From 17858f06af306235ca6dc60a117c0dfcf55d0fa8 Mon Sep 17 00:00:00 2001
From: statasarus <55274484+statasaurus@users.noreply.github.com>
Date: Wed, 28 Feb 2024 17:15:44 +0000
Subject: [PATCH 01/13] #95 require higher version of R

---
 DESCRIPTION | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f532941..f34b3ab 100644
--- a/DESCRIPTION
+++ b/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,

From 4b5f896b2223eed962a30dfb8d5ede15112521be Mon Sep 17 00:00:00 2001
From: statasarus <55274484+statasaurus@users.noreply.github.com>
Date: Wed, 28 Feb 2024 17:16:51 +0000
Subject: [PATCH 02/13] #97 fix codelist and pred issues

---
 R/metacore.R     | 15 +++++++++------
 R/spec_builder.R | 25 ++++++++++++++-----------
 2 files changed, 23 insertions(+), 17 deletions(-)

diff --git a/R/metacore.R b/R/metacore.R
index 1f804c0..b2bbfb8 100644
--- a/R/metacore.R
+++ b/R/metacore.R
@@ -189,14 +189,17 @@ MetaCore_filter <- function(value) {
                  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 @@ select_dataset <- function(.data, dataset, simplify = FALSE) {
 
    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)
diff --git a/R/spec_builder.R b/R/spec_builder.R
index f011687..26a0976 100644
--- a/R/spec_builder.R
+++ b/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 @@ read_all_sheets <- function(path){
 #' @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 @@ spec_type_to_ds_spec <- function(doc, cols = c("dataset" = "[N|n]ame|[D|d]ataset
 #' @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 @@ spec_type_to_ds_vars <- function(doc, cols = c("dataset" = "[D|d]ataset|[D|d]oma
 #' @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 @@ spec_type_to_var_spec <- function(doc, cols = c("variable" = "[N|n]ame|[V|v]aria
 #' @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 @@ spec_type_to_value_spec <- function(doc, cols = c("dataset" = "[D|d]ataset|[D|d]
 
    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 @@ spec_type_to_value_spec <- function(doc, cols = c("dataset" = "[D|d]ataset|[D|d]
       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$predecessor)
@@ -453,7 +456,7 @@ spec_type_to_value_spec <- function(doc, cols = c("dataset" = "[D|d]ataset|[D|d]
 #' @return a dataset formatted for the metacore object
 #' @export
 #'
-#' @family spec builder
+#' @family {spec builder}
 spec_type_to_codelist <- function(doc, codelist_cols = c("code_id" = "ID",
                                                          "name" = "[N|n]ame",
                                                          "code" = "^[C|c]ode|^[T|t]erm",
@@ -558,7 +561,7 @@ spec_type_to_codelist <- function(doc, codelist_cols = c("code_id" = "ID",
 #' @return a dataset formatted for the metacore object
 #' @export
 #'
-#' @family spec builder
+#' @family {spec builder}
 #' @importFrom purrr quietly
 spec_type_to_derivations <- function(doc, cols = c("derivation_id" = "ID",
                                                    "derivation" = "[D|d]efinition|[D|d]escription"),
@@ -591,7 +594,7 @@ spec_type_to_derivations <- function(doc, cols = c("derivation_id" = "ID",
    other_derivations <- ls_derivations %>%
       mutate(
          derivation_id = case_when(
-            str_to_lower(.data$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_
             ),

From 0b86d3894d6b2fe4f9b3a100690e1a9d4bb82aed Mon Sep 17 00:00:00 2001
From: statasarus <55274484+statasaurus@users.noreply.github.com>
Date: Wed, 28 Feb 2024 17:17:05 +0000
Subject: [PATCH 03/13] Update documentation

