Index

A

add_job_id (biomero.eventsourcing.Task attribute) add_job_id() (biomero.eventsourcing.WorkflowTracker method), [1] add_result() (biomero.eventsourcing.Task method) (biomero.eventsourcing.WorkflowTracker method), [1]

add_task (biomero.eventsourcing.WorkflowRun attribute) add_task_to_workflow() (biomero.eventsourcing.WorkflowTracker method), [1]

B

biomero.eventsourcing module biomero.slurm_client module

biomero.views module bring_listener_uptodate() (biomero.slurm_client.SlurmClient method)

C

check_job_status() (biomero.slurm_client.SlurmClient method) cleanup() (biomero.slurm_client.SlurmJob method) cleanup_tmp_files() (biomero.slurm_client.SlurmClient method) command (biomero.eventsourcing.ResultDict attribute) complete_task (biomero.eventsourcing.Task attribute) complete_task() (biomero.eventsourcing.WorkflowTracker method), [1]

complete_workflow (biomero.eventsourcing.WorkflowRun attribute) complete_workflow() (biomero.eventsourcing.WorkflowTracker method), [1] completed() (biomero.slurm_client.SlurmJob method) convert_cytype_to_omtype() (biomero.slurm_client.SlurmClient method) convert_url() (biomero.slurm_client.SlurmClient method) copy_zip_locally() (biomero.slurm_client.SlurmClient method)

D

description (biomero.eventsourcing.WorkflowRun attribute)

E

env (biomero.eventsourcing.ResultDict attribute) error_message (biomero.slurm_client.SlurmJob attribute)

extract_data_location_from_log() (biomero.slurm_client.SlurmClient method) extract_job_id() (biomero.slurm_client.SlurmClient method) extract_parts_from_url() (biomero.slurm_client.SlurmClient method)

F

fail_task (biomero.eventsourcing.Task attribute) fail_task() (biomero.eventsourcing.WorkflowTracker method), [1]

fail_workflow (biomero.eventsourcing.WorkflowRun attribute) fail_workflow() (biomero.eventsourcing.WorkflowTracker method), [1] from_config() (biomero.slurm_client.SlurmClient class method)

G

generate_slurm_job_for_workflow() (biomero.slurm_client.SlurmClient method) get_active_job_progress() (biomero.slurm_client.SlurmClient method) get_all_image_versions_and_data_files() (biomero.slurm_client.SlurmClient method) get_average_task_duration() (biomero.views.WorkflowAnalytics method) get_cellpose_command() (biomero.slurm_client.SlurmClient method) get_conversion_command() (biomero.slurm_client.SlurmClient method) get_error() (biomero.slurm_client.SlurmJob method) get_image_versions_and_data_files() (biomero.slurm_client.SlurmClient method) get_job_status_command() (biomero.slurm_client.SlurmClient method) get_jobs() (biomero.views.JobAccounting method) get_jobs_info_command() (biomero.slurm_client.SlurmClient method) get_listeners() (biomero.slurm_client.SlurmClient method)

get_logfile_from_slurm() (biomero.slurm_client.SlurmClient method) get_or_create_github_session() (biomero.slurm_client.SlurmClient method) get_recent_log_command() (biomero.slurm_client.SlurmClient method) get_task_counts() (biomero.views.WorkflowAnalytics method) get_task_failures() (biomero.views.WorkflowAnalytics method) get_task_id() (biomero.views.JobAccounting method) get_task_usage_over_time() (biomero.views.WorkflowAnalytics method) get_unzip_command() (biomero.slurm_client.SlurmClient method) get_update_slurm_scripts_command() (biomero.slurm_client.SlurmClient method) get_workflow_command() (biomero.slurm_client.SlurmClient method) get_workflow_parameters() (biomero.slurm_client.SlurmClient method) get_zip_command() (biomero.slurm_client.SlurmClient method) group (biomero.eventsourcing.WorkflowRun attribute)

I

init_workflows() (biomero.slurm_client.SlurmClient method) INITIAL_VERSION (biomero.eventsourcing.Task attribute) (biomero.eventsourcing.WorkflowRun attribute)

initialize_analytics_system() (biomero.slurm_client.SlurmClient method) initiate_workflow() (biomero.eventsourcing.WorkflowTracker method), [1] input_data (biomero.eventsourcing.Task attribute)

J

job_id (biomero.slurm_client.SlurmJob attribute) job_ids (biomero.eventsourcing.Task attribute)

job_state (biomero.slurm_client.SlurmJob attribute) JobAccounting (class in biomero.views) JobProgress (class in biomero.views)

L

list_active_jobs() (biomero.slurm_client.SlurmClient method) list_all_jobs() (biomero.slurm_client.SlurmClient method)

list_available_converter_versions() (biomero.slurm_client.SlurmClient method) list_completed_jobs() (biomero.slurm_client.SlurmClient method)

M

module biomero.eventsourcing biomero.slurm_client biomero.views

N

name (biomero.eventsourcing.WorkflowRun attribute) (biomero.eventsourcing.WorkflowTracker attribute) (biomero.views.JobAccounting attribute) (biomero.views.JobProgress attribute) (biomero.views.WorkflowAnalytics attribute) (biomero.views.WorkflowProgress attribute)

NoOpWorkflowTracker (class in biomero.eventsourcing)

O

ok (biomero.slurm_client.SlurmJob attribute)

