Index

_

__eq__() (beeflow.common.wf_data.Task method) (beeflow.common.wf_data.Workflow method) __getnewargs__() (beeflow.common.wf_data.Hint method) (beeflow.common.wf_data.InputParameter method) (beeflow.common.wf_data.OutputParameter method) (beeflow.common.wf_data.Requirement method) (beeflow.common.wf_data.StepInput method) (beeflow.common.wf_data.StepOutput method) (beeflow.common.wf_data.TaskStateUpdate method) __hash__ (beeflow.common.wf_data.Workflow attribute) __hash__() (beeflow.common.wf_data.Task method) __init__() (beeflow.common.wf_data.Task method) (beeflow.common.wf_data.Workflow method) __ne__() (beeflow.common.wf_data.Task method) (beeflow.common.wf_data.Workflow method) __new__() (beeflow.common.wf_data.Hint static method) (beeflow.common.wf_data.InputParameter static method) (beeflow.common.wf_data.OutputParameter static method) (beeflow.common.wf_data.Requirement static method) (beeflow.common.wf_data.StepInput static method) (beeflow.common.wf_data.StepOutput static method) (beeflow.common.wf_data.TaskStateUpdate static method)

__repr__() (beeflow.common.wf_data.Hint method) (beeflow.common.wf_data.InputParameter method) (beeflow.common.wf_data.OutputParameter method) (beeflow.common.wf_data.Requirement method) (beeflow.common.wf_data.StepInput method) (beeflow.common.wf_data.StepOutput method) (beeflow.common.wf_data.Task method) (beeflow.common.wf_data.TaskStateUpdate method) (beeflow.common.wf_data.Workflow method) __weakref__ (beeflow.common.wf_data.Task attribute) (beeflow.common.wf_data.Workflow attribute)

A

accept() (beeflow.common.cli_connection.Server method) add_dependencies() (in module beeflow.common.gdb.neo4j_cypher)

add_scheduling_results() (beeflow.common.wf_profiler.WorkflowProfiler method) add_state_change() (beeflow.common.wf_profiler.WorkflowProfiler method) add_task() (beeflow.common.wf_interface.WorkflowInterface method)

B

BaseSlurmWorker (class in beeflow.common.worker.slurm_worker) bee_workdir_init() (in module beeflow.common.config_driver) BeeConfig (class in beeflow.common.config_driver) beeflow.common.build.build_driver module beeflow.common.build.container_drivers module beeflow.common.build_interfaces module beeflow.common.cli_connection module beeflow.common.config_driver module beeflow.common.config_validator module beeflow.common.connection module beeflow.common.container_path module beeflow.common.crt.charliecloud_driver module beeflow.common.crt.crt_driver module beeflow.common.crt.singularity_driver module beeflow.common.crt_interface module beeflow.common.db.sched_db module beeflow.common.db.tm_db module beeflow.common.expr module beeflow.common.gdb.gdb_driver module beeflow.common.gdb.neo4j_cypher module

beeflow.common.gdb.neo4j_driver module beeflow.common.log module beeflow.common.parser.parser module beeflow.common.wf_data module beeflow.common.wf_interface module beeflow.common.wf_profiler module beeflow.common.worker.lsf_worker module beeflow.common.worker.simple_worker module beeflow.common.worker.slurm_worker module beeflow.common.worker.worker module beeflow.common.worker_interface module beeflow.task_manager module beeflow.wf_manager.resources.wf_metadata module BeeflowConnectionError build_main() (in module beeflow.common.build_interfaces) build_text() (beeflow.common.crt.charliecloud_driver.CharliecloudDriver method) (beeflow.common.crt.crt_driver.ContainerRuntimeDriver method) (beeflow.common.crt.singularity_driver.SingularityDriver method) (beeflow.common.crt_interface.ContainerRuntimeInterface method) (beeflow.common.worker.slurm_worker.BaseSlurmWorker method) (beeflow.common.worker.slurm_worker.SlurmWorker method) (beeflow.common.worker.worker.Worker method) BuildDriver (class in beeflow.common.build.build_driver)

