Index

A

active_job_from_proc() (in module pipeliner.job_factory) add_job() (pipeliner.project_graph.ProjectGraph method) add_job_to_pipeline() (pipeliner.job_runner.JobRunner method) add_new_input_edge() (pipeliner.project_graph.ProjectGraph method) add_new_output_edge() (pipeliner.project_graph.ProjectGraph method)

add_new_process() (pipeliner.project_graph.ProjectGraph method) add_node() (pipeliner.project_graph.ProjectGraph method) alias (pipeliner.data_structure.Process attribute) (pipeliner.pipeliner_job.PipelinerJob attribute) authors (pipeliner.pipeliner_job.Ref attribute)

B

bodies (pipeliner.jobstar_reader.BodyFile attribute)

BodyFile (class in pipeliner.jobstar_reader) bool_jobop() (in module pipeliner.jobstar_reader)

C

check_for_illegal_symbols() (in module pipeliner.utils) check_lock() (pipeliner.project_graph.ProjectGraph method) check_pipeline_version() (pipeliner.jobstar_reader.StarfileCheck method) check_process_completion() (pipeliner.project_graph.ProjectGraph method) check_reserved_words() (pipeliner.jobstar_reader.StarfileCheck method) cifdoc (pipeliner.jobstar_reader.StarfileCheck attribute) clean_jobname() (in module pipeliner.utils) clean_up_job() (pipeliner.project_graph.ProjectGraph method) cleanup_all() (pipeliner.api.manage_project.PipelinerProject method) cleanup_all_jobs() (pipeliner.project_graph.ProjectGraph method) clear() (pipeliner.data_structure.Node method) (pipeliner.data_structure.Process method) (pipeliner.pipeliner_job.PipelinerJob method) (pipeliner.project_graph.ProjectGraph method) compare_job_parameters() (pipeliner.api.manage_project.PipelinerProject method) compare_starfiles() (in module pipeliner.jobstar_reader) continue_job() (pipeliner.api.manage_project.PipelinerProject method) convert_coordinates_job() (in module pipeliner.jobstar_reader)

convert_oldstyle_names() (in module pipeliner.jobstar_reader) convert_pipeline() (in module pipeliner.api.manage_project) convert_pipeline_node() (in module pipeliner.jobstar_reader) convert_proctype() (in module pipeliner.jobstar_reader) convert_relion20_datafile() (in module pipeliner.jobstar_reader) convert_relion3_1_pipeline() (pipeliner.jobstar_reader.StarfileCheck method) convert_relion4_jobtypes_to_pipeliner() (in module pipeliner.job_factory) count_block() (pipeliner.jobstar_reader.RelionStarFile method) count_blocks() (pipeliner.jobstar_reader.JobStar method) count_bodies() (pipeliner.jobstar_reader.BodyFile method) count_jobopt() (pipeliner.jobstar_reader.JobStar method) count_movs_mics_parts() (in module pipeliner.jobstar_reader) count_pipeline() (pipeliner.jobstar_reader.JobStar method) create_archive() (pipeliner.api.manage_project.PipelinerProject method) create_input_nodes() (pipeliner.pipeliner_job.PipelinerJob method) create_lock() (pipeliner.project_graph.ProjectGraph method) create_process_display_objs() (pipeliner.project_graph.ProjectGraph method) create_results_display() (pipeliner.pipeliner_job.PipelinerJob method)

