Merge branch 'develop'

OHDSI · Nov 28, 2023 · be58698 · be58698
2 parents 239d686 + 74a57c6
commit be58698
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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/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 6.3.0
-Date: 2023-11-08 13:53:53 UTC
-SHA: 105405047c12c144c4486ecfacb41d68a70be778
+Version: 6.3.1
+Date: 2023-11-28 13:06:47 UTC
+SHA: 23e12a103d0553f25c4b14d5f0a9f39d239484d0
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: DatabaseConnector
 Type: Package
 Title: Connecting to Various Database Platforms
-Version: 6.3.0
-Date: 2023-11-08
+Version: 6.3.1
+Date: 2023-11-28
 Authors@R: c(
     person("Martijn", "Schuemie", email = "[email protected]", role = c("aut", "cre")),
     person("Marc", "Suchard", role = c("aut")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,13 @@
+DatabaseConnector 6.3.1
+=======================
+
+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/DBI.R b/R/DBI.R
@@ -376,8 +376,8 @@ setMethod("dbFetch", "DatabaseConnectorJdbcResult", function(res, n = -1, ...) {
 
 #' @inherit DBI::dbFetch title description params details references return seealso
 #' @export
-setMethod("dbFetch", "DatabaseConnectorDbiResult", function(res, ...) {
-  columns <- DBI::dbFetch(res@resultSet, ...)
+setMethod("dbFetch", "DatabaseConnectorDbiResult", function(res, n = -1, ...) {
+  columns <- DBI::dbFetch(res@resultSet, n, ...)
   columns <- convertFields(res@dbms, columns)
   columns <- dbFetchIntegerToNumeric(columns)
   colnames(columns) <- tolower(colnames(columns))

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{
@@ -217,6 +218,13 @@ insertTable.default <- function(connection,
     )
     tempEmulationSchema <- oracleTempSchema
   }
+  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 <- as.data.frame(data)
+  }
   if (camelCaseToSnakeCase) {
     colnames(data) <- SqlRender::camelCaseToSnakeCase(colnames(data))
   }
@@ -236,18 +244,16 @@ insertTable.default <- function(connection,
   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)
     }
   }

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,4 +1,4 @@
-This update includes 3 changes and 1 bugfixes. (see NEWS.md).
+This update includes 2 bugfixes. (see NEWS.md).
 
 ---
 

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/Connecting.html b/docs/articles/Connecting.html
diff --git a/docs/articles/DbiAndDbplyr.html b/docs/articles/DbiAndDbplyr.html
diff --git a/docs/articles/Querying.html b/docs/articles/Querying.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
   Connecting: Connecting.html
   DbiAndDbplyr: DbiAndDbplyr.html
   Querying: Querying.html
-last_built: 2023-11-08T13:18Z
+last_built: 2023-11-28T09:55Z
 
diff --git a/docs/pull_request_template.html b/docs/pull_request_template.html
diff --git a/docs/reference/DatabaseConnector-package.html b/docs/reference/DatabaseConnector-package.html
diff --git a/docs/reference/DatabaseConnectorDbiResult-class.html b/docs/reference/DatabaseConnectorDbiResult-class.html
diff --git a/docs/reference/DatabaseConnectorDriver-class.html b/docs/reference/DatabaseConnectorDriver-class.html
diff --git a/docs/reference/DatabaseConnectorDriver.html b/docs/reference/DatabaseConnectorDriver.html
diff --git a/docs/reference/DatabaseConnectorJdbcResult-class.html b/docs/reference/DatabaseConnectorJdbcResult-class.html
diff --git a/docs/reference/assertTempEmulationSchemaSet.html b/docs/reference/assertTempEmulationSchemaSet.html
diff --git a/docs/reference/computeDataHash.html b/docs/reference/computeDataHash.html
diff --git a/docs/reference/connect.html b/docs/reference/connect.html
diff --git a/docs/reference/createConnectionDetails.html b/docs/reference/createConnectionDetails.html
diff --git a/docs/reference/createDbiConnectionDetails.html b/docs/reference/createDbiConnectionDetails.html
diff --git a/docs/reference/createZipFile.html b/docs/reference/createZipFile.html
diff --git a/docs/reference/dateAdd.html b/docs/reference/dateAdd.html
diff --git a/docs/reference/dateDiff.html b/docs/reference/dateDiff.html
diff --git a/docs/reference/dateFromParts.html b/docs/reference/dateFromParts.html