional" or "argparse"' + self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name) self.tool_id = self.tool_name - self.xmlfile = '%s.xml' % self.tool_name - if self.args.runmode == "Executable" or self.args.runmode == "system": # binary - no need + self.xmlfile = "%s.xml" % self.tool_name + if self.args.interpreter_name: + exe = "$runMe" + else: + exe = self.args.exe_package + assert ( + exe is not None + ), "No interpeter or executable passed in - nothing to run so cannot build" + self.tool = gxt.Tool( + self.args.tool_name, + self.tool_id, + self.args.tool_version, + self.args.tool_desc, + exe, + ) + self.tinputs = gxtp.Inputs() + self.toutputs = gxtp.Outputs() + self.testparam = [] + if ( + self.args.runmode == "Executable" or self.args.runmode == "system" + ): # binary - no need aCL(self.args.exe_package) # this little CL will just run - else: - rx = open(self.args.script_path, 'r').readlines() - rx = [x.rstrip() for x in rx ] - rxcheck = [x.strip() for x in rx if x.strip() > ''] - assert len(rxcheck) > 0,"Supplied script is empty. Cannot run" - self.script = '\n'.join(rx) - fhandle, self.sfile = tempfile.mkstemp( - prefix=self.tool_name, suffix=".%s" % (args.interpreter_name)) - tscript = open(self.sfile, 'w') - tscript.write(self.script) - tscript.close() - self.indentedScript = " %s" % '\n'.join( - [' %s' % html_escape(x) for x in rx]) - self.escapedScript = "%s" % '\n'.join( - [' %s' % html_escape(x) for x in rx]) - art = '%s.%s' % (self.tool_name, args.interpreter_name) - artifact = open(art, 'wb') - artifact.write(bytes(self.script, "utf8")) - artifact.close() - aCL(self.args.interpreter_name) - aCL(self.sfile) + else: + self.prepScript() self.elog = "%s_error_log.txt" % self.tool_name self.tlog = "%s_runner_log.txt" % self.tool_name - if self.args.parampass == '0': + if self.args.parampass == "0": self.clsimple() else: clsuffix = [] @@ -177,92 +179,120 @@ for i, p in enumerate(self.infiles): appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS]] clsuffix.append(appendme) - xclsuffix.append([p[IOCLPOS],p[ICLPOS],'$%s' % p[ICLPOS]]) - #print('##infile i=%d, appendme=%s' % (i,appendme)) + xclsuffix.append([p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS]]) + # print('##infile i=%d, appendme=%s' % (i,appendme)) for i, p in enumerate(self.outfiles): if p[OOCLPOS] == "STDOUT": - self.lastclredirect = ['>',p[ONAMEPOS]] - self.lastxclredirect = ['>','$%s' % p[OCLPOS]] - #print('##outfiles i=%d lastclredirect = %s' % (i,self.lastclredirect)) + self.lastclredirect = [">", p[ONAMEPOS]] + self.lastxclredirect = [">", "$%s" % p[OCLPOS]] + # print('##outfiles i=%d lastclredirect = %s' % (i,self.lastclredirect)) else: - appendme = [p[OOCLPOS], p[OCLPOS],p[ONAMEPOS]] - clsuffix.append(appendme) - xclsuffix.append([p[OOCLPOS], p[OCLPOS],'$%s' % p[ONAMEPOS]]) - #print('##outfiles i=%d' % i,'appendme',appendme) - for p in self.addpar: + appendme = [p[OOCLPOS], p[OCLPOS], p[ONAMEPOS]] + clsuffix.append(appendme) + xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS]]) + # print('##outfiles i=%d' % i,'appendme',appendme) + for p in self.addpar: appendme = [p[AOCLPOS], p[ACLPOS], p[AVALPOS]] clsuffix.append(appendme) xclsuffix.append([p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS]]) - #print('##adpar %d' % i,'appendme=',appendme) + # print('##adpar %d' % i,'appendme=',appendme) clsuffix.sort() xclsuffix.sort() self.xclsuffix = xclsuffix self.clsuffix = clsuffix - if self.args.parampass == 'positional': + if self.args.parampass == "positional": self.clpositional() else: self.clargparse() - + + def prepScript(self): + aCL = self.cl.append + rx = open(self.args.script_path, "r").readlines() + rx = [x.rstrip() for x in rx] + rxcheck = [x.strip() for x in rx if x.strip() > ""] + assert len(rxcheck) > 0, "Supplied script is empty. Cannot run" + self.script = "\n".join(rx) + fhandle, self.sfile = tempfile.mkstemp( + prefix=self.tool_name, suffix=".%s" % (self.args.interpreter_name) + ) + tscript = open(self.sfile, "w") + tscript.write(self.script) + tscript.close() + self.indentedScript = " %s" % "\n".join([" %s" % html_escape(x) for x in rx]) + self.escapedScript = "%s" % "\n".join([" %s" % html_escape(x) for x in rx]) + art = "%s.%s" % (self.tool_name, self.args.interpreter_name) + artifact = open(art, "wb") + artifact.write(bytes(self.script, "utf8")) + artifact.close() + aCL(self.args.interpreter_name) + aCL(self.sfile) + def cleanuppar(self): """ positional parameters are complicated by their numeric ordinal""" - for i,p in enumerate(self.infiles): - if self.args.parampass == 'positional': - assert p[ICLPOS].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (p[ICLPOS],p[ILABPOS]) + for i, p in enumerate(self.infiles): + if self.args.parampass == "positional": + assert p[ICLPOS].isdigit(), ( + "Positional parameters must be ordinal integers - got %s for %s" + % (p[ICLPOS], p[ILABPOS]) + ) p.append(p[ICLPOS]) if p[ICLPOS].isdigit() or self.args.parampass == "0": - scl = 'input%d' % (i+1) + scl = "input%d" % (i + 1) p[ICLPOS] = scl self.infiles[i] = p - for i,p in enumerate(self.outfiles): # trying to automagically gather using extensions - if self.args.parampass == 'positional' and p[OCLPOS] != "STDOUT": - assert p[OCLPOS].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (p[OCLPOS],p[ONAMEPOS]) + for i, p in enumerate( + self.outfiles + ): # trying to automagically gather using extensions + if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT": + assert p[OCLPOS].isdigit(), ( + "Positional parameters must be ordinal integers - got %s for %s" + % (p[OCLPOS], p[ONAMEPOS]) + ) p.append(p[OCLPOS]) if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT": scl = p[ONAMEPOS] p[OCLPOS] = scl self.outfiles[i] = p - for i,p in enumerate(self.addpar): - if self.args.parampass == 'positional': - assert p[ACLPOS].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (p[ACLPOS],p[ANAMEPOS]) + for i, p in enumerate(self.addpar): + if self.args.parampass == "positional": + assert p[ACLPOS].isdigit(), ( + "Positional parameters must be ordinal integers - got %s for %s" + % (p[ACLPOS], p[ANAMEPOS]) + ) p.append(p[ACLPOS]) if p[ACLPOS].isdigit(): - scl = 'input%s' % p[ACLPOS] + scl = "input%s" % p[ACLPOS] p[ACLPOS] = scl self.addpar[i] = p - - - + def clsimple(self): """ no parameters - uses < and > for i/o """ aCL = self.cl.append - aCL('<') + aCL("<") aCL(self.infiles[0][IPATHPOS]) - aCL('>') + aCL(">") aCL(self.outfiles[0][OCLPOS]) aXCL = self.xmlcl.append - aXCL('<') - aXCL('$%s' % self.infiles[0][ICLPOS]) - aXCL('>') - aXCL('$%s' % self.outfiles[0][ONAMEPOS]) - + aXCL("<") + aXCL("$%s" % self.infiles[0][ICLPOS]) + aXCL(">") + aXCL("$%s" % self.outfiles[0][ONAMEPOS]) def clpositional(self): # inputs in order then params aCL = self.cl.append - for (o_v,k, v) in self.clsuffix: + for (o_v, k, v) in self.clsuffix: if " " in v: aCL("%s" % v) else: aCL(v) aXCL = self.xmlcl.append - for (o_v,k, v) in self.xclsuffix: + for (o_v, k, v) in self.xclsuffix: aXCL(v) if self.lastxclredirect: aXCL(self.lastxclredirect[0]) aXCL(self.lastxclredirect[1]) - - def clargparse(self): """ argparse style @@ -270,23 +300,142 @@ aCL = self.cl.append aXCL = self.xmlcl.append # inputs then params in argparse named form - for (o_v,k, v) in self.xclsuffix: + for (o_v, k, v) in self.xclsuffix: if len(k.strip()) == 1: - k = '-%s' % k + k = "-%s" % k else: - k = '--%s' % k + k = "--%s" % k aXCL(k) aXCL(v) - for (o_v,k, v) in self.clsuffix: + for (o_v, k, v) in self.clsuffix: if len(k.strip()) == 1: - k = '-%s' % k + k = "-%s" % k else: - k = '--%s' % k + k = "--%s" % k aCL(k) aCL(v) - + def getNdash(self, newname): + if self.is_positional: + ndash = 0 + else: + ndash = 2 + if len(newname) < 2: + ndash = 1 + return ndash + def doXMLparam(self): + """flake8 made me do this...""" + for p in self.outfiles: + newname, newfmt, newcl, oldcl = p + ndash = self.getNdash(newcl) + aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash) + aparm.positional = self.is_positional + if self.is_positional: + if oldcl == "STDOUT": + aparm.positional = 9999999 + aparm.command_line_override = "> $%s" % newcl + else: + aparm.positional = int(oldcl) + aparm.command_line_override = "$%s" % newcl + self.toutputs.append(aparm) + tp = gxtp.TestOutput(name=newcl, value="%s_sample" % newcl, format=newfmt) + self.testparam.append(tp) + for p in self.infiles: + newname = p[ICLPOS] + newfmt = p[IFMTPOS] + ndash = self.getNdash(newname) + if not len(p[ILABPOS]) > 0: + alab = p[ICLPOS] + else: + alab = p[ILABPOS] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=p[IHELPOS], + format=newfmt, + multiple=False, + num_dashes=ndash, + ) + aninput.positional = self.is_positional + self.tinputs.append(aninput) + tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname) + self.testparam.append(tparm) + for p in self.addpar: + newname, newval, newlabel, newhelp, newtype, newcl, oldcl = p + if not len(newlabel) > 0: + newlabel = newname + ndash = self.getNdash(newname) + if newtype == "text": + aparm = gxtp.TextParam( + newname, + label=newlabel, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "integer": + aparm = gxtp.IntegerParam( + newname, + label=newname, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + elif newtype == "float": + aparm = gxtp.FloatParam( + newname, + label=newname, + help=newhelp, + value=newval, + num_dashes=ndash, + ) + else: + raise ValueError( + 'Unrecognised parameter type "%s" for\ + additional parameter %s in makeXML' + % (newtype, newname) + ) + aparm.positional = self.is_positional + if self.is_positional: + aninput.positional = int(oldcl) + self.tinputs.append(aparm) + self.tparm = gxtp.TestParam(newname, value=newval) + self.testparam.append(tparm) + + def doNoXMLparam(self): + alab = self.infiles[0][ILABPOS] + if len(alab) == 0: + alab = self.infiles[0][ICLPOS] + max1s = ( + "Maximum one input if parampass is 0 - more than one input files supplied - %s" + % str(self.infiles) + ) + assert len(self.infiles) == 1, max1s + newname = self.infiles[0][ICLPOS] + aninput = gxtp.DataParam( + newname, + optional=False, + label=alab, + help=self.infiles[0][IHELPOS], + format=self.infiles[0][IFMTPOS], + multiple=False, + num_dashes=0, + ) + aninput.command_line_override = "< $%s" % newname + aninput.positional = self.is_positional + self.tinputs.append(aninput) + tp = gxtp.TestParam(name=newname, value="%s_sample" % newname) + self.testparam.append(tp) + newname = self.outfiles[0][OCLPOS] + newfmt = self.outfiles[0][OFMTPOS] + anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0) + anout.command_line_override = "> $%s" % newname + anout.positional = self.is_positional + self.toutputs.append(anout) + tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname, format=newfmt) + self.testparam.append(tp) def makeXML(self): """ @@ -294,159 +443,71 @@ Uses galaxyhtml Hmmm. How to get the command line into correct order... """ - + self.tool.command_line_override = self.xmlcl if self.args.interpreter_name: - exe = "$runMe" - interp = self.args.interpreter_name - else: - interp = None - exe = self.args.exe_package - assert exe is not None, 'No interpeter or executable passed in to makeXML' - tool = gxt.Tool(self.args.tool_name, self.tool_id, - self.args.tool_version, self.args.tool_desc, exe) - tool.command_line_override = self.xmlcl - if interp: - tool.interpreter = interp + self.tool.interpreter = self.interp if self.args.help_text: - helptext = open(self.args.help_text, 'r').readlines() + helptext = open(self.args.help_text, "r").readlines() helptext = [html_escape(x) for x in helptext] - tool.help = ''.join([x for x in helptext]) + self.tool.help = "".join([x for x in helptext]) else: - tool.help = 'Please ask the tool author (%s) for help \ - as none was supplied at tool generation\n' % (self.args.user_email) - tool.version_command = None # do not want - tinputs = gxtp.Inputs() - toutputs = gxtp.Outputs() + self.tool.help = ( + "Please ask the tool author (%s) for help \ + as none was supplied at tool generation\n" + % (self.args.user_email) + ) + self.tool.version_command = None # do not want requirements = gxtp.Requirements() - testparam = [] - is_positional = (self.args.parampass == 'positional') + if self.args.interpreter_name: - if self.args.interpreter_name == 'python': - requirements.append(gxtp.Requirement( - 'package', 'python', self.args.interpreter_version)) - elif self.args.interpreter_name not in ['bash', 'sh']: - requirements.append(gxtp.Requirement( - 'package', self.args.interpreter_name, self.args.interpreter_version)) + if self.args.interpreter_name == "python": + requirements.append( + gxtp.Requirement("package", "python", self.args.interpreter_version) + ) + elif self.args.interpreter_name not in ["bash", "sh"]: + requirements.append( + gxtp.Requirement( + "package", + self.args.interpreter_name, + self.args.interpreter_version, + ) + ) else: if self.args.exe_package and self.args.parampass != "system": - requirements.append(gxtp.Requirement( - 'package', self.args.exe_package, self.args.exe_package_version)) - tool.requirements = requirements - if self.args.parampass == '0': - alab = self.infiles[0][ILABPOS] - if len(alab) == 0: - alab = self.infiles[0][ICLPOS] - max1s = 'Maximum one input if parampass is 0 - more than one input files supplied - %s' % str(self.infiles) - assert len(self.infiles) == 1,max1s - newname = self.infiles[0][ICLPOS] - aninput = gxtp.DataParam(newname, optional=False, label=alab, help=self.infiles[0][IHELPOS], - format=self.infiles[0][IFMTPOS], multiple=False, num_dashes=0) - aninput.command_line_override = '< $%s' % newname - aninput.positional = is_positional - tinputs.append(aninput) - tp = gxtp.TestParam(name=newname, value='%s_sample' % newname) - testparam.append(tp) - newname = self.outfiles[0][OCLPOS] - newfmt = self.outfiles[0][OFMTPOS] - anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0) - anout.command_line_override = '> $%s' % newname - anout.positional = is_positional - toutputs.append(anout) - tp = gxtp.TestOutput(name=newname, value='%s_sample' % newname,format=newfmt) - testparam.append(tp) + requirements.append( + gxtp.Requirement( + "package", self.args.exe_package, self.args.exe_package_version + ) + ) + self.tool.requirements = requirements + if self.args.parampass == "0": + self.doXMLNoparam() else: - for p in self.outfiles: - newname,newfmt,newcl,oldcl = p - if is_positional: - ndash = 0 - else: - ndash = 2 - if len(newcl) < 2: - ndash = 1 - aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash) - aparm.positional = is_positional - if is_positional: - if oldcl == "STDOUT": - aparm.positional = 9999999 - aparm.command_line_override = "> $%s" % newcl - else: - aparm.positional = int(oldcl) - aparm.command_line_override = '$%s' % newcl - toutputs.append(aparm) - tp = gxtp.TestOutput(name=newcl, value='%s_sample' % newcl ,format=newfmt) - testparam.append(tp) - for p in self.infiles: - newname = p[ICLPOS] - newfmt = p[IFMTPOS] - if is_positional: - ndash = 0 - else: - if len(newname) > 1: - ndash = 2 - else: - ndash = 1 - if not len(p[ILABPOS]) > 0: - alab = p[ICLPOS] - else: - alab = p[ILABPOS] - aninput = gxtp.DataParam(newname, optional=False, label=alab, help=p[IHELPOS], - format=newfmt, multiple=False, num_dashes=ndash) - aninput.positional = is_positional - if is_positional: - aninput.positional = is_positional - tinputs.append(aninput) - tparm = gxtp.TestParam(name=newname, value='%s_sample' % newname ) - testparam.append(tparm) - for p in self.addpar: - newname, newval, newlabel, newhelp, newtype, newcl, oldcl = p - if not len(newlabel) > 0: - newlabel = newname - if is_positional: - ndash = 0 - else: - if len(newname) > 1: - ndash = 2 - else: - ndash = 1 - if newtype == "text": - aparm = gxtp.TextParam( - newname, label=newlabel, help=newhelp, value=newval, num_dashes=ndash) - elif newtype == "integer": - aparm = gxtp.IntegerParam( - newname, label=newname, help=newhelp, value=newval, num_dashes=ndash) - elif newtype == "float": - aparm = gxtp.FloatParam( - newname, label=newname, help=newhelp, value=newval, num_dashes=ndash) - else: - raise ValueError('Unrecognised parameter type "%s" for\ - additional parameter %s in makeXML' % (newtype, newname)) - aparm.positional = is_positional - if is_positional: - aninput.positional = int(oldcl) - tinputs.append(aparm) - tparm = gxtp.TestParam(newname, value=newval) - testparam.append(tparm) - tool.outputs = toutputs - tool.inputs = tinputs - if not self.args.runmode in ['Executable','system']: + self.doXMLParam() + self.tool.outputs = self.toutputs + self.tool.inputs = self.tinputs + if self.args.runmode not in ["Executable", "system"]: configfiles = gxtp.Configfiles() configfiles.append(gxtp.Configfile(name="runMe", text=self.script)) - tool.configfiles = configfiles + self.tool.configfiles = configfiles tests = gxtp.Tests() test_a = gxtp.Test() - for tp in testparam: + for tp in self.testparam: test_a.append(tp) tests.append(test_a) - tool.tests = tests - tool.add_comment('Created by %s at %s using the Galaxy Tool Factory.' % ( - self.args.user_email, timenow())) - tool.add_comment('Source in git at: %s' % (toolFactoryURL)) - tool.add_comment( - 'Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573') - exml = tool.export() - xf = open(self.xmlfile, 'w') + self.tool.tests = tests + self.tool.add_comment( + "Created by %s at %s using the Galaxy Tool Factory." + % (self.args.user_email, timenow()) + ) + self.tool.add_comment("Source in git at: %s" % (toolFactoryURL)) + self.tool.add_comment( + "Cite: Creating re-usable tools from scripts doi: 10.1093/bioinformatics/bts573" + ) + exml = self.tool.export() + xf = open(self.xmlfile, "w") xf.write(exml) - xf.write('\n') + xf.write("\n") xf.close() # ready for the tarball @@ -459,49 +520,46 @@ """ retval = self.run() if retval: - sys.stderr.write( - '## Run failed. Cannot build yet. Please fix and retry') + sys.stderr.write("## Run failed. Cannot build yet. Please fix and retry") sys.exit(1) - tdir = 'tfout' + tdir = "tfout" if not os.path.exists(tdir): os.mkdir(tdir) self.makeXML() - testdir = os.path.join(tdir,'test-data') + testdir = os.path.join(tdir, "test-data") if not os.path.exists(testdir): os.mkdir(testdir) # make tests directory for p in self.infiles: pth = p[IPATHPOS] - dest = os.path.join(testdir, '%s_sample' % - p[ICLPOS]) + dest = os.path.join(testdir, "%s_sample" % p[ICLPOS]) shutil.copyfile(pth, dest) for p in self.outfiles: pth = p[OCLPOS] - if p[OOCLPOS] == 'STDOUT' or self.args.parampass == "0": + if p[OOCLPOS] == "STDOUT" or self.args.parampass == "0": pth = p[ONAMEPOS] - dest = os.path.join(testdir,'%s_sample' % p[ONAMEPOS]) + dest = os.path.join(testdir, "%s_sample" % p[ONAMEPOS]) shutil.copyfile(pth, dest) dest = os.path.join(tdir, p[ONAMEPOS]) - shutil.copyfile(pth, dest) + shutil.copyfile(pth, dest) else: pth = p[OCLPOS] - dest = os.path.join(testdir,'%s_sample' % p[OCLPOS]) + dest = os.path.join(testdir, "%s_sample" % p[OCLPOS]) shutil.copyfile(pth, dest) dest = os.path.join(tdir, p[OCLPOS]) - shutil.copyfile(pth, dest) + shutil.copyfile(pth, dest) if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0: - shutil.copyfile(self.tlog, os.path.join( - testdir, 'test1_log.txt')) - if not self.args.runmode in ['Executable','system']: - stname = os.path.join(tdir, '%s' % (self.sfile)) + shutil.copyfile(self.tlog, os.path.join(testdir, "test1_log.txt")) + if self.args.runmode not in ["Executable", "system"]: + stname = os.path.join(tdir, "%s" % (self.sfile)) if not os.path.exists(stname): shutil.copyfile(self.sfile, stname) - xtname = os.path.join(tdir,self.xmlfile) + xtname = os.path.join(tdir, self.xmlfile) if not os.path.exists(xtname): shutil.copyfile(self.xmlfile, xtname) - tarpath = 'toolfactory_%s.tgz' % self.tool_name - tf = tarfile.open(tarpath,"w:gz") - tf.add(name=tdir,arcname=self.tool_name) + tarpath = "toolfactory_%s.tgz" % self.tool_name + tf = tarfile.open(tarpath, "w:gz") + tf.add(name=tdir, arcname=self.tool_name) tf.close() shutil.copyfile(tarpath, self.args.new_tool) return retval @@ -511,26 +569,29 @@ Some devteam tools have this defensive stderr read so I'm keeping with the faith Feel free to update. """ - s = 'run cl=%s' % str(self.cl) - + s = "run cl=%s" % str(self.cl) + logging.debug(s) - scl = ' '.join(self.cl) + scl = " ".join(self.cl) err = None - if self.args.parampass != '0': - ste = open(self.elog, 'wb') + if self.args.parampass != "0": + ste = open(self.elog, "wb") if self.lastclredirect: - sto = open(self.lastclredirect[1],'wb') # is name of an output file + sto = open(self.lastclredirect[1], "wb") # is name of an output file else: - sto = open(self.tlog, 'wb') + sto = open(self.tlog, "wb") sto.write( - bytes('## Executing Toolfactory generated command line = %s\n' % scl, "utf8")) + bytes( + "## Executing Toolfactory generated command line = %s\n" % scl, + "utf8", + ) + ) sto.flush() - p = subprocess.run(self.cl, shell=False, stdout=sto, - stderr=ste) + p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste) sto.close() ste.close() - tmp_stderr = open(self.elog, 'rb') - err = '' + tmp_stderr = open(self.elog, "rb") + err = "" buffsize = 1048576 try: while True: @@ -542,8 +603,8 @@ tmp_stderr.close() retval = p.returncode else: # work around special case of simple scripts that take stdin and write to stdout - sti = open(self.infiles[0][IPATHPOS], 'rb') - sto = open(self.outfiles[0][ONAMEPOS], 'wb') + sti = open(self.infiles[0][IPATHPOS], "rb") + sto = open(self.outfiles[0][ONAMEPOS], "wb") # must use shell to redirect p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti) retval = p.returncode @@ -555,7 +616,7 @@ os.unlink(self.elog) if p.returncode != 0 and err: # problem sys.stderr.write(err) - logging.debug('run done') + logging.debug("run done") return retval @@ -567,40 +628,43 @@ """ parser = argparse.ArgumentParser() a = parser.add_argument - a('--script_path', default='') - a('--tool_name', default=None) - a('--interpreter_name', default=None) - a('--interpreter_version', default=None) - a('--exe_package', default=None) - a('--exe_package_version', default=None) - a('--input_files', default=[], action="append") - a('--output_files', default=[], action="append") - a('--user_email', default='Unknown') - a('--bad_user', default=None) - a('--make_Tool', default=None) - a('--help_text', default=None) - a('--tool_desc', default=None) - a('--tool_version', default=None) - a('--citations', default=None) - a('--additional_parameters', action='append', default=[]) - a('--edit_additional_parameters', action="store_true", default=False) - a('--parampass', default="positional") - a('--tfout', default="./tfout") - a('--new_tool',default="new_tool") - a('--runmode',default=None) + a("--script_path", default="") + a("--tool_name", default=None) + a("--interpreter_name", default=None) + a("--interpreter_version", default=None) + a("--exe_package", default=None) + a("--exe_package_version", default=None) + a("--input_files", default=[], action="append") + a("--output_files", default=[], action="append") + a("--user_email", default="Unknown") + a("--bad_user", default=None) + a("--make_Tool", default=None) + a("--help_text", default=None) + a("--tool_desc", default=None) + a("--tool_version", default=None) + a("--citations", default=None) + a("--additional_parameters", action="append", default=[]) + a("--edit_additional_parameters", action="store_true", default=False) + a("--parampass", default="positional") + a("--tfout", default="./tfout") + a("--new_tool", default="new_tool") + a("--runmode", default=None) args = parser.parse_args() - assert not args.bad_user, 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file' % ( - args.bad_user, args.bad_user) - assert args.tool_name, '## Tool Factory expects a tool name - eg --tool_name=DESeq' - assert (args.interpreter_name or args.exe_package), '## Tool Factory wrapper expects an interpreter - eg --interpreter_name=Rscript or an executable package findable by the dependency management package' - assert args.exe_package or (len(args.script_path) > 0 and os.path.isfile( - args.script_path)), '## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable' - args.input_files = [x.replace('"', '').replace("'", '') - for x in args.input_files] + assert not args.bad_user, ( + 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file' + % (args.bad_user, args.bad_user) + ) + assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq" + assert ( + args.interpreter_name or args.exe_package + ), "## Tool Factory wrapper expects an interpreter or an executable package" + assert args.exe_package or ( + len(args.script_path) > 0 and os.path.isfile(args.script_path) + ), "## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable" + args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files] # remove quotes we need to deal with spaces in CL params for i, x in enumerate(args.additional_parameters): - args.additional_parameters[i] = args.additional_parameters[i].replace( - '"', '') + args.additional_parameters[i] = args.additional_parameters[i].replace('"', "") r = ScriptRunner(args) if args.make_Tool: retcode = r.makeTooltar()
--- a/toolfactory/rgToolFactory2.xml Sat Aug 08 19:55:55 2020 -0400 +++ b/toolfactory/rgToolFactory2.xml Mon Aug 10 23:24:41 2020 -0400 @@ -122,6 +122,7 @@ </macros> <requirements> <requirement type="package">python</requirement> + <requirement type="package">lxml</requirement> </requirements> <command interpreter="python"><![CDATA[ #import os
--- a/toolfactory/sample_toolfactory_tools.ga Sat Aug 08 19:55:55 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,443 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "workflow to generate a bunch of sample toolfactory tools", - "steps": { - "0": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "rgToolFactory2.py" - } - ], - "label": "rgToolFactory2.py", - "name": "Input dataset", - "outputs": [], - "position": { - "bottom": 235.25, - "height": 81, - "left": 711.84375, - "right": 911.84375, - "top": 154.25, - "width": 200, - "x": 711.84375, - "y": 154.25 - }, - "tool_id": null, - "tool_state": "{\"optional\": false}", - "tool_version": null, - "type": "data_input", - "uuid": "b717b6ee-51d0-415d-876d-f19b42f67666", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "09acd6fd-4e2b-44a8-8757-35eca8d0de89" - } - ] - }, - "1": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "README.md" - } - ], - "label": "README.md", - "name": "Input dataset", - "outputs": [], - "position": { - "bottom": 760.25, - "height": 61, - "left": 711.84375, - "right": 911.84375, - "top": 699.25, - "width": 200, - "x": 711.84375, - "y": 699.25 - }, - "tool_id": null, - "tool_state": "{\"optional\": false}", - "tool_version": null, - "type": "data_input", - "uuid": "8aefae07-4fd1-44a6-bea2-5d377567ac27", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "5f8453d0-abd1-41d9-a4a7-1f8b82f1f095" - } - ] - }, - "2": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "testtext" - } - ], - "label": "testtext", - "name": "Input dataset", - "outputs": [], - "position": { - "bottom": 235.25, - "height": 61, - "left": 989.84375, - "right": 1189.84375, - "top": 174.25, - "width": 200, - "x": 989.84375, - "y": 174.25 - }, - "tool_id": null, - "tool_state": "{\"optional\": false}", - "tool_version": null, - "type": "data_input", - "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa" - } - ] - }, - "3": { - "annotation": "", - "content_id": "rgTF2", - "errors": null, - "id": 3, - "input_connections": { - "ppass|history_inputs_0|input_files": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "toolfactory", - "outputs": [ - { - "name": "ToolFactory_Outputs", - "type": "input" - }, - { - "name": "new_tool", - "type": "tgz" - } - ], - "position": { - "bottom": 636.25, - "height": 222, - "left": 989.84375, - "right": 1189.84375, - "top": 414.25, - "width": 200, - "x": 989.84375, - "y": 414.25 - }, - "post_job_actions": {}, - "tool_id": "rgTF2", - "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"bash\", \"__current_case__\": 5, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"rev | tac\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"tacrev\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"0\", \"__current_case__\": 2, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input file\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"2\"}]}, \"tool_name\": \"tacrev\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.00", - "type": "tool", - "uuid": "8fab16a0-5303-4e5c-8bf6-d6ebc70aa9af", - "workflow_outputs": [ - { - "label": null, - "output_name": "ToolFactory_Outputs", - "uuid": "68d1a0b8-d897-48e9-a304-25d289e139e9" - }, - { - "label": null, - "output_name": "new_tool", - "uuid": "8669863e-a1a5-4ed6-a412-c7f341f66176" - } - ] - }, - "4": { - "annotation": "", - "content_id": "rgTF2", - "errors": null, - "id": 4, - "input_connections": { - "ppass|history_inputs_0|input_files": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "toolfactory", - "outputs": [ - { - "name": "ToolFactory_Outputs", - "type": "input" - }, - { - "name": "new_tool", - "type": "tgz" - } - ], - "position": { - "bottom": 916.25, - "height": 242, - "left": 989.84375, - "right": 1189.84375, - "top": 674.25, - "width": 200, - "x": 989.84375, - "y": 674.25 - }, - "post_job_actions": {}, - "tool_id": "rgTF2", - "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.00", - "type": "tool", - "uuid": "ea0f8bbe-6b0d-4aff-bf06-6192faf8fe22", - "workflow_outputs": [ - { - "label": null, - "output_name": "ToolFactory_Outputs", - "uuid": "70755c1b-6f92-43a3-aacb-8cc508a89b74" - }, - { - "label": null, - "output_name": "new_tool", - "uuid": "ea9482d9-7836-442d-b753-ce4a201fd8c9" - } - ] - }, - "5": { - "annotation": "", - "content_id": "rgTF2", - "errors": null, - "id": 5, - "input_connections": { - "ppass|history_inputs_0|input_files": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "toolfactory", - "outputs": [ - { - "name": "ToolFactory_Outputs", - "type": "input" - }, - { - "name": "new_tool", - "type": "tgz" - } - ], - "position": { - "bottom": 1216.25, - "height": 262, - "left": 989.84375, - "right": 1189.84375, - "top": 954.25, - "width": 200, - "x": 989.84375, - "y": 954.25 - }, - "post_job_actions": {}, - "tool_id": "rgTF2", - "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\nimport argparse\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--infile',default='')\\na('--outfile',default=None)\\nargs = parser.parse_args()\\ninp = args.infile\\noutp = args.outfile\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"reverse argparse\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"infile\", \"input_help\": \"parameter_help\", \"input_CL\": \"infile\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"outfile\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevargparse\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.00", - "type": "tool", - "uuid": "065b274a-ae73-43b0-b015-8b60d90db78f", - "workflow_outputs": [ - { - "label": null, - "output_name": "ToolFactory_Outputs", - "uuid": "bec62d2d-b462-49bb-9646-28fea9136778" - }, - { - "label": null, - "output_name": "new_tool", - "uuid": "2e1ed464-bcff-4354-8bf3-ed01167b280f" - } - ] - }, - "6": { - "annotation": "", - "content_id": "rgTF2", - "errors": null, - "id": 6, - "input_connections": { - "ppass|history_inputs_0|input_files": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "toolfactory", - "outputs": [ - { - "name": "ToolFactory_Outputs", - "type": "input" - }, - { - "name": "new_tool", - "type": "tgz" - } - ], - "position": { - "bottom": 1496.25, - "height": 242, - "left": 989.84375, - "right": 1189.84375, - "top": 1254.25, - "width": 200, - "x": 989.84375, - "y": 1254.25 - }, - "post_job_actions": {}, - "tool_id": "rgTF2", - "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\nappendme = sys.argv[3]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write(appendme)\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"appendme\", \"param_type\": \"text\", \"param_value\": \"added at the end\", \"param_label\": \"append string\", \"param_help\": \"parameter_help\", \"param_CL\": \"3\"}]}, \"tool_name\": \"pyrevaddpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.00", - "type": "tool", - "uuid": "5954323f-4ca1-4957-8250-746703dfa7c5", - "workflow_outputs": [ - { - "label": null, - "output_name": "ToolFactory_Outputs", - "uuid": "6466bf24-51b2-4fae-aac8-fc1d78faac89" - }, - { - "label": null, - "output_name": "new_tool", - "uuid": "f37589e2-3582-4443-bce8-5759485a7220" - } - ] - }, - "7": { - "annotation": "", - "content_id": "rgTF2", - "errors": null, - "id": 7, - "input_connections": { - "ppass|history_inputs_0|input_files": { - "id": 2, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "toolfactory", - "outputs": [ - { - "name": "ToolFactory_Outputs", - "type": "input" - }, - { - "name": "new_tool", - "type": "tgz" - } - ], - "position": { - "bottom": 376.25, - "height": 222, - "left": 1267.84375, - "right": 1467.84375, - "top": 154.25, - "width": 200, - "x": 1267.84375, - "y": 154.25 - }, - "post_job_actions": {}, - "tool_id": "rgTF2", - "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"system\", \"__current_case__\": 1, \"exe_package\": \"sed\", \"exe_package_version\": \"\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"sed runner\", \"help_text\": \"sed '/old/new/g input.txt\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input text\", \"input_help\": \"parameter_help\", \"input_CL\": \"3\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"sedstring\", \"param_type\": \"text\", \"param_value\": \"s/Old/New/g\", \"param_label\": \"parameter_label\", \"param_help\": \"parameter_help\", \"param_CL\": \"1\"}]}, \"tool_name\": \"sedtest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.00", - "type": "tool", - "uuid": "e26df7b6-3899-42fb-8efc-5f13d53668f8", - "workflow_outputs": [ - { - "label": null, - "output_name": "ToolFactory_Outputs", - "uuid": "0a819390-acd4-4be6-aac9-ec3322302b0f" - }, - { - "label": null, - "output_name": "new_tool", - "uuid": "f7555059-144d-4f64-a303-b70d189e6e35" - } - ] - }, - "8": { - "annotation": "", - "content_id": "rgTF2", - "errors": null, - "id": 8, - "input_connections": { - "ppass|history_inputs_0|input_files": { - "id": 5, - "output_name": "new_tool" - } - }, - "inputs": [], - "label": null, - "name": "toolfactory", - "outputs": [ - { - "name": "ToolFactory_Outputs", - "type": "input" - }, - { - "name": "new_tool", - "type": "tgz" - } - ], - "position": { - "bottom": 1271.25, - "height": 242, - "left": 1267.84375, - "right": 1467.84375, - "top": 1029.25, - "width": 200, - "x": 1267.84375, - "y": 1029.25 - }, - "post_job_actions": {}, - "tool_id": "rgTF2", - "tool_state": "{\"__input_ext\": \"tgz\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"import argparse\\nimport tarfile\\nimport os\\nimport tempfile\\nimport subprocess\\n\\n\\\"\\\"\\\"\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\n\\\"\\\"\\\"\\n\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--tooltgz',default='')\\na('--report',default=None)\\na('--toolout',default=None)\\na('--galaxy_root',default=None)\\nargs = parser.parse_args()\\ntoolname = args.toolout.split(os.sep)[-1]\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\ntf = tarfile.open(args.tooltgz,\\\"r:gz\\\")\\ntf.extractall(toolpath)\\ncl = \\\"planemo test --skip_venv --galaxy_root %s %s\\\" % (args.galaxy_root,toolpath)\\ncll = cl.split(' ')\\nsto = open(args.report, 'w')\\np = subprocess.run(cll, shell=False, stdout=sto)\\nretval = p.returncode\\nsto.close()\\n\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"Tool to test toolshed tool archives generated by the tool factory.