---
 man/get_control_term.Rd         | 2 ++
 man/spec_to_metacore.Rd         | 4 ++--
 man/spec_type_to_codelist.Rd    | 4 ++--
 man/spec_type_to_derivations.Rd | 4 ++--
 man/spec_type_to_ds_spec.Rd     | 4 ++--
 man/spec_type_to_ds_vars.Rd     | 4 ++--
 man/spec_type_to_value_spec.Rd  | 4 ++--
 man/spec_type_to_var_spec.Rd    | 4 ++--
 8 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/man/get_control_term.Rd b/man/get_control_term.Rd
index 3171bdd..d5317a4 100644
--- a/man/get_control_term.Rd
+++ b/man/get_control_term.Rd
@@ -24,7 +24,9 @@ lists) for a given variable. The dataset can be optionally specified if there
 is different control terminology for different datasets
 }
 \examples{
+\dontrun{
 meta_ex <- spec_to_metacore(metacore_example("p21_mock.xlsx"))
 get_control_term(meta_ex, QVAL, SUPPAE)
 get_control_term(meta_ex, "QVAL", "SUPPAE")
 }
+}
diff --git a/man/spec_to_metacore.Rd b/man/spec_to_metacore.Rd
index f994fca..cc4cfdd 100644
--- a/man/spec_to_metacore.Rd
+++ b/man/spec_to_metacore.Rd
@@ -21,6 +21,6 @@ given a spec document it returns a metacore object
 \description{
 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.
 }
diff --git a/man/spec_type_to_codelist.Rd b/man/spec_type_to_codelist.Rd
index f4ebb9d..91646ec 100644
--- a/man/spec_type_to_codelist.Rd
+++ b/man/spec_type_to_codelist.Rd
@@ -47,11 +47,11 @@ sheet input). The named vector \verb{*_cols} is used to determine which is the
 correct sheet and renames the columns.
 }
 \seealso{
-Other spec builder: 
+Other {spec builder}: 
 \code{\link{spec_type_to_derivations}()},
 \code{\link{spec_type_to_ds_spec}()},
 \code{\link{spec_type_to_ds_vars}()},
 \code{\link{spec_type_to_value_spec}()},
 \code{\link{spec_type_to_var_spec}()}
 }
-\concept{spec builder}
+\concept{{spec builder}}
diff --git a/man/spec_type_to_derivations.Rd b/man/spec_type_to_derivations.Rd
index 9d90625..eca35fc 100644
--- a/man/spec_type_to_derivations.Rd
+++ b/man/spec_type_to_derivations.Rd
@@ -36,11 +36,11 @@ correct sheet and renames the columns. The derivation will be used for
 "predecessor" origins.
 }
 \seealso{
-Other spec builder: 
+Other {spec builder}: 
 \code{\link{spec_type_to_codelist}()},
 \code{\link{spec_type_to_ds_spec}()},
 \code{\link{spec_type_to_ds_vars}()},
 \code{\link{spec_type_to_value_spec}()},
 \code{\link{spec_type_to_var_spec}()}
 }
-\concept{spec builder}
+\concept{{spec builder}}
diff --git a/man/spec_type_to_ds_spec.Rd b/man/spec_type_to_ds_spec.Rd
index f99d3a5..30f135d 100644
--- a/man/spec_type_to_ds_spec.Rd
+++ b/man/spec_type_to_ds_spec.Rd
@@ -29,11 +29,11 @@ input). The named vector \code{cols} is used to determine which is the correct
 sheet and renames the columns
 }
 \seealso{
-Other spec builder: 
+Other {spec builder}: 
 \code{\link{spec_type_to_codelist}()},
 \code{\link{spec_type_to_derivations}()},
 \code{\link{spec_type_to_ds_vars}()},
 \code{\link{spec_type_to_value_spec}()},
 \code{\link{spec_type_to_var_spec}()}
 }
-\concept{spec builder}
+\concept{{spec builder}}
diff --git a/man/spec_type_to_ds_vars.Rd b/man/spec_type_to_ds_vars.Rd
index 9b0bd29..8d493b9 100644
--- a/man/spec_type_to_ds_vars.Rd
+++ b/man/spec_type_to_ds_vars.Rd
@@ -39,11 +39,11 @@ input). The named vector \code{cols} is used to determine which is the correct
 sheet and renames the columns
 }
 \seealso{
-Other spec builder: 
+Other {spec builder}: 
 \code{\link{spec_type_to_codelist}()},
 \code{\link{spec_type_to_derivations}()},
 \code{\link{spec_type_to_ds_spec}()},
 \code{\link{spec_type_to_value_spec}()},
 \code{\link{spec_type_to_var_spec}()}
 }
-\concept{spec builder}
+\concept{{spec builder}}
diff --git a/man/spec_type_to_value_spec.Rd b/man/spec_type_to_value_spec.Rd
index f9a1a59..84c4ab3 100644
--- a/man/spec_type_to_value_spec.Rd
+++ b/man/spec_type_to_value_spec.Rd
@@ -48,11 +48,11 @@ sheet input). The named vector \code{cols} is used to determine which is the
 correct sheet and renames the columns
 }
 \seealso{
-Other spec builder: 
+Other {spec builder}: 
 \code{\link{spec_type_to_codelist}()},
 \code{\link{spec_type_to_derivations}()},
 \code{\link{spec_type_to_ds_spec}()},
 \code{\link{spec_type_to_ds_vars}()},
 \code{\link{spec_type_to_var_spec}()}
 }
-\concept{spec builder}
+\concept{{spec builder}}
diff --git a/man/spec_type_to_var_spec.Rd b/man/spec_type_to_var_spec.Rd
index 04e8964..ba02179 100644
--- a/man/spec_type_to_var_spec.Rd
+++ b/man/spec_type_to_var_spec.Rd
@@ -30,11 +30,11 @@ input). The named vector \code{cols} is used to determine which is the correct
 sheet and renames the columns. (Note: the keep column will be converted logical)
 }
 \seealso{
-Other spec builder: 
+Other {spec builder}: 
 \code{\link{spec_type_to_codelist}()},
 \code{\link{spec_type_to_derivations}()},
 \code{\link{spec_type_to_ds_spec}()},
 \code{\link{spec_type_to_ds_vars}()},
 \code{\link{spec_type_to_value_spec}()}
 }
-\concept{spec builder}
+\concept{{spec builder}}

