Updated read_redcap_tables to handle non-longitudinal projects and give better error on invalid events or forms

DESCRIPTION

@@ -2,9 +2,10 @@ Package: REDCapCAST
 Title: REDCap Castellated Data Handling
 Version: 23.12.1
 Authors@R: c(
-    person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", role = c("aut", "cre"),
+    person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", 
-           comment = c(ORCID = "0000-0002-7559-1154")),
+    role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")), 
-           person("Paul", "Egeler", email = "paul.egeler@spectrumhealth.org", role = "aut"))
+    person("Paul", "Egeler", email = "paulegeler@gmail.com", role = c("aut"), 
+    comment = c(ORCID = "0000-0001-6948-9498")))
 Description: Originally forked from the R part of 'REDCapRITS' by Paul Egeler. 
     See <https://github.com/pegeler/REDCapRITS>.
     Handles castellated datasets from 'REDCap' projects with repeating instruments. 

NEWS.md

@@ -1,3 +1,9 @@
+# REDCapCAST 24.1.1
+
+### Functions
+
+* Fix: `read_redcap_tables()`: checking form names based on data dictionary to allow handling of non-longitudinal projects. Prints invalid form names and invalid event names. If invalid form names are supplied to `REDCapR::redcap_read()` (which is the backbone), all forms are exported, which is not what we want with a focused approach. Invalid event names will give an output with a rather peculiar formatting.
+
 # REDCapCAST 23.12.1
 
 One new function to ease secure dataset retrieval and a few bug fixes.

R/read_redcap_tables.R

@@ -1,9 +1,10 @@
 #' Download REDCap data
 #'
 #' Implementation of REDCap_split with a focused data acquisition approach using
-#' REDCapR::redcap_read nad only downloading specified fields, forms and/or
+#' REDCapR::redcap_read and only downloading specified fields, forms and/or
 #' events using the built-in focused_metadata including some clean-up.
-#' Works with longitudinal projects with repeating instruments.
+#' Works with classical and longitudinal projects with or without repeating
+#' instruments.
 #' @param uri REDCap database uri
 #' @param token API token
 #' @param records records to download
@@ -39,27 +40,30 @@ read_redcap_tables <- function(uri,
                                )) {
 
 
-  if (!is.null(forms) | !is.null(events)){
+  m <- REDCapR::redcap_metadata_read(redcap_uri = uri, token = token)[["data"]]
-    arm_event_inst <- REDCapR::redcap_event_instruments(redcap_uri = uri,
+
-                                              token = token)
 
   if (!is.null(forms)){
 
-    forms_test <- forms %in% unique(arm_event_inst$data$form)
+    forms_test <- forms %in% unique(m$form_name)
 
     if (any(!forms_test)){
+      print(paste0("The following form names are invalid: ", paste(forms[!forms_test],collapse=", "),"."))
       stop("Not all supplied forms are valid")
     }
   }
 
   if (!is.null(events)){
+    arm_event_inst <- REDCapR::redcap_event_instruments(redcap_uri = uri,
+                                                        token = token)
+
     event_test <- events %in% unique(arm_event_inst$data$unique_event_name)
 
     if (any(!event_test)){
+      print(paste0("The following event names are invalid: ", paste(events[!event_test],collapse=", "),"."))
       stop("Not all supplied event names are valid")
     }
   }
-  }
 
   # Getting dataset
   d <- REDCapR::redcap_read(

man/read_redcap_tables.Rd

@@ -43,9 +43,10 @@ list of instruments
 }
 \description{
 Implementation of REDCap_split with a focused data acquisition approach using
-REDCapR::redcap_read nad only downloading specified fields, forms and/or
+REDCapR::redcap_read and only downloading specified fields, forms and/or
 events using the built-in focused_metadata including some clean-up.
-Works with longitudinal projects with repeating instruments.
+Works with classical and longitudinal projects with or without repeating
+instruments.
 }
 \examples{
 # Examples will be provided later