From 8ae9bd77cb763ec56dc8cf09da8b14e4987f41a1 Mon Sep 17 00:00:00 2001
From: B0r1sD <boris.depoortere@gmail.com>
Date: Wed, 26 Aug 2026 14:28:51 +0200
Subject: [PATCH] feat: cookieless matomo integration (untested)

---
 doc/source/admin/galaxy_options.rst                | 14 ++++++++++++++
 .../config/_galaxy_config_schema_attributes.py     |  1 +
 lib/galaxy/config/sample/galaxy.yml.sample         |  7 +++++++
 lib/galaxy/config/schemas/config_schema.yml        | 11 +++++++++++
 templates/js-app.mako                              |  7 +++++--
 5 files changed, 38 insertions(+), 2 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index ce37cc4fe7a..389613bbb82 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -2144,6 +2144,20 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+``matomo_disable_cookies``
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Run Matomo in "cookieless" mode. When set to true (the default),
+    Galaxy instructs the Matomo tracker to disable all tracking
+    cookies by calling _paq.push(['disableCookies']) before tracking
+    the page view. Set to false to allow Matomo to use cookies. See
+    https://matomo.org/faq/general/faq_157/ for details.
+:Default: ``true``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~
 ``display_servers``
 ~~~~~~~~~~~~~~~~~~~
diff --git a/lib/galaxy/config/_galaxy_config_schema_attributes.py b/lib/galaxy/config/_galaxy_config_schema_attributes.py
index 42f071d66d1..ef9a4e53b14 100644
--- a/lib/galaxy/config/_galaxy_config_schema_attributes.py
+++ b/lib/galaxy/config/_galaxy_config_schema_attributes.py
@@ -165,6 +165,7 @@ class GalaxyAppConfigurationAttributes:
     plausible_domain: str | None
     matomo_server: str | None
     matomo_site_id: str | None
+    matomo_disable_cookies: bool
     display_servers: str
     enable_old_display_applications: bool
     aws_estimate: bool
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 619d45bca3c..b10eaa4dcf3 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1426,6 +1426,13 @@ galaxy:
   # for tracking with Matomo (https://matomo.org/).
   #matomo_site_id: null
 
+  # Run Matomo in "cookieless" mode. When set to true (the default),
+  # Galaxy instructs the Matomo tracker to disable all tracking cookies
+  # by calling _paq.push(['disableCookies']) before tracking the page
+  # view. Set to false to allow Matomo to use cookies. See
+  # https://matomo.org/faq/general/faq_157/ for details.
+  #matomo_disable_cookies: true
+
   # Galaxy can display data at various external browsers.  These options
   # specify which browsers should be available.  URLs and builds
   # available at these browsers are defined in the specified files.
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index 14e76a23008..0b7dc031d82 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -1605,6 +1605,17 @@ mapping:
           Please enter the site ID for the Matomo server so this can be used for tracking
           with Matomo (https://matomo.org/).
 
+      matomo_disable_cookies:
+        type: bool
+        default: true
+        required: false
+        desc: |
+          Run Matomo in "cookieless" mode. When set to true (the default), Galaxy
+          instructs the Matomo tracker to disable all tracking cookies by calling
+          _paq.push(['disableCookies']) before tracking the page view. Set to false
+          to allow Matomo to use cookies. See
+          https://matomo.org/faq/general/faq_157/ for details.
+
       display_servers:
         type: str
         default: hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu
diff --git a/templates/js-app.mako b/templates/js-app.mako
index 6ccceeef0f8..d89c28a5378 100644
--- a/templates/js-app.mako
+++ b/templates/js-app.mako
@@ -61,7 +61,7 @@
             ${ config_plausible_analytics(app.config.plausible_server, app.config.plausible_domain) }
         %endif
         %if app.config.matomo_server and app.config.matomo_site_id:
-            ${ config_matomo_analytics(app.config.matomo_server, app.config.matomo_site_id) }
+            ${ config_matomo_analytics(app.config.matomo_server, app.config.matomo_site_id, app.config.matomo_disable_cookies) }
         %endif
     </body>
 </html>
@@ -93,13 +93,16 @@
     %endif
 </%def>
 
-<%def name="config_matomo_analytics(matomo_server, matomo_site_id)">
+<%def name="config_matomo_analytics(matomo_server, matomo_site_id, matomo_disable_cookies=True)">
     <script type="text/javascript">
         console.log("config_matomo_analytics matomo_server:", '${matomo_server}');
         console.log("config_matomo_analytics matomo_site_id:", '${matomo_site_id}')
         %if matomo_server and matomo_site_id:
             var _paq = window._paq = window._paq || [];
             /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
+            %if matomo_disable_cookies:
+            _paq.push(['disableCookies']);
+            %endif
             _paq.push(['trackPageView']);
             _paq.push(['enableLinkTracking']);
             (function () {