C

cancel_task() (beeflow.common.worker.lsf_worker.LSFWorker method) (beeflow.common.worker.simple_worker.SimpleWorker method) (beeflow.common.worker.slurm_worker.SlurmCLIWorker method) (beeflow.common.worker.slurm_worker.SlurmrestdWorker method) (beeflow.common.worker.slurm_worker.SlurmWorker method) (beeflow.common.worker.worker.Worker method) (beeflow.common.worker_interface.WorkerInterface method) CharliecloudBuildDriver (class in beeflow.common.build.container_drivers) CharliecloudDriver (class in beeflow.common.crt.charliecloud_driver) check_choice() (in module beeflow.common.config_driver) check_slurm_error() (in module beeflow.common.worker.slurm_worker) check_yes() (in module beeflow.common.config_driver) choose_values() (beeflow.common.config_driver.ConfigGenerator method) class_ (beeflow.common.wf_data.Hint attribute) (beeflow.common.wf_data.Requirement attribute) cleanup() (in module beeflow.common.gdb.neo4j_cypher) clear() (beeflow.common.db.sched_db.Resources method) (beeflow.common.db.tm_db.JobQueue method) (beeflow.common.db.tm_db.SubmitQueue method) (beeflow.common.db.tm_db.UpdateQueue method) ClientConnection (class in beeflow.common.cli_connection) close() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) command (beeflow.common.wf_data.Task property) Command (class in beeflow.common.crt.crt_driver) CommandType (class in beeflow.common.crt.crt_driver) ConfigError ConfigGenerator (class in beeflow.common.config_driver)

ConfigOption (class in beeflow.common.config_validator) ConfigSection (class in beeflow.common.config_validator) ConfigValidator (class in beeflow.common.config_validator) connect() (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) Connection (class in beeflow.common.connection) ContainerBuildDriver (class in beeflow.common.build.container_drivers) ContainerRuntimeDriver (class in beeflow.common.crt.crt_driver) ContainerRuntimeInterface (class in beeflow.common.crt_interface) ContainerRuntimeResult (class in beeflow.common.crt.crt_driver) convert_path() (in module beeflow.common.container_path) copy() (beeflow.common.wf_data.Task method) copy_task_outputs() (in module beeflow.common.gdb.neo4j_cypher) count() (beeflow.common.db.tm_db.JobQueue method) (beeflow.common.db.tm_db.SubmitQueue method) create_bee_node() (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (in module beeflow.common.gdb.neo4j_cypher) create_task() (in module beeflow.common.gdb.neo4j_cypher) create_task_hint_nodes() (in module beeflow.common.gdb.neo4j_cypher) create_task_input_nodes() (in module beeflow.common.gdb.neo4j_cypher) create_task_metadata_node() (in module beeflow.common.gdb.neo4j_cypher) create_task_output_nodes() (in module beeflow.common.gdb.neo4j_cypher) create_task_requirement_nodes() (in module beeflow.common.gdb.neo4j_cypher) create_workflow_hint_nodes() (in module beeflow.common.gdb.neo4j_cypher) create_workflow_input_nodes() (in module beeflow.common.gdb.neo4j_cypher) create_workflow_node() (in module beeflow.common.gdb.neo4j_cypher) create_workflow_output_nodes() (in module beeflow.common.gdb.neo4j_cypher) create_workflow_requirement_nodes() (in module beeflow.common.gdb.neo4j_cypher) CwlParseError CwlParser (class in beeflow.common.parser.parser)

D

default (beeflow.common.wf_data.StepInput attribute)

delete() (beeflow.common.connection.Connection method)

E

eval_input() (in module beeflow.common.expr) eval_output() (in module beeflow.common.expr) execute_workflow() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method)

export_graphml() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) extend() (beeflow.common.db.sched_db.Resources method)

F

filepath_completion_input() (in module beeflow.common.config_driver) final_tasks_completed() (in module beeflow.common.gdb.neo4j_cypher)

finalize_task() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method)

G

generate_task_id() (beeflow.common.wf_data.Task method) generate_workflow_id() (in module beeflow.common.wf_data) get() (beeflow.common.cli_connection.ClientConnection method) (beeflow.common.config_driver.BeeConfig class method) (beeflow.common.connection.Connection method) (beeflow.wf_manager.resources.wf_metadata.WFMetadata method) get_ccname() (beeflow.common.crt.charliecloud_driver.CharliecloudDriver static method) get_dependent_tasks() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) get_docker_req() (beeflow.common.build.container_drivers.CharliecloudBuildDriver method) get_full_requirement() (beeflow.common.wf_data.Task method) get_ready_tasks() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) get_requirement() (beeflow.common.wf_data.Task method) get_task_by_id() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) get_task_hints() (in module beeflow.common.gdb.neo4j_cypher) get_task_input() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) get_task_inputs() (in module beeflow.common.gdb.neo4j_cypher) get_task_metadata() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher)

