Adding unit tests for Snowflake

OHDSI · Sep 18, 2023 · fdadefc · fdadefc
1 parent 03f110e
commit fdadefc
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Showing 43 changed files with 204 additions and 15 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -20,7 +20,7 @@ Depends:
  R (>= 4.0.0)
 Imports:
  rJava,
- SqlRender (>= 1.15.2),
+ SqlRender (>= 1.16.0),
  methods,
  stringr,
  readr,
@@ -49,6 +49,8 @@ Suggests:
  duckdb,
  pool,
  ParallelLogger
+Remotes:
+ ohdsi/SqlRender@develop
 License: Apache License
 VignetteBuilder: knitr
 URL: https://ohdsi.github.io/DatabaseConnector/, https://github.com/OHDSI/DatabaseConnector

diff --git a/extras/UploadDataToTestServer.R b/extras/UploadDataToTestServer.R
@@ -52,7 +52,7 @@ fromConnection <- connect(
  password = URLdecode(Sys.getenv("CDM5_SQL_SERVER_PASSWORD")),
  server = Sys.getenv("CDM5_SQL_SERVER_SERVER")
 )
-fromDatabaseSchema <- Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA")
+fromDatabaseSchema <- Sys.getenv("CDM5_SQL_SERVER_CDM54_SCHEMA")
 
 toConnection <- connect(
  dbms = "postgresql",

diff --git a/man/dbAppendTable-DatabaseConnectorConnection-character-method.Rd b/man/dbAppendTable-DatabaseConnectorConnection-character-method.Rd
diff --git a/man/dbClearResult-DatabaseConnectorDbiResult-method.Rd b/man/dbClearResult-DatabaseConnectorDbiResult-method.Rd
diff --git a/man/dbClearResult-DatabaseConnectorJdbcResult-method.Rd b/man/dbClearResult-DatabaseConnectorJdbcResult-method.Rd
diff --git a/man/dbColumnInfo-DatabaseConnectorDbiResult-method.Rd b/man/dbColumnInfo-DatabaseConnectorDbiResult-method.Rd
diff --git a/man/dbColumnInfo-DatabaseConnectorJdbcResult-method.Rd b/man/dbColumnInfo-DatabaseConnectorJdbcResult-method.Rd
diff --git a/man/dbCreateTable-DatabaseConnectorConnection-method.Rd b/man/dbCreateTable-DatabaseConnectorConnection-method.Rd
diff --git a/man/dbDisconnect-DatabaseConnectorConnection-method.Rd b/man/dbDisconnect-DatabaseConnectorConnection-method.Rd
diff --git a/man/dbExecute-DatabaseConnectorConnection-character-method.Rd b/man/dbExecute-DatabaseConnectorConnection-character-method.Rd
diff --git a/man/dbExistsTable-DatabaseConnectorConnection-character-method.Rd b/man/dbExistsTable-DatabaseConnectorConnection-character-method.Rd
diff --git a/man/dbFetch-DatabaseConnectorDbiResult-method.Rd b/man/dbFetch-DatabaseConnectorDbiResult-method.Rd
diff --git a/man/dbFetch-DatabaseConnectorJdbcResult-method.Rd b/man/dbFetch-DatabaseConnectorJdbcResult-method.Rd
diff --git a/man/dbGetInfo-DatabaseConnectorConnection-method.Rd b/man/dbGetInfo-DatabaseConnectorConnection-method.Rd
diff --git a/man/dbGetInfo-DatabaseConnectorDriver-method.Rd b/man/dbGetInfo-DatabaseConnectorDriver-method.Rd
