| Previous changeset 135:7805fdac70ed (2021-04-13) Next changeset 137:63d15caea378 (2021-04-13) |
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toolfactory/galaxyxml/__init__.py toolfactory/galaxyxml/__pycache__/__init__.cpython-38.pyc toolfactory/galaxyxml/tool/__init__.py toolfactory/galaxyxml/tool/__pycache__/__init__.cpython-38.pyc toolfactory/galaxyxml/tool/__pycache__/import_xml.cpython-38.pyc toolfactory/galaxyxml/tool/import_xml.py toolfactory/galaxyxml/tool/parameters/__init__.py toolfactory/galaxyxml/tool/parameters/__pycache__/__init__.cpython-38.pyc |
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| diff -r 7805fdac70ed -r 94f5560de46d toolfactory/galaxyxml/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/galaxyxml/__init__.py Tue Apr 13 00:35:36 2021 +0000 |
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| @@ -0,0 +1,71 @@ +from builtins import ( + object, + str +) + +from lxml import etree + + +class GalaxyXML(object): + def __init__(self): + self.root = etree.Element("root") + + def export(self): + return etree.tostring(self.root, pretty_print=True, encoding="unicode") + + +class Util(object): + @classmethod + def coerce(cls, data, kill_lists=False): + """ + Recursive data sanitisation + + - recurse into lists, dicts, OrderedDict + - remove dict/OrderedDict entries with None value + - kill_lists: True -> replace lists by their first element + """ + 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} + elif isinstance(data, list): + if kill_lists: + return cls.coerce(data[0]) + else: + return [cls.coerce(v, kill_lists=kill_lists) for v in data] + else: + return cls.coerce_value(data) + + @classmethod + def coerce_value(cls, obj): + """Make everything a string! + """ + if isinstance(obj, bool): + if obj: + return "true" + else: + return "false" + elif isinstance(obj, str): + return obj + else: + return str(obj) + + @classmethod + def clean_kwargs(cls, params, final=False): + 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"] + + 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",): + if blacklist in params: + del params[blacklist] + return params |
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| diff -r 7805fdac70ed -r 94f5560de46d toolfactory/galaxyxml/__pycache__/__init__.cpython-38.pyc |
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| diff -r 7805fdac70ed -r 94f5560de46d toolfactory/galaxyxml/tool/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/galaxyxml/tool/__init__.py Tue Apr 13 00:35:36 2021 +0000 |
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| b'@@ -0,0 +1,277 @@\n+import copy\n+import logging\n+\n+from galaxyxml import GalaxyXML, Util\n+from galaxyxml.tool.parameters import (\n+ Expand,\n+ Import,\n+ Inputs,\n+ Macro,\n+ Macros,\n+ Outputs,\n+ XMLParam\n+)\n+\n+from lxml import etree\n+\n+VALID_TOOL_TYPES = ("data_source", "data_source_async")\n+VALID_URL_METHODS = ("get", "post")\n+\n+logging.basicConfig(level=logging.INFO)\n+logger = logging.getLogger(__name__)\n+\n+\n+class Tool(GalaxyXML):\n+ def __init__(\n+ self,\n+ name,\n+ id,\n+ version,\n+ description,\n+ executable,\n+ hidden=False,\n+ tool_type=None,\n+ URL_method=None,\n+ workflow_compatible=True,\n+ interpreter=None,\n+ version_command="interpreter filename.exe --version",\n+ command_override=None,\n+ macros=[],\n+ ):\n+\n+ self.id = id\n+ self.executable = executable\n+ self.interpreter = interpreter\n+ self.command_override = command_override\n+ kwargs = {\n+ "name": name,\n+ "id": id,\n+ "version": version,\n+ "hidden": hidden,\n+ "workflow_compatible": workflow_compatible,\n+ }\n+ self.version_command = version_command\n+\n+ # Remove some of the default values to make tools look a bit nicer\n+ if not hidden:\n+ del kwargs["hidden"]\n+ if workflow_compatible:\n+ del kwargs["workflow_compatible"]\n+\n+ kwargs = Util.coerce(kwargs)\n+ self.root = etree.Element("tool", **kwargs)\n+\n+ if tool_type is not None:\n+ if tool_type not in VALID_TOOL_TYPES:\n+ raise Exception("Tool type must be one of %s" % ",".join(VALID_TOOL_TYPES))\n+ else:\n+ kwargs["tool_type"] = tool_type\n+\n+ if URL_method is not None:\n+ if URL_method in VALID_URL_METHODS:\n+ kwargs["URL_method"] = URL_method\n+ else:\n+ raise Exception("URL_method must be one of %s" % ",".join(VALID_URL_METHODS))\n+\n+ description_node = etree.SubElement(self.root, "description")\n+ description_node.text = description\n+ if len(macros) > 0:\n+ self.macros = Macros()\n+ for m in macros:\n+ self.macros.append(Import(m))\n+ self.inputs = Inputs()\n+ self.outputs = Outputs()\n+\n+ def add_comment(self, comment_txt):\n+ comment = etree.Comment(comment_txt)\n+ self.root.insert(0, comment)\n+\n+ def append_version_command(self):\n+ version_command = etree.SubElement(self.root, "version_command")\n+ try:\n+ version_command.text = etree.CDATA(self.version_command)\n+ except Exception:\n+ pass\n+\n+ def append(self, sub_node):\n+ if issubclass(type(sub_node), XMLParam):\n+ self.root.append(sub_node.node)\n+ else:\n+ self.root.append(sub_node)\n+\n+ def clean_command_string(self, command_line):\n+ clean = []\n+ for x in command_line:\n+ if x is not [] and x is not [""]:\n+ clean.append(x)\n+ return "\\n".join(clean)\n+\n+ def export(self, keep_old_command=False):\n+ # see lib/galaxy/tool_util/linters/xml_order.py\n+ export_xml = copy.deepcopy(self)\n+ try:\n+ export_xml.append(export_xml.macros)\n+ except Exception:\n+ pass\n+\n+ try:\n+ export_xml.append(export_xml.edam_operations)\n+ except Exception:\n+ pass\n+\n+ try:\n+ export_xml.append(export_xml.edam_topics)\n+ except Exception:\n+ pass\n+\n+ try:\n+ export_xml.append(export_xml.requirements)\n+ except Exception:\n+ export_xml.append(Expand(macro="requirements"))\n+\n+ # Add stdio section - now an XMLParameter\n+ try:\n+ stdio_element = export_xml.stdios\n+ except Exception:\n+ std'..b'wargs\n+ command_kwargs = {}\n+ if export_xml.interpreter is not None:\n+ command_kwargs["interpreter"] = export_xml.interpreter\n+ # Add command section\n+ command_node = etree.SubElement(export_xml.root, "command", **command_kwargs)\n+ if keep_old_command:\n+ if getattr(self, "command", None):\n+ command_node.text = etree.CDATA(export_xml.command)\n+ else:\n+ logger.warning("The tool does not have any old command stored. Only the command line is written.")