get_task_output() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) get_task_outputs() (in module beeflow.common.gdb.neo4j_cypher) get_task_requirements() (in module beeflow.common.gdb.neo4j_cypher) get_task_state() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) get_workflow() (beeflow.common.wf_interface.WorkflowInterface method) get_workflow_by_id() (in module beeflow.common.gdb.neo4j_cypher) get_workflow_description() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) get_workflow_hints() (in module beeflow.common.gdb.neo4j_cypher) get_workflow_inputs() (in module beeflow.common.gdb.neo4j_cypher) get_workflow_inputs_and_outputs() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) get_workflow_outputs() (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) get_workflow_requirements() (in module beeflow.common.gdb.neo4j_cypher) get_workflow_requirements_and_hints() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) get_workflow_state() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) get_workflow_tasks() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (in module beeflow.common.gdb.neo4j_cypher) glob (beeflow.common.wf_data.StepOutput attribute) GraphDatabaseDriver (class in beeflow.common.gdb.gdb_driver)

H

handle_error() (beeflow.common.connection.Connection method)

Hint (class in beeflow.common.wf_data)

I

id (beeflow.common.wf_data.InputParameter attribute) (beeflow.common.wf_data.OutputParameter attribute) (beeflow.common.wf_data.StepInput attribute) (beeflow.common.wf_data.StepOutput attribute) info() (in module beeflow.common.config_driver) init() (beeflow.common.config_driver.BeeConfig class method) initialize_ready_tasks() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method)

initialize_workflow() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) InputParameter (class in beeflow.common.wf_data) is_empty() (in module beeflow.common.gdb.neo4j_cypher) is_section_valid() (beeflow.common.config_validator.ConfigValidator method)

J

job_queue (beeflow.common.db.tm_db.TMDB property) job_state (beeflow.common.wf_data.TaskStateUpdate attribute)

JobQueue (class in beeflow.common.db.tm_db) join_path() (in module beeflow.common.config_driver)

L

load_task() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method)

LSFWorker (class in beeflow.common.worker.lsf_worker)

M

main() (in module beeflow.common.parser.parser) metadata (beeflow.common.wf_data.TaskStateUpdate attribute) methods (beeflow.wf_manager.resources.wf_metadata.WFMetadata attribute) module beeflow.common.build.build_driver beeflow.common.build.container_drivers beeflow.common.build_interfaces beeflow.common.cli_connection beeflow.common.config_driver beeflow.common.config_validator beeflow.common.connection beeflow.common.container_path beeflow.common.crt.charliecloud_driver beeflow.common.crt.crt_driver beeflow.common.crt.singularity_driver beeflow.common.crt_interface beeflow.common.db.sched_db beeflow.common.db.tm_db beeflow.common.expr beeflow.common.gdb.gdb_driver beeflow.common.gdb.neo4j_cypher beeflow.common.gdb.neo4j_driver beeflow.common.log beeflow.common.parser.parser beeflow.common.wf_data beeflow.common.wf_interface beeflow.common.wf_profiler beeflow.common.worker.lsf_worker beeflow.common.worker.simple_worker beeflow.common.worker.slurm_worker beeflow.common.worker.worker beeflow.common.worker_interface beeflow.task_manager beeflow.wf_manager.resources.wf_metadata

N

Neo4jDriver (class in beeflow.common.gdb.neo4j_driver)

Neo4jNotRunning new() (in module beeflow.common.config_driver)

O

open_db() (in module beeflow.common.db.sched_db) (in module beeflow.common.db.tm_db) option() (beeflow.common.config_validator.ConfigValidator method)

options() (beeflow.common.config_validator.ConfigValidator method) output (beeflow.common.wf_data.TaskStateUpdate attribute) OutputParameter (class in beeflow.common.wf_data)

