mz-health/OMOP
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OMOP
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replace outputpath with outputfolder for consistency. update documentation.

This commit is contained in:
Adam Black 2021-08-20 11:25:10 -04:00
parent b8425920ff
commit de1c577b6b
5 changed files with 38 additions and 33 deletions
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14
R/executeDdl.R
View File

@ -42,16 +42,16 @@ executeDdl <- function(connectionDetails,
executeForeignKey = TRUE, executeForeignKey = TRUE,
...) { ...) {
outputpath <- tempdir(check = TRUE) outputfolder <- tempdir(check = TRUE)
if(executeDdl) { if(executeDdl) {
filename <- writeDdl(targetDialect = connectionDetails$dbms, filename <- writeDdl(targetDialect = connectionDetails$dbms,
cdmVersion = cdmVersion, cdmVersion = cdmVersion,
cdmDatabaseSchema = cdmDatabaseSchema, cdmDatabaseSchema = cdmDatabaseSchema,
outputpath = outputpath) outputfolder = outputfolder)
sql <- readr::read_file(file.path(outputpath, filename)) sql <- readr::read_file(file.path(outputfolder, filename))
} else { } else {
sql <- "" sql <- ""
} }
@ -60,18 +60,18 @@ executeDdl <- function(connectionDetails,
filename <- writePrimaryKeys(targetDialect = connectionDetails$dbms, filename <- writePrimaryKeys(targetDialect = connectionDetails$dbms,
cdmVersion = cdmVersion, cdmVersion = cdmVersion,
cdmDatabaseSchema = cdmDatabaseSchema, cdmDatabaseSchema = cdmDatabaseSchema,
outputpath = outputpath) outputfolder = outputfolder)
sql <- paste(sql, readr::read_file(file.path(outputpath, filename)), sep = "\n") sql <- paste(sql, readr::read_file(file.path(outputfolder, filename)), sep = "\n")
} }
if(executeForeignKey) { if(executeForeignKey) {
filename <- writeForeignKeys(targetDialect = connectionDetails$dbms, filename <- writeForeignKeys(targetDialect = connectionDetails$dbms,
cdmVersion = cdmVersion, cdmVersion = cdmVersion,
cdmDatabaseSchema = cdmDatabaseSchema, cdmDatabaseSchema = cdmDatabaseSchema,
outputpath = outputpath) outputfolder = outputfolder)
sql <- paste(sql, readr::read_file(file.path(outputpath, filename)), sep = "\n") sql <- paste(sql, readr::read_file(file.path(outputfolder, filename)), sep = "\n")
} }
con <- DatabaseConnector::connect(connectionDetails = connectionDetails) con <- DatabaseConnector::connect(connectionDetails = connectionDetails)

13
man/buildRelease.Rd
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@ -5,15 +5,20 @@
\title{Create OMOP CDM SQL files} \title{Create OMOP CDM SQL files}
\usage{ \usage{
buildRelease( buildRelease(
cdmVersion = listSupportedVersions(), cdmVersions = listSupportedVersions(),
targetDialect = listSupportedDialects() targetDialects = listSupportedDialects(),
outputfolder = file.path(getwd(), "ddl")
) )
} }
\arguments{ \arguments{
\item{cdmVersion}{The version of the CDM you are creating, e.g. 5.3, 5.4. \item{cdmVersions}{The versions of the CDM you are creating, e.g. 5.3, 5.4.
Defaults to all supported CDM versions.} Defaults to all supported CDM versions.}
\item{targetDialect}{The target dialect} \item{targetDialects}{A character vector of target dialects.
Defaults to all supported dialects.}
\item{outputfolder}{The base folder where the SQL files will be written.
Subfolders will be created for each cdmVersion and targetDialect.}
} }
\description{ \description{
Writes DDL, ForeignKey, PrimaryKey and index SQL files for given cdmVersion Writes DDL, ForeignKey, PrimaryKey and index SQL files for given cdmVersion

2
man/buildReleaseZip.Rd
View File

@ -7,7 +7,7 @@
buildReleaseZip( buildReleaseZip(
cdmVersion, cdmVersion,
targetDialect = listSupportedDialects(), targetDialect = listSupportedDialects(),
outputfolder = "output" outputfolder = file.path(getwd(), "ddl")
) )
} }
\arguments{ \arguments{

