Merge pull request #799 from rdmorganiser/dev-2.0.2

RDMO 2.0.2

.github/workflows/pre-commit-autoupdate.yml

@@ -0,0 +1,60 @@
+# This CI job is adapted from:
+# Cookiecutter Django (2013-10-17), BSD-3-Clause license
+# Ref: https://github.com/cookiecutter/cookiecutter-django/blob/2023.10.17/.github/workflows/pre-commit-autoupdate.yml
+
+name: Update pre-commit hooks
+
+on:
+  schedule:
+    # run once a month at midnight of the first day of the month
+    - cron: 0 0 1 * *
+  # run manually from actions tab
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  auto-update:
+    # Disables this workflow from running in a repository that is not part of the indicated organization/user
+    if: github.repository_owner == 'rdmorganiser'
+    permissions:
+      contents: write # for peter-evans/create-pull-request to create branch
+      pull-requests: write # for peter-evans/create-pull-request to create a PR
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+          cache: pip
+      - run: python -m pip install pre-commit
+      - run: pre-commit autoupdate > autoupdate.log
+      - name: Prepare message for pr body
+        run: |
+          grep "updating" autoupdate.log > updates.log
+          sed -i -e 's/\[/- </g' updates.log
+          sed -i -e 's/\]/>/g' updates.log
+          echo -e "## Proposed changes\n\nBumps the pre-commit config with the following updates:\n" > pr-body.md
+          cat updates.log >> pr-body.md
+          echo -e "\n---\nThis PR is auto-generated once a month." >> pr-body.md
+      # Ref: https://github.com/peter-evans/create-pull-request
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@153407881ec5c347639a548ade7d8ad1d6740e38 # v5.0.2
+        with:
+          branch: pre-commit-autoupdate
+          base: dependency-updates
+          committer: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
+          author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
+          title: "build: update pre-commit hooks"
+          commit-message: "build: update pre-commit hooks"
+          add-paths: .pre-commit-config.yaml
+          body-path: pr-body.md
+          labels: |
+            dependencies
+            pre-commit
+            type: maintenance
+          delete-branch: true
+      - name: Write to job summary
+        run: |
+          cat updates.log >> $GITHUB_STEP_SUMMARY

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [RDMO 2.0.2](https://github.com/rdmorganiser/rdmo/compare/2.0.1...2.0.2) (Nov 2, 2023)
+
+* Fix migration to RDMO 2.0 for PostgreSQL
+* Fix Shibboleth urls
+* Fix issue view
+* Fix margins in management interface
 
 ## [RDMO 2.0.1](https://github.com/rdmorganiser/rdmo/compare/2.0.0...2.0.1) (Oct 9, 2023)
 

README.md

@@ -3,7 +3,10 @@ RDMO - Research Data Management Organiser
 
 [![Latest release](https://img.shields.io/pypi/v/rdmo.svg?style=flat)](https://pypi.python.org/pypi/rdmo/)
 [![Python Versions](https://img.shields.io/pypi/pyversions/rdmo.svg?style=flat)](https://www.python.org/)
-[![License](https://img.shields.io/github/license/rdmorganiser/rdmo?style=flat)](https://github.com/rdmorganiser/rdmo/blob/master/LICENSE)
+[![Django Versions](https://img.shields.io/pypi/frameworkversions/django/rdmo)](https://pypi.python.org/pypi/rdmo/)
+[![License](https://img.shields.io/github/license/rdmorganiser/rdmo?style=flat)](https://github.com/rdmorganiser/rdmo/blob/master/LICENSE) \
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![CI Workflow Status](https://github.com/rdmorganiser/rdmo/actions/workflows/ci.yml/badge.svg)](https://github.com/rdmorganiser/rdmo/actions/workflows/ci.yml)
 [![Coverage Status](https://coveralls.io/repos/rdmorganiser/rdmo/badge.svg?branch=master&service=github)](https://coveralls.io/github/rdmorganiser/rdmo?branch=master)
 [![Documentation status](https://readthedocs.org/projects/rdmo/badge/?version=latest)](http://rdmo.readthedocs.io/en/latest/?badge=latest)

rdmo/accounts/urls/__init__.py

@@ -21,8 +21,6 @@
                 shibboleth_login, name='shibboleth_login'),
         re_path('^shibboleth/logout/',
                 shibboleth_logout, name='shibboleth_logout'),
-        re_path('^logout/',
-                auth_views.LogoutView.as_view(next_page=settings.SHIBBOLETH_LOGOUT_URL), name='account_logout'),
     ]
 