\", \"help_text\": \"**What it Does**\\n\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\nIt was generated using the tool factory.\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"tool toolshed tgz archive from history\", \"input_help\": \"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\", \"input_CL\": \"tooltgz\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"report\", \"history_format\": \"txt\", \"history_CL\": \"report\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"toolout\", \"param_type\": \"text\", \"param_value\": \"tools/toolmakers/planemotest\", \"param_label\": \"output path under galaxy root\", \"param_help\": \"This is where the tgz file will be extracted and tested by planemo\", \"param_CL\": \"toolout\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"your galaxy root to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for running planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that root\", \"param_CL\": \"galaxy_root\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.00", - "type": "tool", - "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd", - "workflow_outputs": [ - { - "label": null, - "output_name": "ToolFactory_Outputs", - "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027" - }, - { - "label": null, - "output_name": "new_tool", - "uuid": "744499de-5d7e-4415-b427-315057c81ebc" - } - ] - } - }, - "tags": [], - "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b", - "version": 1 -}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/sample_toolfactory_tools.tgz Mon Aug 10 23:24:41 2020 -0400 @@ -0,0 +1,443 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "workflow to generate a bunch of sample toolfactory tools", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "rgToolFactory2.py" + } + ], + "label": "rgToolFactory2.py", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 235.25, + "height": 81, + "left": 711.84375, + "right": 911.84375, + "top": 154.25, + "width": 200, + "x": 711.84375, + "y": 154.25 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "b717b6ee-51d0-415d-876d-f19b42f67666", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "09acd6fd-4e2b-44a8-8757-35eca8d0de89" + } + ] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "README.md" + } + ], + "label": "README.md", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 760.25, + "height": 61, + "left": 711.84375, + "right": 911.84375, + "top": 699.25, + "width": 200, + "x": 711.84375, + "y": 699.25 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "8aefae07-4fd1-44a6-bea2-5d377567ac27", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "5f8453d0-abd1-41d9-a4a7-1f8b82f1f095" + } + ] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "testtext" + } + ], + "label": "testtext", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 235.25, + "height": 61, + "left": 989.84375, + "right": 1189.84375, + "top": 174.25, + "width": 200, + "x": 989.84375, + "y": 174.25 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa" + } + ] + }, + "3": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 3, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 636.25, + "height": 222, + "left": 989.84375, + "right": 1189.84375, + "top": 414.25, + "width": 200, + "x": 989.84375, + "y": 414.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"bash\", \"__current_case__\": 5, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"rev | tac\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"tacrev\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"0\", \"__current_case__\": 2, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input file\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"2\"}]}, \"tool_name\": \"tacrev\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "8fab16a0-5303-4e5c-8bf6-d6ebc70aa9af", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "68d1a0b8-d897-48e9-a304-25d289e139e9" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "8669863e-a1a5-4ed6-a412-c7f341f66176" + } + ] + }, + "4": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 4, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 916.25, + "height": 242, + "left": 989.84375, + "right": 1189.84375, + "top": 674.25, + "width": 200, + "x": 989.84375, + "y": 674.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "ea0f8bbe-6b0d-4aff-bf06-6192faf8fe22", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "70755c1b-6f92-43a3-aacb-8cc508a89b74" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "ea9482d9-7836-442d-b753-ce4a201fd8c9" + } + ] + }, + "5": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 5, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 1216.25, + "height": 262, + "left": 989.84375, + "right": 1189.84375, + "top": 954.25, + "width": 200, + "x": 989.84375, + "y": 954.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\nimport argparse\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--infile',default='')\\na('--outfile',default=None)\\nargs = parser.parse_args()\\ninp = args.infile\\noutp = args.outfile\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"reverse argparse\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"infile\", \"input_help\": \"parameter_help\", \"input_CL\": \"infile\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"outfile\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevargparse\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "065b274a-ae73-43b0-b015-8b60d90db78f", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "bec62d2d-b462-49bb-9646-28fea9136778" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "2e1ed464-bcff-4354-8bf3-ed01167b280f" + } + ] + }, + "6": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 6, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 1496.25, + "height": 242, + "left": 989.84375, + "right": 1189.84375, + "top": 1254.25, + "width": 200, + "x": 989.84375, + "y": 1254.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\nappendme = sys.argv[3]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write(appendme)\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"appendme\", \"param_type\": \"text\", \"param_value\": \"added at the end\", \"param_label\": \"append string\", \"param_help\": \"parameter_help\", \"param_CL\": \"3\"}]}, \"tool_name\": \"pyrevaddpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "5954323f-4ca1-4957-8250-746703dfa7c5", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "6466bf24-51b2-4fae-aac8-fc1d78faac89" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "f37589e2-3582-4443-bce8-5759485a7220" + } + ] + }, + "7": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 7, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 376.25, + "height": 222, + "left": 1267.84375, + "right": 1467.84375, + "top": 154.25, + "width": 200, + "x": 1267.84375, + "y": 154.