Index

Symbols

$HOME

_

__init__() (jip.options.Options method) (jip.tools.Tool method)

A

account (jip.db.Job attribute), [1] add() (jip.options.Options method) (jip.pipelines.Pipeline method) add_edge() (jip.pipelines.Pipeline method) add_folder() (jip.tools.Scanner method) add_input() (jip.options.Options method) add_link() (jip.pipelines.Edge method) add_module() (jip.tools.Scanner method) add_option() (jip.options.Options method)

add_output() (jip.options.Options method) additional_options (jip.db.Job attribute) append() (jip.options.Option method) apply() (jip.profiles.Profile method) apply_overwrite() (jip.profiles.Profile method) apply_to_pipeline() (jip.profiles.Profile method) archived (jip.db.Job attribute), [1] args (jip.tools.Tool attribute)

B

bash() (jip.pipelines.Job method) (jip.pipelines.Pipeline method) (jip.tools.PythonBlockUtils method)

C

cancel() (in module jip.jobs) (jip.cluster.Cluster method) check_file() (jip.options.Option method) (jip.tools.PythonBlockUtils method) (jip.tools.Tool method) check_files() (jip.options.Option method) check_output_files() (in module jip.jobs) check_queued_jobs() (in module jip.jobs) children (jip.db.Job attribute) children() (jip.pipelines.Node method) clean() (in module jip.jobs) cleanup() (jip.tools.Tool method) clone() (jip.tools.Tool method) Cluster (class in jip.cluster) ClusterImplementationError colorize() (in module jip.cli) command (jip.db.Job attribute), [1]

commit_session() (in module jip.db) Config (class in jip.configuration) configuration (jip.db.Job attribute), [1] confirm() (in module jip.cli) context() (jip.pipelines.Pipeline method) copy() (jip.options.Option method) create_date (jip.db.Job attribute), [1] create_dispatcher_graph() (in module jip.executils) create_executions() (in module jip.jobs) create_groups() (in module jip.jobs) create_job_env() (in module jip.jobs) create_jobs() (in module jip.jobs) create_session() (in module jip.db) create_table() (in module jip.cli)

D

delete() (in module jip.db) (in module jip.jobs) dependencies (jip.db.Job attribute), [1] depends_on() (jip.pipelines.Node method)

dir (jip.profiles.Profile attribute) DispatcherNode (class in jip.executils) dry() (in module jip.cli)

E

Edge (class in jip.pipelines) edges (jip.pipelines.Pipeline attribute) ensure() (jip.tools.Tool method) env (jip.db.Job attribute), [1] environment (in module jip.templates) (jip.db.Job attribute), [1] environment variable $HOME JIP_CONFIG JIP_DB JIP_MODULES, [1], [2] JIP_PATH, [1] PATH PYTHONPATH

err (jip.profiles.Profile attribute) exclude() (jip.pipelines.Pipeline method) expand() (jip.options.Option method) (jip.pipelines.Pipeline method) ext_filter() (in module jip.templates) extra (jip.db.Job attribute), [1]

F

find() (jip.tools.Scanner method) finish_date (jip.db.Job attribute), [1] flat_list() (in module jip.utils) from_argparse() (jip.options.Options class method) from_dict() (jip.profiles.Profile class method)

from_docopt() (jip.options.Options class method) from_file() (jip.profiles.Profile class method) from_job() (jip.profiles.Profile class method) from_node() (in module jip.jobs)

G

get() (in module jip.cluster) (in module jip.db) (in module jip.profiles) (jip.configuration.Config method) (jip.options.Option method) (jip.pipelines.Pipeline method) get_active_jobs() (in module jip.db) get_all() (in module jip.db) get_by_type() (jip.options.Options method) get_cluster_command() (jip.db.Job method), [1] get_command() (jip.tools.Tool method) get_current_state() (in module jip.db) get_default_input() (jip.options.Options method) get_default_output() (jip.options.Options method) get_edge() (jip.pipelines.Pipeline method) get_incoming_link() (jip.pipelines.Node method) get_input_files() (jip.db.Job method) (jip.tools.Tool method) get_opt() (jip.options.Option method) get_outgoing_link() (jip.pipelines.Node method)

