tests/manualTests/pgrpTesting.R

In RGLab/ImmuneSpaceR: A Thin Wrapper around the ImmuneSpace Data and Tools Portal

# This must be done locally because getParticipantData() is user-specific and takes a long time
testPgrp <- function(dt, groupId) {
  print(dt)
  pgrp_T <- con$getParticipantData(group = groupId, dataType = dt, original_view = TRUE)
  pgrp_F <- con$getParticipantData(group = groupId, dataType = dt, original_view = FALSE)
  orig_T <- con$getDataset(dt, original_view = TRUE)
  orig_F <- con$getDataset(dt, original_view = FALSE)

  res <- list()
  res$pgrp_T_cols <- colnames(pgrp_T)
  res$pgrp_F_cols <- colnames(pgrp_F)
  res$orig_T_cols <- colnames(orig_T)
  res$orig_F_cols <- colnames(orig_F)

  res$view_T <- all.equal(colnames(pgrp_T), colnames(orig_T))
  res$view_F <- all.equal(colnames(pgrp_F), colnames(orig_F))

  print(paste0("view T: ", res$view_T))
  print(paste0("view F: ", res$view_F))

  return(res)
}

library(ImmuneSpaceR)
con <- CreateConnection("")
dataTypes <- c(
  "neut_ab_titer",
  "fcs_sample_files",
  "fcs_analyzed_result",
  "demographics",
  "mbaa",
  "pcr",
  "fcs_control_files",
  "elisa",
  "gene_expression_files",
  "hai",
  "hla_typing",
  "elispot",
  "cohort_membership"
)

chk <- lapply(dataTypes, testPgrp, groupId = 155)