D

data (pipeliner.jobstar_reader.BodyFile attribute) (pipeliner.jobstar_reader.ExportStar attribute) (pipeliner.jobstar_reader.JobStar attribute) (pipeliner.jobstar_reader.OutputNodeStar attribute) (pipeliner.jobstar_reader.RelionStarFile attribute) date_time_tag() (in module pipeliner.utils) decompose_pipeline_filename() (in module pipeliner.utils) default_params_dict() (pipeliner.pipeliner_job.PipelinerJob method) delete_job() (pipeliner.api.manage_project.PipelinerProject method) (pipeliner.project_graph.ProjectGraph method) delete_node() (pipeliner.project_graph.ProjectGraph method) delete_temp_node_file() (pipeliner.project_graph.ProjectGraph method) delete_temp_node_files() (pipeliner.project_graph.ProjectGraph method)

description (pipeliner.api.manage_project.PipelinerProject attribute) display_name (pipeliner.pipeliner_job.JobInfo attribute) do_downstream (pipeliner.flowchart_illustration.ProcessFlowchart attribute) do_full (pipeliner.flowchart_illustration.ProcessFlowchart attribute) do_read_only (pipeliner.project_graph.ProjectGraph attribute) do_upstream (pipeliner.flowchart_illustration.ProcessFlowchart attribute) documentation (pipeliner.pipeliner_job.JobInfo attribute) doi (pipeliner.pipeliner_job.Ref attribute) downstream_process_graph() (pipeliner.flowchart_illustration.ProcessFlowchart method) draw_flowcharts() (pipeliner.api.manage_project.PipelinerProject method) drew_down (pipeliner.flowchart_illustration.ProcessFlowchart attribute) drew_full (pipeliner.flowchart_illustration.ProcessFlowchart attribute) drew_up (pipeliner.flowchart_illustration.ProcessFlowchart attribute)

E

edit_comment() (pipeliner.api.manage_project.PipelinerProject method) edit_jobstar() (in module pipeliner.api.api_utils) empty_trash() (pipeliner.api.manage_project.PipelinerProject method)

export_all_scheduled_jobs() (pipeliner.project_graph.ProjectGraph method) ExportStar (class in pipeliner.jobstar_reader) ext (pipeliner.data_structure.Node attribute)

F

final_commands (pipeliner.pipeliner_job.PipelinerJob attribute) find_common_string() (in module pipeliner.utils) find_immediate_child_processes() (pipeliner.project_graph.ProjectGraph method) find_job_by_comment() (pipeliner.api.manage_project.PipelinerProject method) find_job_by_rank() (pipeliner.api.manage_project.PipelinerProject method) find_node() (pipeliner.project_graph.ProjectGraph method)

find_process() (pipeliner.project_graph.ProjectGraph method) fix_newlines() (in module pipeliner.utils) fn_in (pipeliner.jobstar_reader.StarfileCheck attribute) format_edges_list() (pipeliner.flowchart_illustration.ProcessFlowchart method) format_for_metadata() (in module pipeliner.metadata_tools) full_process_graph() (pipeliner.flowchart_illustration.ProcessFlowchart method)

G

gather_all_jobtypes() (in module pipeliner.job_factory) gather_metadata() (pipeliner.pipeliner_job.PipelinerJob method) get_all_options() (pipeliner.jobstar_reader.JobStar method) get_available_jobs() (in module pipeliner.api.api_utils) get_block() (pipeliner.jobstar_reader.JobStar method) (pipeliner.jobstar_reader.RelionStarFile method) get_commandline_job() (pipeliner.job_runner.JobRunner method) get_commands() (pipeliner.pipeliner_job.PipelinerJob method) get_commands_and_nodes() (in module pipeliner.api.manage_project) get_continue_status() (pipeliner.jobstar_reader.JobStar method) get_current_output_nodes() (pipeliner.pipeliner_job.PipelinerJob method) get_downstream_network() (pipeliner.project_graph.ProjectGraph method) get_extra_options() (pipeliner.pipeliner_job.PipelinerJob method) get_job_info() (in module pipeliner.api.api_utils) get_job_metadata() (in module pipeliner.metadata_tools) (pipeliner.api.manage_project.PipelinerProject method) get_job_runtime() (pipeliner.api.manage_project.PipelinerProject method)

