Provenance DAGs and canonical sample identity — provenance_and

Construct, validate, traverse, and tabulate acyclic scientific provenance graphs, and build auditable sample identity tables that preserve immutable VCF identifiers while supporting public aliases and richer biological groupings.

Usage

new_provenance_node(id, label = id,
  kind = c("input", "transformation", "analysis", "artifact", "report"),
  digest = NA_character_, parameters = list(), software = list(),
  status = c("complete", "planned", "running", "failed", "skipped"),
  started_at = NA_character_, completed_at = NA_character_)

new_provenance_edge(from, to,
  relation = c("derived_from", "consumes", "produces", "documents"),
  artifact = NA_character_)

new_provenance_dag(nodes = list(), edges = list())
add_provenance_node(dag, node)
add_provenance_edge(dag, edge)
provenance_node_table(dag)
provenance_edge_table(dag)
provenance_topological_order(dag)
provenance_ancestors(dag, id)
provenance_descendants(dag, id)
validate_provenance_dag(dag)

new_sample_identity(metadata)
validate_sample_identity(x)
sample_identity_table(x, ordered = FALSE)
resolve_sample_identity(identity, sample_ids)
sample_identity_groups(identity)

Arguments

id: Stable provenance node identifier.
label: Human-readable node label.
kind: Provenance node kind.
digest: Optional content or component digest.
parameters: Named parameter metadata.
software: Named software metadata.
status: Execution status.
started_at, completed_at: Optional timestamps.
from, to: Parent and child node identifiers.
relation: Lineage relationship.
artifact: Optional artifact identifier.
nodes, edges: Lists of provenance nodes and edges.
dag: A PopgenVCFProvenanceDAG.
node, edge: Object to add to a graph.
metadata: Metadata containing the immutable sample column and optional identity columns.
x: A sample identity table or provenance object, as appropriate.
ordered: Whether to apply explicit display ordering.
identity: Metadata or a canonical sample identity table.
sample_ids: Immutable VCF/GDS sample identifiers.

Value

Constructors return validated S3 objects. Table functions return data tables. Traversal functions return character node identifiers or public sample names.

Details

The sample column remains the immutable genotype join key. Optional alias, individual, family, replicate, and display_order columns provide public naming and biological grouping without changing VCF/GDS identity.