Merge branch 'development' into development-keyword-selector

.github/workflows/python.yml

@@ -4,22 +4,20 @@ on: [push, pull_request]
 
 jobs:
   lint:
-    runs-on: ubuntu-20.04
-    strategy:
-      matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
-          architecture: x64
+          python-version: 3.12
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install flake8==6.0.0 flake8-import-order==0.18.2 darglint==1.8.1 codespell mypy types-requests werkzeug
+          python -m pip install flake8==7.1.1 flake8-import-order==0.18.2 darglint==1.8.1 codespell
+          python -m pip install mypy types-requests werkzeug
 
       - name: Lint with flake8
         run: |

.github/workflows/smoke-test.yml

@@ -75,8 +75,8 @@ jobs:
       run: |
         cd yoda/docker/compose
         docker exec provider.yoda sh -c 'set -x ; cd /etc/irods/yoda-ruleset && sudo chown irods:irods -R /etc/irods/yoda-ruleset && sudo -u irods git config remote.origin.fetch "+refs/heads/*:refs/remotes/origin/*" && sudo -u irods git pull && sudo -u irods git status'
-        docker exec provider.yoda sh -c "set -x ; cd /etc/irods/yoda-ruleset && ( sudo -u irods git checkout ${{ steps.extract_branch.outputs.branch }} || sudo -u irods git checkout development) && sudo -u irods python -m pip --no-cache-dir install --user -r /etc/irods/yoda-ruleset/requirements.txt && sudo -u irods make && sudo -u irods make install" 
-        docker exec provider.yoda sh -c "set -x ; sudo -u irods /var/lib/irods/irodsctl restart"
+        docker exec provider.yoda sh -c "set -x ; cd /etc/irods/yoda-ruleset && sudo -u irods git checkout ${{ steps.extract_branch.outputs.branch }} && sudo -u irods python3 -m pip --no-cache-dir install --user --break-system-packages -r /etc/irods/yoda-ruleset/requirements.txt && sudo -u irods make && sudo -u irods make install"
+        docker exec provider.yoda sh -c 'set -x ; sudo -u irods /var/lib/irods/irodsctl restart'
 
     - name: Pull and install branch version of the portal
       shell: bash
@@ -111,7 +111,9 @@ jobs:
         docker logs portal.yoda
         docker logs provider.yoda
         docker exec portal.yoda sh -c 'set -x; cat /var/log/apache2/error.log || echo "Apache error log file not found."'
-        docker exec provider.yoda sh -c 'set -x ; cat /var/lib/irods/log/rodsLog*' || echo "rodsLog not found."'
+        docker exec provider.yoda sh -c 'set -x ; cat /var/log/syslog' || echo "rodsLog not found."'
+        cat ../../copytovault.log
+        cat ../../publication.log
 
 # Uncomment section below when needed for debugging.
 #

admin/templates/admin/admin.html

@@ -3,7 +3,7 @@
 {% block title %}{{ super() }} - Administration{% endblock title %}
 
 {% block scripts %}
-<script src="{{ url_for('static', filename='lib/purify-3.2.1/js/purify.min.js') }}"></script>
+<script src="{{ url_for('static', filename='lib/purify-3.2.3/js/purify.min.js') }}"></script>
 <script src="{{ url_for('admin_bp.static', filename='js/create_preview.js') }}"></script>
 <script src="{{ url_for('admin_bp.static', filename='js/file_formats.js') }}"></script>
 {% endblock scripts %}

app.py

@@ -153,6 +153,7 @@ def load_admin_setting() -> Dict[str, Any]:
 
 # CSRF protection.
 csrf = CSRFProtect(app)
+app.config['WTF_CSRF_TIME_LIMIT'] = None  # Set CSRF token lifetime tied to the life of the session.
 
 
 @app.before_request

deposit/templates/deposit/data.html

@@ -13,7 +13,7 @@
     var path = {{ path|tojson|safe }};
     var view = 'browse';
 </script>
-<script src="{{ url_for('static', filename='lib/purify-3.2.1/js/purify.min.js') }}"></script>
+<script src="{{ url_for('static', filename='lib/purify-3.2.3/js/purify.min.js') }}"></script>
 <script src="{{ url_for('static', filename='lib/datatables-1.13.5/datatables.min.js') }}"></script>
 <script src="{{ url_for('deposit_bp.static', filename='lib/flow-js/flow.min.js') }}"></script>
 <script src="{{ url_for('deposit_bp.static', filename='lib/dragbetter-js/jquery.dragbetter.js') }}"></script>

general/general.py

@@ -3,9 +3,11 @@
 __copyright__ = 'Copyright (c) 2021-2024, Utrecht University'
 __license__   = 'GPLv3, see LICENSE'
 
-from flask import Blueprint, redirect, render_template, Response, url_for
+from flask import Blueprint, redirect, render_template, request, Response, session, url_for
 from flask_wtf.csrf import CSRFError
 
+from util import log_error
+
 general_bp = Blueprint('general_bp', __name__,
                        template_folder='templates/general',
                        static_folder='static/general',
@@ -19,6 +21,8 @@ def index() -> Response:
 
