#!/usr/bin/env python3 import argparse import sys import xml.sax class CLIElement(object): """Represents a tag. option_identifier -- str with parameters (e.g. --param), empty if argument. is_list -- bool whether the element is a list. """ def __init__(self, option_identifier='', mapping_path='', is_list=False): self.option_identifier = option_identifier self.mapping = None # Link to ParametersNode, set after parsing. self.mapping_path = mapping_path self.is_list = is_list def __str__(self): t = (self.option_identifier, self.mapping_path, self.is_list) return 'CLIElement(%s, %s, %s)' % tuple(map(repr, list(t))) class ParametersNode(object): """Represents a tag inside the tags.""" def __init__(self, kind='', name='', description='', value='', type_='', tags='', restrictions='', supported_formats=''): self.name = name self.description = description self.value = value self.type_ = type_ self.tags = tags self.supported_formats = supported_formats self.restrictions = None self.path = None # root if is None self.parent = None # not set, usually a list self.children = {} def computePath(self): """Compute path entry from parent links.""" def __str__(self): t = (self.name, self.description, self.value, self.type_, self.tags, self.supported_formats, self.children) return 'ParametersNode(%s, %s, %s, %s, %s, %s, %s)' % tuple(map(repr, t)) def __repr__(self): return str(self) class Tool(object): """Represents the top-level tag from a CTD file.""" def __init__(self, name='', executable_name='', version='', description='', manual='', doc_url='', category=''): self.name = name self.executable_name = executable_name self.version = version self.description = description self.manual = manual self.doc_url = doc_url self.category = category self.cli_elements = [] self.parameters = None def __str__(self): t = (self.name, self.executable_name, self.version, self.description, self.manual, self.doc_url, self.category) return 'Tool(%s, %s, %s, %s, %s, %s, %s)' % tuple(map(repr, list(t))) class CTDFormatException(Exception): """Raised when there is a format error in CTD.""" class CTDHandler(xml.sax.handler.ContentHandler): def __init__(self): self.result = None # A stack of tag names that are currently open. self.stack = [] # The current parameter to append nodes below. self.parameter_node = None def startElement(self, name, attrs): """Handle start of element.""" # Maintain a stack of open tags. self.stack.append(name) if self.stack == ['tool']: # Create the top level Tool object. self.tool = Tool() self.result = self.tool elif self.stack == ['tool', 'cli', 'clielement']: # Create a new CLIElement object for a tag. if not attrs.get('isList'): raise CTDFormatException('No attribute isList in .') if attrs.get('optionIdentifier') is None: raise CTDFormatException('no attribute optionIdentifier in .') is_list = (attrs.get('isList') == 'false') option_identifier = attrs.get('optionIdentifier') self.tool.cli_elements.append(CLIElement(option_identifier=option_identifier, is_list=is_list)) elif self.stack == ['tool', 'cli', 'clielement', 'mapping']: # Handle a sub entry of a tag. if not attrs.get('referenceName'): raise CTDFormatException('no attribute referenceName in ') self.tool.cli_elements[-1].mapping_path = attrs['referenceName'] elif self.stack == ['tool', 'PARAMETERS']: # Handle the entry by creating a new top parameters node. self.tool.parameters = ParametersNode(kind='node', name='') self.parameter_node = self.tool.parameters elif self.stack[:2] == ['tool', 'PARAMETERS'] and self.stack[-1] == 'NODE': # Create a new node ParametersNode for the entry. if not attrs.get('name'): raise CTDFormatException('no attribute name in ') name = attrs.get('name') node = ParametersNode(kind='node', name=name) node.parent = self.parameter_node self.parameter_node.children[name] = node self.parameter_node = node.parent elif self.stack[:2] == ['tool', 'PARAMETERS'] and self.stack[-1] == 'ITEM': # Create a new item ParametersNode for the entry. if not attrs.get('name'): raise CTDFormatException('no attribute name in ') name = attrs.get('name') value = attrs.get('value') type_ = attrs.get('type') tags = attrs.get('tags') description = attrs.get('description') restrictions = attrs.get('restrictions') supported_formats = attrs.get('supported_formats') child = ParametersNode( kind='item', name=name, description=description, value=value, type_=type_, tags=tags, supported_formats=supported_formats) self.parameter_node.children[name] = child def endElement(self, name): self.stack.pop() if name == 'NODE': self.parameter_node = self.parameter_node.parent def characters(self, content): if self.stack == ['tool', 'name']: self.tool.name += content elif self.stack == ['tool', 'executableName']: self.tool.executable_name += content elif self.stack == ['tool', 'version']: self.tool.version += content elif self.stack == ['tool', 'description']: self.tool.description += content elif self.stack == ['tool', 'manual']: self.tool.manual += content elif self.stack == ['tool', 'docurl']: self.tool.doc_url += content elif self.stack == ['tool', 'category']: self.tool.category += content class CTDParser(object): """Parser for CTD files.""" def __init__(self): self.handler = CTDHandler() def parse(self, path): parser = xml.sax.make_parser() parser.setContentHandler(self.handler) parser.parse(path) return self.handler.result def main(): parser = argparse.ArgumentParser(description='Convert CTD to Galaxy XML') parser.add_argument('-i', '--in-file', metavar='FILE', help='CTD file to read.', dest='in_file', required=True) args = parser.parse_args() ctd_parser = CTDParser() tool = ctd_parser.parse(args.in_file) print(tool) for cli in tool.cli_elements: print(' %s' % cli) print(tool.parameters) if __name__ == '__main__': sys.exit(main())