P

params (biomero.eventsourcing.Task attribute) parse_docker_image_version() (biomero.slurm_client.SlurmClient method) policy() (biomero.views.JobAccounting method) (biomero.views.JobProgress method) (biomero.views.WorkflowAnalytics method) (biomero.views.WorkflowProgress method)

progress (biomero.slurm_client.SlurmJob attribute) pull_descriptor_from_github() (biomero.slurm_client.SlurmClient method)

R

result_message (biomero.eventsourcing.Task attribute) ResultDict (class in biomero.eventsourcing) results (biomero.eventsourcing.Task attribute) run_commands() (biomero.slurm_client.SlurmClient method)

run_commands_split_out() (biomero.slurm_client.SlurmClient method) run_conversion_workflow_job() (biomero.slurm_client.SlurmClient method) run_workflow() (biomero.slurm_client.SlurmClient method) run_workflow_job() (biomero.slurm_client.SlurmClient method)

S

setup_container_images() (biomero.slurm_client.SlurmClient method) setup_converters() (biomero.slurm_client.SlurmClient method) setup_directories() (biomero.slurm_client.SlurmClient method) setup_job_scripts() (biomero.slurm_client.SlurmClient method) setup_listeners() (biomero.slurm_client.SlurmClient method) setup_slurm() (biomero.slurm_client.SlurmClient method) slurm_converters_path (biomero.slurm_client.SlurmClient attribute) slurm_data_path (biomero.slurm_client.SlurmClient attribute) slurm_images_path (biomero.slurm_client.SlurmClient attribute) slurm_model_images (biomero.slurm_client.SlurmClient attribute) slurm_model_paths (biomero.slurm_client.SlurmClient attribute) slurm_model_repos (biomero.slurm_client.SlurmClient attribute) SLURM_POLLING_INTERVAL (biomero.slurm_client.SlurmJob attribute)

slurm_polling_interval (biomero.slurm_client.SlurmJob attribute) slurm_script_path (biomero.slurm_client.SlurmClient attribute) slurm_script_repo (biomero.slurm_client.SlurmClient attribute) SlurmClient (class in biomero.slurm_client) SlurmJob (class in biomero.slurm_client) start_task (biomero.eventsourcing.Task attribute) start_task() (biomero.eventsourcing.WorkflowTracker method), [1] start_workflow (biomero.eventsourcing.WorkflowRun attribute) start_workflow() (biomero.eventsourcing.WorkflowTracker method), [1] status (biomero.eventsourcing.Task attribute) stderr (biomero.eventsourcing.ResultDict attribute) stdout (biomero.eventsourcing.ResultDict attribute) str_to_class() (biomero.slurm_client.SlurmClient method) submit_result (biomero.slurm_client.SlurmJob attribute)

T

Task (class in biomero.eventsourcing) Task.Created (class in biomero.eventsourcing) Task.Event (class in biomero.eventsourcing) Task.JobIdAdded (class in biomero.eventsourcing) Task.ProgressUpdated (class in biomero.eventsourcing) Task.ResultAdded (class in biomero.eventsourcing) Task.StatusUpdated (class in biomero.eventsourcing) Task.TaskCompleted (class in biomero.eventsourcing)

Task.TaskCreated (class in biomero.eventsourcing) Task.TaskFailed (class in biomero.eventsourcing) Task.TaskStarted (class in biomero.eventsourcing) task_id (biomero.slurm_client.SlurmJob attribute) task_name (biomero.eventsourcing.Task attribute) task_version (biomero.eventsourcing.Task attribute) tasks (biomero.eventsourcing.WorkflowRun attribute) transfer_data() (biomero.slurm_client.SlurmClient method)

U

unpack_data() (biomero.slurm_client.SlurmClient method) update_slurm_scripts() (biomero.slurm_client.SlurmClient method) update_task_progress (biomero.eventsourcing.Task attribute) update_task_progress() (biomero.eventsourcing.WorkflowTracker method), [1] update_task_status (biomero.eventsourcing.Task attribute)

update_task_status() (biomero.eventsourcing.WorkflowTracker method), [1] update_view_table() (biomero.views.JobAccounting method) (biomero.views.JobProgress method) (biomero.views.WorkflowAnalytics method) (biomero.views.WorkflowProgress method) user (biomero.eventsourcing.WorkflowRun attribute)

V

validate() (biomero.slurm_client.SlurmClient method)

W

wait_for_completion() (biomero.slurm_client.SlurmJob method) wf_id (biomero.slurm_client.SlurmJob attribute) workflow_id (biomero.eventsourcing.Task attribute) workflow_params_to_envvars() (biomero.slurm_client.SlurmClient method) workflow_params_to_subs() (biomero.slurm_client.SlurmClient method) WorkflowAnalytics (class in biomero.views) WorkflowProgress (class in biomero.views) WorkflowRun (class in biomero.eventsourcing)

WorkflowRun.Created (class in biomero.eventsourcing) WorkflowRun.Event (class in biomero.eventsourcing) WorkflowRun.TaskAdded (class in biomero.eventsourcing) WorkflowRun.WorkflowCompleted (class in biomero.eventsourcing) WorkflowRun.WorkflowFailed (class in biomero.eventsourcing) WorkflowRun.WorkflowInitiated (class in biomero.eventsourcing) WorkflowRun.WorkflowStarted (class in biomero.eventsourcing) WorkflowTracker (class in biomero.eventsourcing)

Z

zip_data_on_slurm_server() (biomero.slurm_client.SlurmClient method)