Package 'PhysioLake'

Description

PhysioExperiment adapter for OmicsLake

PhysioExperiment adapter for OmicsLake

Details

An OmicsLake::LakeAdapter that stores and retrieves PhysioExperiment objects in an OmicsLake with full fidelity.

A PhysioExperiment is a SummarizedExperiment subclass with one extra slot (samplingRate); its provenance, events, and derived estimates live in metadata(). OmicsLake's generic SEAdapter already round-trips assays, colData, rowData, and metadata, but it reconstructs a plain SummarizedExperiment – losing the class identity and the sampling rate. This adapter inherits SEAdapter and adds only that missing piece: it stashes the sampling rate in metadata on put() and rebuilds a PhysioExperiment on get(). Because provenance is carried in metadata(), it survives the round trip unchanged (verified: provenanceHash() is identical before and after), so the ecosystem's per-object (micro) W3C-PROV provenance lands intact next to OmicsLake's cross-dataset (macro) lineage. Assays that are not 2-D matrices (e.g. epoched time x channel x trial arrays), which the generic SEAdapter would collapse when storing them as flat tables, are likewise stashed in metadata and spliced back in their original order on get().

A higher priority() than the generic SEAdapter ensures this adapter is selected for PhysioExperiment objects (which also satisfy SEAdapter).

Value

An R6 generator for the PhysioExperimentAdapter.

Super classes

OmicsLake::LakeAdapter -> OmicsLake::SEAdapter -> PhysioExperimentAdapter

Methods

Public methods

• PhysioExperimentAdapter$name()

• PhysioExperimentAdapter$can_handle()

• PhysioExperimentAdapter$priority()

• PhysioExperimentAdapter$put()

• PhysioExperimentAdapter$get()

• PhysioExperimentAdapter$clone()

Method name()

Adapter type name.

Usage

PhysioExperimentAdapter$name()

Method can_handle()

Whether this adapter handles data.

Usage

PhysioExperimentAdapter$can_handle(data)

Arguments

Method priority()

Selection priority (above the generic SummarizedExperiment adapter, which is 100).

Usage

PhysioExperimentAdapter$priority()

Method put()

Store a PhysioExperiment in the lake.

Usage

PhysioExperimentAdapter$put(lake, name, data)

Arguments

Method get()

Retrieve a PhysioExperiment from the lake.

Usage

PhysioExperimentAdapter$get(lake, name, ref = "@latest")

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

PhysioExperimentAdapter$clone(deep = FALSE)

Arguments

See Also

registerPhysioAdapters(), OmicsLake::register_adapter()

Examples

if (requireNamespace("OmicsLake", quietly = TRUE)) {
  adapter <- PhysioExperimentAdapter$new()
  adapter$name()       # "PhysioExperiment"
  adapter$priority()   # 200, above the generic SummarizedExperiment adapter
}

Description

Returns the companion provenance table written by physioPut().

Usage

physioProvenance(lake, name, provenance_suffix = "__prov")

Arguments

Value

A data.frame of the operation DAG (one row per recorded activity), or NULL if none was stored.

See Also

physioPut()

Examples

if (requireNamespace("OmicsLake", quietly = TRUE)) {
  lake <- OmicsLake::Lake$new(basename(tempfile("lake")), root = tempdir())
  pe <- PhysioExperiment::PhysioExperiment(
    assays = list(raw = matrix(as.numeric(1:20), nrow = 10, ncol = 2)),
    samplingRate = 100
  )
  physioPut(lake, "subj01", pe)
  # NULL here because this object carries no recorded op-DAG.
  physioProvenance(lake, "subj01")
}

Description

Wraps OmicsLake::Lake's put() so that the object's W3C-PROV operation DAG (from PhysioExperiment::provenance()) is stored as a queryable companion table and recorded as a lineage dependency of the object (via put(..., depends_on =)). The ecosystem's per-object (micro) provenance thus becomes a first-class node in OmicsLake's cross-dataset (macro) lineage, visible to lake$tree(), lake$deps(), and lake$impact().

Usage

physioPut(lake, name, x, tags = "physio", provenance_suffix = "__prov")

Arguments

Details

Objects that carry no provenance are stored normally (no companion table).

Value

Invisibly, the provenance table's name, or NA_character_ if the object carried no provenance.

See Also

physioProvenance()

Examples

if (requireNamespace("OmicsLake", quietly = TRUE)) {
  lake <- OmicsLake::Lake$new(basename(tempfile("lake")), root = tempdir())
  pe <- PhysioExperiment::PhysioExperiment(
    assays = list(raw = matrix(as.numeric(1:20), nrow = 10, ncol = 2)),
    samplingRate = 100
  )
  physioPut(lake, "subj01", pe)
  restored <- lake$get("subj01")        # a PhysioExperiment again
  PhysioExperiment::samplingRate(restored)
}

Description

Stores the parts of a run bundle (e.g. the frozen pre-registration, the run manifest, the operation DAG, the terminal artifact, the claims registry, the verification report) as individual OmicsLake entries under a common prefix, wired together with lineage edges so the run's internal structure is queryable via lake$tree() / lake$deps(). Combined with lake$snap(), a whole run becomes a versioned, lineage-tracked lake object — giving the substrate the persistent, queryable store it otherwise lacks (it content-addresses runs but does not persist them).

Usage

physioPutBundle(lake, name, components, edges = list(), tags = "run-bundle")

Arguments

Details

data.frame components are stored as queryable tables; other objects are serialised. Components are stored parents-first (topological order over edges) so each depends_on target already exists.

Value

Invisibly, a named character vector mapping each component key to its stored lake entry name.

See Also

physioPut()

Examples

if (requireNamespace("OmicsLake", quietly = TRUE)) {
  lake <- OmicsLake::Lake$new(basename(tempfile("lake")), root = tempdir())
  components <- list(
    prereg = data.frame(key = "alpha", value = 1),
    result = data.frame(metric = "hr", value = 72)
  )
  # `result` depends on `prereg`; the bundle stores that lineage edge.
  physioPutBundle(lake, "run001", components,
                  edges = list(result = "prereg"))
  lake$deps("run001__result")
}

Description

Registers PhysioLake's adapters (currently PhysioExperimentAdapter) with the OmicsLake adapter registry so that lake$put() / lake$get() handle Physio objects automatically. Called on package load; exported so it can be re-run after OmicsLake::clear_adapters().

Usage

registerPhysioAdapters()

Value

Invisibly TRUE.

Examples

if (requireNamespace("OmicsLake", quietly = TRUE)) {
  # Re-run after OmicsLake::clear_adapters(); also called on package load.
  registerPhysioAdapters()
}