tool_factory_2: toolfactory/galaxyxml/tool/parameters/__init_

comparison toolfactory/galaxyxml/tool/parameters/init.py @ 35:5d38cb3d9be8 draft

added patched galaxyxml code temporarily until PR accepted

author	fubar
date	Sat, 08 Aug 2020 19:55:55 -0400
parents
children	ce2b1f8ea68d

comparison

equal deleted inserted replaced

-:5052ac89c036
+:5d38cb3d9be8
+from builtins import str
+from builtins import object
+from lxml import etree
+from galaxyxml import Util
+class XMLParam(object):
+name = 'node'
+def __init__(self, *args, **kwargs):
+# http://stackoverflow.com/a/12118700
+self.children = []
+kwargs = {k: v for k, v in list(kwargs.items()) if v is not None}
+kwargs = Util.coerce(kwargs, kill_lists=True)
+kwargs = Util.clean_kwargs(kwargs, final=True)
+self.node = etree.Element(self.name, **kwargs)
+def append(self, sub_node):
+if self.acceptable_child(sub_node):
+# If one of ours, they aren't etree nodes, they're custom objects
+if issubclass(type(sub_node), XMLParam):
+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)))
+else:
+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
+# validation routines on. Should only be called when DONE.
+for child in self.children:
+# If any child fails to validate return false.
+if not child.validate():
+return False
+return True
+def cli(self):
+lines = []
+for child in self.children:
+lines.append(child.command_line())
+# lines += child.command_line()
+return '\n'.join(lines)
+def command_line(self):
+return None
+class RequestParamTranslation(XMLParam):
+name = 'request_param_translation'
+def __init__(self, **kwargs):
+self.node = etree.Element(self.name)
+def acceptable_child(self, child):
+return isinstance(child, RequestParamTranslation)
+class RequestParam(XMLParam):
+name = 'request_param'
+def __init__(self, galaxy_name, remote_name, missing, **kwargs):
+# TODO: bulk copy locals into self.attr?
+self.galaxy_name = galaxy_name
+# http://stackoverflow.com/a/1408860
+params = Util.clean_kwargs(locals().copy())
+super(RequestParam, self).__init__(**params)
+def acceptable_child(self, child):
+return isinstance(child, AppendParam) and self.galaxy_name == "URL"
+class AppendParam(XMLParam):
+name = 'append_param'
+def __init__(self, separator="&amp;", first_separator="?", join="=", **kwargs):
+params = Util.clean_kwargs(locals().copy())
+super(AppendParam, self).__init__(**params)
+def acceptable_child(self, child):
+return isinstance(child, AppendParamValue)
+class AppendParamValue(XMLParam):
+name = 'value'
+def __init__(self, name="_export", missing="1", **kwargs):
+params = Util.clean_kwargs(locals().copy())
+super(AppendParamValue, self).__init__(**params)
+def acceptable_child(self, child):
+return False
+class EdamOperations(XMLParam):
+name = 'edam_operations'
+def acceptable_child(self, child):
+return issubclass(type(child), EdamOperation)
+def has_operation(self, edam_operation):
+"""
+Check the presence of a given edam_operation.
+:type edam_operation: STRING
+"""
+for operation in self.children:
+if operation.node.text == edam_operation:
+return True
+return False
+class EdamOperation(XMLParam):
+name = 'edam_operation'
+def __init__(self, value):
+super(EdamOperation, self).__init__()
+self.node.text = str(value)
+class EdamTopics(XMLParam):
+name = 'edam_topics'
+def acceptable_child(self, child):
+return issubclass(type(child), EdamTopic)
+def has_topic(self, edam_topic):
+"""
+Check the presence of a given edam_topic.
+:type edam_topic: STRING
+"""
+for topic in self.children:
+if topic.node.text == edam_topic:
+return True
+return False
+class EdamTopic(XMLParam):
+name = 'edam_topic'
+def __init__(self, value):
+super(EdamTopic, self).__init__()
+self.node.text = str(value)
+class Requirements(XMLParam):
+name = 'requirements'
+# This bodes to be an issue -__-
+def acceptable_child(self, child):
+return issubclass(type(child), Requirement) or issubclass(type(child), Container)
+class Requirement(XMLParam):
+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']
+super(Requirement, self).__init__(**passed_kwargs)
+self.node.text = str(value)
+class Container(XMLParam):
+name = 'container'
+def __init__(self, type, value, **kwargs):
+params = Util.clean_kwargs(locals().copy())
+passed_kwargs = {}
+passed_kwargs['type'] = params['type']
+super(Container, self).__init__(**passed_kwargs)
+self.node.text = str(value)
+class Configfiles(XMLParam):
+name = 'configfiles'
+def acceptable_child(self, child):
