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ExecutionContext

Source: R/ExecutionSettings.R
ExecutionContext.Rd

Describes one Picard pipeline execution and derives the names used to isolate its database and filesystem outputs. This R6 class owns execution mode and pipeline version (the namespace).

Internal: constructed by the pipeline (execute_pipeline()) and by the settings/path helpers (createExecutionSettingsFromConfig(), setOutputFolder(), resolveResultsPath()). Study code and task files never construct it directly.

Methods

Public methods

Method new()

Usage

ExecutionContext$new(
  mode = c("test", "production"),
  pipelineVersion = "dev",
  studyVersion = NULL,
  baseCohortTable = NULL,
  databaseName = NULL,
  execPath = here::here("exec/results"),
  maxTableNameLength = MAX_TEST_COHORT_TABLE_NAME_LENGTH
)

Arguments

mode

Character. Either "test" or "production".

pipelineVersion

Character. The complete execution pipeline version. Defaults to "dev" for test executions. Test pipeline versions are normalized to lowercase snake case. Production pipeline versions are semantic versions, or the literal "prod" for a production run against the configured table whose version is not tracked.

studyVersion

Character or NULL. The study version associated with the execution. Required for a semantic-version production run; NULL for test runs and for pipelineVersion = "prod".

baseCohortTable

Character or NULL. The configured, unsuffixed cohort table. Optional for a run-scoped context shared by multiple database config blocks.

databaseName

Character or NULL. Human-readable database name used in result paths. Optional for a run-scoped context shared by multiple database config blocks.

execPath

Character. Base path for execution results. Defaults to exec/results in the current study project.

maxTableNameLength

Integer. Maximum permitted length of the derived cohort table name. Defaults to 60, a practical cross-database limit for test-derived names. Set to NULL to disable this package-level check.

Method getMode()

Usage

ExecutionContext$getMode()

Returns

Character. Execution mode, either "test" or "production".

Method getPipelineVersion()

Usage

ExecutionContext$getPipelineVersion()

Returns

Character. Normalized execution pipelineVersion.

Method getStudyVersion()

Usage

ExecutionContext$getStudyVersion()

Returns

Character or NULL. Associated production study version.

Method getCohortTable()

Usage

ExecutionContext$getCohortTable()

Returns

Character or NULL. Effective cohort table name for this execution, or NULL for a run-scoped context without a base table.

Method deriveCohortTable()

Apply this run's mode and namespace to a configured base cohort table. Production returns the base table unchanged; test appends the normalized pipeline version and enforces the table-name length ceiling before any database work.

Usage

ExecutionContext$deriveCohortTable(baseCohortTable)

Arguments

baseCohortTable

Character. The configured, unsuffixed cohort table.

Returns

Character. The effective cohort table name for this execution.

Method getResultsPath()

Usage

ExecutionContext$getResultsPath(
  taskName = NULL,
  databaseName = private$.databaseName
)

Arguments

taskName

Character. Task folder or file name.

databaseName

Character or NULL. Database name to use when the context is shared across multiple config blocks.

Returns

Character. Absolute result path for the supplied task.

Method clone()

The objects of this class are cloneable with this method.

Usage

ExecutionContext$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.