From 6e2f3e082562a5e248dc13a7352a5b93f745eb10 Mon Sep 17 00:00:00 2001
From: Laetitia Fesselier <laetitia.fesselier@mail.mcgill.ca>
Date: Tue, 4 Apr 2023 14:43:20 -0400
Subject: [PATCH] Review changes

---
 modules/electrophysiology_uploader/README.md  | 51 +++++++++++++++++++
 .../jsx/UploadViewer.js                       | 14 +++--
 .../php/electrophysiology_uploader.class.inc  |  2 +-
 .../php/upload.class.inc                      |  9 ++--
 4 files changed, 64 insertions(+), 12 deletions(-)
 create mode 100644 modules/electrophysiology_uploader/README.md

diff --git a/modules/electrophysiology_uploader/README.md b/modules/electrophysiology_uploader/README.md
new file mode 100644
index 00000000000..697f0642cb4
--- /dev/null
+++ b/modules/electrophysiology_uploader/README.md
@@ -0,0 +1,51 @@
+# Electrophysiology Uploader
+
+## Purpose
+
+The electrophysiology uploader is intended to allow users to upload and browse electrophysiology files.
+
+
+## Intended Users
+
+The primary users are EEG technicians or site coordinators uploading EEG recordings 
+for registered LORIS candidates and timepoints.
+
+## Scope
+
+The electrophysiology uploader has the following built-in capabilities to facilitate 
+timely eeg insertion into the LORIS database. Specifically, it allows to browse
+uploaded recordings using the `Browse` tab and upload recordings using the `Upload` 
+tab.
+
+EEG recordings can be reuploaded multiple times. Previous upload attempts will be backup in _EEGUploadIncomingPath_/archives/.
+
+## Permissions
+
+#### Module Permission
+
+Permission `electrophysiology_browser_view_allsites` or `electrophysiology_browser_view_site`
+is necessary to have access to the module and gives the user the ability to 
+upload and browse all recordings uploaded to the database.
+
+#### Filesystem Permission
+
+The path on the filesystem where the uploaded files go (_EEGUploadIncomingPath_) should be 
+readable and writable by the web server.
+
+## Configurations
+
+The electrophysiology uploader has the following configurations that affect its usage:
+
+### Install Configurations
+
+To enable the module to handle large files, please follow the
+instructons for [Handling Large File Uploads](../../docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/02_Website_Configuration/Handling_Large_File_Uploads.md).
+
+#### <a name="database_config_link"></a> Database Configurations
+
+EEGUploadIncomingPath - This setting determines where on the filesystem the 
+        uploader is to place the uploaded recordings.
+        **Note**: Uploaded recordings are erased from the 
+        `EEGUploadIncomingPath` following a successful archival and insertion 
+        through the LORIS-MRI pipeline. 
+
diff --git a/modules/electrophysiology_uploader/jsx/UploadViewer.js b/modules/electrophysiology_uploader/jsx/UploadViewer.js
index bd34b379fbb..a1000eeae5e 100644
--- a/modules/electrophysiology_uploader/jsx/UploadViewer.js
+++ b/modules/electrophysiology_uploader/jsx/UploadViewer.js
@@ -77,14 +77,12 @@ export default function UploadViewer(props) {
   ];
 
   return (
-    <>
-      <FilterableDataTable
-        name='eeg_upload_viewer'
-        data={props.data}
-        fields={fields}
-        getFormattedCell={formatColumn}
-      />
-    </>
+    <FilterableDataTable
+      name='eeg_upload_viewer'
+      data={props.data}
+      fields={fields}
+      getFormattedCell={formatColumn}
+    />
   );
 }
 
diff --git a/modules/electrophysiology_uploader/php/electrophysiology_uploader.class.inc b/modules/electrophysiology_uploader/php/electrophysiology_uploader.class.inc
index fc744132ae4..321867fc60d 100644
--- a/modules/electrophysiology_uploader/php/electrophysiology_uploader.class.inc
+++ b/modules/electrophysiology_uploader/php/electrophysiology_uploader.class.inc
@@ -50,7 +50,7 @@ class Electrophysiology_Uploader extends \DataFrameworkMenu
      */
     public function useProjectFilter(): bool
     {
-        return false;
+        return true;
     }
 
     /**
diff --git a/modules/electrophysiology_uploader/php/upload.class.inc b/modules/electrophysiology_uploader/php/upload.class.inc
index f11d6519891..3f649e454ec 100644
--- a/modules/electrophysiology_uploader/php/upload.class.inc
+++ b/modules/electrophysiology_uploader/php/upload.class.inc
@@ -125,8 +125,8 @@ class Upload extends \NDB_Page
         if (empty($request->getUploadedFiles()) && empty($values)) {
             $upload_max_size = \Utility::getMaxUploadSize();
             return new \LORIS\Http\Response\JSON\InternalServerError(
-                "The uploaded file size ($upload_max_size) exceeds " .
-                "the upload_max_filesize or post_max_size directive in php.ini"
+                "The uploaded file size exceeds the upload_max_filesize " .
+                "or post_max_size directive in php.ini ($upload_max_size)"
             );
         }
 
@@ -176,7 +176,10 @@ class Upload extends \NDB_Page
             );
         }
 
-        // Check for existing files
+        // Check for an existing file
+        // If found, add a timestamp suffix to avoid collision
+        // with any other existing upload attempt
+        // and move the renamed file in _EEGUploadIncomingPath_/archives/
         $targetPath = $targetdir->getPathname() . '/' . $filename;
         if (file_exists($targetPath)) {
             $archiveFilename = str_replace(