Closes #21 #25 remove mention of _all in yamls and edits mapping spec vignette

DESCRIPTION

@@ -34,8 +34,8 @@ Remotes:
     gsm=Gilead-BioStats/gsm@gsm-core-test
 Suggests:
     clindata,
-    DT,
     knitr,
+    reactable,
     rmarkdown,
     testthat,
     tibble

R/ApplySpec.R

@@ -18,17 +18,6 @@
 #' @export
 
 ApplySpec <- function(dfSource, columnSpecs, domain) {
-  # Add all columns to the spec if '_all' is present.
-  if ("_all" %in% names(columnSpecs)) {
-    missingColumnSpecs <- setdiff(names(dfSource), names(columnSpecs))
-
-    for (column in missingColumnSpecs) {
-      columnSpecs[[column]] <- list()
-    }
-
-    columnSpecs[["_all"]] <- NULL
-  }
-
   # write a query to select the columns from the source
   columnMapping <- columnSpecs %>%
     imap(

vignettes/mapping_spec.Rmd

@@ -29,9 +29,9 @@ Each of the above 13 domains generally map directly 1-to-1 from a raw source, ex
 
 ```{r raw, echo = FALSE, message = FALSE, error = FALSE}
 library(dplyr)
-library(DT)
 library(gsm)
 library(gsm.mapping)
+library(reactable)
 # Source Data
 lSource <- list(
     Source_SUBJ = clindata::rawplus_dm,
@@ -103,13 +103,41 @@ raw_result <- lapply(names(mappings_wf), function(domain_name) {
 # Combine all domains into one table
 raw_final_table <- do.call(rbind, raw_result)
 row.names(raw_final_table) <- NULL
-raw_final_table %>%
-    DT::datatable(
-      extensions = 'FixedColumns',
-      options = list(
-        scrollX = FALSE,
-        fixedColumns = TRUE
-      ),
-      rownames = FALSE
+# raw_final_table %>%
+#     DT::datatable(
+#       extensions = 'FixedColumns',
+#       options = list(
+#         scrollX = FALSE,
+#         fixedColumns = TRUE
+#       ),
+#       rownames = FALSE
+#     )
+
+reactable(
+  raw_final_table,
+  groupBy = "Domain",
+  defaultPageSize = 5,
+  bordered = FALSE, # Removes unnecessary borders
+  highlight = TRUE, # Highlights row on hover
+  theme = reactableTheme(
+    borderColor = "#dee2e6",
+    backgroundColor = "white",
+    style = list(
+      fontFamily = "Arial, sans-serif",
+      fontSize = "14px"
+    ),
+    headerStyle = list(
+      fontWeight = "bold",
+      fontSize = "16px",
+      backgroundColor = "#f8f9fa",
+      borderBottom = "2px solid #dee2e6"
     )
+  ),
+  columns = list(
+    Domain = colDef(name = "Domain", style = list(fontWeight = "bold", fontSize = "15px")),
+    Source_Variable = colDef(name = "Source Variable"),
+    Mapped_Variable = colDef(name = "Mapped Variable"),
+    Type = colDef(name = "Type")
+  )
+)
 ```