10
man/writeDdl.Rd
View File

@ -10,28 +10,28 @@
writeDdl( writeDdl(
targetDialect, targetDialect,
cdmVersion, cdmVersion,
outputpath, outputfolder,
cdmDatabaseSchema = "@cdmDatabaseSchema" cdmDatabaseSchema = "@cdmDatabaseSchema"
) )
writePrimaryKeys( writePrimaryKeys(
targetDialect, targetDialect,
cdmVersion, cdmVersion,
outputpath, outputfolder,
cdmDatabaseSchema = "@cdmDatabaseSchema" cdmDatabaseSchema = "@cdmDatabaseSchema"
) )
writeForeignKeys( writeForeignKeys(
targetDialect, targetDialect,
cdmVersion, cdmVersion,
outputpath, outputfolder,
cdmDatabaseSchema = "@cdmDatabaseSchema" cdmDatabaseSchema = "@cdmDatabaseSchema"
) )
writeIndex( writeIndex(
targetDialect, targetDialect,
cdmVersion, cdmVersion,
outputpath, outputfolder,
cdmDatabaseSchema = "@cdmDatabaseSchema" cdmDatabaseSchema = "@cdmDatabaseSchema"
) )
} }
@ -40,7 +40,7 @@ writeIndex(
\item{cdmVersion}{The version of the CDM you are creating, e.g. 5.3, 5.4} \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{outputfolder}{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. \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"} Defaults to "@cdmDatabaseSchema"}

32
tests/testthat/test-writeDdl.R
View File

@ -1,10 +1,10 @@
test_that("writeDdl works", { test_that("writeDdl works", {
outputpath <- tempdir(TRUE) outputfolder <- tempdir(TRUE)
filename <- writeDdl(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath) filename <- writeDdl(targetDialect = "postgresql", cdmVersion = "5.4", outputfolder = outputfolder)
expect_true(file.exists(file.path(outputpath, filename))) expect_true(file.exists(file.path(outputfolder, filename)))
sql <- readr::read_file(file.path(outputpath, filename)) sql <- readr::read_file(file.path(outputfolder, filename))
expect_type(sql, "character") expect_type(sql, "character")
expect_gt(nchar(sql), 10) expect_gt(nchar(sql), 10)
@ -13,11 +13,11 @@ test_that("writeDdl works", {
test_that("writePrimaryKeys works", { test_that("writePrimaryKeys works", {
outputpath <- tempdir(TRUE) outputfolder <- tempdir(TRUE)
filename <- writePrimaryKeys(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath) filename <- writePrimaryKeys(targetDialect = "postgresql", cdmVersion = "5.4", outputfolder = outputfolder)
expect_true(file.exists(file.path(outputpath, filename))) expect_true(file.exists(file.path(outputfolder, filename)))
sql <- readr::read_file(file.path(outputpath, filename)) sql <- readr::read_file(file.path(outputfolder, filename))
expect_type(sql, "character") expect_type(sql, "character")
expect_gt(nchar(sql), 10) expect_gt(nchar(sql), 10)
@ -26,11 +26,11 @@ test_that("writePrimaryKeys works", {
test_that("writeForeignKeys works", { test_that("writeForeignKeys works", {
outputpath <- tempdir(TRUE) outputfolder <- tempdir(TRUE)
filename <- writeForeignKeys(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath) filename <- writeForeignKeys(targetDialect = "postgresql", cdmVersion = "5.4", outputfolder = outputfolder)
expect_true(file.exists(file.path(outputpath, filename))) expect_true(file.exists(file.path(outputfolder, filename)))
sql <- readr::read_file(file.path(outputpath, filename)) sql <- readr::read_file(file.path(outputfolder, filename))
expect_type(sql, "character") expect_type(sql, "character")
expect_gt(nchar(sql), 10) expect_gt(nchar(sql), 10)
@ -39,11 +39,11 @@ test_that("writeForeignKeys works", {
test_that("writeIndex works", { test_that("writeIndex works", {
outputpath <- tempdir(TRUE) outputfolder <- tempdir(TRUE)
filename <- writeIndex(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath) filename <- writeIndex(targetDialect = "postgresql", cdmVersion = "5.4", outputfolder = outputfolder)
expect_true(file.exists(file.path(outputpath, filename))) expect_true(file.exists(file.path(outputfolder, filename)))
sql <- readr::read_file(file.path(outputpath, filename)) sql <- readr::read_file(file.path(outputfolder, filename))
expect_type(sql, "character") expect_type(sql, "character")
expect_gt(nchar(sql), 10) expect_gt(nchar(sql), 10)