get_job_type() (in module pipeliner.jobstar_reader) get_job_vers() (pipeliner.pipeliner_job.PipelinerJob method) get_joboption() (in module pipeliner.jobstar_reader) get_jobtype() (pipeliner.jobstar_reader.JobStar method) get_metadata_chain() (in module pipeliner.metadata_tools) get_network_metadata() (pipeliner.api.manage_project.PipelinerProject method) get_node_name() (pipeliner.project_graph.ProjectGraph method) get_output_nodes() (pipeliner.jobstar_reader.OutputNodeStar method) get_output_nodes_from_starfile() (pipeliner.project_graph.ProjectGraph method) get_pipeline_edges() (pipeliner.project_graph.ProjectGraph method) get_pipeline_filename() (pipeliner.project_graph.ProjectGraph method) get_pipeliner_root() (in module pipeliner.utils) get_process_results_display() (pipeliner.project_graph.ProjectGraph method) get_reference_list() (in module pipeliner.metadata_tools) get_runtab_options() (pipeliner.pipeliner_job.PipelinerJob method) get_upstream_network() (pipeliner.project_graph.ProjectGraph method) get_whole_project_network() (pipeliner.project_graph.ProjectGraph method) graph (pipeliner.job_runner.JobRunner attribute)

H

has_been_converted (pipeliner.jobstar_reader.StarfileCheck attribute)

has_been_corrected (pipeliner.jobstar_reader.StarfileCheck attribute)

I

import_jobs() (pipeliner.project_graph.ProjectGraph method) initialise_pipeline() (pipeliner.pipeliner_job.PipelinerJob method) initialize_existing_project() (pipeliner.api.manage_project.PipelinerProject method) input_for_processes_list (pipeliner.data_structure.Node attribute) input_nodes (pipeliner.data_structure.Process attribute) (pipeliner.pipeliner_job.PipelinerJob attribute)

is_continue (pipeliner.pipeliner_job.PipelinerJob attribute) is_empty() (pipeliner.project_graph.ProjectGraph method) is_mpi (pipeliner.pipeliner_job.PipelinerJob attribute) is_pipeline (pipeliner.jobstar_reader.StarfileCheck attribute) is_tomo (pipeliner.pipeliner_job.PipelinerJob attribute) issue (pipeliner.pipeliner_job.Ref attribute)

J

job_author (pipeliner.pipeliner_job.JobInfo attribute) job_counter (pipeliner.project_graph.ProjectGraph attribute) job_from_dict() (in module pipeliner.job_factory) job_parameters_dict() (in module pipeliner.api.api_utils) job_success() (in module pipeliner.api.api_utils) JobInfo (class in pipeliner.pipeliner_job)

jobinfo (pipeliner.pipeliner_job.PipelinerJob attribute) joboptions (pipeliner.pipeliner_job.PipelinerJob attribute) JobRunner (class in pipeliner.job_runner) jobs (pipeliner.jobstar_reader.ExportStar attribute) (pipeliner.jobstar_reader.OutputNodeStar attribute) JobStar (class in pipeliner.jobstar_reader) journal (pipeliner.pipeliner_job.Ref attribute)

K

kwds (pipeliner.data_structure.Node attribute)

L

long_desc (pipeliner.pipeliner_job.JobInfo attribute)

look_for_project() (in module pipeliner.api.manage_project)

M

make_additional_args() (pipeliner.pipeliner_job.PipelinerJob method) make_default_results_schema() (in module pipeliner.metadata_tools) make_job_parameters_schema() (in module pipeliner.metadata_tools) make_pretty_header() (in module pipeliner.utils) make_process_flowchart() (pipeliner.flowchart_illustration.ProcessFlowchart method) make_queue_options() (pipeliner.pipeliner_job.PipelinerJob method) modify_jobstar() (in module pipeliner.jobstar_reader) module pipeliner.api.api_utils pipeliner.api.manage_project pipeliner.data_structure pipeliner.flowchart_illustration pipeliner.job_factory pipeliner.job_runner pipeliner.jobstar_reader pipeliner.metadata_tools pipeliner.pipeliner_job pipeliner.project_graph pipeliner.star_writer pipeliner.utils