\n+ command_node.text = export_xml.executable\n+ else:\n+ if self.command_override:\n+ actual_cli = export_xml.clean_command_string(command_line)\n+ else:\n+ actual_cli = "%s %s" % (export_xml.executable, export_xml.clean_command_string(command_line),)\n+ command_node.text = etree.CDATA(actual_cli.strip())\n+ export_xml.append(command_node)\n+\n+ try:\n+ export_xml.append(export_xml.configfiles)\n+ except Exception:\n+ pass\n+\n+ try:\n+ export_xml.append(export_xml.inputs)\n+ except Exception:\n+ pass\n+ try:\n+ export_xml.append(export_xml.outputs)\n+ except Exception:\n+ pass\n+\n+ try:\n+ export_xml.append(export_xml.tests)\n+ except Exception:\n+ export_xml.append(Expand(macro="%s_tests" % self.id))\n+\n+ help_element = etree.SubElement(export_xml.root, "help")\n+ help_element.text = etree.CDATA(export_xml.help)\n+ export_xml.append(help_element)\n+\n+ try:\n+ export_xml.append(export_xml.citations)\n+ except Exception:\n+ export_xml.append(Expand(macro="citations"))\n+\n+ return super(Tool, export_xml).export()\n+\n+\n+class MacrosTool(Tool):\n+ """\n+ creates a <macros> tag containing macros and tokens\n+ for the inputs and outputs:\n+\n+ for the inputs\n+\n+ - a macro `<xml name="ID_inmacro">` containing all the inputs\n+ - a token `<token name="ID_INMACRO">` containing the CLI for the inputs\n+\n+ where ID is the id used in initialization.\n+\n+ analogously for the outputs `ID_outmacro` and `ID_OUTMACRO`\n+ are created.\n+\n+ TODO all other elements, like requirements are currently ignored\n+ """\n+ def __init__(self, *args, **kwargs):\n+ super(MacrosTool, self).__init__(*args, **kwargs)\n+ self.root = etree.Element(\'macros\')\n+ self.inputs = Macro("%s_inmacro" % self.id)\n+ self.outputs = Macro("%s_outmacro" % self.id)\n+\n+\n+ def export(self, keep_old_command=False): # noqa\n+\n+ export_xml = copy.deepcopy(self)\n+\n+ try:\n+ for child in export_xml.macros:\n+ export_xml.append(child)\n+ except Exception:\n+ pass\n+\n+ command_line = []\n+ try:\n+ command_line.append(export_xml.inputs.cli())\n+ except Exception as e:\n+ logger.warning(str(e))\n+ raise\n+\n+ # Add command section\n+ command_node = etree.SubElement(export_xml.root, \'token\', {"name": "%s_INMACRO" % self.id.upper()})\n+ actual_cli = "%s" % (export_xml.clean_command_string(command_line))\n+ command_node.text = etree.CDATA(actual_cli.strip())\n+\n+ command_line = []\n+ try:\n+ command_line.append(export_xml.outputs.cli())\n+ except Exception:\n+ pass\n+ command_node = etree.SubElement(export_xml.root, \'token\', {"name": "%s_OUTMACRO" % self.id.upper()})\n+ actual_cli = "%s" % (export_xml.clean_command_string(command_line))\n+ command_node.text = etree.CDATA(actual_cli.strip())\n+\n+ try:\n+ export_xml.append(export_xml.inputs)\n+ except Exception:\n+ pass\n+\n+ try:\n+ export_xml.append(export_xml.outputs)\n+ except Exception:\n+ pass\n+\n+ return super(Tool, export_xml).export()\n' |
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| diff -r 7805fdac70ed -r 94f5560de46d toolfactory/galaxyxml/tool/__pycache__/import_xml.cpython-38.pyc |
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| diff -r 7805fdac70ed -r 94f5560de46d toolfactory/galaxyxml/tool/import_xml.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/galaxyxml/tool/import_xml.py Tue Apr 13 00:35:36 2021 +0000 |
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| b'@@ -0,0 +1,785 @@\n+import logging\n+import xml.etree.ElementTree as ET\n+\n+import galaxyxml.tool as gxt\n+import galaxyxml.tool.parameters as gxtp\n+\n+logging.basicConfig(level=logging.INFO)\n+logger = logging.getLogger(__name__)\n+\n+\n+class GalaxyXmlParser(object):\n+ """\n+ Class to import content from an existing Galaxy XML wrapper.\n+ """\n+\n+ def _init_tool(self, xml_root):\n+ """\n+ Init tool from existing xml tool.\n+\n+ :param xml_root: root of the galaxy xml file.