update documentation

.Rbuildignore

@@ -1,2 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^LICENSE\.md$
+.github/*
+ddl/*

LICENSE.md

@@ -0,0 +1,194 @@
+Apache License
+==============
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NAMESPACE

@@ -4,9 +4,10 @@ export(createDdl)
 export(createForeignKeys)
 export(createPrimaryKeys)
 export(downloadCurrentDdl)
+export(executeDdl)
 export(listSupportedVersions)
 export(parseWiki)
-export(writeDDL)
+export(writeDdl)
 export(writeForeignKeys)
 export(writeIndex)
 export(writePrimaryKeys)

errorReport.txt

@@ -1,26 +0,0 @@
-DBMS:
-sql server
-
-Error:
-com.microsoft.sqlserver.jdbc.SQLServerException: 'fpk_NOTE_person_id' is not a constraint.
-
-SQL:
-ALTER TABLE ohdsi.dbo.NOTE DROP CONSTRAINT fpk_NOTE_person_id 
-
-R version:
-R version 3.4.2 (2017-09-28)
-
-Platform:
-x86_64-w64-mingw32
-
-Attached base packages:
-- stats
-- graphics
-- grDevices
-- utils
-- datasets
-- methods
-- base
-
-Other attached packages:
-- CdmDdlBase (0.1.0)

extras/codeToRun.R

@@ -7,17 +7,17 @@ cdmVersion <- "5.3"
 supportedVersions <- listSupportedVersions()
 
 for (cdmVersion in supportedVersions) {
-  for (targetdialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) {
+  for (targetDialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) {
-    writeDDL(targetdialect = targetdialect,
+    writeDdl(targetDialect = targetDialect,
              cdmVersion = cdmVersion)
 
-    writePrimaryKeys(targetdialect = targetdialect,
+    writePrimaryKeys(targetDialect = targetDialect,
                      cdmVersion = cdmVersion)
 
-    writeForeignKeys(targetdialect = targetdialect,
+    writeForeignKeys(targetDialect = targetDialect,
                      cdmVersion = cdmVersion)
 
-    writeIndex(targetdialect = targetdialect,
+    writeIndex(targetDialect = targetDialect,
                cdmVersion = cdmVersion)
   }
 }

man/createForeignKeys.Rd

@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/createForeignKeys.R
-\name{createForeignKeys}
-\alias{createForeignKeys}
-\title{Create a foreign key sql script from two csv files that detail the OMOP CDM Specifications.}
-\usage{
-createForeignKeys(cdmVersion = cdmVersion)
-}
-\arguments{
-\item{cdmVersionNum}{The version of the CDM you are creating, e.g. 5.3.1}
-}
-\description{
-Create a foreign key sql script from two csv files that detail the OMOP CDM Specifications.
-}

man/createPrimaryKeys.Rd

@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/createPrimaryKeys.R
-\name{createPrimaryKeys}
-\alias{createPrimaryKeys}
-\title{Create a primary key sql script from two csv files that detail the OMOP CDM Specifications.}
-\usage{
-createPrimaryKeys(cdmVersion = cdmVersion)
-}
-\arguments{
-\item{cdmVersionNum}{The version of the CDM you are creating, e.g. 5.3}
-}
-\description{
-Create a primary key sql script from two csv files that detail the OMOP CDM Specifications.
-}

man/writeDDL.Rd

@@ -1,19 +1,61 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/writeDDL.R
+% Please edit documentation in R/writeDdl.R
-\name{writeDDL}
+\name{writeDdl}
-\alias{writeDDL}
+\alias{writeDdl}
+\alias{writePrimaryKeys}
+\alias{writeForeignKeys}
+\alias{writeIndex}
 \title{Write DDL script}
 \usage{
-writeDDL(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabaseSchema")
+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{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 for which you are creating the DDL. e.g. 5.3.1}
+\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 DDL script
+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.
+}}
+

man/writeForeignKeys.Rd

@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/writeForeignKeys.R
-\name{writeForeignKeys}
-\alias{writeForeignKeys}
-\title{Write constraint script}
-\usage{
-writeForeignKeys(
-  targetdialect,
-  cdmVersion,
-  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 that you are creating the primary keys for}
-
-\item{cdmDatabaseSchema}{The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"}
-}
-\description{
-Write constraint script
-}

man/writeIndex.Rd

@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/writeIndex.R
-\name{writeIndex}
-\alias{writeIndex}
-\title{Write Index script}
-\usage{
-writeIndex(targetdialect, cdmVersion, 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 that you are creating the indices for. e.g. 5.3.1}
-
-\item{cdmDatabaseSchema}{The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"}
-}
-\description{
-Write Index script
-}

man/writePrimaryKeys.Rd

@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/writePrimaryKeys.R
-\name{writePrimaryKeys}
-\alias{writePrimaryKeys}
-\title{Write primary key script}
-\usage{
-writePrimaryKeys(
-  targetdialect,
-  cdmVersion,
-  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 that you are creating the primary keys for}
-
-\item{cdmDatabaseSchema}{The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"}
-}
-\description{
-Write primary key script
-}