P

params (beeflow.common.wf_data.Hint attribute) (beeflow.common.wf_data.Requirement attribute) parse_args() (in module beeflow.common.parser.parser) parse_job() (beeflow.common.parser.parser.CwlParser method) parse_requirements() (beeflow.common.parser.parser.CwlParser method) parse_step() (beeflow.common.parser.parser.CwlParser method) parse_step_inputs() (beeflow.common.parser.parser.CwlParser static method) parse_step_outputs() (beeflow.common.parser.parser.CwlParser static method) parse_workflow() (beeflow.common.parser.parser.CwlParser method) patch() (beeflow.common.connection.Connection method) PathError pause_workflow() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) pop() (beeflow.common.db.tm_db.JobQueue method) (beeflow.common.db.tm_db.SubmitQueue method) position (beeflow.common.wf_data.StepInput attribute) post() (beeflow.common.connection.Connection method) prefix (beeflow.common.wf_data.StepInput attribute) prepare() (beeflow.common.worker.worker.Worker method) print_wrap() (in module beeflow.common.config_driver) process_container_name() (beeflow.common.build.build_driver.BuildDriver method) (beeflow.common.build.container_drivers.CharliecloudBuildDriver method) process_copy_container() (beeflow.common.build.build_driver.BuildDriver method) (beeflow.common.build.container_drivers.CharliecloudBuildDriver method)

process_docker_file() (beeflow.common.build.build_driver.BuildDriver method) (beeflow.common.build.container_drivers.CharliecloudBuildDriver method) (beeflow.common.build.container_drivers.SingularityBuildDriver method) process_docker_image_id() (beeflow.common.build.build_driver.BuildDriver method) (beeflow.common.build.container_drivers.CharliecloudBuildDriver method) (beeflow.common.build.container_drivers.SingularityBuildDriver method) process_docker_import() (beeflow.common.build.build_driver.BuildDriver method) (beeflow.common.build.container_drivers.CharliecloudBuildDriver method) (beeflow.common.build.container_drivers.SingularityBuildDriver method) process_docker_load() (beeflow.common.build.build_driver.BuildDriver method) (beeflow.common.build.container_drivers.CharliecloudBuildDriver method) (beeflow.common.build.container_drivers.SingularityBuildDriver method) process_docker_output_directory() (beeflow.common.build.build_driver.BuildDriver method) (beeflow.common.build.container_drivers.CharliecloudBuildDriver method) (beeflow.common.build.container_drivers.SingularityBuildDriver method) process_docker_pull() (beeflow.common.build.build_driver.BuildDriver method) (beeflow.common.build.container_drivers.CharliecloudBuildDriver method) (beeflow.common.build.container_drivers.SingularityBuildDriver method) push() (beeflow.common.db.tm_db.JobQueue method) (beeflow.common.db.tm_db.SubmitQueue method) (beeflow.common.db.tm_db.UpdateQueue method) put() (beeflow.common.cli_connection.ClientConnection method) (beeflow.common.connection.Connection method)

Q

query_job() (beeflow.common.worker.lsf_worker.LSFWorker method) query_task() (beeflow.common.worker.lsf_worker.LSFWorker method) (beeflow.common.worker.simple_worker.SimpleWorker method) (beeflow.common.worker.slurm_worker.SlurmCLIWorker method) (beeflow.common.worker.slurm_worker.SlurmrestdWorker method) (beeflow.common.worker.slurm_worker.SlurmWorker method) (beeflow.common.worker.worker.Worker method) (beeflow.common.worker_interface.WorkerInterface method)

R

remove_by_id() (beeflow.common.db.tm_db.JobQueue method) Requirement (class in beeflow.common.wf_data) reset_tasks_metadata() (in module beeflow.common.gdb.neo4j_cypher) reset_workflow() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) reset_workflow_id() (in module beeflow.common.gdb.neo4j_cypher) resolve_path() (beeflow.common.config_driver.BeeConfig static method) resolve_priority() (beeflow.common.build.build_driver.BuildDriver method) resources (beeflow.common.db.sched_db.SchedDB property)

Resources (class in beeflow.common.db.sched_db) restart_task() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) resume_workflow() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) run_text() (beeflow.common.crt.charliecloud_driver.CharliecloudDriver method) (beeflow.common.crt.crt_driver.ContainerRuntimeDriver method) (beeflow.common.crt.singularity_driver.SingularityDriver method) (beeflow.common.crt_interface.ContainerRuntimeInterface method)

