Index

_

__init__() (sophios.wic_types.GraphData method)

A

absolute_paths() (in module sophios.cwl_subinterpreter) add_graph_edge() (in module sophios.utils_graphs) add_subgraphs() (in module sophios.utils_graphs)

add_yamldict_keyval_in() (in module sophios.utils_cwl) add_yamldict_keyval_out() (in module sophios.utils_cwl) apply_args() (in module sophios.inlineing)

B

build_cmd() (in module sophios.run_local)

C

canonicalize_inputs_dict() (in module sophios.utils_cwl) canonicalize_outputs_dict() (in module sophios.utils_cwl) canonicalize_steps_dict() (in module sophios.utils_cwl) canonicalize_steps_list() (in module sophios.utils_cwl) canonicalize_type() (in module sophios.utils_cwl) check_args_match_inputs() (in module sophios.python_cwl_adapter) cli_watcher() (in module sophios.cwl_subinterpreter) compile_workflow() (in module sophios.compiler) compile_workflow_generate_schema() (in module sophios.schemas.wic_schema) compile_workflow_once() (in module sophios.compiler) compiled_cwl (sophios.wic_types.NodeData attribute) CompilerInfo (class in sophios.wic_types) copy_cwl_input_output_dict() (in module sophios.utils_cwl)

copy_output_files() (in module sophios.run_local) cwl (sophios.wic_types.Tool attribute) cwl_prepend_dockerFile_include_path() (in module sophios.plugins) cwl_prepend_dockerFile_include_path_rosetree() (in module sophios.plugins) cwl_schema() (in module sophios.schemas.wic_schema) cwl_type_to_jsonschema_type() (in module sophios.schemas.wic_schema) cwl_type_to_jsonschema_type_schema() (in module sophios.schemas.wic_schema) cwl_update_inline_runtag() (in module sophios.plugins) cwl_update_inline_runtag_rosetree() (in module sophios.plugins) cwl_update_outputs_optional() (in module sophios.plugins) cwl_update_outputs_optional_rosetree() (in module sophios.plugins) cwltool_main() (in module sophios.run_local) cwltool_main_pf() (in module sophios.run_local)

D

data (sophios.wic_types.RoseTree attribute) default_schema() (in module sophios.schemas.wic_schema) desugar_into_canonical_normal_form() (in module sophios.utils_cwl)

dockerPull_append_noentrypoint() (in module sophios.plugins) dockerPull_append_noentrypoint_rosetree() (in module sophios.plugins) dockerPull_append_noentrypoint_tools() (in module sophios.plugins)

E

env (sophios.wic_types.CompilerInfo attribute) EnvData (class in sophios.wic_types) explicit_edge_calls (sophios.wic_types.EnvData attribute) (sophios.wic_types.NodeData attribute)

explicit_edge_defs (sophios.wic_types.EnvData attribute) (sophios.wic_types.NodeData attribute) extract_implementation() (in module sophios.utils)

F

file_watcher_glob() (in module sophios.cwl_subinterpreter) filter() (sophios.plugins.NoPartialFailureNullWarning method) (sophios.plugins.NoPreviouslyDefinedFilter method) (sophios.plugins.NoResolvedFilter method)

flatten() (in module sophios.utils) flatten_forest() (in module sophios.utils) flatten_graphdata() (in module sophios.utils_graphs) flatten_rose_tree() (in module sophios.utils)

G

generate_CWL_CommandLineTool() (in module sophios.python_cwl_adapter) generate_run_script() (in module sophios.run_local) get_absolute_paths() (in module sophios.input_output) get_args() (in module sophios.cli) get_basic_config() (in module sophios.input_output) get_config() (in module sophios.input_output) get_graph_reps() (in module sophios.utils_graphs) get_home_paths() (in module sophios.input_output) get_inference_rules() (in module sophios.inference) get_inlineable_subworkflows() (in module sophios.inlineing) get_input_mappings() (in module sophios.utils) get_inputs_workflow() (in module sophios.python_cwl_adapter) get_known_and_unknown_args() (in module sophios.cli) get_main_args() (in module sophios.python_cwl_adapter) get_module() (in module sophios.python_cwl_adapter)

get_output_mapping() (in module sophios.utils) get_py_paths() (in module sophios.plugins) get_step_name_1() (in module sophios.utils) get_steps_keys() (in module sophios.utils) get_subkeys() (in module sophios.utils) get_tools_cwl() (in module sophios.plugins) get_validator() (in module sophios.schemas.wic_schema) get_workflow_outputs() (in module sophios.utils_cwl) get_workflow_paths() (in module sophios.plugins) get_yml_paths() (in module sophios.plugins) graph (sophios.wic_types.NodeData attribute) GraphData (class in sophios.wic_types) graphdata (sophios.wic_types.GraphReps attribute) graphdata_to_cytoscape() (in module sophios.utils_graphs) GraphReps (class in sophios.wic_types) graphviz (sophios.wic_types.GraphReps attribute)

