## ----include = FALSE----------------------------------------------------------
NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true")
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = NOT_CRAN
)

## ----warning=FALSE, message=FALSE---------------------------------------------
# library(DBI)
# library(duckdb)
# library(dplyr)
# library(CDMConnector)
# library(CodelistGenerator)

## ----warning=FALSE------------------------------------------------------------
# requireEunomia()
# db <- dbConnect(duckdb(), dbdir = eunomiaDir())
# cdm <- cdmFromCon(db,
#                   cdmSchema = "main",
#                   writeSchema = "main",
#                   writePrefix = "cg_")
# cdm

## -----------------------------------------------------------------------------
# cdm$concept |> glimpse()
# cdm$concept_relationship |> glimpse()
# cdm$concept_ancestor |> glimpse()
# cdm$concept_synonym |> glimpse()
# cdm$drug_strength |> glimpse()

## -----------------------------------------------------------------------------
# vocabularyVersion(cdm)

## -----------------------------------------------------------------------------
# availableVocabularies(cdm)

## ----eval = FALSE-------------------------------------------------------------
# library(readr)
# library(DBI)
# library(duckdb)
# library(omopgenerics)
# library(here)
# 
# vocab_folder <- here() # add path to directory
# 
# # read in files
# concept <- read_delim(here(vocab_folder, "CONCEPT.csv"),
#                       "\t",
#                       escape_double = FALSE, trim_ws = TRUE
# )
# concept_relationship <- read_delim(here(vocab_folder, "CONCEPT_RELATIONSHIP.csv"),
#                                    "\t",
#                                    escape_double = FALSE, trim_ws = TRUE
# )
# concept_ancestor <- read_delim(here(vocab_folder, "CONCEPT_ANCESTOR.csv"),
#                                "\t",
#                                escape_double = FALSE, trim_ws = TRUE
# )
# concept_synonym <- read_delim(here(vocab_folder, "CONCEPT_SYNONYM.csv"),
#                               "\t",
#                               escape_double = FALSE, trim_ws = TRUE
# )
# vocabulary <- read_delim(here(vocab_folder, "VOCABULARY.csv"), "\t",
#                          escape_double = FALSE, trim_ws = TRUE
# )
# 
# # write to duckdb
# db <- dbConnect(duckdb(), here(vocab_folder,"vocab.duckdb"))
# dbWriteTable(db, "concept", concept, overwrite = TRUE)
# dbWriteTable(db, "concept_relationship", concept_relationship, overwrite = TRUE)
# dbWriteTable(db, "concept_ancestor", concept_ancestor, overwrite = TRUE)
# dbWriteTable(db, "concept_synonym", concept_synonym, overwrite = TRUE)
# dbWriteTable(db, "vocabulary", vocabulary, overwrite = TRUE)
# # add empty person and observation period tables
# person_cols <- omopColumns("person")
# person <- data.frame(matrix(ncol = length(person_cols), nrow = 0))
# colnames(person) <- person_cols
# dbWriteTable(db, "person", person, overwrite = TRUE)
# observation_period_cols <- omopColumns("observation_period")
# observation_period <- data.frame(matrix(ncol = length(observation_period_cols), nrow = 0))
# colnames(observation_period) <- observation_period_cols
# dbWriteTable(db, "observation_period", observation_period, overwrite = TRUE)
# dbDisconnect(db)

## ----eval = FALSE-------------------------------------------------------------
# db <- dbConnect(duckdb(), here(vocab_folder,"vocab.duckdb"))
# cdm <- cdmFromCon(db, "main", "main", cdmName = "vocabularise", .softValidation = TRUE)