From 6f9b55741573b52e242771d1a0b7075a1c2acee5 Mon Sep 17 00:00:00 2001
From: statasarus <55274484+statasaurus@users.noreply.github.com>
Date: Thu, 29 Feb 2024 09:29:26 +0000
Subject: [PATCH 04/13] remove 3.5 and go back to old pipe

---
 .github/workflows/check-standard.yaml | 1 -
 R/metacore.R                          | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
index 524fb30..3fe639a 100644
--- a/.github/workflows/check-standard.yaml
+++ b/.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"}
diff --git a/R/metacore.R b/R/metacore.R
index b2bbfb8..68be91f 100644
--- a/R/metacore.R
+++ b/R/metacore.R
@@ -199,7 +199,7 @@ MetaCore_filter <- function(value) {
 
    private$.codelist <- private$.codelist %>%
       right_join(private$.value_spec %>%
-                    distinct(.data$code_id) |>
+                    distinct(.data$code_id) %>%
                     na.omit(), by = "code_id", multiple = "all")
 
    private$.supp <- private$.supp %>% filter(dataset == value)

From 76826934f3891219ca965c52c3cbd3b5effb3354 Mon Sep 17 00:00:00 2001
From: statasarus <55274484+statasaurus@users.noreply.github.com>
Date: Thu, 7 Mar 2024 12:54:37 +0000
Subject: [PATCH 05/13] correct how Comments a pulled in

I realised I wasn't ever pulling the information from the comment
---
 R/spec_builder.R             | 14 ++++++++++++++
 tests/testthat/test-reader.R |  4 +++-
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/R/spec_builder.R b/R/spec_builder.R
index 26a0976..de777ae 100644
--- a/R/spec_builder.R
+++ b/R/spec_builder.R
@@ -590,7 +590,21 @@ spec_type_to_derivations <- function(doc, cols = c("derivation_id" = "ID",
    if(class(ls_derivations)[1] == "list"){
       ls_derivations <- ls_derivations %>%
          reduce(bind_rows)
+      # Get the comments
+      if(any(str_detect(names(doc), "[C|c]omment"))){
+         comments <- doc[str_detect(names(doc), "[C|c]omment")][[1]] |>
+            select(matches("ID|Description"))
+         with_comments <- ls_derivations |>
+            filter(str_to_lower(.data$origin) == "assigned") |>
+            left_join(comments, by = c("comment" = "ID" )) |>
+            mutate(comment = .data$Description) |>
+            select(-.data$Description)
+         ls_derivations <- ls_derivations |>
+            filter(str_to_lower(origin) != "assigned") |>
+            bind_rows(with_comments)
+      }
    }
+
    other_derivations <- ls_derivations %>%
       mutate(
          derivation_id = case_when(
diff --git a/tests/testthat/test-reader.R b/tests/testthat/test-reader.R
index e1860e6..31c6adc 100644
--- a/tests/testthat/test-reader.R
+++ b/tests/testthat/test-reader.R
@@ -466,10 +466,12 @@ test_that("derivation reader tests", {
       select(derivation_id = ID,
              derivation = Description) %>%
       mutate(derivation_id = paste0("MT.", derivation_id))
+
    ref_deriv <- spec$Variables %>%
       filter(Origin %in% c("Assigned")) %>%
+      left_join(select(spec$Comments, ID, Description), by = c("Comment" = "ID")) %>%
       mutate(derivation_id = paste0("MT.", Dataset, ".", Variable),
-             derivation = Comment) %>%
+             derivation = Description) %>%
       select(starts_with("derivation")) %>%
       bind_rows(ref_deriv, .) %>%
       arrange(derivation_id) %>%

