test repeating instruments w/ sparse records

ref #143

inst/misc/example.credentials

@@ -23,3 +23,4 @@ redcap_uri,username,project_id,token,comment
 "https://bbmc.ouhsc.edu/redcap/api/","myusername","2545","0BF11B9CB01F0B8F8EE203B7E07DEFD9","DAG Write"
 "https://bbmc.ouhsc.edu/redcap/api/","myusername","2593","1C31398F332FCACA4C0A7B93B18D5CD4","super-wide #2--5,785 columns"
 "https://bbmc.ouhsc.edu/redcap/api/","myusername","2597","5C1526186C4D04AE0A0630743E69B53C","super-wide #3--35,000 columns"
+"https://bbmc.ouhsc.edu/redcap/api/","myusername","2603","56F43A10D01D6578A46393394D76D88F","Repeating Instruments --Sparse"

inst/test-data/specific-redcapr/read-batch-repeating-sparse/batch-size-1.R

@@ -0,0 +1,14 @@
+structure(list(record_id = c(1, 1, 1, 1, 2, 2, 3, 4, 5), redcap_repeat_instrument = c(NA, 
+"bp", "bp", "bp", NA, "bp", NA, NA, NA), redcap_repeat_instance = c(NA, 
+1, 2, 3, NA, 1, NA, NA, NA), date_enrolled = structure(c(18183, 
+NA, NA, NA, 17929, NA, 18935, 18935, NA), class = "Date"), first_name = c("aaa", 
+NA, NA, NA, "bbb", NA, "empty 3", "empty 4", "empty 5"), dob = structure(c(14896, 
+NA, NA, NA, 14642, NA, NA, NA, NA), class = "Date"), age = c(8.9, 
+NA, NA, NA, 9.6, NA, NA, NA, NA), ethnicity = c(1, NA, NA, NA, 
+0, NA, NA, NA, NA), race = c(4, NA, NA, NA, 6, NA, NA, NA, NA
+), sex = c(0, NA, NA, NA, 1, NA, NA, NA, NA), demographics_complete = c(2, 
+NA, NA, NA, 2, NA, 0, 0, 0), date_bp = structure(c(NA, 18183, 
+18183, 18183, NA, 12512, NA, NA, NA), class = "Date"), bp_systolic = c(NA, 
+110, 111, 112, NA, 114, NA, NA, NA), bp_diastolic = c(NA, 100, 
+101, 102, NA, 104, NA, NA, NA), bp_complete = c(NA, 2, 2, 2, 
+NA, 2, NA, NA, NA)), row.names = c(NA, -9L), class = "data.frame")

inst/test-data/specific-redcapr/read-batch-repeating-sparse/batch-size-3.R

@@ -0,0 +1,14 @@
+structure(list(record_id = c(1, 1, 1, 1, 2, 2, 3, 4, 5), redcap_repeat_instrument = c(NA, 
+"bp", "bp", "bp", NA, "bp", NA, NA, NA), redcap_repeat_instance = c(NA, 
+1, 2, 3, NA, 1, NA, NA, NA), date_enrolled = structure(c(18183, 
+NA, NA, NA, 17929, NA, 18935, 18935, NA), class = "Date"), first_name = c("aaa", 
+NA, NA, NA, "bbb", NA, "empty 3", "empty 4", "empty 5"), dob = structure(c(14896, 
+NA, NA, NA, 14642, NA, NA, NA, NA), class = "Date"), age = c(8.9, 
+NA, NA, NA, 9.6, NA, NA, NA, NA), ethnicity = c(1, NA, NA, NA, 
+0, NA, NA, NA, NA), race = c(4, NA, NA, NA, 6, NA, NA, NA, NA
+), sex = c(0, NA, NA, NA, 1, NA, NA, NA, NA), demographics_complete = c(2, 
+NA, NA, NA, 2, NA, 0, 0, 0), date_bp = structure(c(NA, 18183, 
+18183, 18183, NA, 12512, NA, NA, NA), class = "Date"), bp_systolic = c(NA, 
+110, 111, 112, NA, 114, NA, NA, NA), bp_diastolic = c(NA, 100, 
+101, 102, NA, 104, NA, NA, NA), bp_complete = c(NA, 2, 2, 2, 
+NA, 2, NA, NA, NA)), row.names = c(NA, -9L), class = "data.frame")