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"system\", \"__current_case__\": 1, \"exe_package\": \"sed\", \"exe_package_version\": \"\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"sed runner\", \"help_text\": \"sed '/old/new/g input.txt\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input text\", \"input_help\": \"parameter_help\", \"input_CL\": \"3\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"sedstring\", \"param_type\": \"text\", \"param_value\": \"s/Old/New/g\", \"param_label\": \"parameter_label\", \"param_help\": \"parameter_help\", \"param_CL\": \"1\"}]}, \"tool_name\": \"sedtest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "e26df7b6-3899-42fb-8efc-5f13d53668f8", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "0a819390-acd4-4be6-aac9-ec3322302b0f" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "f7555059-144d-4f64-a303-b70d189e6e35" + } + ] + }, + "8": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 8, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 5, + "output_name": "new_tool" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 1271.25, + "height": 242, + "left": 1267.84375, + "right": 1467.84375, + "top": 1029.25, + "width": 200, + "x": 1267.84375, + "y": 1029.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"tgz\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"import argparse\\nimport tarfile\\nimport os\\nimport tempfile\\nimport subprocess\\n\\n\\\"\\\"\\\"\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\n\\\"\\\"\\\"\\n\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--tooltgz',default='')\\na('--report',default=None)\\na('--toolout',default=None)\\na('--galaxy_root',default=None)\\nargs = parser.parse_args()\\ntoolname = args.toolout.split(os.sep)[-1]\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\ntf = tarfile.open(args.tooltgz,\\\"r:gz\\\")\\ntf.extractall(toolpath)\\ncl = \\\"planemo test --skip_venv --galaxy_root %s %s\\\" % (args.galaxy_root,toolpath)\\ncll = cl.split(' ')\\nsto = open(args.report, 'w')\\np = subprocess.run(cll, shell=False, stdout=sto)\\nretval = p.returncode\\nsto.close()\\n\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"Tool to test toolshed tool archives generated by the tool factory.\", \"help_text\": \"**What it Does**\\n\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\nIt was generated using the tool factory.\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"tool toolshed tgz archive from history\", \"input_help\": \"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\", \"input_CL\": \"tooltgz\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"report\", \"history_format\": \"txt\", \"history_CL\": \"report\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"toolout\", \"param_type\": \"text\", \"param_value\": \"tools/toolmakers/planemotest\", \"param_label\": \"output path under galaxy root\", \"param_help\": \"This is where the tgz file will be extracted and tested by planemo\", \"param_CL\": \"toolout\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"your galaxy root to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for running planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that root\", \"param_CL\": \"galaxy_root\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "744499de-5d7e-4415-b427-315057c81ebc" + } + ] + } + }, + "tags": [], + "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b", + "version": 1 +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/tfworkflowsample.ga Mon Aug 10 23:24:41 2020 -0400 @@ -0,0 +1,443 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "workflow to generate a bunch of sample toolfactory tools", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "rgToolFactory2.py" + } + ], + "label": "rgToolFactory2.py", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 235.25, + "height": 81, + "left": 711.84375, + "right": 911.84375, + "top": 154.25, + "width": 200, + "x": 711.84375, + "y": 154.25 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "b717b6ee-51d0-415d-876d-f19b42f67666", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "09acd6fd-4e2b-44a8-8757-35eca8d0de89" + } + ] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "README.md" + } + ], + "label": "README.md", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 760.25, + "height": 61, + "left": 711.84375, + "right": 911.84375, + "top": 699.25, + "width": 200, + "x": 711.84375, + "y": 699.25 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "8aefae07-4fd1-44a6-bea2-5d377567ac27", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "5f8453d0-abd1-41d9-a4a7-1f8b82f1f095" + } + ] + }, + "2": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "testtext" + } + ], + "label": "testtext", + "name": "Input dataset", + "outputs": [], + "position": { + "bottom": 235.25, + "height": 61, + "left": 989.84375, + "right": 1189.84375, + "top": 174.25, + "width": 200, + "x": 989.84375, + "y": 174.25 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "02a35533-a67b-44c0-bce8-96a8adddc5a9", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "abe4a1b1-2c0b-44d1-95f8-4f9bb38e9daa" + } + ] + }, + "3": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 3, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 636.25, + "height": 222, + "left": 989.84375, + "right": 1189.84375, + "top": 414.25, + "width": 200, + "x": 989.84375, + "y": 414.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"bash\", \"__current_case__\": 5, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"rev | tac\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"tacrev\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"0\", \"__current_case__\": 2, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input file\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"2\"}]}, \"tool_name\": \"tacrev\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "8fab16a0-5303-4e5c-8bf6-d6ebc70aa9af", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "68d1a0b8-d897-48e9-a304-25d289e139e9" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "8669863e-a1a5-4ed6-a412-c7f341f66176" + } + ] + }, + "4": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 4, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 916.25, + "height": 242, + "left": 989.84375, + "right": 1189.84375, + "top": 674.25, + "width": 200, + "x": 989.84375, + "y": 674.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "ea0f8bbe-6b0d-4aff-bf06-6192faf8fe22", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "70755c1b-6f92-43a3-aacb-8cc508a89b74" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "ea9482d9-7836-442d-b753-ce4a201fd8c9" + } + ] + }, + "5": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 5, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 1216.25, + "height": 262, + "left": 989.84375, + "right": 1189.84375, + "top": 954.25, + "width": 200, + "x": 989.84375, + "y": 954.