From 9669445bce1a4bb3956445b02c926cc88c522745 Mon Sep 17 00:00:00 2001
From: statasarus <55274484+statasaurus@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:01:24 +0100
Subject: [PATCH 06/13] add some tests and fix note

---
 R/spec_builder.R             |  2 +-
 R/xml_builders.R             |  8 ++++++--
 tests/testthat/test-reader.R | 11 +++++++++--
 3 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/R/spec_builder.R b/R/spec_builder.R
index de777ae..b746436 100644
--- a/R/spec_builder.R
+++ b/R/spec_builder.R
@@ -600,7 +600,7 @@ spec_type_to_derivations <- function(doc, cols = c("derivation_id" = "ID",
             mutate(comment = .data$Description) |>
             select(-.data$Description)
          ls_derivations <- ls_derivations |>
-            filter(str_to_lower(origin) != "assigned") |>
+            filter(str_to_lower(.data$origin) != "assigned") |>
             bind_rows(with_comments)
       }
    }
diff --git a/R/xml_builders.R b/R/xml_builders.R
index 8526098..f3e6ae6 100644
--- a/R/xml_builders.R
+++ b/R/xml_builders.R
@@ -357,8 +357,12 @@ xml_to_codelist <- function(doc) {
             version = xml_attr(node, "Version"),
             type = "external_library"
          )
-      }) %>%
-      nest(codes = c(.data$dictionary, .data$version))
+      })
+   if(nrow(external_libs) > 0){
+      external_libs <- external_libs |>
+         nest(codes = c(.data$dictionary, .data$version))
+   }
+
 
    # Combinging the code decode with the permitted values
    bind_rows(code_decode, permitted_val, external_libs) %>%
diff --git a/tests/testthat/test-reader.R b/tests/testthat/test-reader.R
index 31c6adc..d4c2623 100644
--- a/tests/testthat/test-reader.R
+++ b/tests/testthat/test-reader.R
@@ -255,10 +255,18 @@ test_that("Test var_spec readers", {
    spec_var_spec <- spec_type_to_var_spec(spec) %>%
       arrange(variable) %>%
       select(variable, type, length, label, format)
-   # remove common as it is derived when reading in specs but left alone from defines
+
+   spec2 <- spec
+   spec2$Variables |>
+      select(-Dataset)
+   no_ds <- spec_type_to_var_spec(spec2) |>
+      arrange(variable) %>%
+      select(variable, type, length, label, format)
+   expect_equal(no_ds, spec_var_spec)
 
    # Tests
    expect_equal(def_var_spec, ref_var_spec)
+   # remove common as it is derived when reading in specs but left alone from defines
    expect_equal(spec_var_spec,
                 ref_var_spec %>%
                    select(-common))
@@ -397,7 +405,6 @@ test_that("values_spec reader tests", {
                 map(~paste0(.[1], " '", .[2])),
              where = if_else(where == "NA 'NA", NA_character_, paste0(where, "'")))
 
-
    # Tests
    expect_equal(def_value_spec, ref_value_spec)
    expect_equal(spec_value_spec,  ref_value_spec)

From e21eb69f34e74f4ebb0df4cbc5a879c9d3300a3f Mon Sep 17 00:00:00 2001
From: statasarus <55274484+statasaurus@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:02:07 +0100
Subject: [PATCH 07/13] remove 3.6

---
 .github/workflows/check-standard.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
index 3fe639a..7f99670 100644
--- a/.github/workflows/check-standard.yaml
+++ b/.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: '3.6', 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"}
 

From 3f6cbf3dee648741b3a6f3d351ff9370a59ed7cc Mon Sep 17 00:00:00 2001
From: Tamara Senior <tamara.senior@roche.com>
Date: Fri, 12 Apr 2024 17:34:42 +0200
Subject: [PATCH 08/13] initial commit

