Merge branch 'develop'

# Conflicts:
#	.github/workflows/R_CMD_check_Hades.yaml
#	.github/workflows/R_CMD_check_main_weekly.yaml

.github/workflows/R_CMD_check_Hades.yaml

@@ -28,22 +28,22 @@ jobs:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
-      CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+      CDM5_ORACLE_CDM54_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM54_SCHEMA }}
       CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
       CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
       CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
       CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
-      CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
+      CDM5_POSTGRESQL_CDM54_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM54_SCHEMA }}
       CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
       CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
       CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
       CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
-      CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
+      CDM5_SQL_SERVER_CDM54_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM54_SCHEMA }}
       CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
       CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
       CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
       CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
-      CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+      CDM5_REDSHIFT_CDM54_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM54_SCHEMA }}
       CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
       CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
       CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
@@ -52,10 +52,16 @@ jobs:
       CDM_SNOWFLAKE_OHDSI_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_OHDSI_SCHEMA }}
       CDM_SNOWFLAKE_PASSWORD: ${{ secrets.CDM_SNOWFLAKE_PASSWORD }}
       CDM_SNOWFLAKE_CONNECTION_STRING: ${{ secrets.CDM_SNOWFLAKE_CONNECTION_STRING }}
-      CDM_SNOWFLAKE_USER: ${{ secrets.CDM_SNOWFLAKE_USER }}   
+      CDM_SNOWFLAKE_USER: ${{ secrets.CDM_SNOWFLAKE_USER }}      
       CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
       CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
       CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+      CDM5_SPARK_CDM_SCHEMA: ${{ secrets.CDM5_SPARK_CDM_SCHEMA }}
+      CDM5_SPARK_OHDSI_SCHEMA: ${{ secrets.CDM5_SPARK_OHDSI_SCHEMA }}
+      CDM_BIG_QUERY_CONNECTION_STRING: ${{ secrets.CDM_BIG_QUERY_CONNECTION_STRING }}
+      CDM_BIG_QUERY_KEY_FILE: ${{ secrets.CDM_BIG_QUERY_KEY_FILE }}
+      CDM_BIG_QUERY_CDM_SCHEMA: ${{ secrets.CDM_BIG_QUERY_CDM_SCHEMA }}
+      CDM_BIG_QUERY_OHDSI_SCHEMA: ${{ secrets.CDM_BIG_QUERY_OHDSI_SCHEMA }}
 
     steps:
       - uses: actions/checkout@v3
@@ -174,4 +180,3 @@ jobs:
         if: ${{ env.new_version != '' }}
         run: |
           curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/
-

.github/workflows/R_CMD_check_main_weekly.yaml

@@ -20,22 +20,22 @@ jobs:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
-      CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+      CDM5_ORACLE_CDM54_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM54_SCHEMA }}
       CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
       CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
       CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
       CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
-      CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
+      CDM5_POSTGRESQL_CDM54_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM54_SCHEMA }}
       CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
       CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
       CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
       CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
-      CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
+      CDM5_SQL_SERVER_CDM54_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM54_SCHEMA }}
       CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
       CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
       CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
       CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
-      CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+      CDM5_REDSHIFT_CDM54_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM54_SCHEMA }}
       CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
       CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
       CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
@@ -44,10 +44,12 @@ jobs:
       CDM_SNOWFLAKE_OHDSI_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_OHDSI_SCHEMA }}
       CDM_SNOWFLAKE_PASSWORD: ${{ secrets.CDM_SNOWFLAKE_PASSWORD }}
       CDM_SNOWFLAKE_CONNECTION_STRING: ${{ secrets.CDM_SNOWFLAKE_CONNECTION_STRING }}
-      CDM_SNOWFLAKE_USER: ${{ secrets.CDM_SNOWFLAKE_USER }}   
+      CDM_SNOWFLAKE_USER: ${{ secrets.CDM_SNOWFLAKE_USER }}     
       CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
       CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
       CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+      CDM5_SPARK_CDM_SCHEMA: ${{ secrets.CDM5_SPARK_CDM_SCHEMA }}
+      CDM5_SPARK_OHDSI_SCHEMA: ${{ secrets.CDM5_SPARK_OHDSI_SCHEMA }}
 
     steps:
       - uses: actions/checkout@v3
@@ -69,4 +71,4 @@ jobs:
         with:
           args: 'c("--no-manual", "--as-cran")'
           error-on: '"warning"'
-          check-dir: '"check"'
+          check-dir: '"check"'

