Merge pull request #72 from DanChaltiel/fix/71-several-subject-identi…

…fiers

Fix/71 several subject identifiers

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: EDCimport
-Version: 0.4.1.9055
+Version: 0.4.1.9056
 Title: Import Data from EDC Software
 Authors@R: 
     c(person(given = "Dan",

R/sanity_checks.R

@@ -281,7 +281,7 @@ edc_data_condition = function(.data, message, issue_n, max_subjid,
   if(nrow(.data)>0){
     if(is.character(csv_path)){
       assert(str_ends(csv_path, "\\.csv"), call=parent.frame())
-      write.csv2(.data, csv_path)
+      write.csv2(.data, csv_path, row.names=FALSE)
     }
     message = format_inline(message)
 
@@ -294,7 +294,14 @@ edc_data_condition = function(.data, message, issue_n, max_subjid,
     }
 
     if(!is.null(col_subjid)){
-      if(!tolower(col_subjid) %in% tolower(names(.data))){
+      col_found = tolower(col_subjid) %in% tolower(names(.data))
+      if(sum(col_found)>1){
+        cli_warn("Found {length(col_found)} subject identifiers in the input dataset:
+                 {.val {col_subjid[col_found]}}. Defaulting to the first one.", 
+                  class="edc_data_condition_subjid_multiple_warn", call=parent.frame())
+        col_subjid = col_subjid[col_found][1]
+      }
+      if(!any(col_found)){
         cli_abort("Could not find column {col_subjid} in the input dataset.", 
                   class="edc_data_condition_subjid_error", call=parent.frame())
       }

tests/testthat/_snaps/sanity.md

@@ -0,0 +1,52 @@
+# edc_data_warn snapshot
+
+    Code
+      db0 %>% filter(age > 60) %>% edc_data_warn("Age should not be >60")
+    Condition
+      Warning:
+      Issue #xx: Age should not be >60 (10 patients: #1, #7, #9, #11, #12, ...)
+    Code
+      db0 %>% filter(age > 70) %>% edc_data_warn("Age should not be >70", issue_n = NULL)
+    Condition
+      Warning:
+      Age should not be >70 (2 patients: #9 and #12)
+    Code
+      db0 %>% filter(age > 20) %>% edc_data_warn("Age should not be >20", issue_n = 1,
+        max_subjid = 2)
+    Condition
+      Warning:
+      Issue #01: Age should not be >20 (50 patients: #1, #2, ...)
+    Code
+      db0 %>% filter(age > 70) %>% edc_data_warn("Age should not be >70", issue_n = NULL,
+        col_subjid = c("SUBJID", "PATNO"))
+    Condition
+      Warning:
+      Age should not be >70 (2 patients: #9 and #12)
+    Code
+      db0 %>% filter(age > 70) %>% edc_data_warn("Age should not be >70", issue_n = 2,
+        col_subjid = c("SUBJID", "group"))
+    Condition
+      Warning in `edc_data_warn()`:
+      Found 2 subject identifiers in the input dataset: "SUBJID" and "group". Defaulting to the first one.
+      Warning:
+      Issue #02: Age should not be >70 (2 patients: #9 and #12)
+    Code
+      db0 %>% filter(age > 70) %>% edc_data_warn("Age should not be >70", issue_n = 3,
+        col_subjid = c("group", "SUBJID"))
+    Condition
+      Warning in `edc_data_warn()`:
+      Found 2 subject identifiers in the input dataset: "group" and "SUBJID". Defaulting to the first one.
+      Warning:
+      Issue #03: Age should not be >70 (2 patients: #A and #B)
+    Code
+      edc_data_warnings()
+    Output
+      # A tibble: 5 x 4
+        issue_n message               subjid     fun     
+        <chr>   <chr>                 <list>     <chr>   
+      1 01      Age should not be >20 <chr [50]> cli_warn
+      2 02      Age should not be >70 <chr [2]>  cli_warn
+      3 03      Age should not be >70 <chr [2]>  cli_warn
+      4 xx      Age should not be >60 <chr [10]> cli_warn
+      5 <NA>    Age should not be >70 <chr [2]>  cli_warn
+

tests/testthat/test-sanity.R

@@ -0,0 +1,93 @@
+
+test_that("edc_data_warn snapshot", {
+  clean_lookup()
+  tm = edc_example()
+  attach(tm)
+
+  expect_snapshot({
+    #default
+    db0 %>%
+      filter(age>60) %>%
+      edc_data_warn("Age should not be >60")
+
+    #no issue_n
+    db0 %>%
+      filter(age>70) %>%
+      edc_data_warn("Age should not be >70", issue_n=NULL)
+
+    #with issue_n & max_subjid
+    db0 %>%
+      filter(age>20) %>%
+      edc_data_warn("Age should not be >20", issue_n=1, max_subjid=2)
+
+    #multiple subjid proposals
+    db0 %>%
+      filter(age>70) %>%
+      edc_data_warn("Age should not be >70", issue_n=NULL, col_subjid=c("SUBJID", "PATNO"))
+
+
+    ## WARNINGS
+
+    #warning, multiple subjid found
+    db0 %>%
+      filter(age>70) %>%
+      edc_data_warn("Age should not be >70", issue_n=2, col_subjid=c("SUBJID", "group"))
+
+    #warning, multiple subjid found, reverse order
+    db0 %>%
+      filter(age>70) %>%
+      edc_data_warn("Age should not be >70", issue_n=3, col_subjid=c("group", "SUBJID"))
+
+
+    edc_data_warnings()
+  })
+
+})
+
+test_that("edc_data_warn errors", {
+  clean_lookup()
+  tm = edc_example()
+  attach(tm)
+
+  #error expected
+  db0 %>%
+    filter(age>70) %>%
+    edc_data_stop("Age should never be >70", issue_n=99) %>% 
+    expect_error()
+
+  #error subjid not found
+  db0 %>%
+    filter(age>70) %>%
+    edc_data_warn("Age should not be >70", issue_n=98, col_subjid=c("PATNO")) %>% 
+    expect_error(class="edc_data_condition_subjid_error")
+
+})
+
+test_that("edc_data_warn CSV", {
+  clean_lookup()
+  tm = edc_example()
+  attach(tm)
+
+  path = tempfile(fileext=".csv")
+
+  expect_false(file_exists(path))
+
+  input = db0 %>%
+    as.data.frame() %>% 
+    filter(age>70) %>%
+    select(SUBJID, age, group) %>% 
+    labelled::remove_labels()
+
+  input %>% 
+    edc_data_warn("Age should not be >70", issue_n=99, csv_path=path) %>% 
+    expect_warning()
+
+  output = read.csv2(path)
+
+  expect_equal(input, output, tolerance = 0.01)
+
+  #cleanup
+  unlink(path)
+  expect_false(file_exists(path))
+
+})