 @general_bp.app_errorhandler(CSRFError)
 def csrf_error(e: Exception) -> Response:
+    username = session.get("login_username", "N/A")
+    log_error(f"CSRF error occurred for user {username} on path {request.path}.")
     return redirect(url_for('user_bp.login'))
 
 

group_manager/templates/group_manager/index.html

@@ -9,7 +9,7 @@
 {% endblock style %}
 
 {% block scripts %}
-    <script src="{{ url_for('static', filename='lib/purify-3.2.1/js/purify.min.js') }}"></script>
+    <script src="{{ url_for('static', filename='lib/purify-3.2.3/js/purify.min.js') }}"></script>
     <script src="{{ url_for('group_manager_bp.static', filename='js/group_manager.js') }}"></script>
     <script src="{{ url_for('group_manager_bp.static', filename='lib/select2/select2.full.min.js') }}"></script>
     <script>

research/templates/research/browse.html

@@ -3,7 +3,7 @@
 {% block title %}{{ super() }} - Research{% endblock title %}
 
 {% block scripts %}
-<script src="{{ url_for('static', filename='lib/purify-3.2.1/js/purify.min.js') }}"></script>
+<script src="{{ url_for('static', filename='lib/purify-3.2.3/js/purify.min.js') }}"></script>
 <script src="{{ url_for('static', filename='lib/datatables-1.13.5/datatables.min.js') }}"></script>
 <script src="{{ url_for('research_bp.static', filename='lib/flow-js/flow.min.js') }}"></script>
 <script src="{{ url_for('research_bp.static', filename='js/research.js') }}"></script>
@@ -81,18 +81,18 @@ <h5 class="modal-title">
 </div>
 
 <div class="modal" tabindex="-1" role="dialog" id="cleanup-collection">
-    <div class="modal-dialog">
+    <div class="modal-dialog modal-dialog-scrollable">
         <div class="modal-content">
-            <div class="modal-body">
-                <h5 class="modal-title">Clean up collection</h5>
-                <div class="alert alert-warning" id="alert-panel-cleanup-collection">
+            <div class="modal-header d-flex flex-column align-items-start">
+                <h5 class="modal-title mb-2">Clean up collection</h5>
+                <div class="alert alert-warning w-100" id="alert-panel-cleanup-collection">
                     <span></span>
                 </div>
-
                 <p><b><span id="collection"></span></b></p>
+            </div>
 
+            <div class="modal-body">
                 <div id="cleanup-files"></div>
-
             </div>
             <div class="modal-footer">
                 <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Cancel</button>

search/templates/search/search.html

@@ -3,7 +3,7 @@
 {% block title %}{{ super() }} - Search{% endblock title %}
 
 {% block scripts %}
-<script src="{{ url_for('static', filename='lib/purify-3.2.1/js/purify.min.js') }}"></script>
+<script src="{{ url_for('static', filename='lib/purify-3.2.3/js/purify.min.js') }}"></script>
 <script src="{{ url_for('static', filename='lib/datatables-1.13.5/datatables.min.js') }}"></script>
 <script src="{{ url_for('search_bp.static', filename='js/revision.js') }}"></script>
 <script src="{{ url_for('search_bp.static', filename='js/search.js') }}"></script>

user/templates/user/data_transfer.html

@@ -64,7 +64,7 @@ <h1>Data Transfer</h1>
     "irods_home": "/{{ config.get('IRODS_DEFAULT_ZONE') }}/home",
     "irods_user_name": "{{ g.user }}",
     "irods_zone_name": "{{ config.get('IRODS_DEFAULT_ZONE') }}",
-    "irods_authentication_scheme": "pam",
+    "irods_authentication_scheme": "pam_password",
     "irods_encryption_algorithm": "AES-256-CBC",
     "irods_encryption_key_size": 32,
     "irods_encryption_num_hash_rounds": 16,
@@ -91,7 +91,7 @@ <h1>Data Transfer</h1>
 irods_port: 1247
 irods_user_name: "{{ g.user }}"
 irods_zone_name: "{{ config.get('IRODS_DEFAULT_ZONE') }}"
-irods_authentication_scheme: "pam"
+irods_authentication_scheme: "pam_password"
 irods_encryption_algorithm: "AES-256-CBC"
 irods_encryption_key_size: 32
 irods_encryption_num_hash_rounds: 16

vault/templates/vault/browse.html

@@ -8,7 +8,7 @@
 {% endblock style %}
 
 {% block scripts %}
-<script src="{{ url_for('static', filename='lib/purify-3.2.1/js/purify.min.js') }}"></script>
+<script src="{{ url_for('static', filename='lib/purify-3.2.3/js/purify.min.js') }}"></script>
 <script src="{{ url_for('static', filename='lib/datatables-1.13.5/datatables.min.js') }}"></script>
 <script src="{{ url_for('vault_bp.static', filename='js/vault.js') }}"></script>
 <script src="{{ url_for('vault_bp.static', filename='js/dlgSelectCollection.js') }}"></script>