---
 NAMESPACE       |  1 +
 NEWS.md         |  5 ++++-
 R/metacore.R    | 36 ++++++++++++++++++++++++++++++++++++
 man/get_keys.Rd | 25 +++++++++++++++++++++++++
 4 files changed, 66 insertions(+), 1 deletion(-)
 create mode 100644 man/get_keys.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 6824bb1..c9023a7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ export(check_inconsistent_types)
 export(create_tbl)
 export(define_to_metacore)
 export(get_control_term)
+export(get_keys)
 export(is_metacore)
 export(load_metacore)
 export(metacore)
diff --git a/NEWS.md b/NEWS.md
index 10058b6..40be616 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,7 @@
-# Metacroe 0.1.2
+# Metacore 0.1.3
+- Add `get_keys` function which returns the dataset keys for a given dataset
+
+# Metacore 0.1.2
 - Update to resolve issues from the dplyr updates
 
 # Metacore 0.1.1
diff --git a/R/metacore.R b/R/metacore.R
index 68be91f..d70e9df 100644
--- a/R/metacore.R
+++ b/R/metacore.R
@@ -413,6 +413,42 @@ get_control_term <- function(metacode, variable, dataset = NULL){
 }
 
 
+#' Get Dataset Keys
+#'
+#' Returns the dataset keys for a given dataset
+#'
+#' @param metacode metacore object
+#' @param dataset A dataset name
+#'
+#' @return a 2-column tibble with dataset key variables and key sequence
+#' @export
+#'
+#' @importFrom rlang as_label enexpr as_name
+#'
+#' @examples
+#' \dontrun{
+#' meta_ex <- spec_to_metacore(metacore_example("p21_mock.xlsx"))
+#' get_keys(meta_ex, "AE")
+#' }
+get_keys <- function(metacode, dataset){
+   dataset_val <- ifelse(str_detect(as_label(enexpr(dataset)), "\""),
+                         as_name(dataset), as_label(enexpr(dataset))) # to make the filter more explicit
+
+   subset_data <- metacode$ds_vars %>%
+      filter(dataset == dataset_val)
+   if(nrow(subset_data) == 0){
+      stop(paste0(dataset_val, " not found in the value_spec table. Please check the dataset name"))
+   }
+
+   keys <- subset_data %>%
+      filter(!is.na(key_seq)) %>%
+      select(variable, key_seq)
+
+   keys <- keys[order(keys$key_seq),]
+
+   return(keys)
+}
+
 
 #' save metacore object
 #'
diff --git a/man/get_keys.Rd b/man/get_keys.Rd
new file mode 100644
index 0000000..64c6c40
--- /dev/null
+++ b/man/get_keys.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/metacore.R
+\name{get_keys}
+\alias{get_keys}
+\title{Get Dataset Keys}
+\usage{
+get_keys(metacode, dataset)
+}
+\arguments{
+\item{metacode}{metacore object}
+
+\item{dataset}{A dataset name}
+}
+\value{
+a 2-column tibble with dataset key variables and key sequence
+}
+\description{
+Returns the dataset keys for a given dataset
+}
+\examples{
+\dontrun{
+meta_ex <- spec_to_metacore(metacore_example("p21_mock.xlsx"))
+get_keys(meta_ex, "AE")
+}
+}

From 86fe5ec11d9a3de17938e8d426e3b064ea27cc08 Mon Sep 17 00:00:00 2001
From: Tamara Senior <tamara.senior@roche.com>
Date: Fri, 12 Apr 2024 17:57:55 +0200
Subject: [PATCH 09/13] update description

---
 DESCRIPTION | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index f34b3ab..ddc2f29 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,6 +21,10 @@ Authors@R:
              role = "aut",
              email = "mike.stackhouse@atorusresearch.com",
              comment = c(ORCID = "0000-0001-6030-723X")),
+      person(given = "Tamara",
+             family = "Senior",
+             role = "aut",
+             email = "tamara.senior@roche.com"),
       person(given = "GSK/Atorus JPT",
              role = c("cph", "fnd")))
 Description: Create an immutable container holding metadata for the purpose of better enabling programming activities and functionality of other packages within the clinical programming workflow.