+return issubclass(type(child), Configfile) or issubclass(type(child), ConfigfileDefaultInputs)
+class Configfile(XMLParam):
+name = 'configfile'
+def __init__(self, name, text, **kwargs):
+params = Util.clean_kwargs(locals().copy())
+passed_kwargs = {}
+passed_kwargs['name'] = params['name']
+super(Configfile, self).__init__(**passed_kwargs)
+self.node.text = etree.CDATA(str(text))
+class ConfigfileDefaultInputs(XMLParam):
+name = 'inputs'
+def __init__(self, name, **kwargs):
+params = Util.clean_kwargs(locals().copy())
+passed_kwargs = {}
+passed_kwargs['name'] = params['name']
+super(ConfigfileDefaultInputs, self).__init__(**passed_kwargs)
+class Inputs(XMLParam):
+name = 'inputs'
+# This bodes to be an issue -__-
+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)
+def acceptable_child(self, child):
+return issubclass(type(child), InputParameter)
+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
+# Handle positional parameters
+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']
+else:
+self.num_dashes = 0
+self.space_between_arg = " "
+# Not sure about this :(
+# https://wiki.galaxyproject.org/Tools/BestPractices#Parameter_help
+if 'label' in kwargs:
+# TODO: replace with positional attribute
+if len(self.flag()) > 0:
+if kwargs['label'] is None:
+kwargs[
+'label'] = 'Author did not provide help for this parameter... '
+if not self.positional:
+kwargs['argument'] = self.flag()
+super(InputParameter, self).__init__(**kwargs)
+def command_line(self):
+before = self.command_line_before()
+cli = self.command_line_actual()
+after = self.command_line_after()
+complete = [x for x in (before, cli, after) if x is not None]
+return '\n'.join(complete)
+def command_line_before(self):
+try:
+return self.command_line_before_override
+except Exception:
+return None
+def command_line_after(self):
+try:
+return self.command_line_after_override
+except Exception:
+return None
+def command_line_actual(self):
+try:
+return self.command_line_override
+except Exception:
+if self.positional:
+return self.mako_name()
+else:
+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
+def flag(self):
+flag = '-' * self.num_dashes
+return flag + self.mako_identifier
+class Section(InputParameter):
+name = 'section'
+def __init__(self, name, title, expanded=None, help=None, **kwargs):
+params = Util.clean_kwargs(locals().copy())
+super(Section, self).__init__(**params)
+def acceptable_child(self, child):
+return issubclass(type(child), InputParameter)
+class Repeat(InputParameter):
+name = 'repeat'
+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_override
+super(Repeat, self).__init__(**params)
+def acceptable_child(self, child):
+return issubclass(type(child), InputParameter)
+def command_line_actual(self):
+if hasattr(self, 'command_line_override'):
+return self.command_line_override
+else:
+return "%s" % self.mako_name()
+class Conditional(InputParameter):
+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)
+def validate(self):
+# Find a way to check if one of the kids is a WHEN
+pass
+class When(InputParameter):
+name = 'when'
+def __init__(self, value):
+params = Util.clean_kwargs(locals().copy())
+super(When, self).__init__(None, **params)
+def acceptable_child(self, child):
+return issubclass(type(child), InputParameter)
+class Param(InputParameter):
+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
+super(Param, self).__init__(**params)
+if type(self) == Param:
+raise Exception(
+"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)
+class TextParam(Param):
+type = 'text'
+def __init__(self, name, optional=None, label=None, help=None,
+value=None, **kwargs):
+params = Util.clean_kwargs(locals().copy())
+super(TextParam, self).__init__(**params)
+def command_line_actual(self):
+try:
+return self.command_line_override
+except Exception:
+if self.positional:
+return self.mako_name()
+else:
+return f"{self.flag}{self.space_between_arg}'{self.mako_name()}'"
+class _NumericParam(Param):
+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'
+class FloatParam(_NumericParam):
+type = 'float'
+class BooleanParam(Param):
+type = 'boolean'
+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)
+if truevalue is None:
+# If truevalue and falsevalue are None, then we use "auto", the IUC
+# recommended default.
+#
+# truevalue is set to the parameter's value, and falsevalue is not.
+#
+# 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()
+if falsevalue is None:
+self.node.attrib['falsevalue'] = ""
