OCDocker.Workbench.Planner module

Command-planning helpers for workbench specs.

OCDocker.Workbench.Planner.build_run_manifest(spec, plan, *, run_id, status='defined', workspace=None)[source]

Create an initial run manifest from a spec and command plan.

Parameters:

  • spec (WorkbenchSpec) – Input value.

  • plan (PlannedCommand) – Input value.

  • run_id (str) – Input value.

  • status (RunStatus) – Input value.

  • workspace (str | Path | None) – Input value.

Returns:

Returned value.

Return type:

RunManifest

OCDocker.Workbench.Planner.plan_command(spec, *, ocdocker_executable='ocdocker', snakemake_executable='snakemake')[source]

Dispatch command planning for any supported workbench spec.

Parameters:

  • spec (WorkbenchSpec) – Input value.

  • ocdocker_executable (str) – Input value.

  • snakemake_executable (str) – Input value.

Returns:

Returned value.

Return type:

PlannedCommand

OCDocker.Workbench.Planner.plan_ocscore_train_command(spec, *, executable='ocdocker')[source]

Build an ocdocker ocscore train command plan without running it.

Parameters:

  • spec (OCScoreStudySpec | OCScoreAblationSpec) – Input value.

  • executable (str) – Input value.

Returns:

Returned value.

Return type:

PlannedCommand

OCDocker.Workbench.Planner.plan_snakemake_command(workflow, *, executable='snakemake')[source]

Build a Snakemake command plan without executing the workflow.

Parameters:

  • workflow (SnakemakeWorkflowSpec) – Input value.

  • executable (str) – Input value.

Returns:

Returned value.

Return type:

PlannedCommand

OCDocker.Workbench.Planner.plan_vs_campaign_command(spec, *, executable='snakemake')[source]

Build a Snakemake command plan for a VS campaign spec.

Parameters:

  • spec (VSCampaignSpec) – Input value.

  • executable (str) – Input value.

Returns:

Returned value.

Return type:

PlannedCommand