\n+ :type xml_root: :class:`xml.etree._Element`\n+ """\n+ version_cmd = None\n+ description = None\n+ for child in xml_root:\n+ if child.tag == "description":\n+ description = child.text\n+ elif child.tag == "command":\n+ executable = child.text.split()[0]\n+ command = child.text\n+ elif child.tag == "version_command":\n+ version_cmd = child.text\n+\n+ tool = gxt.Tool(\n+ xml_root.attrib["name"],\n+ xml_root.attrib["id"],\n+ xml_root.attrib.get("version", None),\n+ description,\n+ executable,\n+ hidden=xml_root.attrib.get("hidden", False),\n+ tool_type=xml_root.attrib.get("tool_type", None),\n+ URL_method=xml_root.attrib.get("URL_method", None),\n+ workflow_compatible=xml_root.attrib.get("workflow_compatible", True),\n+ version_command=version_cmd,\n+ )\n+ tool.command = command\n+ return tool\n+\n+ def _load_description(self, tool, desc_root):\n+ """\n+ <description> is already loaded during initiation.\n+\n+ :param tool: Tool object from galaxyxml.\n+ :type tool: :class:`galaxyxml.tool.Tool`\n+ :param desc_root: root of <description> tag.\n+ :type desc_root: :class:`xml.etree._Element`\n+ """\n+ logger.info("<description> is loaded during initiation of the object.")\n+\n+ def _load_version_command(self, tool, vers_root):\n+ """\n+ <version_command> is already loaded during initiation.\n+\n+ :param tool: Tool object from galaxyxml.\n+ :type tool: :class:`galaxyxml.tool.Tool`\n+ :param vers_root: root of <version_command> tag.\n+ :type vers_root: :class:`xml.etree._Element`\n+ """\n+ logger.info("<version_command> is loaded during initiation of the object.")\n+\n+ def _load_stdio(self, tool, stdio_root):\n+ """\n+\n+ :param tool: <test> root to append <stdio> to.\n+ :param stdio_root: root of <param> tag.\n+ :param stdio_root: :class:`xml.etree._Element`\n+ """\n+ tool.stdios = gxtp.Stdios()\n+ for std in stdio_root:\n+ slevel = std.attrib[\'level\']\n+ srange = std.attrib[\'range\']\n+ tool.stdios.append(gxtp.Stdio(level=slevel, range=srange))\n+ logger.info("<stdio> loaded.")\n+\n+ def _load_command(self, tool, desc_root):\n+ """\n+ <command> is already loaded during initiation.\n+\n+ :param tool: Tool object from galaxyxml.\n+ :type tool: :class:`galaxyxml.tool.Tool`\n+ :param desc_root: root of <command> tag.\n+ :type desc_root: :class:`xml.etree._Element`\n+ """\n+ logger.info("<command> is loaded during initiation of the object.")\n+\n+ def _load_help(self, tool, help_root):\n+ """\n+ Load the content of the <help> into the tool.\n+\n+ :param tool: Tool object from galaxyxml.\n+ :type tool: :class:`galaxyxml.tool.Tool`\n+ :param requirements_root: root of <help> tag.\n+ :type requirements_root: :class:`xml.etree._Element`\n+ """\n+ tool.help = help_root.text\n+\n+ def _load_requirements(self, tool, requirements_root):\n+ """\n+ Add <requirements> to the tool.\n+\n+ :param tool: Tool object from galaxyxml.\n+ :type tool: :class:`galaxyxml.tool.Tool`\n+ :param requirements_root: root of <requirements> tag.\n+ '..b'file=output_root.attrib.get("file", None),\n+ ftype=output_root.attrib.get("ftype", None),\n+ sort=output_root.attrib.get("sort", None),\n+ value=output_root.attrib.get("value", None),\n+ md5=output_root.attrib.get("md5", None),\n+ checksum=output_root.attrib.get("checksum", None),\n+ compare=output_root.attrib.get("compare", None),\n+ lines_diff=output_root.attrib.get("lines_diff", None),\n+ delta=output_root.attrib.get("delta", None),\n+ )\n+ )\n+\n+ def _load_output_collection(self, test_root, output_root):\n+ """\n+ Add <output_collection> to the <test>.