add cubi templates to list view (#1961)

config/settings/base.py

@@ -853,6 +853,13 @@ def set_logging(level=None):
 ONTOLOGYACCESS_QUERY_LIMIT = env.int('ONTOLOGYACCESS_QUERY_LIMIT', 250)
 
 
+# Isatemplates settings
+# Enable templates from cubi-isa-templates
+ISATEMPLATES_ENABLE_CUBI_TEMPLATES = env.bool(
+    'ISATEMPLATES_ENABLE_CUBI_TEMPLATES', True
+)
+
+
 # Settings for HTTP AuthBasic
 BASICAUTH_REALM = env.str(
     'BASICAUTH_REALM', 'Log in with your SODAR user name and password.'

config/settings/test.py

@@ -131,6 +131,9 @@
     'bih_proteomics_smb',
 ]
 
+# Isatemplates app settings
+ISATEMPLATES_ENABLE_CUBI_TEMPLATES = True
+
 # UI test settings
 PROJECTROLES_TEST_UI_CHROME_OPTIONS = [
     'headless',

docs_manual/source/admin_settings.rst

@@ -229,6 +229,14 @@ Ontology Access Settings
 ``ONTOLOGYACCESS_QUERY_LIMIT``
     Term query limit (integer).
 
+ISA Templates Settings
+----------------------
+
+``ISATEMPLATES_ENABLE_CUBI_TEMPLATES``
+    Enable templates from the
+    `cubi-isa-templates <https://github.com/bihealth/cubi-isa-templates/>`_
+    repository (boolean).
+
 
 SODAR Docker Compose Settings
 =============================

isatemplates/models.py

@@ -45,7 +45,7 @@ class CookiecutterISATemplate(models.Model):
         default=True, help_text='Display template for users in UI'
     )
 
-    # ; User who last edited the template
+    #: User who last edited the template
     user = models.ForeignKey(
         AUTH_USER_MODEL,
         related_name='cookiecutter_templates',

isatemplates/templates/isatemplates/list.html

@@ -9,10 +9,6 @@
 {% block css %}
   {{ block.super }}
   <style type="text/css">
-    table#sodar-it-list-table thead tr th:nth-child(2),
-    table#sodar-it-list-table tbody tr td:nth-child(2) {
-      white-space: nowrap;
-    }
     table#sodar-it-list-table thead tr th:nth-child(4),
     table#sodar-it-list-table tbody tr td:nth-child(4) {
       width: 170px;
@@ -44,6 +40,12 @@
         display: none;
       }
     }
+    @media screen and (max-width: 900px) {
+      table#sodar-it-cubi-table thead tr th:nth-child(2),
+      table#sodar-it-cubi-table tbody tr td:nth-child(2) {
+        display: none;
+      }
+    }
   </style>
 {% endblock css %}
 
@@ -81,7 +83,7 @@ <h4>
           {% for t in templates %}
             <tr class="sodar-it-list-item">
               <td>{{ t.description }}</td>
-              <td class="text-monospace">{{ t.name }}</td>
+              <td class="text-monospace text-nowrap">{{ t.name }}</td>
               {% if t.user %}
                 <td>
                   {% get_user_html t.user as t_user %}
@@ -126,10 +128,47 @@ <h4>
             </tr>
           {% endfor %}
           {% if templates.count == 0 %}
-            <td class="bg-faded font-italic text-center"
-                id="sodar-it-list-empty" colspan="6">
-              No custom ISA-Tab templates imported.
-            </td>
+            <tr id="sodar-it-list-empty">
+              <td class="bg-faded font-italic text-center" colspan="6">
+                No custom ISA-Tab templates imported.
+              </td>
+            </tr>
+          {% endif %}
+        </tbody>
+      </table>
+    </div>
+  </div>
+
+  <div class="card" id="sodar-it-cubi-list">
+    <div class="card-header">
+      <h4>
+        <i class="iconify" data-icon="mdi:file-table-box-multiple-outline"></i>
+        CUBI Templates
+        {% get_info_link "Templates from the cubi-isa-templates repository" as info_link %}
+        {{ info_link | safe }}
+      </h4>
+    </div>
+    <div class="card-body p-0">
+      <table class="table table-striped sodar-card-table" id="sodar-it-cubi-table">
+        <thead>
+          <tr>
+            <th>Description</th>
+            <th>Name</th>
+          </tr>
+        </thead>
+        <tbody>
+          {% for t in cubi_templates %}
+            <tr class="sodar-it-cubi-item">
+              <td>{{ t.description | capfirst }}</td>
+              <td class="text-monospace text-nowrap">{{ t.name }}</td>
+            </tr>
+          {% endfor %}
+          {% if not cubi_templates %}
+            <tr id="sodar-it-cubi-empty">
+              <td class="bg-faded font-italic text-center" colspan="2">
+                CUBI templates are disabled in the site Django settings.
+              </td>
+            </tr>
           {% endif %}
         </tbody>
       </table>

