Switched from checkmate to admiraldev assertions; added tests for exa…

…mple + validations

R/derive_blfl.R

@@ -205,65 +205,31 @@ derive_blfl <- function(sdtm_in,
                         baseline_visits = character(),
                         baseline_timepoints = character()) {
   # Check assertions --------------------------------------------------------
-  assertion_collection <- checkmate::makeAssertCollection()
-  # Assert that sdtm_in is a data frame,
-  checkmate::assert_data_frame(sdtm_in,
-                               col.names = "strict",
-                               min.rows = 1L,
-                               add = assertion_collection)
-
-  # Assert that the input dataset has a "DOMAIN" column
-  checkmate::assert_names(names(sdtm_in),
-                          must.include = c("DOMAIN", sdtm.oak:::oak_id_vars()),
-                          .var.name = "Columns of 'sdtm_inaset'",
-                          add = assertion_collection)
+  # Check variables are character scalars
+  admiraldev::assert_character_scalar(tgt_var)
+  admiraldev::assert_character_scalar(ref_var)
 
-  # Assert dm_domain is data.frame
-  checkmate::assert_data_frame(dm_domain,
-                               col.names = "strict",
-                               min.rows = 1L,
-                               add = assertion_collection)
-
-  # Check if USUBJID and reference_date is present in the DM
-  checkmate::assert_names(names(dm_domain),
-                          must.include = c("USUBJID", ref_var),
-                          .var.name = "Columns of 'dm_domain'",
-                          add = assertion_collection)
-
-  checkmate::assert_character(tgt_var,
-                              min.chars = 1L,
-                              len = 1L,
-                              add = assertion_collection)
-
-  checkmate::assert_names(tgt_var,
-                          type = "strict",
-                          add = assertion_collection)
-
-  checkmate::assert_character(ref_var,
-                              min.chars = 1L,
-                              len = 1L,
-                              add = assertion_collection)
+  # Assert that sdtm_in is a data frame, contains DOMAIN and oak id vars
+  admiraldev::assert_data_frame(
+    sdtm_in,
+    required_vars = rlang::syms(c("DOMAIN", sdtm.oak:::oak_id_vars()))
+    )
 
-  checkmate::assert_names(ref_var,
-                          type = "strict",
-                          add = assertion_collection)
-
-  checkmate::reportAssertions(assertion_collection)
+  # Assert dm_domain is data.frame
+  admiraldev::assert_data_frame(
+    dm_domain,
+    required_vars = rlang::syms(c("USUBJID", ref_var))
+  )
 
   # Get domain from input dataset
   domain <- unique(sdtm_in$DOMAIN)
-  checkmate::assert_character(domain,
-                              min.chars = 1L,
-                              len = 1L,
-                              add = assertion_collection)
+
+  admiraldev::assert_character_scalar(domain)
 
   # Assert that tgt_var is a concatenation of domain and "BLFL" or "LOBXFL"
-  checkmate::assert_choice(
-    tgt_var,
-    choices = c(paste0(domain, "BLFL"),
-                paste0(domain, "LOBXFL")),
-    add = assertion_collection
-  )
+  admiraldev::assert_character_scalar(tgt_var,
+                                      values = c(paste0(domain, "BLFL"),
+                                                 paste0(domain, "LOBXFL")))
 
   # Determine domain prefixed columns
   suffixes <-
@@ -274,14 +240,12 @@ derive_blfl <- function(sdtm_in,
     setNames(tolower(suffixes))
 
   # Assert that the input dataset has a "DTC" column
-  checkmate::assert_names(names(sdtm_in),
-                          must.include = c(domain_prefixed_names[c("orres",
-                                                                   "stat",
-                                                                   "testcd",
-                                                                   "dtc")]),
-                          .var.name = "Columns of 'sdtm_in'",
-                          add = assertion_collection)
-  checkmate::reportAssertions(assertion_collection)
+  admiraldev::assert_data_frame(
+    sdtm_in,
+    required_vars = rlang::syms(c(domain_prefixed_names[c("orres",
+                                                          "stat",
+                                                          "testcd",
+                                                          "dtc")])))
 
