Build a pre-submit Trio submission bundle

This is the higher-level R interface for the new submission workflow. It can prepare dataset/evidence files, prepare metric metadata, build the five-table submission object, and return the payload/JSON for inspection before calling submitTrioSubmission().

Usage

prepareTrioSubmissionBundle(
  trio,
  dataset_args,
  task_args,
  evidence_task_map,
  prepare_files = FALSE,
  file_args = list(),
  prepare_metrics = FALSE,
  metric_args = list(),
  build_payload = TRUE,
  build_json = FALSE
)

Arguments

trio

A Trio object.

dataset_args

Named list passed to buildDatasetSubmission().

task_args

Named list passed to buildDatasetTaskSubmission().

evidence_task_map

Named character vector mapping Trio evidence names to submission task names.

prepare_files

Logical; if TRUE, call prepareTrioSubmissionFiles().

file_args

Named list of additional arguments for prepareTrioSubmissionFiles(), excluding trio.

prepare_metrics

Logical; if TRUE, call prepareTrioSubmissionMetrics().

metric_args

Named list of additional arguments for prepareTrioSubmissionMetrics(), excluding trio.

build_payload

Logical; if TRUE, attach the nested payload structure.

build_json

Logical; if TRUE, attach the JSON string.

Value

A named list containing the built submission, plus optional files, metrics, payload, and json.

Examples

data <- data.frame(feature = c(1, 2, 3), row.names = paste0("sample", 1:3))
labels <- factor(c("A", "B", "A"))
names(labels) <- rownames(data)
trio <- Trio$new(
  data = data,
  evidence = list(class_labels = list(
    evidence = labels,
    metrics = "macroF1Metric"
  )),
  metrics = list(macroF1Metric = macroF1Metric),
  name = "example_dataset",
  description = "A small example dataset."
)
dataset_args <- list(
  dataType = "omics",
  dataModality = "transcriptomics",
  technology = "RNA-seq",
  tissue = "blood",
  status = "healthy"
)
task_args <- list(
  taskStage = "prediction",
  taskType = "classification",
  taskName = "class_prediction"
)
bundle <- prepareTrioSubmissionBundle(
  trio = trio,
  dataset_args = dataset_args,
  task_args = task_args,
  evidence_task_map = c(class_labels = "class_prediction")
)
names(bundle)
#> [1] "submission" "files"      "metrics"    "payload"