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\nimport argparse\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--infile',default='')\\na('--outfile',default=None)\\nargs = parser.parse_args()\\ninp = args.infile\\noutp = args.outfile\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"reverse argparse\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"infile\", \"input_help\": \"parameter_help\", \"input_CL\": \"infile\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"outfile\", \"history_format\": \"txt\", \"history_CL\": \"outfile\"}], \"edit_params\": \"yes\", \"additional_parameters\": []}, \"tool_name\": \"pyrevargparse\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "065b274a-ae73-43b0-b015-8b60d90db78f", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "bec62d2d-b462-49bb-9646-28fea9136778" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "2e1ed464-bcff-4354-8bf3-ed01167b280f" + } + ] + }, + "6": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 6, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 1496.25, + "height": 242, + "left": 989.84375, + "right": 1189.84375, + "top": 1254.25, + "width": 200, + "x": 989.84375, + "y": 1254.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"# reverse order of text by row\\nimport sys\\ninp = sys.argv[1]\\noutp = sys.argv[2]\\nappendme = sys.argv[3]\\ni = open(inp,'r').readlines()\\no = open(outp,'w')\\nfor row in i:\\n rs = row.rstrip()\\n rs = list(rs)\\n rs.reverse()\\n o.write(''.join(rs))\\n o.write(appendme)\\n o.write('\\\\n')\\no.close()\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"pyrevpos\", \"help_text\": \"**What it Does**\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"inputfile\", \"input_help\": \"parameter_help\", \"input_CL\": \"1\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"2\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"appendme\", \"param_type\": \"text\", \"param_value\": \"added at the end\", \"param_label\": \"append string\", \"param_help\": \"parameter_help\", \"param_CL\": \"3\"}]}, \"tool_name\": \"pyrevaddpos\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "5954323f-4ca1-4957-8250-746703dfa7c5", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "6466bf24-51b2-4fae-aac8-fc1d78faac89" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "f37589e2-3582-4443-bce8-5759485a7220" + } + ] + }, + "7": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 7, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 376.25, + "height": 222, + "left": 1267.84375, + "right": 1467.84375, + "top": 154.25, + "width": 200, + "x": 1267.84375, + "y": 154.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"system\", \"__current_case__\": 1, \"exe_package\": \"sed\", \"exe_package_version\": \"\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"sed runner\", \"help_text\": \"sed '/old/new/g input.txt\", \"citations\": []}, \"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"txt\"], \"input_label\": \"input text\", \"input_help\": \"parameter_help\", \"input_CL\": \"3\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"sedstring\", \"param_type\": \"text\", \"param_value\": \"s/Old/New/g\", \"param_label\": \"parameter_label\", \"param_help\": \"parameter_help\", \"param_CL\": \"1\"}]}, \"tool_name\": \"sedtest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "e26df7b6-3899-42fb-8efc-5f13d53668f8", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "0a819390-acd4-4be6-aac9-ec3322302b0f" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "f7555059-144d-4f64-a303-b70d189e6e35" + } + ] + }, + "8": { + "annotation": "", + "content_id": "rgTF2", + "errors": null, + "id": 8, + "input_connections": { + "ppass|history_inputs_0|input_files": { + "id": 5, + "output_name": "new_tool" + } + }, + "inputs": [], + "label": null, + "name": "toolfactory", + "outputs": [ + { + "name": "ToolFactory_Outputs", + "type": "input" + }, + { + "name": "new_tool", + "type": "tgz" + } + ], + "position": { + "bottom": 1271.25, + "height": 242, + "left": 1267.84375, + "right": 1467.84375, + "top": 1029.25, + "width": 200, + "x": 1267.84375, + "y": 1029.25 + }, + "post_job_actions": {}, + "tool_id": "rgTF2", + "tool_state": "{\"__input_ext\": \"tgz\", \"chromInfo\": \"/home/ross/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"interexe\": {\"interpreter\": \"python\", \"__current_case__\": 2, \"interpreter_version\": \"\", \"exe_package_version\": \"\", \"dynScript\": \"import argparse\\nimport tarfile\\nimport os\\nimport tempfile\\nimport subprocess\\n\\n\\\"\\\"\\\"\\nplanemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/galaxy/tools/tool_makers/pyrevargparse/ &> pyrevargparse\\n\\\"\\\"\\\"\\n\\nparser = argparse.ArgumentParser()\\na = parser.add_argument\\na('--tooltgz',default='')\\na('--report',default=None)\\na('--toolout',default=None)\\na('--galaxy_root',default=None)\\nargs = parser.parse_args()\\ntoolname = args.toolout.split(os.sep)[-1]\\ntoolpath = os.path.join(args.galaxy_root,args.toolout)\\ntf = tarfile.open(args.tooltgz,\\\"r:gz\\\")\\ntf.extractall(toolpath)\\ncl = \\\"planemo test --skip_venv --galaxy_root %s %s\\\" % (args.galaxy_root,toolpath)\\ncll = cl.split(' ')\\nsto = open(args.report, 'w')\\np = subprocess.run(cll, shell=False, stdout=sto)\\nretval = p.returncode\\nsto.close()\\n\"}, \"makeMode\": {\"make_Tool\": \"yes\", \"__current_case__\": 0, \"tool_version\": \"0.01\", \"tool_desc\": \"Tool to test toolshed tool archives generated by the tool factory.\", \"help_text\": \"**What it Does**\\n\\nGiven a toolshed tgz file generated by a tool factory run, this will unpack it and run planemo test, returning the planemo stdout as a report\\nIt was generated using the tool factory.\", \"citations\": []}, \"ppass\": {\"parampass\": \"argparse\", \"__current_case__\": 0, \"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"tool toolshed tgz archive from history\", \"input_help\": \"Run planemo test on a tool shed tool archive tgz format file generated by the ToolFactory or Planemo\", \"input_CL\": \"tooltgz\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"report\", \"history_format\": \"txt\", \"history_CL\": \"report\"}], \"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"toolout\", \"param_type\": \"text\", \"param_value\": \"tools/toolmakers/planemotest\", \"param_label\": \"output path under galaxy root\", \"param_help\": \"This is where the tgz file will be extracted and tested by planemo\", \"param_CL\": \"toolout\"}, {\"__index__\": 1, \"param_name\": \"galaxy_root\", \"param_type\": \"text\", \"param_value\": \"/home/ross/galaxy\", \"param_label\": \"your galaxy root to use for running planemo\", \"param_help\": \"This will form the galaxy_root parameter for running planemo using an existing Galaxy source tree, and the tgz will be extracted at a path relative to that root\", \"param_CL\": \"galaxy_root\"}]}, \"tool_name\": \"planemotest\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.00", + "type": "tool", + "uuid": "c72a7aae-3801-431b-a331-be6938d34fbd", + "workflow_outputs": [ + { + "label": null, + "output_name": "ToolFactory_Outputs", + "uuid": "75aa9815-5bd6-44a7-8210-889d3b7e5027" + }, + { + "label": null, + "output_name": "new_tool", + "uuid": "744499de-5d7e-4415-b427-315057c81ebc" + } + ] + } + }, + "tags": [], + "uuid": "490d9c7f-eea3-4616-a8b7-13510da0430b", + "version": 1 +}