diff --git a/man/dbGetQuery-DatabaseConnectorConnection-character-method.Rd b/man/dbGetQuery-DatabaseConnectorConnection-character-method.Rd
diff --git a/man/dbGetRowCount-DatabaseConnectorDbiResult-method.Rd b/man/dbGetRowCount-DatabaseConnectorDbiResult-method.Rd
diff --git a/man/dbGetRowCount-DatabaseConnectorJdbcResult-method.Rd b/man/dbGetRowCount-DatabaseConnectorJdbcResult-method.Rd
diff --git a/man/dbGetRowsAffected-DatabaseConnectorDbiResult-method.Rd b/man/dbGetRowsAffected-DatabaseConnectorDbiResult-method.Rd
diff --git a/man/dbGetRowsAffected-DatabaseConnectorJdbcResult-method.Rd b/man/dbGetRowsAffected-DatabaseConnectorJdbcResult-method.Rd
diff --git a/man/dbGetStatement-DatabaseConnectorDbiResult-method.Rd b/man/dbGetStatement-DatabaseConnectorDbiResult-method.Rd
diff --git a/man/dbGetStatement-DatabaseConnectorJdbcResult-method.Rd b/man/dbGetStatement-DatabaseConnectorJdbcResult-method.Rd
diff --git a/man/dbHasCompleted-DatabaseConnectorDbiResult-method.Rd b/man/dbHasCompleted-DatabaseConnectorDbiResult-method.Rd
diff --git a/man/dbHasCompleted-DatabaseConnectorJdbcResult-method.Rd b/man/dbHasCompleted-DatabaseConnectorJdbcResult-method.Rd
diff --git a/man/dbIsValid-DatabaseConnectorDbiConnection-method.Rd b/man/dbIsValid-DatabaseConnectorDbiConnection-method.Rd
diff --git a/man/dbIsValid-DatabaseConnectorJdbcConnection-method.Rd b/man/dbIsValid-DatabaseConnectorJdbcConnection-method.Rd
diff --git a/man/dbListFields-DatabaseConnectorConnection-character-method.Rd b/man/dbListFields-DatabaseConnectorConnection-character-method.Rd
diff --git a/man/dbListTables-DatabaseConnectorConnection-method.Rd b/man/dbListTables-DatabaseConnectorConnection-method.Rd
diff --git a/man/dbReadTable-DatabaseConnectorConnection-character-method.Rd b/man/dbReadTable-DatabaseConnectorConnection-character-method.Rd
diff --git a/man/dbRemoveTable-DatabaseConnectorConnection-ANY-method.Rd b/man/dbRemoveTable-DatabaseConnectorConnection-ANY-method.Rd
diff --git a/man/dbSendQuery-DatabaseConnectorDbiConnection-character-method.Rd b/man/dbSendQuery-DatabaseConnectorDbiConnection-character-method.Rd
diff --git a/man/dbSendQuery-DatabaseConnectorJdbcConnection-character-method.Rd b/man/dbSendQuery-DatabaseConnectorJdbcConnection-character-method.Rd
diff --git a/man/dbSendStatement-DatabaseConnectorConnection-character-method.Rd b/man/dbSendStatement-DatabaseConnectorConnection-character-method.Rd
diff --git a/man/dbWriteTable-DatabaseConnectorConnection-ANY-method.Rd b/man/dbWriteTable-DatabaseConnectorConnection-ANY-method.Rd
diff --git a/tests/testthat/dbplyrTestFunction.R b/tests/testthat/dbplyrTestFunction.R
@@ -6,7 +6,8 @@ testDbplyrFunctions <- function(connectionDetails, cdmDatabaseSchema) {
  assertTempEmulationSchemaSet(connectionDetails$dbms)
 