\n+\n+ :param root: <test> root to append <output> to.\n+ :param repeat_root: root of <output_collection> tag.\n+ :param repeat_root: :class:`xml.etree._Element`\n+ """\n+ collection = gxtp.TestOutputCollection(\n+ name=output_root.attrib.get("name", None),\n+ ftype=output_root.attrib.get("ftype", None),\n+ sort=output_root.attrib.get("sort", None),\n+ value=output_root.attrib.get("value", None),\n+ compare=output_root.attrib.get("compare", None),\n+ lines_diff=output_root.attrib.get("lines_diff", None),\n+ delta=output_root.attrib.get("delta", None),\n+ )\n+ # Deal with child nodes\n+ self.load_inputs(collection, output_root)\n+ test_root.append(collection)\n+\n+ def _load_element(self, test_root, element_root):\n+ """\n+ Add <element> to the <test>.\n+\n+ :param root: <test> root to append <output> to.\n+ :param repeat_root: root of <output_collection> tag.\n+ :param repeat_root: :class:`xml.etree._Element`\n+ """\n+ test_root.append(gxtp.TestOCElement(\n+ name=element_root.attrib.get("name", None),\n+ ftype=element_root.attrib.get("ftype", None),\n+ file=element_root.attrib.get("file", None)\n+ )\n+ )\n+\n+ def _load_repeat(self, test_root, repeat_root):\n+ """\n+ Add <repeat> to the <test>.\n+\n+ :param root: <test> root to append <output> to.\n+ :param output_root: root of <repeat> tag.\n+ :param output_root: :class:`xml.etree._Element`\n+ """\n+ repeat = gxtp.TestRepeat(\n+ repeat_root.attrib.get("name", None),\n+ repeat_root.attrib.get("title", None),\n+ min=repeat_root.attrib.get("min", None),\n+ max=repeat_root.attrib.get("max", None),\n+ default=repeat_root.attrib.get("default", None)\n+ )\n+ # Deal with child nodes\n+ self.load_inputs(repeat, repeat_root)\n+ test_root.append(repeat)\n+\n+ def load_inputs(self, repeat, repeat_root):\n+ """\n+ Add children to repeat/collection for test\n+\n+ :param repeat_root: repeat to attach inputs to.\n+ :param repeat: root of <repeat> or <collection> tag.\n+ :type repeat_root: :class:`xml.etree._Element`\n+ """\n+ for rep_child in repeat_root:\n+ try:\n+ getattr(self, "_load_{}".format(rep_child.tag))(repeat, rep_child)\n+ except AttributeError:\n+ logger.warning(rep_child.tag + " tag is not processed for <" + repeat_root.tag + "> tag.")\n+\n+ def load_tests(self, root, tests_root):\n+ """\n+ Add <tests> to the root.\n+\n+ :param root: root to attach <tests> to (<tool>).\n+ :param tests_root: root of <tests> tag.\n+ :type tests_root: :class:`xml.etree._Element`\n+ """\n+ for test_root in tests_root:\n+ test = gxtp.Test()\n+ for test_child in test_root:\n+ try:\n+ getattr(self, "_load_{}".format(test_child.tag))(test, test_child)\n+ except AttributeError:\n+ logger.warning(test_child.tag + " tag is not processed within <test>.")\n+ root.append(test)\n' |
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| diff -r 7805fdac70ed -r 94f5560de46d toolfactory/galaxyxml/tool/parameters/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolfactory/galaxyxml/tool/parameters/__init__.py Tue Apr 13 00:35:36 2021 +0000 |
