planemo.autopygen package

Subpackages

• planemo.autopygen.commands package
  • Submodules
  • planemo.autopygen.commands.command_utils module
    • DefinitionNotFoundException
    • ParamTypeNotSupported
    • create_body_expression()
    • create_element_with_body()
    • create_flag()
    • transform_param_info()
  • Module contents
• planemo.autopygen.source_file_parsing package
  • Submodules
  • planemo.autopygen.source_file_parsing.constants module
  • planemo.autopygen.source_file_parsing.decoy_parser module
    • CustomParserUnavailableException
    • DecoyParser
      • DecoyParser.Action
      • DecoyParser.Section
      • DecoyParser.Subparsers
      • DecoyParser.add_argument()
      • DecoyParser.add_argument_for_arg_group()
      • DecoyParser.add_argument_group()
      • DecoyParser.add_subparsers()
      • DecoyParser.create_custom_add_argument_group()
      • DecoyParser.report_arguments_and_groups()
      • DecoyParser.save_action()
    • obtain_class_def()
  • planemo.autopygen.source_file_parsing.local_module_parsing module
    • UnknownNamesRemoval
      • UnknownNamesRemoval.visit_ClassDef()
      • UnknownNamesRemoval.visit_Name()
    • handle_local_module_names()
  • planemo.autopygen.source_file_parsing.parser_discovery_and_init module
    • ArgumentCreationDiscovery
      • ArgumentCreationDiscovery.is_call_on_parser_or_group()
      • ArgumentCreationDiscovery.report_findings()
      • ArgumentCreationDiscovery.visit_Call()
    • GroupAndSubparsersDiscovery
      • GroupAndSubparsersDiscovery.report_findings()
      • GroupAndSubparsersDiscovery.visit_Assign()
    • ImportDiscovery
      • ImportDiscovery.report_findings()
      • ImportDiscovery.visit_Import()
      • ImportDiscovery.visit_ImportFrom()
    • SimpleParserDiscoveryAndReplacement
      • SimpleParserDiscoveryAndReplacement.imported_using_from()
      • SimpleParserDiscoveryAndReplacement.imported_using_import()
      • SimpleParserDiscoveryAndReplacement.is_simple_assignment()
      • SimpleParserDiscoveryAndReplacement.report_findings()
      • SimpleParserDiscoveryAndReplacement.visit_Assign()
    • get_parser_init_and_actions()
    • is_this_x_creation()
  • planemo.autopygen.source_file_parsing.parsing_commons module
    • CustomAST
    • CustomVisitor
      • CustomVisitor.report_findings()
      • CustomVisitor.visit_and_report()
    • Discovery
    • add_parents()
    • create_module_tree_from_path()
    • create_module_tree_from_str()
  • planemo.autopygen.source_file_parsing.parsing_exceptions module
    • ArgParseImportNotFound
    • ArgParserNotUsed
    • ArgumentParsingDiscoveryError
    • CouldNotFixNameError
  • planemo.autopygen.source_file_parsing.unknown_names_discovery module
    • UnknownNameInit
      • UnknownNameInit.report_findings()
      • UnknownNameInit.visit_Assign()
      • UnknownNameInit.visit_ClassDef()
    • UnknownNamesDiscovery
      • UnknownNamesDiscovery.report_findings()
      • UnknownNamesDiscovery.visit_ClassDef()
      • UnknownNamesDiscovery.visit_ListComp()
      • UnknownNamesDiscovery.visit_Name()
    • initialize_variables_in_module()
  • Module contents
• planemo.autopygen.xml package
  • Submodules
  • planemo.autopygen.xml.xml_utils module
    • formatted_xml_elem()
    • options()
    • param()
    • repeat()
  • Module contents