S

save() (beeflow.common.config_driver.ConfigGenerator method) (beeflow.common.wf_profiler.WorkflowProfiler method) SchedDB (class in beeflow.common.db.sched_db) section() (beeflow.common.config_validator.ConfigValidator method) sections (beeflow.common.config_validator.ConfigValidator property) send() (in module beeflow.common.cli_connection) Server (class in beeflow.common.cli_connection) server() (in module beeflow.common.cli_connection) set_init_task_inputs() (in module beeflow.common.gdb.neo4j_cypher) set_paused_tasks_to_running() (in module beeflow.common.gdb.neo4j_cypher) set_runnable_tasks_to_ready() (in module beeflow.common.gdb.neo4j_cypher) set_running_tasks_to_paused() (in module beeflow.common.gdb.neo4j_cypher) set_task_input() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) set_task_input_type() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (in module beeflow.common.gdb.neo4j_cypher) set_task_metadata() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) set_task_output() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) set_task_output_glob() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (in module beeflow.common.gdb.neo4j_cypher)

set_task_state() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) set_workflow_state() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method) (in module beeflow.common.gdb.neo4j_cypher) setup() (in module beeflow.common.log) show() (in module beeflow.common.config_driver) SimpleWorker (class in beeflow.common.worker.simple_worker) SingularityBuildDriver (class in beeflow.common.build.container_drivers) SingularityDriver (class in beeflow.common.crt.singularity_driver) SlurmCLIWorker (class in beeflow.common.worker.slurm_worker) SlurmrestdWorker (class in beeflow.common.worker.slurm_worker) SlurmWorker (class in beeflow.common.worker.slurm_worker) source (beeflow.common.wf_data.OutputParameter attribute) (beeflow.common.wf_data.StepInput attribute) StepInput (class in beeflow.common.wf_data) StepOutput (class in beeflow.common.wf_data) submit_job() (beeflow.common.worker.lsf_worker.LSFWorker method) (beeflow.common.worker.slurm_worker.BaseSlurmWorker method) submit_queue (beeflow.common.db.tm_db.TMDB property) submit_task() (beeflow.common.worker.lsf_worker.LSFWorker method) (beeflow.common.worker.simple_worker.SimpleWorker method) (beeflow.common.worker.slurm_worker.BaseSlurmWorker method) (beeflow.common.worker.slurm_worker.SlurmWorker method) (beeflow.common.worker.worker.Worker method) (beeflow.common.worker_interface.WorkerInterface method) SubmitQueue (class in beeflow.common.db.tm_db)

T

Task (class in beeflow.common.wf_data) task_id (beeflow.common.wf_data.TaskStateUpdate attribute) task_info (beeflow.common.wf_data.TaskStateUpdate attribute) task_save_path() (beeflow.common.worker.worker.Worker method) TaskStateUpdate (class in beeflow.common.wf_data)

TMDB (class in beeflow.common.db.tm_db) type (beeflow.common.wf_data.InputParameter attribute) (beeflow.common.wf_data.OutputParameter attribute) (beeflow.common.wf_data.StepInput attribute) (beeflow.common.wf_data.StepOutput attribute)

U

update_job_state() (beeflow.common.db.tm_db.JobQueue method) update_queue (beeflow.common.db.tm_db.TMDB property)

UpdateQueue (class in beeflow.common.db.tm_db) updates() (beeflow.common.db.tm_db.UpdateQueue method) userconfig_path() (beeflow.common.config_driver.BeeConfig class method)

V

validate() (beeflow.common.config_validator.ConfigOption method) (beeflow.common.config_validator.ConfigValidator method) (in module beeflow.common.config_driver) validate_chrun_opts() (in module beeflow.common.config_driver)

value (beeflow.common.wf_data.InputParameter attribute) (beeflow.common.wf_data.OutputParameter attribute) (beeflow.common.wf_data.StepInput attribute) (beeflow.common.wf_data.StepOutput attribute) value_from (beeflow.common.wf_data.StepInput attribute)

W

wf_id (beeflow.common.wf_data.TaskStateUpdate attribute) WFMetadata (class in beeflow.wf_manager.resources.wf_metadata) Worker (class in beeflow.common.worker.worker) WorkerError WorkerInterface (class in beeflow.common.worker_interface) Workflow (class in beeflow.common.wf_data) workflow_completed() (beeflow.common.gdb.gdb_driver.GraphDatabaseDriver method) (beeflow.common.gdb.neo4j_driver.Neo4jDriver method) (beeflow.common.wf_interface.WorkflowInterface method)

workflow_id (beeflow.common.wf_interface.WorkflowInterface property) WorkflowInterface (class in beeflow.common.wf_interface) WorkflowProfiler (class in beeflow.common.wf_profiler) write_script() (beeflow.common.worker.lsf_worker.LSFWorker method) (beeflow.common.worker.slurm_worker.BaseSlurmWorker method)