From 43a67e704b292788a859076c9dbe90ffd23ef206 Mon Sep 17 00:00:00 2001
From: tamarasenior <102166057+tamarasenior@users.noreply.github.com>
Date: Fri, 19 Apr 2024 14:26:07 +0100
Subject: [PATCH 10/13] Update R/metacore.R

Co-authored-by: Jana Stoilova <43623360+anajens@users.noreply.github.com>
---
 R/metacore.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/metacore.R b/R/metacore.R
index d70e9df..3bcb754 100644
--- a/R/metacore.R
+++ b/R/metacore.R
@@ -429,6 +429,7 @@ get_control_term <- function(metacode, variable, dataset = NULL){
 #' \dontrun{
 #' meta_ex <- spec_to_metacore(metacore_example("p21_mock.xlsx"))
 #' get_keys(meta_ex, "AE")
+#' get_keys(meta_ex, AE)
 #' }
 get_keys <- function(metacode, dataset){
    dataset_val <- ifelse(str_detect(as_label(enexpr(dataset)), "\""),

From ced13e33d958eef9c5b48f6708402f19090c219e Mon Sep 17 00:00:00 2001
From: Tamara Senior <tamara.senior@roche.com>
Date: Thu, 25 Apr 2024 15:14:22 +0200
Subject: [PATCH 11/13] Write unit tests

---
 R/metacore.R                   |  2 +-
 man/get_keys.Rd                |  1 +
 tests/testthat/test-metacore.R | 15 +++++++++++++++
 3 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/R/metacore.R b/R/metacore.R
index 3bcb754..fa0c338 100644
--- a/R/metacore.R
+++ b/R/metacore.R
@@ -438,7 +438,7 @@ get_keys <- function(metacode, dataset){
    subset_data <- metacode$ds_vars %>%
       filter(dataset == dataset_val)
    if(nrow(subset_data) == 0){
-      stop(paste0(dataset_val, " not found in the value_spec table. Please check the dataset name"))
+      stop(paste0(dataset_val, " not found in the ds_vars table. Please check the dataset name"))
    }
 
    keys <- subset_data %>%
diff --git a/man/get_keys.Rd b/man/get_keys.Rd
index 64c6c40..84687b1 100644
--- a/man/get_keys.Rd
+++ b/man/get_keys.Rd
@@ -21,5 +21,6 @@ Returns the dataset keys for a given dataset
 \dontrun{
 meta_ex <- spec_to_metacore(metacore_example("p21_mock.xlsx"))
 get_keys(meta_ex, "AE")
+get_keys(meta_ex, AE)
 }
 }
diff --git a/tests/testthat/test-metacore.R b/tests/testthat/test-metacore.R
index 840d1ce..a8f3c23 100644
--- a/tests/testthat/test-metacore.R
+++ b/tests/testthat/test-metacore.R
@@ -137,3 +137,18 @@ test_that("pulling out control terminology works", {
    )
    })
 
+test_that("get_keys works", {
+   test <- spec_to_metacore(metacore_example("p21_mock.xlsx"), quiet = TRUE)
+   #Testing Errors
+   ## Domain not in ds_vars table
+   expect_error(get_keys(test, DS))
+   ## Missing dataset name
+   expect_error(get_keys(test))
+   #Testing Correct Output
+   expect_equal(
+      get_keys(test, DM),
+      tibble(variable = c("STUDYID", "USUBJID"), key_seq = c(1L, 2L)) %>%
+         add_labs(variable = "Variable Name",
+                  key_seq = "Sequence Key")
+   )
+})

From 49ee0578231755e706bdff0f2c857fbc5c8f7368 Mon Sep 17 00:00:00 2001
From: statasarus <55274484+statasaurus@users.noreply.github.com>
Date: Wed, 1 May 2024 15:13:32 +0100
Subject: [PATCH 12/13] Update news

---
 NEWS.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 40be616..62787e4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,6 @@
 # Metacore 0.1.3
-- Add `get_keys` function which returns the dataset keys for a given dataset
+- Add `get_keys` function which returns the dataset keys for a given dataset [#102](https://github.com/atorus-research/metacore/issues/102) 
+- Fix issues with `select_dataset(simplify = TRUE)` [#97](https://github.com/atorus-research/metacore/issues/97) 
 
 # Metacore 0.1.2
 - Update to resolve issues from the dplyr updates

From 0fe12f548d2b39fc6eb74541b9a85f21085836d9 Mon Sep 17 00:00:00 2001
From: statasarus <55274484+statasaurus@users.noreply.github.com>
Date: Wed, 1 May 2024 15:21:53 +0100
Subject: [PATCH 13/13] add rhub workflow

---
 .github/workflows/rhub.yaml | 95 +++++++++++++++++++++++++++++++++++++
 1 file changed, 95 insertions(+)
 create mode 100644 .github/workflows/rhub.yaml

diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
new file mode 100644
index 0000000..74ec7b0
--- /dev/null
+++ b/.github/workflows/rhub.yaml
@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}