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| b'@@ -0,0 +1,1012 @@\n+import logging\n+from builtins import (\n+ object,\n+ str\n+)\n+\n+from galaxy.tool_util.parser.util import _parse_name\n+\n+from galaxyxml import Util\n+\n+from lxml import etree\n+\n+logging.basicConfig(level=logging.INFO)\n+logger = logging.getLogger(__name__)\n+\n+\n+class XMLParam(object):\n+ name = "node"\n+\n+ def __init__(self, *args, **kwargs):\n+ # http://stackoverflow.com/a/12118700\n+ self.children = []\n+ self.parent = None\n+ kwargs = {k: v for k, v in list(kwargs.items()) if v is not None}\n+ kwargs = Util.coerce(kwargs, kill_lists=True)\n+ kwargs = Util.clean_kwargs(kwargs, final=True)\n+ self.node = etree.Element(self.name, **kwargs)\n+\n+ def __getattr__(self, name):\n+ """\n+ Allow to access keys of the node "attributes" (i.e. the dict\n+ self.node.attrib) as attributes.\n+ """\n+ # https://stackoverflow.com/questions/47299243/recursionerror-when-python-copy-deepcopy\n+ if name == "__setstate__":\n+ raise AttributeError(name)\n+ try:\n+ return self.node.attrib[name]\n+ except KeyError:\n+ raise AttributeError(name)\n+\n+ def append(self, sub_node):\n+ if self.acceptable_child(sub_node):\n+ # If one of ours, they aren\'t etree nodes, they\'re custom objects\n+ if issubclass(type(sub_node), XMLParam):\n+ self.node.append(sub_node.node)\n+ self.children.append(sub_node)\n+ self.children[-1].parent = self\n+ else:\n+ raise Exception(\n+ "Child was unacceptable to parent (%s is not appropriate for %s)" % (type(self), type(sub_node))\n+ )\n+ else:\n+ raise Exception(\n+ "Child was unacceptable to parent (%s is not appropriate for %s)" % (type(self), type(sub_node))\n+ )\n+\n+ def validate(self):\n+ # Very few need validation, but some nodes we may want to have\n+ # validation routines on. Should only be called when DONE.\n+ for child in self.children:\n+ # If any child fails to validate return false.\n+ if not child.validate():\n+ return False\n+ return True\n+\n+ def cli(self):\n+ lines = []\n+ for child in self.children:\n+ lines.append(child.command_line())\n+ return "\\n".join(lines)\n+\n+ def command_line(self, mako_path=None):\n+ """\n+ genetate the command line for the node (and its childres)\n+\n+ mako_path override the path to the node\n+ """\n+ return None\n+\n+\n+class Stdios(XMLParam):\n+ name = "stdio"\n+\n+ def acceptable_child(self, child):\n+ return isinstance(child, Stdio)\n+\n+\n+class Stdio(XMLParam):\n+ name = "exit_code"\n+\n+ def __init__(self, range="1:", level="fatal", **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(Stdio, self).__init__(**params)\n+\n+\n+class Macros(XMLParam):\n+ name = "macros"\n+\n+ def acceptable_child(self, child):\n+ return isinstance(child, (Macro, Import))\n+\n+\n+class Macro(XMLParam):\n+ name = "xml"\n+\n+ def __init__(self, name):\n+ params = Util.clean_kwargs(locals().copy())\n+ passed_kwargs = {}\n+ passed_kwargs[\'name\'] = params[\'name\']\n+ super(Macro, self).__init__(**passed_kwargs)\n+\n+ def acceptable_child(self, child):\n+ return issubclass(type(child), XMLParam) and not isinstance(child, Macro)\n+\n+\n+class Import(XMLParam):\n+ name = "import"\n+\n+ def __init__(self, value):\n+ super(Import, self).