Submodules

planemo.autopygen.argument_parser_conversion module

Functions used to extract initialized ArgumentParser from target source code, and to transform it into easily usable ParamInfo class containing all the necessary info for ‘inputs’ element initialization

planemo.autopygen.argument_parser_conversion.command_from_decoy(parser: DecoyParser, data_inputs: Dict[str, str], reserved_names: Set[str], name_map: Dict[str, str], section_map: Dict[str, str], depth: int = 0, starting_namespace: str = '', skip_default_namespace: bool = False) → str

The function generates commands from decoy parser. It requires name and section maps that have already been initialised and contain correct mapping

planemo.autopygen.argument_parser_conversion.generate_xml_from_section(section: Section, data_inputs: Dict[str, str], reserved_names: Set[str], name_map: Dict[str, str], section_map: Dict[str, str], dont_wrap_in_section: bool = False) → Tuple[List[_Element], List[Any], ParamInfo | None]

planemo.autopygen.argument_parser_conversion.obtain_and_convert_parser(path: str) → DecoyParser | None

Function parses python source code located at ‘path’, extracts initialized argument parser from the source file and returns it

Parameters

pathstr

path to the source file containing argument parser init

Returns

Initialized argument parser, or None, in case error happened

planemo.autopygen.argument_parser_conversion.obtain_and_convert_parser_from_str(text: str) → ArgumentParser | None

Function parses python source code stored in text and extracts argument parser

Parameters

textstr

variable containing target source code

Returns

Initialized argument parser, or None, in case error happened

planemo.autopygen.argument_parser_conversion.obtain_param_info(action: Action, data_inputs: Dict[str, str], reserved_names: Set[str], name_map: Dict[str, str], section_map: Dict[str, str]) → ParamInfo

planemo.autopygen.argument_parser_conversion.obtain_parser(tree: Module) → DecoyParser | None

planemo.autopygen.argument_parser_conversion.transform_section_name(section_name: str) → str

planemo.autopygen.argument_parser_conversion.update_name_map(name: str, name_map: Dict[str, str], reserved_names: Set[str])

Updates names that are equal to one of the values in ‘reserved_names’ Doesn’t change names already present in the mapping

Parameters

name : name_map : reserved_names :

planemo.autopygen.argument_parser_conversion.xml_from_decoy(parser: DecoyParser, data_inputs: Dict[str, str], reserved_names: Set[str], name_map: Dict[str, str], section_map: Dict[str, str], dont_wrap_default_section: bool = True) → Tuple[List[Any], List[Any], ParamInfo | None]

planemo.autopygen.argument_parser_conversion.xml_to_string(nodes: List[_Element], indent: int)

planemo.autopygen.param_info module

class planemo.autopygen.param_info.ParamDataType(*values)

Bases: Enum

BOOLEAN = 'boolean'

DATA = 'data'

FLOAT = 'float'

INTEGER = 'integer'

SELECT = 'select'

TEXT = 'text'

UNDEFINED = "##!_FIXME_!## argument uses complex type it's type cannot be determined"

class planemo.autopygen.param_info.ParamInfo(is_positional: bool, param_type: ParamTypeFlags, type: ParamDataType, name: str, argument: str, label: str, section: str, section_label: str, default_val: Any, custom_attributes: Dict[str, str], nargs: float | int = 0, help: str | None = None, optional: bool = False, choices: List[Any] | None = None, format: str | None = None)

Bases: object

Class containing data of a single extracted parameter

argument: str

choices: List[Any] | None = None

custom_attributes: Dict[str, str]

default_val: Any

format: str | None = None

help: str | None = None

is_positional: bool

label: str

name: str

nargs: float | int = 0

optional: bool = False

param_type: ParamTypeFlags

section: str

section_label: str

type: ParamDataType

class planemo.autopygen.param_info.ParamTypeFlags(is_flag: bool = False, is_repeat: bool = False, is_selection: bool = False, is_extend: bool = False, is_version: bool = False, is_help: bool = False, is_output: bool = False)

Bases: object

is_extend: bool = False

is_flag: bool = False

is_help: bool = False

is_output: bool = False

is_repeat: bool = False

is_selection: bool = False

is_version: bool = False

Module contents