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 6.2.4
-Date: 2023-09-07 07:52:51 UTC
-SHA: 0275322b097fac96668c8804dd0acd8466c1442c
+Version: 6.3.0
+Date: 2023-11-08 13:53:53 UTC
+SHA: 105405047c12c144c4486ecfacb41d68a70be778

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: DatabaseConnector
 Type: Package
 Title: Connecting to Various Database Platforms
-Version: 6.2.4
-Date: 2023-09-07
+Version: 6.3.0
+Date: 2023-11-08
 Authors@R: c(
     person("Martijn", "Schuemie", email = "schuemie@ohdsi.org", role = c("aut", "cre")),
     person("Marc", "Suchard", role = c("aut")),
@@ -20,7 +20,7 @@ Depends:
     R (>= 4.0.0)
 Imports:
     rJava,
-    SqlRender (>= 1.15.2),
+    SqlRender (>= 1.16.0),
     methods,
     stringr,
     readr,

NEWS.md

@@ -1,3 +1,19 @@
+DatabaseConnector 6.3.0
+=======================
+
+Changes:
+
+1. On Snowflake always using `QUOTED_IDENTIFIERS_IGNORE_CASE=TRUE` to avoid name mismatches when using quotes.
+
+2. Updated Redshift drivers.
+
+3. Added unit tests for all supported platforms.
+
+Bugfixes:
+
+1. Fix bug on BigQuery where wait time was too short to avoid rate limit error.
+
+
 DatabaseConnector 6.2.4
 =======================
 

R/Connect.R

@@ -34,13 +34,30 @@ checkIfDbmsIsSupported <- function(dbms) {
     "synapse",
     "duckdb"
   )
+  deprecated <- c(
+    "hive",
+    "impala",
+    "netezza",
+    "pdw"
+  )
   if (!dbms %in% supportedDbmss) {
     abort(sprintf(
       "DBMS '%s' not supported. Please use one of these values: '%s'",
       dbms,
       paste(supportedDbmss, collapse = "', '")
     ))
   }
+  if (dbms %in% deprecated) {
+    warn(sprintf(
+      paste(c("DBMS '%s' has been deprecated. Current functionality is provided as is.",
+            "No futher support will be provided.",
+            "Please consider switching to a different database platform."),
+            collapse = " "),
+      dbms),
+      .frequency = "regularly",
+      .frequency_id = "deprecated_dbms"
+    )
+  }
 }
 
 checkDetailValidation <- function(connectionDetails, name) {
@@ -484,8 +501,8 @@ connectPostgreSql <- function(connectionDetails) {
 
 connectRedShift <- function(connectionDetails) {
   inform("Connecting using Redshift driver")
-  jarPath <- findPathToJar("^RedshiftJDBC.*\\.jar$", connectionDetails$pathToDriver)
-  if (grepl("RedshiftJDBC42", jarPath)) {
+  jarPath <- findPathToJar("^[Rr]edshift.*\\.jar$", connectionDetails$pathToDriver)
+  if (grepl("RedshiftJDBC42", jarPath) || grepl("redshift-jdbc42", jarPath)) {
     driver <- getJbcDriverSingleton("com.amazon.redshift.jdbc42.Driver", jarPath)
   } else {
     driver <- getJbcDriverSingleton("com.amazon.redshift.jdbc4.Driver", jarPath)
@@ -709,7 +726,8 @@ connectSnowflake <- function(connectionDetails) {
       user = connectionDetails$user(),
       password = connectionDetails$password(),
       dbms = connectionDetails$dbms,
-      "CLIENT_TIMESTAMP_TYPE_MAPPING"="TIMESTAMP_NTZ"
+      "CLIENT_TIMESTAMP_TYPE_MAPPING"="TIMESTAMP_NTZ",
+      "QUOTED_IDENTIFIERS_IGNORE_CASE"="TRUE"
     )
   }
   return(connection)