inst/test-data/specific-redcapr/read-batch-repeating-sparse/batch-szie-2.R

@@ -0,0 +1,14 @@
+structure(list(record_id = c(1, 1, 1, 1, 2, 2, 3, 4, 5), redcap_repeat_instrument = c(NA, 
+"bp", "bp", "bp", NA, "bp", NA, NA, NA), redcap_repeat_instance = c(NA, 
+1, 2, 3, NA, 1, NA, NA, NA), date_enrolled = structure(c(18183, 
+NA, NA, NA, 17929, NA, 18935, 18935, NA), class = "Date"), first_name = c("aaa", 
+NA, NA, NA, "bbb", NA, "empty 3", "empty 4", "empty 5"), dob = structure(c(14896, 
+NA, NA, NA, 14642, NA, NA, NA, NA), class = "Date"), age = c(8.9, 
+NA, NA, NA, 9.6, NA, NA, NA, NA), ethnicity = c(1, NA, NA, NA, 
+0, NA, NA, NA, NA), race = c(4, NA, NA, NA, 6, NA, NA, NA, NA
+), sex = c(0, NA, NA, NA, 1, NA, NA, NA, NA), demographics_complete = c(2, 
+NA, NA, NA, 2, NA, 0, 0, 0), date_bp = structure(c(NA, 18183, 
+18183, 18183, NA, 12512, NA, NA, NA), class = "Date"), bp_systolic = c(NA, 
+110, 111, 112, NA, 114, NA, NA, NA), bp_diastolic = c(NA, 100, 
+101, 102, NA, 104, NA, NA, NA), bp_complete = c(NA, 2, 2, 2, 
+NA, 2, NA, NA, NA)), row.names = c(NA, -9L), class = "data.frame")

inst/test-data/specific-redcapr/read-batch-repeating-sparse/default.R

@@ -0,0 +1,14 @@
+structure(list(record_id = c(1, 1, 1, 1, 2, 2, 3, 4, 5), redcap_repeat_instrument = c(NA, 
+"bp", "bp", "bp", NA, "bp", NA, NA, NA), redcap_repeat_instance = c(NA, 
+1, 2, 3, NA, 1, NA, NA, NA), date_enrolled = structure(c(18183, 
+NA, NA, NA, 17929, NA, 18935, 18935, NA), class = "Date"), first_name = c("aaa", 
+NA, NA, NA, "bbb", NA, "empty 3", "empty 4", "empty 5"), dob = structure(c(14896, 
+NA, NA, NA, 14642, NA, NA, NA, NA), class = "Date"), age = c(8.9, 
+NA, NA, NA, 9.6, NA, NA, NA, NA), ethnicity = c(1, NA, NA, NA, 
+0, NA, NA, NA, NA), race = c(4, NA, NA, NA, 6, NA, NA, NA, NA
+), sex = c(0, NA, NA, NA, 1, NA, NA, NA, NA), demographics_complete = c(2, 
+NA, NA, NA, 2, NA, 0, 0, 0), date_bp = structure(c(NA, 18183, 
+18183, 18183, NA, 12512, NA, NA, NA), class = "Date"), bp_systolic = c(NA, 
+110, 111, 112, NA, 114, NA, NA, NA), bp_diastolic = c(NA, 100, 
+101, 102, NA, 104, NA, NA, NA), bp_complete = c(NA, 2, 2, 2, 
+NA, 2, NA, NA, NA)), row.names = c(NA, -9L), class = "data.frame")

