Add toolmsg webhook to EU

group_vars/sn06/toolmsg.yml

@@ -0,0 +1,40 @@
+---
+# This file is used to define custom messages for tools that are displayed in the tool form
+# The toolmsg webhook wil be triggered and the message will be displayed in the tool form if the tool_id matches
+
+# Format:
+# toolmsg_messages:
+#   - tool_id: to match subject.startsWith(tool_id)
+#              Best to use remove version numbers and trailing slash
+#              e.g. toolshed.g2.bx.psu.edu/repos/galaxyp/diann/diann
+#     message: A custom HTML message to be displayed for this tool
+#     class: bootstrap class [primary, info, success, warning, danger]
+
+# Example 1: Display a warning message for the tool ncbi_blastp_wrapper, the message will be in bold format
+# toolmsg_messages:
+#   - tool_id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper
+#     message: <strong>We recommend using Diamond instead.</strong>
+#     class: warning
+
+# Example 2: Display a warning message for the tool ncbi_blastp_wrapper, the message will be in bold format and will have a link to the Diamond tool
+# toolmsg_messages:
+#   - tool_id: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper
+#     message: >
+#       <strong>We recommend using
+#       <a href="https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fdiamond%2Fbg_diamond%2F2.1.11%2Bgalaxy0&version=latest"
+#           target="_blank"
+#       >
+#         Diamond
+#       </a>
+#       instead.</strong>
+#     class: warning
+
+toolmsg_messages:
+  - tool_id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc
+    message: >
+      <strong>We recommend using
+      <a href="https://usegalaxy.eu/?tool_id=falco" target="_blank">
+        Falco
+      </a>
+      instead. Falco is 3 times faster and offers the same functionality as FASTQC.</strong>
+    class: warning

roles/usegalaxy-eu.webhooks/defaults/main.yml

@@ -1,2 +1,3 @@
-galaxy_webhook_url: "https://github.com/usegalaxy-eu/galaxy-webhooks"
-galaxy_webhook_dir: "{{ galaxy_mutable_data_dir }}/webhooks"
+galaxy_webhook_url: 'https://github.com/usegalaxy-eu/galaxy-webhooks'
+galaxy_webhook_dir: '{{ galaxy_mutable_data_dir }}/webhooks'
+galaxy_webhook_plugins_template_dir: 'templates/galaxy/webhooks/'

roles/usegalaxy-eu.webhooks/tasks/main.yml

@@ -1,6 +1,21 @@
 - name: Clone webhook repository
-  git:
-    repo: "{{ galaxy_webhook_url }}"
-    dest: "{{ galaxy_webhook_dir }}"
+  ansible.builtin.git:
+    repo: '{{ galaxy_webhook_url }}'
+    dest: '{{ galaxy_webhook_dir }}'
     version: master
-    force: "yes"
+    force: 'yes'
+
+- name: Create toolmsg plugins directory in webhook directory
+  ansible.builtin.file:
+    path: '{{ galaxy_webhook_dir }}/toolmsg_24.2'
+    state: directory
+    mode: '0755'
+
+- name: Template toolmsg_24.2 webhook files
+  ansible.builtin.template:
+    src: '{{ item }}'
+    dest: "{{ galaxy_webhook_dir }}/toolmsg_24.2/{{ item | basename | regex_replace('\\.j2$', '') }}"
+    mode: 0644
+  with_fileglob:
+    - '{{ galaxy_webhook_plugins_template_dir }}/toolmsg_24.2/*'
+  notify: Restart Galaxy

sn06.yml

@@ -51,6 +51,7 @@
     - group_vars/sn06/sn06.yml
     - group_vars/sn06/themes_conf.yml
     - group_vars/sn06/subdomains.yml
+    - group_vars/sn06/toolmsg.yml
     - group_vars/tiaas.yml # All of the training infrastructure
     - group_vars/gxconfig.yml # The base galaxy configuration
     - group_vars/toolbox.yml # User controlled toolbox

templates/galaxy/webhooks/toolmsg_24.2/GALAXY_VERSION

@@ -0,0 +1 @@
+galaxy >= 24.2

templates/galaxy/webhooks/toolmsg_24.2/config.yml.j2

@@ -0,0 +1,4 @@
+id: toolmsg
+type:
+  - onload
+activate: true

templates/galaxy/webhooks/toolmsg_24.2/script.js.j2

@@ -0,0 +1,82 @@
+// Custom messages for tool forms
+
+const enableDebug = false;
+const debugLog = (msg) => enableDebug && console.debug("[ToolMsg]: " + msg);
+
+const WAIT_TOOL_MAX_TRIES = 3;
+const WAIT_TOOL_INTERVAL = 500;
+const toolMessages = [
+    {% if toolmsg_messages is defined and toolmsg_messages %}
+        {% for message in toolmsg_messages %}
+        {
+            tool_id: "{{ message.tool_id }}",
+            message: `{{ message.message }}`,
+            class: "{{ message.class }}"
+        },
+        {% endfor %}
+    {% endif %}
+];
+
+function waitToolFormLoad() {
+    tries++;
+    let matched = false;
+    const element = document.querySelector('div[tool_id]');
+    if (element) {
+        debugLog('Tool form has been loaded');
+        matched = showToolMessages();
+        tries = WAIT_TOOL_MAX_TRIES;
+    } else {
+        debugLog("No tool form detected (tries: " + tries + ")");
+    }
+    tries < WAIT_TOOL_MAX_TRIES
+        && !matched
+        && setTimeout(waitToolFormLoad, WAIT_TOOL_INTERVAL);
+}
+
+function isCurrentToolForm(toolId) {
+    const elements = document.querySelectorAll('[tool_id]');
+    for (let element of elements) {
+        const thisToolId = element.getAttribute('tool_id');
+        if (thisToolId && thisToolId.startsWith(toolId)) {
+            debugLog(toolId + " matches " + thisToolId);
+            return true;
+        }
+    }
+    debugLog(toolId + " not found in page.");
+    return false;
+}
+
+function showToolMessages() {
+    let match = false;
+    toolMessages.forEach( (toolMessage) => {
+        if (isCurrentToolForm(toolMessage.tool_id)) {
+            const newElement = document.createElement('p');
+            newElement.className = 'alert alert-' + toolMessage.class + ' my-3';
+            newElement.innerHTML = toolMessage.message;
+            const referenceElement = document.getElementById('tool-card-body');
+            if (referenceElement) {
+                referenceElement.parentNode.insertBefore(newElement, referenceElement);
+            } else {
+                debugLog('Reference element with id="tool-card-body" not found.');
+            }
+            match = true;
+        }
+    })
+    return match;
+}
+
+let tries = 0;
+let lastUrlPath = null;
+
+// Add observer for Vue pathname changes
+const observer = new MutationObserver( () => {
+    if (lastUrlPath !== window.location.href) {
+        debugLog("Triggered mutation observer");
+        tries = 0;
+        lastUrlPath = window.location.href;
+        setTimeout(waitToolFormLoad, 500);
+    }
+});
+
+// Observe the document body for changes (or another relevant element)
+observer.observe(document.body, { childList: true, subtree: true });