| Previous changeset 137:63d15caea378 (2021-04-13) Next changeset 139:6b414af9ca11 (2021-04-17) |
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Commit message:
Uploaded |
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modified:
toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
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removed:
toolfactory/galaxyxml/__init__.py toolfactory/galaxyxml/tool/__init__.py toolfactory/galaxyxml/tool/import_xml.py toolfactory/galaxyxml/tool/parameters/__init__.py |
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| diff -r 63d15caea378 -r 1dba6c7687a9 toolfactory/galaxyxml/__init__.py --- a/toolfactory/galaxyxml/__init__.py Tue Apr 13 03:06:27 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,71 +0,0 @@ -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 63d15caea378 -r 1dba6c7687a9 toolfactory/galaxyxml/tool/__init__.py --- a/toolfactory/galaxyxml/tool/__init__.py Tue Apr 13 03:06:27 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,277 +0,0 @@\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 63d15caea378 -r 1dba6c7687a9 toolfactory/galaxyxml/tool/import_xml.py --- a/toolfactory/galaxyxml/tool/import_xml.py Tue Apr 13 03:06:27 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,785 +0,0 @@\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 63d15caea378 -r 1dba6c7687a9 toolfactory/galaxyxml/tool/parameters/__init__.py --- a/toolfactory/galaxyxml/tool/parameters/__init__.py Tue Apr 13 03:06:27 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1012 +0,0 @@\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' |
| b |
| diff -r 63d15caea378 -r 1dba6c7687a9 toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Tue Apr 13 03:06:27 2021 +0000 +++ b/toolfactory/rgToolFactory2.py Wed Apr 14 07:05:22 2021 +0000 |
| [ |
| @@ -1044,9 +1044,9 @@ supplied test outputs are sent to repdir for display """ penv = os.environ - pconfig = os.path.join(self.args.tool_dir,'.planemo.yml') + pconfig = os.path.join(self.args.tool_dir, '.planemo.yml') penv["PLANEMO_GLOBAL_CONFIG_PATH"] = pconfig - self.set_planemo_galaxy_root(self.args.galaxy_root,config_path=pconfig) + self.set_planemo_galaxy_root(self.args.galaxy_root, config_path=pconfig) xreal = "%s.xml" % self.tool_name tool_test_path = os.path.join( self.repdir, f"{self.tool_name}_planemo_test_report.html" @@ -1071,7 +1071,7 @@ p = subprocess.run( cll, shell=False, - env = penv, + env=penv, cwd=self.tooloutdir, stderr=tout, stdout=tout, @@ -1081,7 +1081,7 @@ def set_planemo_galaxy_root(self, galaxyroot='/galaxy-central', config_path=".planemo.yml"): # bug in planemo - bogus '--dev-wheels' passed to run_tests.sh as at april 2021 - need a fiddled copy so it is ignored until fixed - CONFIG_TEMPLATE = f"""## Planemo Global Configuration File. + CONFIG_TEMPLATE = """## Planemo Global Configuration File. ## Everything in this file is completely optional - these values can all be ## configured via command line options for the corresponding commands. |
| b |
| diff -r 63d15caea378 -r 1dba6c7687a9 toolfactory/rgToolFactory2.xml --- a/toolfactory/rgToolFactory2.xml Tue Apr 13 03:06:27 2021 +0000 +++ b/toolfactory/rgToolFactory2.xml Wed Apr 14 07:05:22 2021 +0000 |
| b |
| @@ -180,7 +180,7 @@ </macros> <requirements> - <!-- <requirement type="package" version="0.4.13">galaxyxml</requirement> --> + <requirement type="package" version="0.4.14">galaxyxml</requirement> <requirement type="package" version="0.15.0">bioblend</requirement> <requirement type="package" version="0.10.6">ephemeris</requirement> <requirement type="package" version="0.74.3">planemo</requirement> |