Index

A

add_job_id (biomero.eventsourcing.Task attribute) add_job_id() (biomero.eventsourcing.WorkflowTracker method), [1] add_launcher_task() (biomero.eventsourcing.WorkflowTracker method) 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] atomic_get() (in module biomero.ssh_recovery) atomic_put() (in module biomero.ssh_recovery)

B

biomero.detached module biomero.eventsourcing module biomero.maintenance module biomero.provenance module biomero.remote_scripts module biomero.remote_shallower module

biomero.slurm_client module biomero.ssh_recovery module biomero.views module bounded_read_timeout() (in module biomero.ssh_recovery) bring_listener_uptodate() (biomero.slurm_client.SlurmClient method) build_helper_command() (in module biomero.remote_shallower) build_sbatch_wrap_command() (biomero.slurm_client.SlurmClient method)

C

cancel_slurm_jobs() (biomero.slurm_client.SlurmClient method) check_job_status() (biomero.slurm_client.SlurmClient method) check_remote_commands_available() (biomero.slurm_client.SlurmClient method) claim_launcher (biomero.eventsourcing.Task attribute) claim_launcher_task() (biomero.eventsourcing.WorkflowTracker method) claimed_at (biomero.eventsourcing.Task attribute) claimed_by (biomero.eventsourcing.Task attribute) cleanup() (biomero.slurm_client.SlurmJob method) cleanup_tmp_files() (biomero.slurm_client.SlurmClient method) command (biomero.eventsourcing.ResultDict attribute) commit_open_transaction() (biomero.eventsourcing.WorkflowTracker method)

complete_task (biomero.eventsourcing.Task attribute) complete_task() (biomero.eventsourcing.WorkflowTracker method), [1] complete_workflow() (biomero.eventsourcing.WorkflowRun method) (biomero.eventsourcing.WorkflowTracker method), [1] completed (biomero.eventsourcing.Task attribute) completed() (biomero.slurm_client.SlurmJob method) completed_receipts() (in module biomero.remote_shallower) contract_version (biomero.remote_shallower.HelperSettings attribute) convert_param_type_to_omtype() (biomero.slurm_client.SlurmClient method) convert_url() (biomero.slurm_client.SlurmClient method) copy_zip_locally() (biomero.slurm_client.SlurmClient method) create_then_publish_script() (in module biomero.remote_scripts)

D

delay (biomero.ssh_recovery.OutageWindow attribute) description (biomero.eventsourcing.WorkflowRun attribute)

detached_mode_enabled() (in module biomero.detached) download() (in module biomero.ssh_recovery)

E

ended_without_success() (biomero.slurm_client.SlurmJob static method) env (biomero.eventsourcing.ResultDict attribute) error_message (biomero.slurm_client.SlurmJob attribute)

evidence (biomero.eventsourcing.Task.StorageProvenanceRecorded 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 method) (biomero.eventsourcing.WorkflowTracker method), [1]

failed (biomero.eventsourcing.Task attribute) find_launcher_task() (biomero.eventsourcing.WorkflowTracker method) finished() (biomero.maintenance.MetadataRefresh method) from_config() (biomero.slurm_client.SlurmClient class method) from_job_id() (biomero.slurm_client.SlurmJob class method)