tests/testthat/test-read-batch-repeating-sparse.R

@@ -0,0 +1,129 @@
+library(testthat)
+
+credential  <- retrieve_credential_testing(project_id = 2603L)
+update_expectation  <- FALSE
+
+test_that("smoke test", {
+  testthat::skip_on_cran()
+  expect_message(
+    returned_object <-
+      redcap_read(
+        redcap_uri    = credential$redcap_uri,
+        token         = credential$token
+      )
+  )
+})
+
+test_that("default", {
+  testthat::skip_on_cran()
+  path_expected <- "test-data/specific-redcapr/read-batch-repeating-sparse/default.R"
+  expected_outcome_message <- "\\d+ records and \\d+ columns were read from REDCap in \\d+(\\.\\d+\\W|\\W)seconds\\."
+
+  expect_message(
+    regexp          = expected_outcome_message,
+    returned_object <-
+      redcap_read(
+        redcap_uri    = credential$redcap_uri,
+        token         = credential$token#,
+        # batch_size    = 1
+      )
+  )
+
+  if (update_expectation) save_expected(returned_object$data, path_expected)
+  expected_data_frame <- retrieve_expected(path_expected)
+
+  expect_equal(returned_object$data, expected=expected_data_frame, label="The returned data.frame should be correct", ignore_attr = TRUE) # dput(returned_object$data)
+  expect_equal(returned_object$status_code, expected="200")
+  expect_true(returned_object$records_collapsed=="", "A subset of records was not requested.")
+  expect_true(returned_object$fields_collapsed=="", "A subset of fields was not requested.")
+  expect_true(returned_object$filter_logic=="", "A filter was not specified.")
+  expect_match(returned_object$outcome_message, regexp=expected_outcome_message, perl=TRUE)
+  expect_true(returned_object$success)
+})
+
+
+test_that("batch size 3", {
+  testthat::skip_on_cran()
+  path_expected <- "test-data/specific-redcapr/read-batch-repeating-sparse/batch-size-3.R"
+  expected_outcome_message <- "\\d+ records and \\d+ columns were read from REDCap in \\d+(\\.\\d+\\W|\\W)seconds\\."
+
+  expect_message(
+    regexp          = expected_outcome_message,
+    returned_object <-
+      redcap_read(
+        redcap_uri    = credential$redcap_uri,
+        token         = credential$token,
+        batch_size    = 3
+      )
+  )
+
+  if (update_expectation) save_expected(returned_object$data, path_expected)
+  expected_data_frame <- retrieve_expected(path_expected)
+
+  expect_equal(returned_object$data, expected=expected_data_frame, label="The returned data.frame should be correct", ignore_attr = TRUE) # dput(returned_object$data)
+  expect_equal(returned_object$status_code, expected="200; 200")
+  expect_true(returned_object$records_collapsed=="", "A subset of records was not requested.")
+  expect_true(returned_object$fields_collapsed=="", "A subset of fields was not requested.")
+  expect_true(returned_object$filter_logic=="", "A filter was not specified.")
+  expect_match(returned_object$outcome_message, regexp=expected_outcome_message, perl=TRUE)
+  expect_true(returned_object$success)
+})
+
+
+test_that("batch size 2", {
+  testthat::skip_on_cran()
+  path_expected <- "test-data/specific-redcapr/read-batch-repeating-sparse/batch-szie-2.R"
+  expected_outcome_message <- "\\d+ records and \\d+ columns were read from REDCap in \\d+(\\.\\d+\\W|\\W)seconds\\."
+
+  expect_message(
+    regexp          = expected_outcome_message,
+    returned_object <-
+      redcap_read(
+        redcap_uri    = credential$redcap_uri,
+        token         = credential$token,
+        batch_size    = 2
+      )
+  )
+
+  if (update_expectation) save_expected(returned_object$data, path_expected)
+  expected_data_frame <- retrieve_expected(path_expected)
+
+  expect_equal(returned_object$data, expected=expected_data_frame, label="The returned data.frame should be correct", ignore_attr = TRUE) # dput(returned_object$data)
+  expect_equal(returned_object$status_code, expected="200; 200; 200")
+  expect_true(returned_object$records_collapsed=="", "A subset of records was not requested.")
+  expect_true(returned_object$fields_collapsed=="", "A subset of fields was not requested.")
+  expect_true(returned_object$filter_logic=="", "A filter was not specified.")
+  expect_match(returned_object$outcome_message, regexp=expected_outcome_message, perl=TRUE)
+  expect_true(returned_object$success)
+})
+
+
+test_that("batch size 1", {
+  testthat::skip_on_cran()
+  path_expected <- "test-data/specific-redcapr/read-batch-repeating-sparse/batch-size-1.R"
+  expected_outcome_message <- "\\d+ records and \\d+ columns were read from REDCap in \\d+(\\.\\d+\\W|\\W)seconds\\."
+
+  expect_message(
+    regexp          = expected_outcome_message,
+    returned_object <-
+      redcap_read(
+        redcap_uri    = credential$redcap_uri,
+        token         = credential$token,
+        batch_size    = 1
+      )
+  )
+
+  if (update_expectation) save_expected(returned_object$data, path_expected)
+  expected_data_frame <- retrieve_expected(path_expected)
+
+  expect_equal(returned_object$data, expected=expected_data_frame, label="The returned data.frame should be correct", ignore_attr = TRUE) # dput(returned_object$data)
+  expect_equal(returned_object$status_code, expected="200; 200; 200; 200; 200")
+  expect_true(returned_object$records_collapsed=="", "A subset of records was not requested.")
+  expect_true(returned_object$fields_collapsed=="", "A subset of fields was not requested.")
+  expect_true(returned_object$filter_logic=="", "A filter was not specified.")
+  expect_match(returned_object$outcome_message, regexp=expected_outcome_message, perl=TRUE)
+  expect_true(returned_object$success)
+})
+
+rm(credential)
+