Merge pull request #223 from CHOP-CGTInformatics/fix-dag-export-bug

Fix DAG export bug

Author: ezraporter

.github/workflows/R-CMD-check.yaml

@@ -31,6 +31,7 @@ jobs:
       REDCAPTIDIER_LONGITUDINAL_DAG_API: ${{ secrets.REDCAPTIDIER_LONGITUDINAL_DAG_API }}
       REDCAPTIDIER_MIXED_STRUCTURE_API: ${{ secrets.REDCAPTIDIER_MIXED_STRUCTURE_API }}
       REDCAPTIDIER_MDC_API: ${{ secrets.REDCAPTIDIER_MDC_API }}
+      REDCAPTIDIER_DAG_ACCESS_API: ${{ secrets.REDCAPTIDIER_DAG_ACCESS_API }}
     steps:
       - name: Update Ubuntu, Install cURL Headers, add Libraries
         run: |

.github/workflows/test-coverage.yaml

@@ -30,6 +30,7 @@ jobs:
       REDCAPTIDIER_DAG_API: ${{ secrets.REDCAPTIDIER_DAG_API }}
       REDCAPTIDIER_LONGITUDINAL_DAG_API: ${{ secrets.REDCAPTIDIER_LONGITUDINAL_DAG_API }}
       REDCAPTIDIER_MDC_API: ${{ secrets.REDCAPTIDIER_MDC_API }}
+      REDCAPTIDIER_DAG_ACCESS_API: ${{ secrets.REDCAPTIDIER_DAG_ACCESS_API }}
     steps:
       - name: Update Ubuntu, Install cURL Headers, add Libraries
         run: |

R/read_redcap.R

@@ -204,11 +204,13 @@ read_redcap <- function(redcap_uri,
   # If DAGs detected and requested in label format, trigger an API call and
   # update column data for redcap_data_access_group
   if ("redcap_data_access_group" %in% names(db_data) && raw_or_label != "raw") {
-    dag_data <- redcap_dag_read(
-      redcap_uri = redcap_uri,
-      token = token,
-      verbose = !suppress_redcapr_messages
-    )$data
+    dag_data <- try_redcapr({
+      redcap_dag_read(
+        redcap_uri = redcap_uri,
+        token = token,
+        verbose = !suppress_redcapr_messages
+      )
+    })
 
     db_data <- update_dag_cols(
       data = db_data,

R/utils.R

@@ -805,19 +805,22 @@ try_redcapr <- function(expr, call = caller_env()) {
         "i" = "URI: `{condition$redcap_uri}`"
       )
       condition$class <- c("cannot_post", condition$class)
+    } else if (!is.null(out$outcome_message) && str_detect(
+      out$outcome_message,
+      "You must have 'API Export' privileges and 'Data Access Groups' privileges"
+    )
+    ) {
+      condition$info <- c(
+        "!" = "You do not have sufficient privileges to export data access groups.",
+        "i" = "Set `export_data_access_groups = FALSE` if you do not intend to export data access groups."
+      )
+      condition$class <- c("dag_access_error", condition$class)
+      condition$parent <- append_outcome_message(quo, out$outcome_message)
     } else {
       condition$class <- c("unexpected_error", condition$class)
 
       if (!is.null(out$outcome_message)) {
-        # Throw error containing outcome message and attach that as the parent
-        # Get the name of the function called inside try_redcapr so it can be mentioned in the error message
-        calling_fn <- quo_get_expr(quo)
-        # Handle case where try_redcapr had multiline expr
-        if (inherits(calling_fn, "{")) {
-          calling_fn <- calling_fn[[2]]
-        }
-
-        condition$parent <- catch_cnd(abort(out$outcome_message, call = calling_fn))
+        condition$parent <- append_outcome_message(quo, out$outcome_message)
       }
     }
     cli_abort(
@@ -834,6 +837,18 @@ try_redcapr <- function(expr, call = caller_env()) {
   out$data
 }
 
+append_outcome_message <- function(quo, outcome_message) {
+  # Throw error containing outcome message and attach that as the parent
+  # Get the name of the function called inside try_redcapr so it can be mentioned in the error message
+  calling_fn <- quo_get_expr(quo)
+  # Handle case where try_redcapr had multiline expr
+  if (inherits(calling_fn, "{")) {
+    calling_fn <- calling_fn[[2]]
+  }
+
+  catch_cnd(abort(outcome_message, call = calling_fn))
+}
+
 
