fix: Excel API exception handling. (#4627)

* Extracted creation of temp file from output stream, so exception gets handled correctly * Added explicit error message when writing xls cell contents * Fixed error handling for all xls api mappings
molgenis · Jan 23, 2025 · ab7be0c · ab7be0c
1 parent 9e3c3af
commit ab7be0c
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Showing 2 changed files with 28 additions and 15 deletions.
diff --git a/...molgenis-emx2-io/src/main/java/org/molgenis/emx2/io/tablestore/TableStoreForXlsxFile.java b/...molgenis-emx2-io/src/main/java/org/molgenis/emx2/io/tablestore/TableStoreForXlsxFile.java
@@ -116,7 +116,19 @@ private void writeRowsToSheet(
       // write a contents row
       org.apache.poi.ss.usermodel.Row excelRow = sheet.createRow(rowNum);
       for (Map.Entry<String, Integer> entry : columnNameIndexMap.entrySet()) {
-        excelRow.createCell(entry.getValue()).setCellValue(row.getString(entry.getKey()));
+        try {
+          excelRow.createCell(entry.getValue()).setCellValue(row.getString(entry.getKey()));
+        } catch (IllegalArgumentException e) {
+          throw new MolgenisException(
+              "Error writing table '"
+                  + name
+                  + "', column '"
+                  + entry.getKey()
+                  + "', at row "
+                  + rowNum
+                  + ": "
+                  + e.getMessage());
+        }
       }
       rowNum++;
     }

diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ExcelApi.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ExcelApi.java
@@ -75,14 +75,15 @@ static void getExcel(Context ctx) throws IOException {
     boolean includeSystemColumns = includeSystemColumns(ctx);
     Path tempDir = Files.createTempDirectory(MolgenisWebservice.TEMPFILES_DELETE_ON_EXIT);
     tempDir.toFile().deleteOnExit();
-    try (OutputStream outputStream = ctx.res().getOutputStream()) {
-      Path excelFile = tempDir.resolve("download.xlsx");
-      if (ctx.queryParam("emx1") != null) {
-        MolgenisIO.toEmx1ExcelFile(excelFile, schema);
-      } else {
-        MolgenisIO.toExcelFile(excelFile, schema, includeSystemColumns);
-      }
 
+    Path excelFile = tempDir.resolve("download.xlsx");
+    if (ctx.queryParam("emx1") != null) {
+      MolgenisIO.toEmx1ExcelFile(excelFile, schema);
+    } else {
+      MolgenisIO.toExcelFile(excelFile, schema, includeSystemColumns);
+    }
+
+    try (OutputStream outputStream = ctx.outputStream()) {
       ctx.contentType("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
       ctx.header(
           "Content-Disposition",
@@ -99,11 +100,11 @@ static void getExcelTable(Context ctx) throws IOException {
     Table table = MolgenisWebservice.getTableByIdOrName(ctx);
     Path tempDir = Files.createTempDirectory(MolgenisWebservice.TEMPFILES_DELETE_ON_EXIT);
     tempDir.toFile().deleteOnExit();
+    Path excelFile = tempDir.resolve("download.xlsx");
+    TableStore excelStore = new TableStoreForXlsxFile(excelFile);
+    excelStore.writeTable(
+        table.getName(), getDownloadColumns(ctx, table), getDownloadRows(ctx, table));
     try (OutputStream outputStream = ctx.res().getOutputStream()) {
-      Path excelFile = tempDir.resolve("download.xlsx");
-      TableStore excelStore = new TableStoreForXlsxFile(excelFile);
-      excelStore.writeTable(
-          table.getName(), getDownloadColumns(ctx, table), getDownloadRows(ctx, table));
       ctx.contentType("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
       ctx.header(
           "Content-Disposition",
@@ -121,10 +122,10 @@ static void getExcelTable(Context ctx) throws IOException {
   static void getExcelReport(Context ctx) throws IOException {
     Path tempDir = Files.createTempDirectory(MolgenisWebservice.TEMPFILES_DELETE_ON_EXIT);
     tempDir.toFile().deleteOnExit();
+    Path excelFile = tempDir.resolve("download.xlsx");
+    TableStore excelStore = new TableStoreForXlsxFile(excelFile);
+    generateReportsToStore(ctx, excelStore);
     try (OutputStream outputStream = ctx.res().getOutputStream()) {
-      Path excelFile = tempDir.resolve("download.xlsx");
-      TableStore excelStore = new TableStoreForXlsxFile(excelFile);
-      generateReportsToStore(ctx, excelStore);
       ctx.contentType("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
       ctx.header("Content-Disposition", "attachment; filename=report.xlsx");
       outputStream.write(Files.readAllBytes(excelFile));