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Prepare Trio files and download metadata for submission

Source: R/SubmissionDataset.R
prepareTrioSubmissionFiles.Rd

This helper reuses the good parts of the old writeCTD() workflow for the new submission path. It can either save dataset/evidence files locally so the user can upload them, or reuse an existing downloadable source already attached to the Trio.

Usage

prepareTrioSubmissionFiles(
  trio,
  name = trio$name,
  outputDir = ".",
  saveData = NULL,
  saveEvidence = NULL,
  useExistingSource = NULL,
  figshareUrl = NULL,
  datasetFileName = NULL,
  evidenceFileName = NULL,
  verifyFigshare = FALSE,
  skipMd5Check = FALSE
)

Arguments

trio

A Trio object.

name

Dataset name used for generated filenames. Defaults to trio$name.

outputDir

Directory for generated .rds files. Defaults to ".".

saveData

Logical indicating whether to save trio$data to an RDS file. If NULL and interactive, the user is prompted.

saveEvidence

Logical indicating whether to save all supporting evidence to a single RDS file. If NULL and interactive, defaults to TRUE.

useExistingSource

Logical indicating whether to keep using trio$dataSource/trio$dataSourceID rather than preparing uploaded files. If NULL and interactive, the user is prompted when an existing source is available.

figshareUrl

Optional Figshare URL to verify against prepared files.

datasetFileName

Optional dataset filename to match inside the Figshare article.

evidenceFileName

Optional evidence filename to match inside the Figshare article.

verifyFigshare

Logical; if TRUE, verify the prepared files against the Figshare article metadata.

skipMd5Check

Logical; if TRUE, allow verification without MD5 matching.

Value

A named list describing the saved files and/or reusable download sources for dataset and evidence.

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."
)
files <- prepareTrioSubmissionFiles(
  trio,
  outputDir = tempdir(),
  saveData = TRUE,
  saveEvidence = TRUE,
  useExistingSource = FALSE
)
names(files)
#> [1] "dataset"  "evidence"