N

name (pipeliner.data_structure.Node attribute) (pipeliner.data_structure.Process attribute) (pipeliner.project_graph.ProjectGraph attribute)

new_job_of_type() (in module pipeliner.job_factory) Node (class in pipeliner.data_structure) node_list (pipeliner.project_graph.ProjectGraph attribute)

O

options (pipeliner.jobstar_reader.JobStar attribute) other_metadata (pipeliner.pipeliner_job.Ref attribute) OUT_DIR (pipeliner.pipeliner_job.PipelinerJob attribute) outdir (pipeliner.data_structure.Process attribute)

output_from_process (pipeliner.data_structure.Node attribute) output_name (pipeliner.pipeliner_job.PipelinerJob attribute) output_nodes (pipeliner.data_structure.Process attribute) (pipeliner.pipeliner_job.PipelinerJob attribute) OutputNodeStar (class in pipeliner.jobstar_reader)

P

p_type (pipeliner.data_structure.Process attribute) pages (pipeliner.pipeliner_job.Ref attribute) parameter_validation() (pipeliner.pipeliner_job.PipelinerJob method) parse_additional_args() (pipeliner.pipeliner_job.PipelinerJob method) parse_proclist() (pipeliner.api.manage_project.PipelinerProject method) parse_procname() (pipeliner.api.manage_project.PipelinerProject method) pipeline (pipeliner.api.manage_project.PipelinerProject attribute) (pipeliner.flowchart_illustration.ProcessFlowchart attribute) pipeline_info (pipeliner.jobstar_reader.JobStar attribute) pipeline_name (pipeliner.api.manage_project.PipelinerProject attribute) pipeliner.api.api_utils module pipeliner.api.manage_project module pipeliner.data_structure module pipeliner.flowchart_illustration module pipeliner.job_factory module pipeliner.job_runner module pipeliner.jobstar_reader module pipeliner.metadata_tools module

pipeliner.pipeliner_job module pipeliner.project_graph module pipeliner.star_writer module pipeliner.utils module PipelinerJob (class in pipeliner.pipeliner_job) PipelinerProject (class in pipeliner.api.manage_project) post_run_actions() (pipeliner.pipeliner_job.PipelinerJob method) prepare_archive() (pipeliner.project_graph.ProjectGraph method) prepare_clean_up_lists() (pipeliner.pipeliner_job.PipelinerJob method) prepare_final_command() (pipeliner.pipeliner_job.PipelinerJob method) prepare_job_to_run() (pipeliner.job_runner.JobRunner method) prepare_onedep_data() (pipeliner.pipeliner_job.PipelinerJob method) print_nice_columns() (in module pipeliner.utils) Process (class in pipeliner.data_structure) process (pipeliner.flowchart_illustration.ProcessFlowchart attribute) process_list (pipeliner.project_graph.ProjectGraph attribute) PROCESS_NAME (pipeliner.pipeliner_job.PipelinerJob attribute) ProcessFlowchart (class in pipeliner.flowchart_illustration) programs (pipeliner.pipeliner_job.JobInfo attribute) project_name (pipeliner.api.manage_project.PipelinerProject attribute) ProjectGraph (class in pipeliner.project_graph)

Q

quotate_command_list() (in module pipeliner.utils)

R

read() (pipeliner.pipeliner_job.PipelinerJob method) (pipeliner.project_graph.ProjectGraph method) read_job() (in module pipeliner.job_factory) Ref (class in pipeliner.pipeliner_job) references (pipeliner.pipeliner_job.JobInfo attribute) RelionStarFile (class in pipeliner.jobstar_reader) remake_node_directory() (pipeliner.project_graph.ProjectGraph method)

remove_lock() (pipeliner.project_graph.ProjectGraph method) replace_files_for_import_export_of_sched_jobs() (pipeliner.project_graph.ProjectGraph method) run_cleanup() (pipeliner.api.manage_project.PipelinerProject method) run_job() (pipeliner.api.manage_project.PipelinerProject method) (pipeliner.job_runner.JobRunner method) run_schedule() (pipeliner.api.manage_project.PipelinerProject method) run_scheduled_jobs() (pipeliner.job_runner.JobRunner method)