get_output_files() (jip.db.Job method), [1] (jip.tools.Tool method) get_parents() (in module jip.jobs) get_pipe_parent() (in module jip.jobs) get_pipe_targets() (jip.db.Job method), [1] get_specs() (in module jip.profiles) get_stream_input() (jip.pipelines.Node method) get_streaming_link() (jip.pipelines.Edge method) get_subgraph() (in module jip.jobs) glob() (jip.options.Option method) glob_inputs() (jip.options.Options method) group() (jip.pipelines.Node method) group_from (jip.db.Job attribute) group_to (jip.db.Job attribute) groups() (jip.pipelines.Pipeline method)

H

has_incoming() (jip.pipelines.Node method) has_outgoing() (jip.pipelines.Node method) has_streaming_link() (jip.pipelines.Edge method)

help() (jip.options.Options method) (jip.tools.Tool method) hold() (in module jip.jobs) hosts (jip.db.Job attribute), [1]

I

id (jip.db.Job attribute), [1] ignored() (in module jip.utils) in_files (jip.db.Job attribute) incoming() (jip.pipelines.Node method) init() (in module jip.db) (jip.tools.Tool method) interpreter (jip.db.Job attribute), [1]

is_dependency() (jip.options.Option method) is_done() (jip.db.Job method), [1] (jip.tools.Tool method) is_list() (jip.options.Option method) is_stream() (jip.options.Option method) is_stream_source() (jip.db.Job method), [1] is_stream_target() (jip.db.Job method), [1]

J

jip.cli (module) jip.cluster (module) jip.configuration (module) jip.db (module) jip.executils (module) jip.jobs (module) jip.options (module) jip.pipelines (module) jip.profiles (module) jip.templates (module) jip.tools (module)

jip.utils (module) JIP_CONFIG JIP_DB JIP_MODULES, [1], [2] JIP_PATH, [1] JipUndefined (class in jip.templates) Job (class in jip.db) (class in jip.pipelines) job (jip.pipelines.Node attribute) job() (jip.pipelines.Pipeline method) (jip.tools.PythonBlockUtils method) job_id (jip.db.Job attribute), [1]

K

keep_on_fail (jip.db.Job attribute), [1]

L

list() (jip.cluster.Cluster method) list_dir() (in module jip.utils) load() (jip.profiles.Profile method)

load_args() (jip.profiles.Profile method) LSF (class in jip.cluster)

M

make_absolute() (jip.options.Option method) (jip.options.Options method) max_memory (jip.db.Job attribute), [1]

max_time (jip.db.Job attribute), [1] merge() (jip.profiles.Profile method)

N

name (jip.db.Job attribute), [1] (jip.pipelines.Job attribute) (jip.pipelines.Node attribute) (jip.profiles.Profile attribute) name() (jip.pipelines.Pipeline method) (jip.tools.PythonBlockUtils method) Node (class in jip.pipelines)

nodes (jip.db.Job attribute), [1] nodes() (jip.pipelines.Pipeline method)

O

on_success (jip.db.Job attribute) on_success() (jip.pipelines.Node method) Option (class in jip.options) Options (class in jip.options)

options (jip.tools.Tool attribute) out_files (jip.db.Job attribute) outgoing() (jip.pipelines.Node method)

P

parent_filter() (in module jip.templates) parents() (jip.pipelines.Node method) parse() (jip.options.Options method) parse_args() (in module jip.cli) (jip.tools.Tool method) parse_job_ids() (in module jip.cli) parse_mem() (in module jip.utils) parse_time() (in module jip.utils) ParserException PATH path (jip.db.Job attribute), [1] (jip.tools.Tool attribute) PBS (class in jip.cluster) pipe_form (jip.db.Job attribute) pipe_targets (jip.db.Job attribute), [1] pipe_to (jip.db.Job attribute)