  connection <- connect(connectionDetails)
- on.exit(disconnect(connection))
+ on.exit(dropEmulatedTempTables(connection))
+ on.exit(disconnect(connection), add = TRUE)
 
  person <- tbl(connection, inDatabaseSchema(cdmDatabaseSchema, "person"))
  observationPeriod <- tbl(connection, inDatabaseSchema(cdmDatabaseSchema, "observation_period"))
@@ -178,7 +179,6 @@ testDbplyrFunctions <- function(connectionDetails, cdmDatabaseSchema) {
  # names(dumbNameCars) <- c("Car speed", "Dist. to Stop")
  # copy_to(connection, dumbNameCars, name = "dn_cars")
 
- dropEmulatedTempTables(connection)
  # disconnect(connection)
  invisible(NULL)
 }
diff --git a/tests/testthat/test-BatchProcess.R b/tests/testthat/test-BatchProcess.R
@@ -111,4 +111,26 @@ test_that("renderTranslateQueryApplyBatched works", {
 
  disconnect(connection)
  unlink(dbFile)
+
+ # Snowflake --------------------------------------------------
+ details <- createConnectionDetails(
+ dbms = "snowflake",
+ user = Sys.getenv("CDM_SNOWFLAKE_USER"),
+ password = URLdecode(Sys.getenv("CDM_SNOWFLAKE_PASSWORD")),
+ connectionString = Sys.getenv("CDM_SNOWFLAKE_CONNECTION_STRING")
+ )
+ connection <- connect(details)
+ cdmDatabaseSchema <- Sys.getenv("CDM_SNOWFLAKE_CDM53_SCHEMA")
+
+ sql <- "SELECT TOP 10 * FROM @cdm_database_schema.vocabulary;"
+ data <- renderTranslateQueryApplyBatched(connection,
+ sql,
+ fun,
+ args,
+ cdm_database_schema = cdmDatabaseSchema
+ )
+ data <- do.call(rbind, data)
+ expect_true("test" %in% colnames(data))
+ expect_true(all(data$test == "MY STRING"))
+ disconnect(connection)
 })
diff --git a/tests/testthat/test-connection.R b/tests/testthat/test-connection.R
@@ -253,17 +253,17 @@ test_that("Open and close connection using connection strings with separate user
  # expect_equal(dbms(connection), "spark")
  # expect_true(disconnect(connection))
 
- # Snowflake --------------------------------------------------
- # Disable Snowflake unit tests until we have a testing server
- # details <- createConnectionDetails(
- # dbms = "snowflake",
- # connectionString = Sys.getenv("CDM5_SNOWFLAKE_CONNECTION_STRING"),
- # user = Sys.getenv("CDM5_SNOWFLAKE_USER"),
- # password = URLdecode(Sys.getenv("CDM5_SNOWFLAKE_PASSWORD"))
- # )
- # connection <- connect(details)
- # expect_true(inherits(connection, "DatabaseConnectorConnection"))
- # expect_true(disconnect(connection))
+ # Snowflake  --------------------------------------------------
+ details <- createConnectionDetails(
+  dbms = "snowflake",
+  user = Sys.getenv("CDM_SNOWFLAKE_USER"),
+  password = URLdecode(Sys.getenv("CDM_SNOWFLAKE_PASSWORD")),
+  connectionString = Sys.getenv("CDM_SNOWFLAKE_CONNECTION_STRING")
+ )
+ connection <- connect(details)
+ expect_true(inherits(connection, "DatabaseConnectorConnection"))
+ expect_equal(dbms(connection), "snowflake")
+ expect_true(disconnect(connection))
 })
 
 test_that("Error is thrown when using incorrect dbms argument", {

diff --git a/tests/testthat/test-dataHash.R b/tests/testthat/test-dataHash.R
@@ -106,4 +106,17 @@ test_that("Compute data hash", {
 
  disconnect(connection)
  unlink(dbFile)
+
+ # Snowflake ------------------------------------------------------------------
+ details <- createConnectionDetails(
+ dbms = "snowflake",
+ user = Sys.getenv("CDM_SNOWFLAKE_USER"),
+ password = URLdecode(Sys.getenv("CDM_SNOWFLAKE_PASSWORD")),
+ connectionString = Sys.getenv("CDM_SNOWFLAKE_CONNECTION_STRING")
+ )
+ connection <- connect(details)
+ hash <- computeDataHash(connection, Sys.getenv("CDM_SNOWFLAKE_CDM53_SCHEMA"))
+ expect_true(is.character(hash))
+
+ disconnect(connection)
 })
diff --git a/tests/testthat/test-dbplyr.R b/tests/testthat/test-dbplyr.R
@@ -117,6 +117,19 @@ test_that("Test dbplyr on DuckDB", {
  unlink(databaseFile) 
 })
 
+test_that("Test dbplyr on Snowflake", {
+ # Snowflake ----------------------------------------------
+ connectionDetails <- createConnectionDetails(
+ dbms = "snowflake",
+ user = Sys.getenv("CDM_SNOWFLAKE_USER"),
+ password = URLdecode(Sys.getenv("CDM_SNOWFLAKE_PASSWORD")),
+ connectionString = Sys.getenv("CDM_SNOWFLAKE_CONNECTION_STRING")
+ )
+ cdmDatabaseSchema <- Sys.getenv("CDM_SNOWFLAKE_CDM53_SCHEMA")
+ options(sqlRenderTempEmulationSchema = Sys.getenv("CDM_SNOWFLAKE_OHDSI_SCHEMA"))
+ testDbplyrFunctions(connectionDetails, cdmDatabaseSchema)
+})
+
 test_that("Test dbplyr date functions on non-dbplyr data", {
  date <- c(as.Date("2000-02-01"), as.Date("2000-12-31"), as.Date("2000-01-31"))