Closes #49: add get_terms() from admiral.test

R/get_terms.R

@@ -0,0 +1,71 @@
+#' An example function as expected by the `get_terms_fun` parameter of
+#' `admiral::create_query_data()`
+#'
+#' @param basket_select A basket_select object defining the terms
+#'
+#' @param version MedDRA version
+#'
+#' @param keep_id Should `GRPID` be included in the output?
+#'
+#' @param temp_env Temporary environment
+get_terms <- function(basket_select,
+                      version,
+                      keep_id,
+                      temp_env) {
+  if (basket_select$type == "smq") {
+    if (is.null(temp_env$admiral_smq_db)) {
+      data("admiral_smq_db", envir = temp_env)
+    }
+    if (!is.null(basket_select$name)) {
+      is_in_smq <- temp_env$admiral_smq_db$smq_name == basket_select$name
+    } else {
+      is_in_smq <- temp_env$admiral_smq_db$smq_id == basket_select$id
+    }
+    if (basket_select$scope == "NARROW") {
+      is_in_scope <- temp_env$admiral_smq_db$scope == "narrow"
+    } else {
+      is_in_scope <- rep(TRUE, nrow(temp_env$admiral_smq_db))
+    }
+    if (keep_id) {
+      select_id <- c(GRPID = "smq_id")
+    } else {
+      select_id <- NULL
+    }
+    keep_cols <- c(
+      TERMNAME = "termname",
+      SRCVAR = "termvar",
+      GRPNAME = "smq_name",
+      select_id
+    )
+
+    structure(
+      temp_env$admiral_smq_db[is_in_smq & is_in_scope, keep_cols],
+      names = names(keep_cols)
+    )
+  } else if (basket_select$type == "sdg") {
+    if (is.null(temp_env$admiral_sdg_db)) {
+      data("admiral_sdg_db", envir = temp_env)
+    }
+    if (!is.null(basket_select$name)) {
+      is_in_sdq <- temp_env$admiral_sdg_db$sdg_name == basket_select$name
+    } else {
+      is_in_sdq <- temp_env$admiral_sdg_db$sdg_id == basket_select$id
+    }
+    if (keep_id) {
+      select_id <- c(GRPID = "sdg_id")
+    } else {
+      select_id <- NULL
+    }
+    keep_cols <- c(
+      TERMNAME = "termname",
+      SRCVAR = "termvar",
+      GRPNAME = "sdg_name",
+      select_id
+    )
+
+    structure(
+      temp_env$admiral_sdg_db[is_in_sdq, keep_cols],
+      names = names(keep_cols)
+    )
+  }
+}

inst/WORDLIST

@@ -2,27 +2,21 @@ ADEG
 ADaM
 AE
 AELAT
-Arancibia
 CDISC
-Changelog
 Contestí
 DM
 DS
 EG
 EXLAT
 EXLOC
-Farrugia
-Github
-GSK
+GRPID
 Gopi
-LinkedIn
 MH
+MedDRA
 NEI
-Onboarding
 Pharmacokinetic
 Pharmacokinetics
-QS
-README
+Pharmaverse
 Rodríguez
 SDG
 SDTM
@@ -33,20 +27,10 @@ SUPPDS
 SUPPTR
 SV
 TAs
-USUBJIDs
 VFQ
+Vegesna
 ae
-admiraldata
-admiraltemplate
-admiralxxx
-adxx
 anonymized
-dev
 nolint
-onboarding
 pharmaverse
 qs
-renv
-repo
-https
-Vegesna