Interactively prepare a Trio submission bundle

This high-level helper provides a writeCTD()-style console workflow for the new five-table submission path. It collects dataset, task, evidence, and metric metadata; optionally prepares local files for upload and verifies a Figshare article; optionally uploads custom metrics to a GitHub gist; and returns all submission tables ready for review before calling submitTrioSubmission().

Usage

writeSubmission(
  trio,
  n_tasks = NULL,
  dataset_defaults = list(),
  task_defaults = list(),
  evidence_defaults = list(),
  metric_defaults = list(),
  prepare_files = TRUE,
  file_args = list(),
  upload_custom_metrics = FALSE,
  githubPat = Sys.getenv("GITHUB_PAT"),
  gistPublic = TRUE,
  review = TRUE,
  submit = NULL,
  url = submission_webapp_url,
  submittedBy = NULL,
  build_payload = TRUE,
  build_json = FALSE
)

Arguments

trio

A Trio object.

n_tasks

Optional number of tasks to define. If NULL, interactive sessions prompt for it and non-interactive sessions require it through task_defaults or n_tasks.

dataset_defaults

Optional named list passed into collectDatasetSubmissionInfo().

task_defaults

Optional named list passed into collectTaskSubmissionInfo().

evidence_defaults

Optional named list passed into collectEvidenceSubmissionInfo().

metric_defaults

Optional named list passed into collectMetricSubmissionInfo().

prepare_files

Logical; if TRUE, prepare dataset/evidence files or reuse an existing source.

file_args

Optional named list passed into prepareTrioSubmissionFiles().

upload_custom_metrics

Logical; if TRUE, upload custom metrics to a GitHub gist.

githubPat

Optional GitHub personal access token. Defaults to the current GITHUB_PAT environment variable.

gistPublic

Logical; whether any created gist should be public.

review

Logical; if TRUE, print a compact review summary before returning.

submit

Logical; if TRUE, submit the built payload at the end. If NULL, interactive sessions ask whether to submit after the review step.

url

Optional Google Apps Script endpoint URL used when submit = TRUE.

submittedBy

Optional submitter email or identifier used when submit = TRUE.

build_payload

Logical; if TRUE, attach the nested payload object.

build_json

Logical; if TRUE, attach the JSON string.

Value

A named list containing collected arguments, optional prepared file and metric metadata, the final submission, and optional payload/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."
)
result <- writeSubmission(
  trio = trio,
  n_tasks = 1,
  dataset_defaults = list(
    dataType = "omics",
    dataModality = "transcriptomics",
    technology = "RNA-seq",
    tissue = "blood",
    status = "healthy"
  ),
  task_defaults = list(
    taskStage = "prediction",
    taskType = "classification",
    taskName = "class_prediction"
  ),
  evidence_defaults = list(
    taskName = "class_prediction",
    evidenceType = "experimental_ground_truth"
  ),
  metric_defaults = list(metricType = "label_based"),
  prepare_files = FALSE,
  build_json = FALSE,
  review = FALSE
)
names(result)
#> [1] "dataset_args"  "task_args"     "evidence_args" "metric_args"  
#> [5] "files"         "metrics"       "submission"    "payload"