## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(metacore)
library(dplyr)
library(purrr)
library(stringr)

## ----error=TRUE---------------------------------------------------------------
try({
spec_to_metacore(metacore_example("mock_spec.xlsx"))
})

## -----------------------------------------------------------------------------
metacore:::spec_type(metacore_example("mock_spec.xlsx"))

## -----------------------------------------------------------------------------
doc <- read_all_sheets(metacore_example("mock_spec.xlsx"))
doc %>% map(head)

## ----error=TRUE---------------------------------------------------------------
try({
spec_type_to_ds_spec(doc)
})

## -----------------------------------------------------------------------------
doc$Domains %>% names()

## -----------------------------------------------------------------------------
ds_spec <- spec_type_to_ds_spec(doc,
  cols = c(
    "dataset" = "Name",
    "structure" = "Data Structure",
    "label" = "Label"
  )
)
head(ds_spec)

## ----error=TRUE---------------------------------------------------------------
try({
spec_type_to_ds_vars(doc)
})

## -----------------------------------------------------------------------------
doc$Variables %>% head()

ds_vars <- spec_type_to_ds_vars(doc,
  cols = c(
    "dataset" = "Domain",
    "variable" = "[V|v]ariable [N|n]ame",
    "order" = "[V|v]ariable [O|o]rder",
    "mandatory" = "[M|m]andatory"
    # Note that in version 0.3.0 `keep` was renamed to `mandatory` to better align with CDISC terminology. See below for details.
  ),
  key_seq_cols = c(
    "dataset" = "Domain Name",
    "key_seq" = "Key"
  ),
  sheet = "[V|v]ar|Domains"
)

head(ds_vars)

## ----eval=FALSE, include=FALSE------------------------------------------------
# ds_vars <- spec_type_to_ds_vars(doc,
#   cols = c(
#     "dataset" = "Domain",
#     "variable" = "[V|v]ariable [N|n]ame",
#     "order" = "[V|v]ariable [O|o]rder",
#     "keep" = "[M|m]andatory"
#   )
# )

## -----------------------------------------------------------------------------
var_spec <- spec_type_to_var_spec(doc, cols = c(
  "variable" = "Variable Name",
  "length" = "[L|l]ength",
  "label" = "[L|l]abel",
  "type" = "[T|t]ype",
  "dataset" = "[D|d]ataset|[D|d]omain",
  "format" = "Format"
))
head(var_spec)

## -----------------------------------------------------------------------------
var_spec <- var_spec %>%
  mutate(format = if_else(str_detect(format, "\\."), format, ""))

## -----------------------------------------------------------------------------
value_spec <- spec_type_to_value_spec(doc,
  cols = c(
    "dataset" = "VLM Name|Domain",
    "variable" = "VLM Name|Variable Name",
    "origin" = "[O|o]rigin",
    "type" = "[T|t]ype",
    "code_id" = "Controlled Term",
    "where" = "Parameter Code",
    "derivation_id" = "Method",
    "predecessor" = "Method"
  ),
  where_sep_sheet = FALSE
)
head(value_spec)

## -----------------------------------------------------------------------------
derivation <- spec_type_to_derivations(doc,
  cols = c(
    "derivation_id" = "Name",
    "derivation" = "[D|d]efinition|[D|d]escription"
  ),
  var_cols = c(
    "dataset" = "Domain Name",
    "variable" = "Variable Name|VLM",
    "origin" = "[O|o]rigin",
    "predecessor" = "Comment",
    "comment" = "Comment"
  )
)
head(derivation)

## -----------------------------------------------------------------------------
codelist <- spec_type_to_codelist(doc,
  codelist_cols = c(
    "code_id" = "Codelist Code",
    "name" = "Codelist Name",
    "code" = "Coded Value",
    "decode" = "Decoded Value"
  ),
  simplify = TRUE,
  dict_cols = NULL
)
head(codelist)

## -----------------------------------------------------------------------------
metacore(ds_spec, ds_vars, var_spec, value_spec,
  derivation, codelist,
  verbose = "message"
)