R/DBI.R

@@ -455,7 +455,7 @@ setMethod(
       )
     }
     rowsAffected <- executeSql(connection = conn, sql = statement)
-    rowsAffected <- rJava::.jnew("java/lang/Integer", as.integer(rowsAffected))
+    rowsAffected <- rJava::.jnew("java/lang/Double", as.double(sum(rowsAffected)))
     result <- new("DatabaseConnectorJdbcResult",
                   content = rowsAffected,
                   type = "rowsAffected",

R/Drivers.R

@@ -91,7 +91,7 @@ downloadJdbcDrivers <- function(dbms, pathToDriver = Sys.getenv("DATABASECONNECT
   jdbcDriverSources <- utils::read.csv(text = 
     "row,dbms, fileName, baseUrl
     1,postgresql,postgresqlV42.2.18.zip,https://ohdsi.github.io/DatabaseConnectorJars/
-    2,redshift,redShiftV2.1.0.9.zip,https://ohdsi.github.io/DatabaseConnectorJars/
+    2,redshift,redshift-jdbc42-2.1.0.20.zip,https://s3.amazonaws.com/redshift-downloads/drivers/jdbc/2.1.0.20/
     3,sql server,sqlServerV9.2.0.zip,https://ohdsi.github.io/DatabaseConnectorJars/
     4,oracle,oracleV19.8.zip,https://ohdsi.github.io/DatabaseConnectorJars/
     5,spark,DatabricksJDBC42-2.6.32.1054.zip,https://databricks-bi-artifacts.s3.us-east-2.amazonaws.com/simbaspark-drivers/jdbc/2.6.32/
@@ -162,7 +162,7 @@ getJbcDriverSingleton <- function(driverClass = "", classPath = "") {
 }
 
 checkPathToDriver <- function(pathToDriver, dbms) {
-  if (!is.null(dbms) && dbms %in% c("sqlite", "sqlite extended")) {
+  if (!is.null(dbms) && dbms %in% c("sqlite", "sqlite extended", "duckdb")) {
     return()
   }
   if (pathToDriver == "") {

R/Sql.R

@@ -255,44 +255,33 @@ lowLevelExecuteSql <- function(connection, sql) {
   UseMethod("lowLevelExecuteSql", connection)
 }
 
-delayIfNecessary <- function(sql, regex, executionTimeList, threshold) {
+ddlExecutionTimes <- new.env()
+insertExecutionTimes <- new.env()
+
+delayIfNecessary <- function(sql, regex, executionTimes, threshold) {
   regexGroups <- stringr::str_match(sql, stringr::regex(regex, ignore_case = TRUE))
   tableName <- regexGroups[3]
   if (!is.na(tableName) && !is.null(tableName)) {
     currentTime <- Sys.time()
-    lastExecutedTime <- executionTimeList[[tableName]]
+    lastExecutedTime <- executionTimes[[tableName]]
     if (!is.na(lastExecutedTime) && !is.null(lastExecutedTime)) {
-      delta <- currentTime - lastExecutedTime
+      delta <- difftime(currentTime, lastExecutedTime, units = "secs") 
       if (delta < threshold) {
         Sys.sleep(threshold - delta)
       }
     }
-
-    executionTimeList[[tableName]] <- currentTime
+    executionTimes[[tableName]] <- currentTime
   }
-  return(executionTimeList)
 }
 
 delayIfNecessaryForDdl <- function(sql) {
-  ddlList <- getOption("ddlList")
-  if (is.null(ddlList)) {
-    ddlList <- list()
-  }
-
   regexForDdl <- "(^CREATE\\s+TABLE\\s+IF\\s+EXISTS|^CREATE\\s+TABLE|^DROP\\s+TABLE\\s+IF\\s+EXISTS|^DROP\\s+TABLE)\\s+([a-zA-Z0-9_$#-]*\\.?\\s*(?:[a-zA-Z0-9_]+)*)"
-  updatedList <- delayIfNecessary(sql, regexForDdl, ddlList, 5)
-  options(ddlList = updatedList)
+  delayIfNecessary(sql, regexForDdl, ddlExecutionTimes, 5)
 }
 
 delayIfNecessaryForInsert <- function(sql) {
-  insetList <- getOption("insetList")
-  if (is.null(insetList)) {
-    insetList <- list()
-  }
-
   regexForInsert <- "(^INSERT\\s+INTO)\\s+([a-zA-Z0-9_$#-]*\\.?\\s*(?:[a-zA-Z0-9_]+)*)"
-  updatedList <- delayIfNecessary(sql, regexForInsert, insetList, 5)
-  options(insetList = updatedList)
+  delayIfNecessary(sql, regexForInsert, insertExecutionTimes, 5)
 }
 
