Fix bulk import for Postgres on MacOs.

OHDSI · Nov 28, 2023 · 9919fbc · 9919fbc
1 parent 59c8d38
commit 9919fbc
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Showing 4 changed files with 23 additions and 14 deletions.
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
@@ -8,5 +8,8 @@ org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning
+org.eclipse.jdt.core.compiler.release=disabled
 org.eclipse.jdt.core.compiler.source=1.8
diff --git a/NEWS.md b/NEWS.md
@@ -5,6 +5,8 @@ Bugfixes:
 
 1. Fixed `dbFetch()` for DBI drivers, no longer ignoring `n` argument.
 
+2. Fix bulk import for Postgres on MacOs.
+
 
 DatabaseConnector 6.3.0
 =======================

diff --git a/R/BulkLoad.R b/R/BulkLoad.R
@@ -286,7 +286,6 @@ bulkLoadHive <- function(connection, sqlTableName, sqlFieldNames, data) {
   )
 }
 
-
 bulkLoadPostgres <- function(connection, sqlTableName, sqlFieldNames, sqlDataTypes, data) {
   logTrace(sprintf("Inserting %d rows into table '%s' using PostgreSQL bulk load", nrow(data), sqlTableName))
   startTime <- Sys.time()
@@ -306,13 +305,12 @@ bulkLoadPostgres <- function(connection, sqlTableName, sqlFieldNames, sqlDataTyp
   password <- attr(connection, "password")()
 
   if (.Platform$OS.type == "windows") {
-    winPsqlPath <- Sys.getenv("POSTGRES_PATH")
-    command <- file.path(winPsqlPath, "psql.exe")
-    if (!file.exists(command)) {
-      abort(paste("Could not find psql.exe in ", winPsqlPath))
-    }
+    command <- file.path(Sys.getenv("POSTGRES_PATH"), "psql.exe")
   } else {
-    command <- "psql"
+    command <- file.path(Sys.getenv("POSTGRES_PATH"), "psql")
+  }
+  if (!file.exists(command)) {
+    abort(paste("Could not find psql.exe in ", Sys.getenv("POSTGRES_PATH")))
   }
   headers <- paste0("(", sqlFieldNames, ")")
   if (is.null(port)) {

diff --git a/R/InsertTable.R b/R/InsertTable.R
@@ -130,7 +130,8 @@ validateInt64Insert <- function() {
 #'
 #' PostgreSQL:
 #' Uses the 'psql' executable to upload. Set the POSTGRES_PATH environment variable  to the Postgres
-#' binary path, e.g. 'C:/Program Files/PostgreSQL/11/bin'.
+#' binary path, e.g. 'C:/Program Files/PostgreSQL/11/bin' on Windows or '/Library/PostgreSQL/16/bin' 
+#' on MacOs.
 #'
 #' @examples
 #' \dontrun{
@@ -233,21 +234,26 @@ insertTable.default <- function(connection,
   if (!is.null(databaseSchema)) {
     tableName <- paste(databaseSchema, tableName, sep = ".")
   }
+  if (Andromeda::isAndromedaTable(data)) {
+    warn("Batch-wise uploading of Andromeda tables currently not supported. Loading entire table in memory.",
+        .frequency = "regularly",
+        .frequency_id = "useMppBulkLoad"
+    )
+    data <- collect(data)
+  }
   if (is.vector(data) && !is.list(data)) {
     data <- data.frame(x = data)
   }
-  if (length(data) < 1) {
+  if (ncol(data) < 1) {
     abort("data must have at least one column")
   }
   if (is.null(names(data))) {
     names(data) <- paste("V", 1:length(data), sep = "")
   }
-  if (length(data[[1]]) > 0) {
-    if (!is.data.frame(data)) {
+  if (!is.data.frame(data)) {
+    if (nrow(data) > 0) {
       data <- as.data.frame(data, row.names = 1:length(data[[1]]))
-    }
-  } else {
-    if (!is.data.frame(data)) {
+    } else {
       data <- as.data.frame(data)
     }
   }