 if settings.ACCOUNT or settings.SOCIALACCOUNT:

rdmo/management/assets/js/components/nested/NestedPage.js

@@ -52,7 +52,7 @@ const NestedPage = ({ config, page, configActions, elementActions }) => {
                                options={getUriPrefixes(page.elements)} />
             </div>
           </div>
-          <div className="checkboxes">
+          <div className="mt-10">
             <span className="mr-10">{gettext('Show elements:')}</span>
             <Link className="mr-10" onClick={toggleQuestionSets}>{gettext('Question sets')}</Link>
           </div>

rdmo/management/assets/js/components/nested/NestedQuestionSet.js

@@ -50,7 +50,7 @@ const NestedQuestionSet = ({ config, questionset, configActions, elementActions
                                options={getUriPrefixes(questionset.elements)} />
             </div>
           </div>
-          <div className="checkboxes">
+          <div className="mt-10">
             <span className="mr-10">{gettext('Show elements:')}</span>
             <Link className="mr-10" onClick={toggleQuestionSets}>{gettext('Question sets')}</Link>
           </div>

rdmo/management/assets/js/components/nested/NestedSection.js

@@ -53,7 +53,7 @@ const NestedCatalog = ({ config, section, configActions, elementActions }) => {
                                options={getUriPrefixes(section.elements)} />
             </div>
           </div>
-          <div className="checkboxes">
+          <div className="mt-10">
             <span className="mr-10">{gettext('Show elements:')}</span>
             <Link className="mr-10" onClick={togglePages}>{gettext('Pages')}</Link>
             <Link className="mr-10" onClick={toggleQuestionSets}>{gettext('Question sets')}</Link>

rdmo/projects/tests/test_view_issue.py

@@ -49,6 +49,26 @@
 
 issue_status = ('open', 'in_progress', 'closed')
 
+@pytest.mark.parametrize('username,password', users)
+@pytest.mark.parametrize('project_id', projects)
+@pytest.mark.parametrize('issue_id', issues)
+def test_issue(db, client, username, password, project_id, issue_id):
+    client.login(username=username, password=password)
+    issue = Issue.objects.filter(project_id=project_id, id=issue_id).first()
+
+    url = reverse('issue', args=[project_id, issue_id])
+    response = client.get(url)
+
+    if issue:
+        if project_id in view_issue_permission_map.get(username, []):
+            assert response.status_code == 200
+        elif password:
+            assert response.status_code == 403
+        else:
+            assert response.status_code == 302
+    else:
+        assert response.status_code == 404
+
 
 @pytest.mark.parametrize('username,password', users)
 @pytest.mark.parametrize('project_id', projects)

rdmo/projects/views/issue.py

@@ -33,13 +33,14 @@ def get_permission_object(self):
 
     def get_context_data(self, **kwargs):
         project = self.get_object().project
+        project.catalog.prefetch_elements()
         conditions = self.get_object().task.conditions.all()
 
         sources = []
         for condition in conditions:
             sources.append({
                 'source': condition.source,
-                'questions': condition.source.questions.filter(questionset__section__catalog=project.catalog),
+                'questions': filter(lambda q: q.attribute == condition.source, project.catalog.questions),
                 'values': condition.source.values.filter(project=project, snapshot=None)
             })
 

rdmo/questions/migrations/0074_data_migration.py

@@ -1,6 +1,6 @@
 from __future__ import unicode_literals
 
-from django.db import migrations
+from django.db import connection, migrations
 
 
 def run_data_migration(apps, schema_editor):
@@ -39,6 +39,20 @@ def run_data_migration(apps, schema_editor):
             question.questionset_id = None
             question.save()
 
+    if connection.vendor == 'postgresql':
+        # reset the autoincrement value for the page and questionset tables
+        with connection.cursor() as cursor:
+            cursor.execute('''
+                SELECT SETVAL(
+                    pg_get_serial_sequence('questions_page', 'id'),
+                    (SELECT MAX(id) FROM questions_page)
+                );
+                SELECT SETVAL(
+                    pg_get_serial_sequence('questions_questionset', 'id'),
+                    (SELECT MAX(id) FROM questions_questionset)
+                );
+            ''')
+
 
 class Migration(migrations.Migration):