Fix issues simplification

.github/workflows/check-standard.yaml

@@ -26,7 +26,6 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: '3.5', repos: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: '3.6', repos: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metacore
 Title: A Centralized Metadata Object Focus on Clinical Trial Data Programming Workflows
-Version: 0.1.2
+Version: 0.1.3
 Authors@R: 
     c(person(given = "Christina",
              family = "Fillmore",
@@ -27,7 +27,9 @@ Description: Create an immutable container holding metadata for the purpose of b
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE, r6 = FALSE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.1
+Depends: 
+    R (>= 3.6)
 Suggests: 
     testthat,
     knitr,

R/metacore.R

@@ -189,14 +189,17 @@
                  multiple = "all") %>%
       distinct(variable, .keep_all = TRUE) # for when duplicates gett through and have different lables but the same name
 
+   # Get values/variables that need derivations
+   val_deriv <- private$.value_spec %>%
+      distinct(.data$derivation_id) %>%
+      na.omit()
+
    private$.derivations <- private$.derivations %>%
-      right_join(private$.value_spec %>%
-                    select(derivation_id) %>%
-                    na.omit(), by = "derivation_id", multiple = "all")
+      right_join(val_deriv, by = "derivation_id", multiple = "all")
 
    private$.codelist <- private$.codelist %>%
       right_join(private$.value_spec %>%
-                    select(code_id) %>%
+                    distinct(.data$code_id) %>%
                     na.omit(), by = "code_id", multiple = "all")
 
    private$.supp <- private$.supp %>% filter(dataset == value)
@@ -330,13 +333,13 @@
 
    if (simplify) {
 
-      suppressMessages(
+     test <-  suppressMessages(
          list(
             cl$ds_vars,
             cl$var_spec,
             cl$value_spec,
             cl$derivations,
-            cl$codelist,
+            select(cl$codelist, code_id, codes),
             cl$supp
          ) %>%
             reduce(left_join)

R/spec_builder.R

@@ -2,8 +2,8 @@
 #'
 #' This function takes the location of an excel specification document and reads
 #' it in as a meta core object. At the moment it only supports specification in
-#' the format of pinnacle 21 specifications. But, the @family spec builder can
-#' be used as building blocks for bespoke specification documents
+#' the format of pinnacle 21 specifications. But, the section level spec builder can
+#' be used as building blocks for bespoke specification documents.
 #'
 #' @param path string of file location
 #' @param quiet Option to quietly load in, this will suppress warnings, but not
@@ -96,7 +96,7 @@
 #' @return a dataset formatted for the metacore object
 #' @export
 #'
-#' @family spec builder
+#' @family {spec builder}
 spec_type_to_ds_spec <- function(doc, cols = c("dataset" = "[N|n]ame|[D|d]ataset|[D|d]omain",
                                                "structure" = "[S|s]tructure",
                                                "label" = "[L|l]abel|[D|d]escription"), sheet = NULL){
@@ -140,7 +140,7 @@
 #' @return a dataset formatted for the metacore object
 #' @export
 #'
-#' @family spec builder
+#' @family {spec builder}
 spec_type_to_ds_vars <- function(doc, cols = c("dataset" = "[D|d]ataset|[D|d]omain",
                                                "variable" = "[V|v]ariable [[N|n]ame]?|[V|v]ariables?",
                                                "order" = "[V|v]ariable [O|o]rder|[O|o]rder",
@@ -214,7 +214,7 @@
 #' @return a dataset formatted for the metacore object
 #' @export
 #'
-#' @family spec builder
+#' @family {spec builder}
 spec_type_to_var_spec <- function(doc, cols = c("variable" = "[N|n]ame|[V|v]ariables?",
                                                 "length" = "[L|l]ength",
                                                 "label" = "[L|l]abel",
@@ -314,7 +314,7 @@
 #' @return a dataset formatted for the metacore object
 #' @export
 #'
-#' @family spec builder
+#' @family {spec builder}
 spec_type_to_value_spec <- function(doc, cols = c("dataset" = "[D|d]ataset|[D|d]omain",
                                                   "variable" = "[N|n]ame|[V|v]ariables?",
                                                   "origin" = "[O|o]rigin",
@@ -408,7 +408,10 @@
 
    if(!"derivation_id" %in% names(cols)){
       out <- out %>%
-         mutate(derivation_id = paste0(dataset, ".", variable))
+         mutate(derivation_id =
+                   if_else(str_to_lower(.data$origin) == "assigned",
+                      paste0(dataset, ".", variable),
+                      paste0("pred.", dataset, ".", variable)))
    }
 
    # Get missing columns
@@ -421,7 +424,7 @@
       mutate(sig_dig = as.integer(.data$sig_dig),
              derivation_id = case_when(
                 !is.na(.data$derivation_id) ~ .data$derivation_id,
-                str_to_lower(.data$origin) == "predecessor" ~ as.character(.data$predecessor),
+                str_to_lower(.data$origin) == "predecessor" ~ paste0("pred.", as.character(.data$predecessor)),
                 str_to_lower(.data$origin) == "assigned" ~ paste0(.data$dataset, ".", .data$variable))
       ) %>%
       select(-.data$predecessor)
@@ -453,7 +456,7 @@
 #' @return a dataset formatted for the metacore object
 #' @export
 #'
-#' @family spec builder
+#' @family {spec builder}
 spec_type_to_codelist <- function(doc, codelist_cols = c("code_id" = "ID",
                                                          "name" = "[N|n]ame",
                                                          "code" = "^[C|c]ode|^[T|t]erm",
@@ -558,7 +561,7 @@
 #' @return a dataset formatted for the metacore object
 #' @export
 #'
-#' @family spec builder
+#' @family {spec builder}
 #' @importFrom purrr quietly
 spec_type_to_derivations <- function(doc, cols = c("derivation_id" = "ID",
                                                    "derivation" = "[D|d]efinition|[D|d]escription"),
@@ -591,7 +594,7 @@
    other_derivations <- ls_derivations %>%
       mutate(
          derivation_id = case_when(
-            str_to_lower(.data$origin) == "predecessor" ~ as.character(.data$predecessor),
+            str_to_lower(.data$origin) == "predecessor" ~ paste0("pred.", as.character(.data$predecessor)),
             str_to_lower(.data$origin) == "assigned" ~ paste0(.data$dataset, ".", .data$variable),
             TRUE ~ NA_character_
             ),