I

ignore_aliases() (sophios.input_output.NoAliasDumper method) import_python_file() (in module sophios.python_cwl_adapter) inline_subworkflow() (in module sophios.inlineing) inline_subworkflow_cwl() (in module sophios.inlineing)

inline_subworkflow_wic_tag() (in module sophios.inlineing) input_mapping (sophios.wic_types.EnvData attribute) inputs_file_workflow (sophios.wic_types.EnvData attribute) inputs_workflow (sophios.wic_types.NodeData attribute) insert_step_into_workflow() (in module sophios.compiler)

L

logging_filters() (in module sophios.plugins)

M

main() (in module sophios.cwl_subinterpreter) (in module sophios.main) make_plugins_dag() (in module sophios.utils_graphs) make_tool_dag() (in module sophios.utils_graphs) maybe_add_requirements() (in module sophios.utils_cwl) merge_yml_trees() (in module sophios.ast) module sophios.ast sophios.cli sophios.compiler sophios.cwl_subinterpreter sophios.inference sophios.inlineing sophios.input_output sophios.main sophios.plugins sophios.python_cwl_adapter sophios.run_local sophios.schemas.wic_schema sophios.utils sophios.utils_cwl sophios.utils_graphs sophios.wic_types

move_adapters_and_examples() (in module sophios.input_output) move_slash_last() (in module sophios.inlineing)

N

name (sophios.wic_types.NodeData attribute) named_empty_schema() (in module sophios.schemas.wic_schema) named_id_schema() (in module sophios.schemas.wic_schema) named_null_schema() (in module sophios.schemas.wic_schema) named_schema() (in module sophios.schemas.wic_schema) namespaces (sophios.wic_types.NodeData attribute)

networkx (sophios.wic_types.GraphReps attribute) NoAliasDumper (class in sophios.input_output) NodeData (class in sophios.wic_types) NoPartialFailureNullWarning (class in sophios.plugins) NoPreviouslyDefinedFilter (class in sophios.plugins) NoResolvedFilter (class in sophios.plugins)

O

output_mapping (sophios.wic_types.EnvData attribute)

P

parse_int_string_tuple() (in module sophios.utils) parse_provenance_output_files() (in module sophios.utils) parse_provenance_output_files_() (in module sophios.utils) parse_step_name_str() (in module sophios.utils)

partition_by_lowest_common_ancestor() (in module sophios.utils) perform_edge_inference() (in module sophios.inference) plugin_ns (sophios.wic_types.StepId attribute) pretty_print_forest() (in module sophios.utils) python_script_generate_cwl() (in module sophios.ast)

R

read_ast_from_disk() (in module sophios.ast) read_config_from_disk() (in module sophios.input_output) read_lines_pairs() (in module sophios.input_output) recursively_contains_dict_key() (in module sophios.utils) recursively_delete_dict_key() (in module sophios.utils) reindex_wic_steps() (in module sophios.utils) remove_entrypoints() (in module sophios.plugins) remove_entrypoints_docker() (in module sophios.plugins) remove_entrypoints_podman() (in module sophios.plugins)

remove_id_tags() (in module sophios.utils_cwl) rerun_cwltool() (in module sophios.cwl_subinterpreter) restore_namespaced_output_name() (in module sophios.utils) rose (sophios.wic_types.CompilerInfo attribute) RoseTree (class in sophios.wic_types) run_cwl_serialized_async() (in module sophios.run_local) run_cwl_workflow() (in module sophios.run_local) run_local() (in module sophios.run_local) run_path (sophios.wic_types.Tool attribute)

S

shorten_namespaced_output_name() (in module sophios.utils) sophios.ast module sophios.cli module sophios.compiler module sophios.cwl_subinterpreter module sophios.inference module sophios.inlineing module sophios.input_output module sophios.main module sophios.plugins module sophios.python_cwl_adapter module

sophios.run_local module sophios.schemas.wic_schema module sophios.utils module sophios.utils_cwl module sophios.utils_graphs module sophios.wic_types module stage_input_files() (in module sophios.run_local) stem (sophios.wic_types.StepId attribute) step_id (sophios.wic_types.YamlTree attribute) step_name_1 (sophios.wic_types.NodeData attribute) step_name_str() (in module sophios.utils) StepId (class in sophios.wic_types) sub_forests (sophios.wic_types.YamlForest attribute) sub_trees (sophios.wic_types.RoseTree attribute)

T

Tool (class in sophios.wic_types) tool (sophios.wic_types.NodeData attribute)

tree_to_forest() (in module sophios.ast) types_match() (in module sophios.inference)

V

validate_cwl() (in module sophios.plugins)

vars_workflow_output_internal (sophios.wic_types.EnvData attribute)

W

wic_main_schema() (in module sophios.schemas.wic_schema) wic_tag_schema() (in module sophios.schemas.wic_schema) workflow_inputs_file (sophios.wic_types.NodeData attribute)

write_absolute_yaml_tags() (in module sophios.input_output) write_config_to_disk() (in module sophios.input_output) write_to_disk() (in module sophios.input_output)

Y

yaml_tree (sophios.wic_types.YamlForest attribute) YamlForest (class in sophios.wic_types)

YamlTree (class in sophios.wic_types) yml (sophios.wic_types.NodeData attribute) (sophios.wic_types.YamlTree attribute)