G

generate_slurm_job_for_workflow() (biomero.slurm_client.SlurmClient method) generic_descriptor_from_github() (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_authoritative_config_path() (biomero.slurm_client.SlurmClient class method) get_average_task_duration() (biomero.views.WorkflowAnalytics method) get_canonical_input_manifest() (biomero.eventsourcing.WorkflowTracker method) get_canonical_inputs() (biomero.eventsourcing.WorkflowTracker method) get_cellpose_command() (biomero.slurm_client.SlurmClient method) get_config_paths() (biomero.slurm_client.SlurmClient class method) get_config_write_path() (biomero.slurm_client.SlurmClient class method) get_conversion_command() (biomero.slurm_client.SlurmClient method) get_conversion_logfile_from_slurm() (biomero.slurm_client.SlurmClient method) get_error() (biomero.slurm_client.SlurmJob method) get_file_attachment_params() (biomero.slurm_client.SlurmClient method) get_image_pull_status() (biomero.slurm_client.SlurmClient method) get_image_versions_and_data_files() (biomero.slurm_client.SlurmClient method) get_job_params() (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_remote_shallower_receipts() (biomero.slurm_client.SlurmClient method) get_shallower_job_params() (biomero.slurm_client.SlurmClient method) get_submission_job_name() (biomero.slurm_client.SlurmClient static method) get_submission_state_prefix() (biomero.slurm_client.SlurmClient method) get_task() (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() (biomero.slurm_client.SlurmClient method) get_workflow_command() (biomero.slurm_client.SlurmClient method) get_workflow_parameters() (biomero.slurm_client.SlurmClient method) get_workflow_tasks() (biomero.slurm_client.SlurmClient method) get_zip_command() (biomero.slurm_client.SlurmClient method) group (biomero.eventsourcing.WorkflowRun attribute)

H

heartbeat_error (biomero.ssh_recovery.RecoveryState attribute) heartbeats (biomero.ssh_recovery.RecoveryState attribute)

helper_job_name() (in module biomero.remote_shallower) HelperJob (class in biomero.remote_shallower) HelperSettings (class in biomero.remote_shallower)

I

image (biomero.remote_shallower.HelperJob attribute) image_spec() (in module biomero.remote_shallower) IncompleteTransfer 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)

installed_tool_version() (in module biomero.remote_shallower) io_timeout() (in module biomero.ssh_recovery) is_claimed_by_other() (biomero.eventsourcing.Task method) is_finished() (biomero.maintenance.MetadataRefresh method) is_launcher_task() (in module biomero.eventsourcing) is_terminal() (biomero.slurm_client.SlurmJob static method) is_transient() (in module biomero.ssh_recovery) is_workflow_cancel_requested() (biomero.eventsourcing.WorkflowTracker method) is_workflow_finished() (biomero.eventsourcing.WorkflowTracker method) iter_workflow_tasks() (biomero.eventsourcing.WorkflowTracker method)

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

limit_channel_open() (in module biomero.ssh_recovery) 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) load_config() (biomero.slurm_client.SlurmClient class method) lock_wait_seconds (biomero.remote_shallower.HelperSettings attribute) locked_script() (in module biomero.remote_scripts)

M

manifest_path (biomero.remote_shallower.HelperJob attribute) manifest_schema (biomero.remote_shallower.HelperSettings attribute) metadata_refresh_statuses() (in module biomero.maintenance) MetadataAnnotation (class in biomero.provenance) MetadataChange (class in biomero.provenance) MetadataRefresh (class in biomero.maintenance) MetadataRefresh.Created (class in biomero.maintenance) MetadataRefresh.Event (class in biomero.maintenance) MetadataRefresh.Finished (class in biomero.maintenance) MetadataRefresh.Progress (class in biomero.maintenance)

MetadataRefresh.Started (class in biomero.maintenance) module biomero.detached biomero.eventsourcing biomero.maintenance biomero.provenance biomero.remote_scripts biomero.remote_shallower biomero.slurm_client biomero.ssh_recovery 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)

native_timeouts() (in module biomero.ssh_recovery) next_pause() (biomero.ssh_recovery.OutageWindow method) NoOpWorkflowTracker (class in biomero.eventsourcing)

