In nf-osi/nfportalutils: NF Portal Utilities

knitr::opts_chunk$set(echo = TRUE)

library(nfportalutils)
library(DiagrammeR)

syn_login(Sys.getenv("SYNAPSE_AUTH_TOKEN"))

dsp <- tryCatch({ jsonlite::read_json(path = params$dsp) }, error = function(e) NULL)

project_id <- params$project_id
schema_url <- params$schema_url

Parameters

Project: r project_id
Report run date: r Sys.Date()

Data sharing plan: r params$dsp
NF data model: r schema_url
Schematic API service: https://schematic.api.sagebionetworks.org/v1/

cat("> [!WARNING]\n", 
    "*Data Sharing Plan data could not be retrieved.", 
    "Some projects may not have a structured data sharing plan available.",
    "However, check path or formatting if one was truly expected to exist.",
    "Some checks will be skipped.*")

Datasets

Data Sharing Plan vs Project Assets

cat("*Skipped comparison check because DSP could not be retrieved.*")
data_not_expected <- FALSE

tryCatch({
  if(!is.null(dsp$dataSharingWaived)) {
    data_not_expected <- dsp$dataSharingWaived == TRUE
  } else if(!length(dsp$dataDeposit)) {
     data_not_expected <- TRUE
  }

  if(data_not_expected) {
    cat("*Skipped comparison check because DSP indicates **Data Not Expected** or there are no datasets listed.*")
  } else {
    expectation <- data.table::rbindlist(dsp$dataDeposit, fill = T)
    dsp_datasets <- setNames(paste0("D", 1:nrow(expectation)),  expectation$dataLabel)
    in_project <- data.table::rbindlist(list_project_datasets(project_id), fill = T)
    project_datasets <- setNames(in_project$id, in_project$name)
    cat(
      "```mermaid",
      dsp_dataset_mapping(dsp_datasets, project_datasets),
      "```",
      sep = "\n")
  }
},
error = function(e) cat("Something went wrong with comparing DSP and project. Error:\n", e$message))

Metadata Revalidation

cat("*Defaulting to metadata revalidation without DSP information.*")

if(data_not_expected) cat("*Skipped revalidation check because data sharing plan indicates **Data Not Expected**.*")

tryCatch({
  results <- meta_qc_project(project_id, schema_url = schema_url)
  if(!is.null(results)) {
    results$result <- ifelse(results$result, ":thumbsup:", ":x:")
    knitr::kable(results)
  } else {
    htmltools::div("Datasets could not be detected. Check project structure.")
  }},
  error = function(e) {
    htmltools::div("Something went wrong with project dataset review. Error message:", 
                   htmltools::code(e$message)) 
  }
)

Governance

cat("*Skipped governance check because DSP could not be retrieved.*")

items <- htmltools::tagList()

outside_us <- dsp$governance$dataCharacterization$dataIsOutsideUSA$response
if(outside_us) {
  items <- htmltools::tagAppendChild(items, htmltools::tags$li("Yes, data is outside US"))
}

ext_gov <- dsp$governance$contributorDUO$DUOPX_details
if(!is.null(ext_gov) || ext_gov != "") {
  items <- htmltools::tagAppendChild(items, htmltools::tags$li("This project has an extended governance request:", htmltools::tags$em(ext_gov)))
}

if(length(items)) {
  htmltools::tagList(
    htmltools::div(
      htmltools::tags$ul(
        items
      )
    )
  )
} else {
  htmltools::div("Project does not indicate special governance items qualifying for review.")
}