+def command_line_actual(self):
+if hasattr(self, 'command_line_override'):
+return self.command_line_override
+else:
+return "%s" % self.mako_name()
+class DataParam(Param):
+type = 'data'
+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'
+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']
+super(SelectParam, self).__init__(**params)
+if options is not None and default is not None:
+if default not in options:
+raise Exception("Specified a default that isn't in options")
+if options:
+for k, v in list(sorted(options.items())):
+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)
+class SelectOption(InputParameter):
+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']
+super(SelectOption, self).__init__(None, **passed_kwargs)
+self.node.text = str(text)
+class Options(InputParameter):
+name = 'options'
+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)
+def acceptable_child(self, child):
+return issubclass(type(child), Column) or issubclass(type(child), Filter)
+class Column(InputParameter):
+name = 'column'
+def __init__(self, name, index, **kwargs):
+params = Util.clean_kwargs(locals().copy())
+super(Column, self).__init__(**params)
+class Filter(InputParameter):
+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):
+params = Util.clean_kwargs(locals().copy())
+super(Filter, self).__init__(**params)
+class ValidatorParam(InputParameter):
+name = 'validator'
+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'
+def acceptable_child(self, child):
+return isinstance(child, OutputData) or isinstance(child, OutputCollection)
+class OutputData(XMLParam):
+"""Copypasta of InputParameter, needs work
+"""
+name = 'data'
+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']
+else:
+self.num_dashes = 0
+self.space_between_arg = " "
+params = Util.clean_kwargs(locals().copy())
+super(OutputData, self).__init__(**params)
+def command_line(self):
+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
+def flag(self):
+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)
+class OutputFilter(XMLParam):
+name = 'filter'
+def __init__(self, text, **kwargs):
+params = Util.clean_kwargs(locals().copy())
+del params['text']
+super(OutputFilter, self).__init__(**params)
+self.node.text = text
+def acceptable_child(self, child):
+return False
+class ChangeFormat(XMLParam):
+name = 'change_format'
+def __init__(self, **kwargs):
+params = Util.clean_kwargs(locals().copy())
+super(ChangeFormat, self).__init__(**params)
+def acceptable_child(self, child):
+return isinstance(child, ChangeFormatWhen)
+class ChangeFormatWhen(XMLParam):
+name = 'when'
+def __init__(self, input, format, value, **kwargs):
+params = Util.clean_kwargs(locals().copy())
+super(ChangeFormatWhen, self).__init__(**params)
+def acceptable_child(self, child):
+return False
+class OutputCollection(XMLParam):
+name = 'collection'
+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) \
+or isinstance(child, DiscoverDatasets)
+class DiscoverDatasets(XMLParam):
+name = 'discover_datasets'
+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'
+def acceptable_child(self, child):
+return issubclass(type(child), Test)
+class Test(XMLParam):
+name = 'test'
+def acceptable_child(self, child):
+return isinstance(child, TestParam) or isinstance(child, TestOutput)
+class TestParam(XMLParam):
+name = 'param'
+def __init__(self, name, value=None, ftype=None, dbkey=None, **kwargs):
+params = Util.clean_kwargs(locals().copy())
+super(TestParam, self).__init__(**params)
+class TestOutput(XMLParam):
+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):
+params = Util.clean_kwargs(locals().copy())
+super(TestOutput, self).__init__(**params)
+class Citations(XMLParam):
+name = 'citations'
+def acceptable_child(self, child):
+return issubclass(type(child), Citation)
+def has_citation(self, type, value):
+"""
+Check the presence of a given citation.
+:type type: STRING
+:type value: STRING
+"""
+for citation in self.children:
+if citation.node.attrib['type'] == type and citation.node.text == value:
+return True
+return False
+class Citation(XMLParam):
+name = 'citation'
+def __init__(self, type, value):
+passed_kwargs = {}
+passed_kwargs['type'] = type
+super(Citation, self).__init__(**passed_kwargs)
+self.node.text = str(value)

Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/galaxyxml/tool/parameters/__init__.py @ 35:5d38cb3d9be8 draft

comparison toolfactory/galaxyxml/tool/parameters/init.py @ 35:5d38cb3d9be8 draft