isatemplates/tests/test_ui.py

@@ -1,5 +1,8 @@
 """UI tests for the isatemplates app"""
 
+from cubi_isa_templates import _TEMPLATES as CUBI_TEMPLATES
+
+from django.test import override_settings
 from django.urls import reverse
 
 from selenium.common.exceptions import NoSuchElementException
@@ -30,9 +33,17 @@ def test_get_no_templates(self):
         self.assertIsNotNone(
             self.selenium.find_element(By.ID, 'sodar-it-list-empty')
         )
+        self.assertEqual(
+            len(
+                self.selenium.find_elements(By.CLASS_NAME, 'sodar-it-cubi-item')
+            ),
+            len(CUBI_TEMPLATES),
+        )
+        with self.assertRaises(NoSuchElementException):
+            self.selenium.find_element(By.ID, 'sodar-it-cubi-empty')
 
     def test_get_existing_template(self):
-        """Test ISATemplateListView GET with existing template"""
+        """Test GET with existing template"""
         self.template = self.make_isa_template(
             name=TEMPLATE_NAME,
             description=TEMPLATE_DESC,
@@ -49,3 +60,21 @@ def test_get_existing_template(self):
         )
         with self.assertRaises(NoSuchElementException):
             self.selenium.find_element(By.ID, 'sodar-it-list-empty')
+        self.assertEqual(
+            len(
+                self.selenium.find_elements(By.CLASS_NAME, 'sodar-it-cubi-item')
+            ),
+            len(CUBI_TEMPLATES),
+        )
+        with self.assertRaises(NoSuchElementException):
+            self.selenium.find_element(By.ID, 'sodar-it-cubi-empty')
+
+    @override_settings(ISATEMPLATES_ENABLE_CUBI_TEMPLATES=False)
+    def test_get_disable_cubi_templates(self):
+        """Test GET with cubi templates disabled"""
+        self.login_and_redirect(self.superuser, self.url)
+        with self.assertRaises(NoSuchElementException):
+            self.selenium.find_element(By.CLASS_NAME, 'sodar-it-cubi-item')
+        self.assertIsNotNone(
+            self.selenium.find_element(By.ID, 'sodar-it-cubi-empty')
+        )

isatemplates/tests/test_views.py

@@ -2,6 +2,9 @@
 
 import json
 
+from cubi_isa_templates import _TEMPLATES as CUBI_TEMPLATES
+
+from django.test import override_settings
 from django.urls import reverse
 
 from test_plus.test import TestCase
@@ -46,3 +49,15 @@ def test_get(self):
             response.context['templates'][0].sodar_uuid,
             self.template.sodar_uuid,
         )
+        self.assertEqual(
+            len(response.context['cubi_templates']), len(CUBI_TEMPLATES)
+        )
+
+    @override_settings(ISATEMPLATES_ENABLE_CUBI_TEMPLATES=False)
+    def test_get_disable_cubi_templates(self):
+        """Test GET with cubi templates disabled"""
+        with self.login(self.superuser):
+            response = self.client.get(self.url)
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.context['templates'].count(), 1)
+        self.assertEqual(response.context['cubi_templates'], None)

isatemplates/views.py

@@ -1,5 +1,8 @@
 """UI views for the isatemplates app"""
 
+from cubi_isa_templates import _TEMPLATES as CUBI_TEMPLATES
+
+from django.conf import settings
 from django.views.generic import TemplateView
 
 # Projectroles dependency
@@ -19,4 +22,9 @@ def get_context_data(self, **kwargs):
         context['templates'] = CookiecutterISATemplate.objects.all().order_by(
             'name'
         )
+        context['cubi_templates'] = None
+        if settings.ISATEMPLATES_ENABLE_CUBI_TEMPLATES:
+            context['cubi_templates'] = sorted(
+                CUBI_TEMPLATES, key=lambda x: x.description.lower()
+            )
         return context