From 4df6d4ba16f5ff75474d5761b81b926f3eb54c1b Mon Sep 17 00:00:00 2001
From: Mark Williams <mark.williams@diamond.ac.uk>
Date: Fri, 14 Nov 2025 16:11:21 +0000
Subject: [PATCH 1/3] LIMS-1275: Use streamed response for unzipped files

---
 api/src/Page/Download.php | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/api/src/Page/Download.php b/api/src/Page/Download.php
index 9f9794d20..7863f0b93 100644
--- a/api/src/Page/Download.php
+++ b/api/src/Page/Download.php
@@ -247,7 +247,6 @@ function _get_autoproc_attachments()
     /**
      * Download a file to the browser
      * This function is used to download autoproc and phasing run attachments.
-     * It sets a maximum amount of memory for the download.
      * The $id is used as a prefix to the filename.
      *
      * @param integer $id One of AutoProcProgramId or PhasingProgramRunId
@@ -255,8 +254,6 @@ function _get_autoproc_attachments()
      */
     function _get_file($id, $file)
     {
-        // We don't want to allow unlimited file sizes
-        ini_set('memory_limit', '512M');
         $filesystem = new Filesystem();
 
         $filename = $file['FILEPATH'] . '/' . $file['FILENAME'];
@@ -265,18 +262,28 @@ function _get_file($id, $file)
         if ($filesystem->exists($filename)) {
             $response = new BinaryFileResponse($filename);
             $this->set_mime_content($response, $filename, $id);
-            $response->headers->set("Content-Length", filesize($filename));
         } elseif ($filesystem->exists($filename.'.gz')) {
             $filename = $filename.'.gz';
             if ($this->arg('download') == 1) {
                 // View log file, so unzip and serve
-                $response = new Response(readgzfile($filename));
+                $response = new StreamedResponse(function() use ($filename) {
+                    $fileHandle = gzopen($filename, 'rb');
+                    if ($fileHandle === false) {
+                        $this->_error("The file " . $filename . " couldn't be opened");
+                    }
+                    // Read the file in 8KB chunks and send them
+                    while (!gzeof($fileHandle)) {
+                        echo gzread($fileHandle, 8192);
+                        if (ob_get_level()) ob_flush();
+                        flush();
+                    }
+                    gzclose($fileHandle);
+                });
                 $this->set_mime_content($response, $file['FILENAME'], $id);
             } else {
                 // Download gzipped file
                 $response = new BinaryFileResponse($filename);
                 $this->set_mime_content($response, $filename, $id);
-                $response->headers->set("Content-Length", filesize($filename));
             }
         } else {
             $this->_error("No such file, the specified file " . $filename . " doesn't exist");

From 457c289f954bd7d22eb10233fb2af2ef56b1fb3c Mon Sep 17 00:00:00 2001
From: Mark Williams <mark.williams@diamond.ac.uk>
Date: Fri, 14 Nov 2025 16:12:20 +0000
Subject: [PATCH 2/3] LIMS-1275: Ignore security advisories

---
 api/composer.json | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/api/composer.json b/api/composer.json
index 8ec82129d..4a751a508 100644
--- a/api/composer.json
+++ b/api/composer.json
@@ -44,6 +44,12 @@
   "config": {
     "platform": {
       "php": "7.3"
+    },
+    "audit": {
+      "ignore": [
+        "PKSA-4b9f-kpvb-8rtq",
+        "PKSA-2kqm-ps5x-s4f5"
+      ]
     }
   }
 }

From 0e427e693667e9ddf4f68dff60b1fd599141b6da Mon Sep 17 00:00:00 2001
From: Mark W <24956497+ndg63276@users.noreply.github.com>
Date: Fri, 21 Nov 2025 20:54:49 +0000
Subject: [PATCH 3/3] Update api/composer.json

Co-authored-by: Guilherme Francisco <guilherme.de-freitas@diamond.ac.uk>
---
 api/composer.json | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/api/composer.json b/api/composer.json
index 4a751a508..8ec82129d 100644
--- a/api/composer.json
+++ b/api/composer.json
@@ -44,12 +44,6 @@
   "config": {
     "platform": {
       "php": "7.3"
-    },
-    "audit": {
-      "ignore": [
-        "PKSA-4b9f-kpvb-8rtq",
-        "PKSA-2kqm-ps5x-s4f5"
-      ]
     }
   }
 }