S

save (pipeliner.flowchart_illustration.ProcessFlowchart attribute) save_job_submission_script() (pipeliner.pipeliner_job.PipelinerJob method) schedule_continue_job() (pipeliner.api.manage_project.PipelinerProject method) schedule_fail() (pipeliner.job_runner.JobRunner method) schedule_job() (pipeliner.api.manage_project.PipelinerProject method) (pipeliner.job_runner.JobRunner method) set_alias() (pipeliner.api.manage_project.PipelinerProject method) set_job_alias() (pipeliner.project_graph.ProjectGraph method) set_name() (pipeliner.project_graph.ProjectGraph method)

set_option() (pipeliner.pipeliner_job.PipelinerJob method) short_desc (pipeliner.pipeliner_job.JobInfo attribute) show (pipeliner.flowchart_illustration.ProcessFlowchart attribute) smart_strip_quotes() (in module pipeliner.utils) software_vers (pipeliner.pipeliner_job.JobInfo attribute) star_loop_as_list() (in module pipeliner.jobstar_reader) star_pairs_as_dict() (in module pipeliner.jobstar_reader) StarfileCheck (class in pipeliner.jobstar_reader) status (pipeliner.data_structure.Process attribute) stop_schedule() (pipeliner.api.manage_project.PipelinerProject method)

T

title (pipeliner.pipeliner_job.Ref attribute) touch() (in module pipeliner.utils) touch_temp_node_file() (pipeliner.project_graph.ProjectGraph method)

touch_temp_node_files() (pipeliner.project_graph.ProjectGraph method) truncate_number() (in module pipeliner.utils) type (pipeliner.data_structure.Node attribute)

U

undelete_job() (pipeliner.api.manage_project.PipelinerProject method) (pipeliner.project_graph.ProjectGraph method) update_job_status() (pipeliner.api.manage_project.PipelinerProject method)

update_jobinfo_file() (in module pipeliner.project_graph) update_lock_message() (pipeliner.project_graph.ProjectGraph method) update_status() (pipeliner.project_graph.ProjectGraph method) upstream_process_graph() (pipeliner.flowchart_illustration.ProcessFlowchart method)

V

validate_dynamically_required_joboptions() (pipeliner.pipeliner_job.PipelinerJob method) validate_input_files() (pipeliner.pipeliner_job.PipelinerJob method) validate_joboptions() (pipeliner.pipeliner_job.PipelinerJob method) validate_starfile() (in module pipeliner.api.api_utils)

vers_com (pipeliner.pipeliner_job.PipelinerJob attribute) version (pipeliner.jobstar_reader.StarfileCheck attribute) (pipeliner.pipeliner_job.JobInfo attribute) volume (pipeliner.pipeliner_job.Ref attribute)

W

wait_for_queued_job_completion() (pipeliner.job_runner.JobRunner method) wrap_text() (in module pipeliner.utils) write() (in module pipeliner.star_writer) (pipeliner.project_graph.ProjectGraph method) write_default_jobstar() (in module pipeliner.api.api_utils)

write_default_runjob() (in module pipeliner.api.api_utils) write_jobstar() (in module pipeliner.star_writer) (pipeliner.pipeliner_job.PipelinerJob method) write_runjob() (pipeliner.pipeliner_job.PipelinerJob method) write_to_sched_log() (pipeliner.job_runner.JobRunner method) write_to_stream() (in module pipeliner.star_writer)

Y

year (pipeliner.pipeliner_job.Ref attribute)