Immutable artifact lineage — artifact-lineage • popgenVCF

Creates immutable module-execution and artifact records, assigns SHA256 content identities, validates producer and consumer relationships, derives a provenance DAG, verifies current content, exports interoperable lineage files, and embeds the lineage in portable reproducible projects.

Usage

new_lineage_execution(
  id,
  module,
  status = c("complete", "planned", "running", "failed", "skipped"),
  parameters = list(),
  software = list(),
  started_at = NA_character_,
  completed_at = NA_character_
)

new_lineage_artifact(
  id,
  module,
  name,
  type,
  format,
  producer,
  consumers = character(),
  path = NULL,
  object = NULL,
  metadata = list()
)

new_artifact_lineage(executions = list(), artifacts = list())

validate_artifact_lineage(lineage)

lineage_execution_table(lineage)

lineage_artifact_table(lineage)

artifact_lineage_dag(lineage, validate = TRUE)

verify_artifact_lineage(lineage, objects = list())

write_artifact_lineage(
  lineage,
  directory,
  formats = c("tsv", "json", "graphml", "dot")
)

set_project_artifact_lineage(project, lineage)

Arguments

id: Stable execution or artifact identifier.
module: Analysis module name.
status: Execution status.
parameters, software: Named execution metadata lists.
started_at, completed_at: Optional timestamps.
name: Stable artifact name.
type: Artifact type.
format: Artifact format.
producer: Identifier of the single producing execution.
consumers: Identifiers of consuming executions.
path: Existing artifact file path.
object: In-memory artifact when no file exists.
metadata: Named artifact metadata.
executions: List of PopgenVCFLineageExecution records.
artifacts: List of PopgenVCFLineageArtifact records.
lineage: A PopgenVCFArtifactLineage.
validate: Whether to validate before deriving the DAG.
objects: Named list of current in-memory objects indexed by artifact ID.
directory: Output directory.
formats: Export formats: TSV, JSON, GraphML, or DOT.
project: A PopgenVCFProject.

Value

Constructors return validated lineage objects. Table functions return data tables. artifact_lineage_dag() returns a PopgenVCFProvenanceDAG. verify_artifact_lineage() returns TRUE. The writer returns paths to created files, and set_project_artifact_lineage() returns an updated project.

Details

Each artifact has exactly one producer and zero or more consumers. File artifacts are hashed from bytes. In-memory artifacts are hashed from serialized R content. Artifact and execution identifiers occupy separate namespaces, and a producer cannot consume its own artifact.