From eb3d27926f30d3e8f16944bc7872c48ff98707fe Mon Sep 17 00:00:00 2001
From: Adam Black <adam.black@odysseusinc.com>
Date: Thu, 19 Aug 2021 16:22:08 -0400
Subject: [PATCH] Add imports and update docs.

---
 .Rbuildignore             |  1 +
 NAMESPACE                 |  3 ++
 R/WikiParser.R            |  2 +-
 R/createDdl.R             |  1 +
 R/downloadCurrentDdl.R    |  2 +-
 man/downloadCurrentDdl.Rd |  1 -
 man/writeDdl.Rd           | 61 +++++++++++++++++++++++++++++++++++++++
 7 files changed, 68 insertions(+), 3 deletions(-)
 create mode 100644 man/writeDdl.Rd

diff --git a/.Rbuildignore b/.Rbuildignore
index 51cbb5f..070fca2 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 .github/*
+extras/*
diff --git a/NAMESPACE b/NAMESPACE
index fc60bbb..92dc0be 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -13,3 +13,6 @@ export(writeDdl)
 export(writeForeignKeys)
 export(writeIndex)
 export(writePrimaryKeys)
+importFrom(utils,download.file)
+importFrom(utils,read.csv)
+importFrom(utils,write.csv)
diff --git a/R/WikiParser.R b/R/WikiParser.R
index b471633..1e5ee13 100644
--- a/R/WikiParser.R
+++ b/R/WikiParser.R
@@ -23,7 +23,7 @@
 #'
 #' @param mdFilesLocation Path to the root folder of the Wiki repository.
 #' @param output_file     Path to where the output CSV file should be written.
-#'
+#' @importFrom utils write.csv
 #' @export
 parseWiki <- function(mdFilesLocation, output_file) {
   # mdFilesLocation <- "../CommonDataModel.wiki"
diff --git a/R/createDdl.R b/R/createDdl.R
index 74464e6..d1a66dc 100644
--- a/R/createDdl.R
+++ b/R/createDdl.R
@@ -26,6 +26,7 @@
 #'
 #' @param cdmVersion The version of the CDM you are creating, e.g. 5.3, 5.4
 #' @return A character string containing the OHDSQL DDL
+#' @importFrom utils read.csv
 #' @export
 #' @examples
 #' ddl <- createDdl("5.4")
diff --git a/R/downloadCurrentDdl.R b/R/downloadCurrentDdl.R
index 8bd9de3..469208b 100644
--- a/R/downloadCurrentDdl.R
+++ b/R/downloadCurrentDdl.R
@@ -14,7 +14,7 @@
 #' downloadCurrentDdl("OHDSI/CommonDataModel",
 #'  pathToCsv="Sql%20Server/OMOP%20CDM%20sql%20server%20ddl.txt")
 #' }
-#'
+#' @importFrom utils download.file
 #' @export
 
 downloadCurrentDdl <- function(githubPath="OHDSI/CommonDataModel",
diff --git a/man/downloadCurrentDdl.Rd b/man/downloadCurrentDdl.Rd
index 867c863..f3068d2 100644
--- a/man/downloadCurrentDdl.Rd
+++ b/man/downloadCurrentDdl.Rd
@@ -30,5 +30,4 @@ The default location is
 downloadCurrentDdl("OHDSI/CommonDataModel",
  pathToCsv="Sql\%20Server/OMOP\%20CDM\%20sql\%20server\%20ddl.txt")
 }
-
 }
diff --git a/man/writeDdl.Rd b/man/writeDdl.Rd
new file mode 100644
index 0000000..c245499
--- /dev/null
+++ b/man/writeDdl.Rd
@@ -0,0 +1,61 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/writeDdl.R
+\name{writeDdl}
+\alias{writeDdl}
+\alias{writePrimaryKeys}
+\alias{writeForeignKeys}
+\alias{writeIndex}
+\title{Write DDL script}
+\usage{
+writeDdl(
+  targetDialect,
+  cdmVersion,
+  outputpath,
+  cdmDatabaseSchema = "@cdmDatabaseSchema"
+)
+
+writePrimaryKeys(
+  targetDialect,
+  cdmVersion,
+  outputpath,
+  cdmDatabaseSchema = "@cdmDatabaseSchema"
+)
+
+writeForeignKeys(
+  targetDialect,
+  cdmVersion,
+  outputpath,
+  cdmDatabaseSchema = "@cdmDatabaseSchema"
+)
+
+writeIndex(
+  targetDialect,
+  cdmVersion,
+  outputpath,
+  cdmDatabaseSchema = "@cdmDatabaseSchema"
+)
+}
+\arguments{
+\item{targetDialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"}
+
+\item{cdmVersion}{The version of the CDM you are creating, e.g. 5.3, 5.4}
+
+\item{outputpath}{The directory or folder where the SQL file should be saved.}
+
+\item{cdmDatabaseSchema}{The schema of the CDM instance where the DDL will be run. For example, this would be "ohdsi.dbo" when testing on sql server.
+Defaults to "@cdmDatabaseSchema"}
+}
+\description{
+Write the DDL to a SQL file. The SQL will be rendered (parameters replaced) and translated to the target SQL
+dialect. By default the @cdmDatabaseSchema parameter is kept in the SQL file and needs to be replaced before
+execution.
+}
+\section{Functions}{
+\itemize{
+\item \code{writePrimaryKeys}: writePrimaryKeys Write the SQL code that creates the primary keys to a file.
+
+\item \code{writeForeignKeys}: writeForeignKeys Write the SQL code that creates the foreign keys to a file.
+
+\item \code{writeIndex}: writeIndex Write the rendered and translated sql that creates recommended indexes to a file.
+}}
+