O

ok (biomero.slurm_client.SlurmJob attribute) open() (biomero.slurm_client.SlurmClient method) originator_id_type (biomero.eventsourcing.Task.Created attribute) (biomero.eventsourcing.Task.Event attribute) (biomero.eventsourcing.Task.TaskCreated attribute) (biomero.eventsourcing.WorkflowRun.Created attribute) (biomero.eventsourcing.WorkflowRun.Event attribute) (biomero.eventsourcing.WorkflowRun.WorkflowInitiated attribute) (biomero.maintenance.MetadataRefresh.Created attribute) (biomero.maintenance.MetadataRefresh.Event attribute)

outage_deadline (biomero.ssh_recovery.OutageWindow attribute) OutageWindow (class in biomero.ssh_recovery) output_path (biomero.remote_shallower.HelperJob attribute)

P

params (biomero.eventsourcing.Task attribute) parse_batch_report() (in module biomero.remote_shallower) parse_docker_image_version() (biomero.slurm_client.SlurmClient method) pending_deadline (biomero.ssh_recovery.OutageWindow attribute) pending_metadata_refreshes() (in module biomero.maintenance) plan_metadata_refresh() (in module biomero.provenance) policy() (biomero.views.JobAccounting method) (biomero.views.JobProgress method) (biomero.views.WorkflowAnalytics method) (biomero.views.WorkflowProgress method)

polling_interval (biomero.remote_shallower.HelperSettings attribute) positive_job_ids() (biomero.slurm_client.SlurmClient static method) prepare_converters() (biomero.slurm_client.SlurmClient method) progress (biomero.slurm_client.SlurmJob attribute) progressed() (biomero.maintenance.MetadataRefresh method) publish_or_verify_manifest() (in module biomero.remote_shallower) pulse() (biomero.ssh_recovery.RecoveryState method)

Q

queue_metadata_refresh() (in module biomero.maintenance)

R

raise_if_cancel_requested() (biomero.eventsourcing.WorkflowTracker method) raise_if_cancelled() (biomero.ssh_recovery.RecoveryState static method) read_only() (in module biomero.ssh_recovery) ReadOnlyCommandTimeout record_canonical_inputs (biomero.eventsourcing.WorkflowRun attribute) record_canonical_inputs() (biomero.eventsourcing.WorkflowTracker method) record_storage_provenance (biomero.eventsourcing.Task attribute) record_storage_provenance() (biomero.eventsourcing.WorkflowTracker method) RecoveryPending RecoveryState (class in biomero.ssh_recovery) release_database_connections() (biomero.eventsourcing.WorkflowTracker method) release_launcher (biomero.eventsourcing.Task attribute) release_launcher_task() (biomero.eventsourcing.WorkflowTracker method) RemoteOperationStillPending remove_state_files_command() (in module biomero.remote_scripts) remove_submission_receipts() (biomero.slurm_client.SlurmClient method) render_workflow_metadata() (in module biomero.provenance) request_cancel (biomero.eventsourcing.WorkflowRun attribute) request_workflow_cancel() (biomero.eventsourcing.WorkflowTracker method)

resolve_metadata_versions() (in module biomero.provenance) resolve_task() (biomero.views.JobAccounting method) (biomero.views.WorkflowAnalytics method) (biomero.views.WorkflowProgress method) resolve_workflow() (biomero.views.JobAccounting method) (biomero.views.WorkflowAnalytics method) (biomero.views.WorkflowProgress method) result_message (biomero.eventsourcing.Task attribute) ResultDict (class in biomero.eventsourcing) results (biomero.eventsourcing.Task attribute) retry() (in module biomero.ssh_recovery) run_commands() (biomero.slurm_client.SlurmClient method) run_commands_read_only() (biomero.slurm_client.SlurmClient method) run_commands_split_out() (biomero.slurm_client.SlurmClient method) run_conversion_workflow_job() (biomero.slurm_client.SlurmClient method) run_once_script() (in module biomero.remote_scripts) run_read_only() (biomero.slurm_client.SlurmClient method) run_workflow() (biomero.slurm_client.SlurmClient method) run_workflow_job() (biomero.slurm_client.SlurmClient method)