   # End of assertions, work begins ------------------------------------------
   # Create copy of input dataset for modification and processing

tests/testthat/_snaps/derive_blfl.md

@@ -0,0 +1,107 @@
+# derive_blfl example works
+
+    {
+      "type": "list",
+      "attributes": {
+        "class": {
+          "type": "character",
+          "attributes": {},
+          "value": ["tbl_df", "tbl", "data.frame"]
+        },
+        "row.names": {
+          "type": "integer",
+          "attributes": {},
+          "value": [1, 2, 3, 4, 5, 6, 7, 8, 9]
+        },
+        "names": {
+          "type": "character",
+          "attributes": {},
+          "value": ["DOMAIN", "oak_id", "raw_source", "patient_number", "USUBJID", "VSDTC", "VSTESTCD", "VSORRES", "VSSTAT", "VSLOBXFL"]
+        }
+      },
+      "value": [
+        {
+          "type": "character",
+          "attributes": {},
+          "value": ["VS", "VS", "VS", "VS", "VS", "VS", "VS", "VS", "VS"]
+        },
+        {
+          "type": "integer",
+          "attributes": {},
+          "value": [1, 2, 1, 2, 1, 2, 1, 1, 2]
+        },
+        {
+          "type": "character",
+          "attributes": {},
+          "value": ["VTLS1", "VTLS1", "VTLS1", "VTLS1", "VTLS2", "VTLS2", "VTLS1", "VTLS1", "VTLS1"]
+        },
+        {
+          "type": "integer",
+          "attributes": {},
+          "value": [375, 375, 375, 375, 375, 375, 376, 376, 376]
+        },
+        {
+          "type": "character",
+          "attributes": {},
+          "value": ["test_study-375", "test_study-375", "test_study-375", "test_study-375", "test_study-375", "test_study-375", "test_study-376", "test_study-376", "test_study-376"]
+        },
+        {
+          "type": "character",
+          "attributes": {},
+          "value": ["2020-09-01T13:31", "2020-10-01T11:20", "2020-09-28T10:10", "2020-10-01T13:31", "2020-09-28T10:10", "2020-09-28T10:05", "2020-09-20", "2020-09-20", "2020-09-20"]
+        },
+        {
+          "type": "character",
+          "attributes": {},
+          "value": ["DIABP", "DIABP", "PULSE", "PULSE", "SYSBP", "SYSBP", "DIABP", "PULSE", "PULSE"]
+        },
+        {
+          "type": "character",
+          "attributes": {},
+          "value": ["90", "90", "ND", "85", "120", "120", "75", null, "110"]
+        },
+        {
+          "type": "character",
+          "attributes": {},
+          "value": [null, null, null, null, null, null, null, "NOT DONE", null]
+        },
+        {
+          "type": "character",
+          "attributes": {},
+          "value": ["Y", null, null, null, null, "Y", "Y", null, "Y"]
+        }
+      ]
+    }
+
+# derive_blfl sdmt_in validations work
+
+    Required variable `DOMAIN` is missing
+
+---
+
+    Required variables `oak_id`, `raw_source` and `patient_number` are missing
+
+---
+
+    Required variables `VSORRES`, `VSSTAT`, `VSTESTCD` and `VSDTC` are missing
+
+# derive_blfl dm_domain validations work
+
+    Required variables `USUBJID` and `RFXSTDTC` are missing
+
+# derive_blfl tgt_var and ref_var validations work
+
+    `tgt_var` must be a character scalar but is a list
+
+---
+
+    `ref_var` must be a character scalar but is a data frame
+
+---
+
+    `tgt_var` must be one of 'VSBLFL' or 'VSLOBXFL' but is 'DMLOBXFL'
+
+# derive_blfl DOMAIN validation works
+
+    `domain` must be a character scalar but is `4`
+