 #' @title
 #' Check whether a REDCap database has repeat forms

tests/testthat/test-read_redcap.R

@@ -755,3 +755,18 @@ test_that("update_dag_cols() works for haven labels", {
   expect_equal(out$redcap_data_access_group, expected_vec)
   expect_equal(out, expected_out)
 })
+
+test_that("read_redcap() handles insufficient DAG access", {
+  read_redcap(
+    Sys.getenv("REDCAP_URI"),
+    Sys.getenv("REDCAPTIDIER_DAG_ACCESS_API")
+  ) |>
+    expect_error(class = "dag_access_error")
+
+  read_redcap(
+    Sys.getenv("REDCAP_URI"),
+    Sys.getenv("REDCAPTIDIER_DAG_ACCESS_API"),
+    export_data_access_groups = FALSE
+  ) |>
+    expect_no_error()
+})

utility/cli_message_examples.R

@@ -151,3 +151,7 @@ read_redcap(Sys.getenv("REDCAP_URI"), Sys.getenv("REDCAPTIDIER_CLASSIC_API")) %>
 # missing data codes
 
 read_redcap(redcap_uri, Sys.getenv("REDCAPTIDIER_MDC_API"))
+
+# No DAG export access
+
+read_redcap(Sys.getenv("REDCAP_URI"), Sys.getenv("REDCAPTIDIER_DAG_ACCESS_API"))

utility/cli_message_examples_reprex.md

@@ -112,8 +112,8 @@ read_redcap(redcap_uri, classic_token, export_survey_fields = 123)
 
 read_redcap(redcap_uri, classic_token, export_survey_fields = c(TRUE, TRUE))
 #> Error in `read_redcap()`:
-#> ✖ You've supplied `TRUE` and `TRUE` for `export_survey_fields` which is
-#>   not a valid value
+#> ✖ You've supplied `TRUE` `TRUE` for `export_survey_fields` which is not
+#>   a valid value
 #> ! Must have length 1, but has length 2
 
 ## suppress_redcapr_messages
@@ -126,8 +126,8 @@ read_redcap(redcap_uri, classic_token, suppress_redcapr_messages = 123)
 
 read_redcap(redcap_uri, classic_token, suppress_redcapr_messages = c(TRUE, TRUE))
 #> Error in `read_redcap()`:
-#> ✖ You've supplied `TRUE` and `TRUE` for `suppress_redcapr_messages`
-#>   which is not a valid value
+#> ✖ You've supplied `TRUE` `TRUE` for `suppress_redcapr_messages` which is
+#>   not a valid value
 #> ! Must have length 1, but has length 2
 
 # data access groups
@@ -255,7 +255,7 @@ withr::with_tempdir({
 })
 #> Error:
 #> ✖ File
-#>   ''/private/var/folders/qc/mmjjyjq50530z9r_7mfqcqfhxkkk67/T/Rtmph4LQ3Z/filee5aa7b9bea48/temp.csv''
+#>   ''/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/RtmpQCmzPP/file1411b189a9c52/temp.csv''
 #>   already exists.
 #> ℹ Overwriting files is disabled by default. Set `overwrite = TRUE` to overwrite
 #>   existing file.
@@ -296,7 +296,7 @@ withr::with_tempdir({
     write_redcap_xlsx(file = filepath)
 })
 #> Warning in write_redcap_xlsx(., file = filepath): ! No extension provided for `file`:
-#>   '/private/var/folders/qc/mmjjyjq50530z9r_7mfqcqfhxkkk67/T/Rtmph4LQ3Z/filee5aa11455c98/temp'
+#>   '/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/RtmpQCmzPP/file1411b1319086f/temp'
 #> ℹ The extension '.xlsx' will be appended to the file name.
 
 # Printed supertibble
@@ -338,6 +338,18 @@ read_redcap(redcap_uri, Sys.getenv("REDCAPTIDIER_MDC_API"))
 #> 1 form_1           Form 1            <tibble [3 × 9]> <tibble>        nonrepeat…
 #> # ℹ 5 more variables: data_rows <int>, data_cols <int>, data_size <lbstr_by>,
 #> #   data_na_pct <formttbl>, form_complete_pct <formttbl>
+
+# No DAG export access
+
+read_redcap(Sys.getenv("REDCAP_URI"), Sys.getenv("REDCAPTIDIER_DAG_ACCESS_API"))
+#> Error in `read_redcap()`:
+#> ✖ The REDCapR export operation was not successful.
+#> ! You do not have sufficient privileges to export data access groups.
+#> ℹ Set `export_data_access_groups = FALSE` if you do not intend to export data
+#>   access groups.
+#> Caused by error in `redcap_dag_read()`:
+#> ! The REDCapR read/export operation was not successful.  The error message was:
+#> ERROR: Insufficient user privileges: You must have 'API Export' privileges and 'Data Access Groups' privileges in the project.
 ```
 
-<sup>Created on 2024-10-16 with [reprex v2.1.0](https://reprex.tidyverse.org)</sup>
+<sup>Created on 2025-05-30 with [reprex v2.1.0](https://reprex.tidyverse.org)</sup>