__init__()\n+ self.node.text = value\n+\n+ def acceptable_child(self, child):\n+ return issubclass(type(child), XMLParam) and not isinstance(child, Macro)\n+\n+\n+class Expand(XMLParam):\n+ """\n+ <expand macro="...">\n+ """\n+ name = "expand"\n+\n+ def __init__(self, macro):\n+ params = Util.clean_kwargs(locals().copy())\n+ passed_kwargs = {}'..b'\n+\n+ def acceptable_child(self, child):\n+ return issubclass(type(child), Test) \\\n+ or isinstance(child, Expand)\n+\n+\n+class Test(XMLParam):\n+ name = "test"\n+\n+ def acceptable_child(self, child):\n+ return isinstance(child, TestParam) \\\n+ or isinstance(child, TestOutput) \\\n+ or isinstance(child, TestOutputCollection) \\\n+ or isinstance(child, TestRepeat) \\\n+ or isinstance(child, Expand)\n+\n+\n+class TestParam(XMLParam):\n+ name = "param"\n+\n+ def __init__(self, name, value=None, ftype=None, dbkey=None, **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(TestParam, self).__init__(**params)\n+\n+\n+class TestOutput(XMLParam):\n+ name = "output"\n+\n+ def __init__(\n+ self,\n+ name=None,\n+ file=None,\n+ ftype=None,\n+ sort=None,\n+ value=None,\n+ md5=None,\n+ checksum=None,\n+ compare=None,\n+ lines_diff=None,\n+ delta=None,\n+ **kwargs,\n+ ):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(TestOutput, self).__init__(**params)\n+\n+\n+class TestOCElement(XMLParam):\n+ name = "element"\n+\n+ def __init__(self, name=None, file=None, ftype=None, **kwargs):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(TestOCElement, self).__init__(**params)\n+\n+\n+class TestOutputCollection(XMLParam):\n+ name = "output_collection"\n+\n+ def __init__(\n+ self,\n+ name=None,\n+ ftype=None,\n+ sort=None,\n+ value=None,\n+ compare=None,\n+ lines_diff=None,\n+ delta=None,\n+ **kwargs,\n+ ):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(TestOutputCollection, self).__init__(**params)\n+\n+ def acceptable_child(self, child):\n+ return isinstance(child, TestOCElement)\n+\n+ def command_line_before(self, mako_path):\n+ return "<output_collection name = \'%s\'>" % self.name\n+\n+ def command_line_after(self):\n+ return "</output_collection>"\n+\n+ def command_line_actual(self, mako_path):\n+ lines = []\n+ for child in self.children:\n+ lines.append(child.command_line())\n+ return "\\n".join(lines)\n+\n+\n+class TestRepeat(XMLParam):\n+ name = "repeat"\n+\n+ def __init__(\n+ self,\n+ name=None,\n+ ftype=None,\n+ sort=None,\n+ value=None,\n+ compare=None,\n+ lines_diff=None,\n+ delta=None,\n+ **kwargs,\n+ ):\n+ params = Util.clean_kwargs(locals().copy())\n+ super(TestRepeat, self).__init__(**params)\n+\n+ def acceptable_child(self, child):\n+ return issubclass(type(child), TestParam) \\\n+ or issubclass(type(child), TestOutput) \\\n+ or issubclass(type(child), TestOutputCollection)\n+\n+ def command_line_before(self, mako_path):\n+ return "<repeat name = \'%s\'>" % self.name\n+\n+ def command_line_after(self):\n+ return "</repeat>"\n+\n+ def command_line_actual(self, mako_path):\n+ lines = []\n+ for child in self.children:\n+ lines.append(child.command_line())\n+ return "\\n".join(lines)\n+\n+\n+class Citations(XMLParam):\n+ name = "citations"\n+\n+ def acceptable_child(self, child):\n+ return issubclass(type(child), Citation) \\\n+ or isinstance(child, Expand)\n+\n+ def has_citation(self, type, value):\n+ """\n+ Check the presence of a given citation.\n+\n+ :type type: STRING\n+ :type value: STRING\n+ """\n+ for citation in self.children:\n+ if citation.node.attrib[\'type\'] == type \\\n+ and citation.node.text == value:\n+ return True\n+ return False\n+\n+\n+class Citation(XMLParam):\n+ name = "citation"\n+\n+ def __init__(self, type, value):\n+ passed_kwargs = {}\n+ passed_kwargs["type"] = type\n+ super(Citation, self).__init__(**passed_kwargs)\n+ self.node.text = str(value)\n' |
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