S

scope() (in module biomero.ssh_recovery) seconds_left() (biomero.ssh_recovery.OutageWindow method) seconds_left_in_outage() (biomero.ssh_recovery.RecoveryState method) 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) sftp_timeout() (in module biomero.ssh_recovery) sha256_of_json() (in module biomero.remote_shallower) shallow_results_on_slurm() (biomero.slurm_client.SlurmClient method) shallow_workflow_results() (in module biomero.remote_shallower) sif_path (biomero.remote_shallower.HelperJob attribute) 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) SSHRecoveryCancelled SSHRecoveryTimeout start_if_new() (biomero.ssh_recovery.OutageWindow method) 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] started() (biomero.maintenance.MetadataRefresh method) state_dir (biomero.remote_shallower.HelperJob attribute) state_name() (biomero.slurm_client.SlurmJob static method) status (biomero.eventsourcing.Task attribute) stderr (biomero.eventsourcing.ResultDict attribute) stdout (biomero.eventsourcing.ResultDict attribute) storage_metadata_view() (in module biomero.provenance) str_to_class() (biomero.slurm_client.SlurmClient method) submit_job_once() (biomero.slurm_client.SlurmClient method) submit_once_script() (in module biomero.remote_scripts) submit_result (biomero.slurm_client.SlurmJob attribute)

T

target_key (biomero.eventsourcing.Task.StorageProvenanceRecorded attribute) task (biomero.remote_shallower.HelperJob attribute) Task (class in biomero.eventsourcing) Task.Created (class in biomero.eventsourcing) Task.Event (class in biomero.eventsourcing) Task.JobIdAdded (class in biomero.eventsourcing) Task.LauncherClaimed (class in biomero.eventsourcing) Task.LauncherReleased (class in biomero.eventsourcing) Task.ProgressUpdated (class in biomero.eventsourcing) Task.ResultAdded (class in biomero.eventsourcing) Task.StatusUpdated (class in biomero.eventsourcing) Task.StorageProvenanceRecorded (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.remote_shallower.HelperJob attribute) (biomero.slurm_client.SlurmJob attribute) task_name (biomero.eventsourcing.Task attribute) task_version (biomero.eventsourcing.Task attribute) tasks (biomero.eventsourcing.WorkflowRun attribute) timeout (biomero.ssh_recovery.OutageWindow attribute) (biomero.ssh_recovery.RecoveryState attribute) topics (biomero.views.JobAccounting attribute) (biomero.views.JobProgress attribute) (biomero.views.WorkflowAnalytics attribute) (biomero.views.WorkflowProgress attribute) tracker_repository() (in module biomero.views) transfer_data() (biomero.slurm_client.SlurmClient method) transient_reason() (in module biomero.ssh_recovery)

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)

validate_installed_tool() (in module biomero.remote_shallower) verify_task_canonical_inputs() (in module biomero.remote_shallower)

W

wait() (biomero.ssh_recovery.RecoveryState method) wait_for_completion() (biomero.slurm_client.SlurmJob method) wait_for_helper_job() (in module biomero.remote_shallower) wf_id (biomero.slurm_client.SlurmJob attribute) windows (biomero.ssh_recovery.RecoveryState attribute) workflow_bilayers_folder_params_to_subs() (biomero.slurm_client.SlurmClient method) workflow_id (biomero.eventsourcing.Task attribute) workflow_params_to_envvars() (biomero.slurm_client.SlurmClient method) workflow_params_to_subs() (biomero.slurm_client.SlurmClient method) workflow_template_subs() (biomero.slurm_client.SlurmClient method) WorkflowAnalytics (class in biomero.views) WorkflowCancelled

WorkflowInterrupted WorkflowProgress (class in biomero.views) WorkflowRun (class in biomero.eventsourcing) WorkflowRun.CancelRequested (class in biomero.eventsourcing) WorkflowRun.CanonicalInputsRecorded (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)