 #' @export
@@ -302,18 +291,23 @@ lowLevelExecuteSql.default <- function(connection, sql) {
 
   statement <- rJava::.jcall(connection@jConnection, "Ljava/sql/Statement;", "createStatement")
   on.exit(rJava::.jcall(statement, "V", "close"))
-  hasResultSet <- rJava::.jcall(statement, "Z", "execute", as.character(sql), check = FALSE)
+  if (dbms(connection) == "spark") {
+    # For some queries the DataBricks JDBC driver will throw an error saying no ROWCOUNT is returned
+    # when using executeLargeUpdate, so using execute instead. 
+    rJava::.jcall(statement, "Z", "execute", as.character(sql), check = FALSE)
+    rowsAffected <- rJava::.jcall(statement, "I", "getUpdateCount", check = FALSE)
+    if (rowsAffected == -1) {
+      rowsAffected <- 0
+    }
+  } else {
+    rowsAffected <- rJava::.jcall(statement, "J", "executeLargeUpdate", as.character(sql), check = FALSE)
+  }
 
   if (dbms(connection) == "bigquery") {
     delayIfNecessaryForDdl(sql)
     delayIfNecessaryForInsert(sql)
   }
 
-  rowsAffected <- 0
-  if (!hasResultSet) {
-    rowsAffected <- rJava::.jcall(statement, "I", "getUpdateCount", check = FALSE)
-  }
-
   delta <- Sys.time() - startTime
   logTrace(paste("Executing SQL took", delta, attr(delta, "units")))
   invisible(rowsAffected)
@@ -421,9 +415,9 @@ executeSql <- function(connection,
 
   batched <- runAsBatch && supportsBatchUpdates(connection)
   sqlStatements <- SqlRender::splitSql(sql)
+  rowsAffected <- c()
   if (batched) {
     batchSize <- 1000
-    rowsAffected <- 0
     for (start in seq(1, length(sqlStatements), by = batchSize)) {
       end <- min(start + batchSize - 1, length(sqlStatements))
 
@@ -441,7 +435,7 @@ executeSql <- function(connection,
       tryCatch(
         {
           startQuery <- Sys.time()
-          rowsAffected <- c(rowsAffected, rJava::.jcall(statement, "[I", "executeBatch"))
+          rowsAffected <- c(rowsAffected, rJava::.jcall(statement, "[J", "executeLargeBatch"))
           delta <- Sys.time() - startQuery
           if (profile) {
             inform(paste("Statements", start, "through", end, "took", delta, attr(delta, "units")))
@@ -471,7 +465,7 @@ executeSql <- function(connection,
       tryCatch(
         {
           startQuery <- Sys.time()
-          lowLevelExecuteSql(connection, sqlStatement)
+          rowsAffected <- c(rowsAffected, lowLevelExecuteSql(connection, sqlStatement))
           delta <- Sys.time() - startQuery
           if (profile) {
             inform(paste("Statement ", i, "took", delta, attr(delta, "units")))
@@ -498,9 +492,7 @@ executeSql <- function(connection,
     delta <- Sys.time() - startTime
     inform(paste("Executing SQL took", signif(delta, 3), attr(delta, "units")))
   }
-  if (batched) {
     invisible(rowsAffected)
-  }
 }
 
 convertFields <- function(dbms, result) {

cran-comments.md

@@ -1,4 +1,4 @@
-This update includes 1 changes and 2 bugfixes, including the fix requested by Prof. Hornik. (see NEWS.md).
+This update includes 3 changes and 1 bugfixes. (see NEWS.md).
 
 ---
 
@@ -14,4 +14,4 @@ There were no ERRORs or WARNINGs.
 
 ## Downstream dependencies
 
-DatabaseConnector is used by CDMConnector, which was tested with this new version. No issues were found.
+DatabaseConnector is used by Achilles, CohortAlgebra, CohortExplorer, TreatmentPatterns, and CDMConnector, which were tested with this new version. No issues were found.