inst/tinytest/more_test_ctrdata_mongo_remote_ro.R

In ctrdata: Retrieve and Analyze Clinical Trials in Public Registers

## RH 2019-09-28

#### SETUP ####
if (!at_home()) exit_file("Reason: not at_home")
source("setup_ctrdata.R")

if (!checkInternet())      exit_file("Reason: no internet connectivity")
if (!checkMongoRemoteRo()) exit_file("Reason: no remote ro MongoDB")

# create database object
dbc <- nodbi::src_mongo(
  db = mongoRemoteRoDb,
  collection = mongoRemoteRoCollection,
  url = mongoRemoteRoUrl)

# database has been pre-loaded
# and can only be accessed as
# read-only, static collection

#### CTGOV and EUCTR ####

# test
expect_message(
  suppressWarnings(
    dbFindFields(
      namepart = "date",
      con = dbc)),
  "Finding fields|Using cache")

# test
tmp <- suppressMessages(
  dbGetFieldsIntoDf(
    fields = c(
      "a2_eudract_number",
      "overall_status",
      "record_last_import",
      "primary_completion_date",
      "x6_date_on_which_this_record_was_first_entered_in_the_eudract_database",
      "study_design_info.intervention_model",
      "e71_human_pharmacology_phase_i"),
    con = dbc))

# tests
expect_equal(dim(tmp)[2], 8)

# test
expect_true("Date" %in%
              class(tmp[["record_last_import"]]))

# test
expect_true("character" %in%
              class(tmp[["study_design_info.intervention_model"]]))


#### close ####
try({
  dbc$con$disconnect()
},
silent = TRUE)