Pipeline (class in jip.pipelines) pipeline (class in jip.tools) (jip.db.Job attribute), [1] pipeline() (jip.tools.Tool method) pipeline_name (jip.db.Job attribute) pipeline_name() (jip.pipelines.Node method) (jip.pipelines.Pipeline method) priority (jip.db.Job attribute), [1] Profile (class in jip.profiles) project (jip.db.Job attribute), [1] PythonBlock (class in jip.tools) PythonBlockUtils (class in jip.tools) PYTHONPATH PythonTool (class in jip.tools) pytool (class in jip.tools)

Q

query() (in module jip.db) query_by_files() (in module jip.db)

queue (jip.db.Job attribute), [1]

R

raw() (jip.options.Option method) read_ids_from_pipe() (in module jip.cli) remove() (jip.pipelines.Pipeline method) remove_links() (jip.pipelines.Edge method) render_table() (in module jip.cli) render_template() (in module jip.templates) RenderError replace_filter() (in module jip.templates)

resolve_job_range() (in module jip.cli) resolve_jobs() (in module jip.jobs) resolve_log() (jip.cluster.Cluster method) restore_configuration() (jip.db.Job method) rreplace() (in module jip.utils) run() (jip.db.Job method), [1] (jip.executils.DispatcherNode method) (jip.pipelines.Job method) (jip.pipelines.Pipeline method) (jip.tools.PythonBlock method) (jip.tools.PythonBlockUtils method) run_job() (in module jip.jobs)

S

save() (in module jip.db) scan() (jip.tools.Scanner method) scan_files() (jip.tools.Scanner method) scan_modules() (jip.tools.Scanner method) Scanner (class in jip.tools) ScriptTool (class in jip.tools) set() (jip.options.Option method) (jip.pipelines.Node method) (jip.tools.PythonBlockUtils method) set_state() (in module jip.jobs) setup() (jip.tools.Tool method) SGE (class in jip.cluster) show_commands() (in module jip.cli) show_dry() (in module jip.cli) show_job_profiles() (in module jip.cli) show_job_states() (in module jip.cli) show_job_tree() (in module jip.cli) show_options() (in module jip.cli) skip() (jip.pipelines.Pipeline method)

Slurm (class in jip.cluster) specs (in module jip.profiles) start_date (jip.db.Job attribute), [1] state (jip.db.Job attribute), [1] STATE_CANCELED (in module jip.db) STATE_COLORS (in module jip.cli) STATE_DONE (in module jip.db) STATE_FAILED (in module jip.db) STATE_HOLD (in module jip.db) STATE_QUEUED (in module jip.db) STATE_RUNNING (in module jip.db) stderr (jip.db.Job attribute), [1] stdout (jip.db.Job attribute), [1] SubmissionError submit() (jip.cluster.Cluster method) submit_job() (in module jip.jobs)

T

table_to_string() (in module jip.cli) tasks (jip.db.Job attribute), [1] tasks_per_node (jip.db.Job attribute), [1] temp (jip.db.Job attribute), [1] terminate() (jip.db.Job method), [1] (jip.tools.PythonBlock method) threads (jip.db.Job attribute), [1] to_cmd() (jip.options.Option method) (jip.options.Options method) to_dict() (jip.options.Options method)

Tool (class in jip.tools) tool (class in jip.tools) (jip.db.Job attribute), [1] tool_name (jip.db.Job attribute), [1] ToolNotFoundException topological_order() (in module jip.jobs) (jip.pipelines.Pipeline method) TYPE_INPUT (in module jip.options) TYPE_OPTION (in module jip.options) TYPE_OUTPUT (in module jip.options)

U

update() (jip.cluster.Cluster method) (jip.profiles.Profile method) update_archived() (in module jip.db) update_job_states() (in module jip.db)

usage() (jip.options.Options method) user (jip.db.Job attribute), [1]

V

validate() (jip.db.Job method), [1] (jip.options.Option method) (jip.options.Options method) (jip.pipelines.Pipeline method) (jip.tools.Tool method) validation_error() (jip.tools.PythonBlockUtils method) (jip.tools.Tool method)

ValidationError value (jip.options.Option attribute)

W

wait() (jip.executils.DispatcherNode method)

working_directory (jip.db.Job attribute), [1]