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.maintenance module biomero.provenance module biomero.remote_shallower module

biomero.slurm_client module biomero.views module bring_listener_uptodate() (biomero.slurm_client.SlurmClient method) build_command() (in module biomero.remote_shallower)

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) completed_receipts() (in module biomero.remote_shallower) 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)

D

description (biomero.eventsourcing.WorkflowRun attribute)

E

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 attribute)

fail_workflow() (biomero.eventsourcing.WorkflowTracker method), [1] 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_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

image_spec() (in module biomero.remote_shallower) 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) is_terminal() (biomero.slurm_client.SlurmJob static 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

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)

M

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.eventsourcing biomero.maintenance biomero.provenance biomero.remote_shallower 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) 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)

P

params (biomero.eventsourcing.Task attribute) parse_docker_image_version() (biomero.slurm_client.SlurmClient method) 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)

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

Q

queue_metadata_refresh() (in module biomero.maintenance)

R

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) render_workflow_metadata() (in module biomero.provenance) 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) run() (in module biomero.remote_shallower) 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) shallow_results_on_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) storage_metadata_view() (in module biomero.provenance) str_to_class() (biomero.slurm_client.SlurmClient method) submit_result (biomero.slurm_client.SlurmJob attribute)

T

target_key (biomero.eventsourcing.Task.StorageProvenanceRecorded 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.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.slurm_client.SlurmJob attribute) task_name (biomero.eventsourcing.Task attribute) task_version (biomero.eventsourcing.Task attribute) tasks (biomero.eventsourcing.WorkflowRun 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)

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)

W

wait_for_completion() (biomero.slurm_client.SlurmJob method) wf_id (biomero.slurm_client.SlurmJob 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) WorkflowProgress (class in biomero.views)

WorkflowRun (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)