Merge branch 'feature/b-and-i-24-14' of https://github.com/CenterForO…

…penScience/osf.io into fix-source-tags

* 'feature/b-and-i-24-14' of https://github.com/CenterForOpenScience/osf.io:
  refactor handle_duplicate_notifications and add tests
  Shorten lines; rename script for test clarity
  fix flake8 errors
  add admin screen to manage duplicate notifications
  [ENG-2814] Allow Read-only and Read/Write contributors to view a project's draft registrations (CenterForOpenScience#10660)
  [CR][ENG-5997] merge develop into b-and-i branch (CenterForOpenScience#10691)
  add exception handling in case state doesn't change
  [ENG-4527] Fix citation to use registered date (CenterForOpenScience#10678)
  restrict state changes more and allow no-ops
  split apart change provider views from general preprint view and machine_state change viewa
  Re-add permissions changes for files on withdrawn registrations (CenterForOpenScience#10671)
  [ENG-4903] Fixes issue with email confirmation links failing due to database congestion (CenterForOpenScience#10662)

# Conflicts:
#	addons/boa/requirements.txt
#	addons/box/requirements.txt
#	addons/dataverse/requirements.txt
#	addons/dropbox/requirements.txt
#	addons/github/requirements.txt
#	addons/gitlab/requirements.txt
#	addons/mendeley/requirements.txt
#	addons/owncloud/requirements.txt
#	addons/s3/requirements.txt
#	addons/twofactor/requirements.txt
#	addons/wiki/requirements.txt
#	addons/zotero/requirements.txt
#	api/base/utils.py
#	api/users/serializers.py
#	api_tests/draft_registrations/views/test_draft_registration_list.py
#	api_tests/nodes/views/test_node_draft_registration_list.py
#	api_tests/users/views/test_user_draft_registration_list.py
#	api_tests/users/views/test_user_settings.py
#	docker-compose.yml
#	poetry.lock
#	pyproject.toml
#	requirements.txt
#	requirements/dev.txt
#	requirements/release.txt
#	tests/test_views.py
#	website/util/metrics.py

.github/workflows/test-build.yml

@@ -21,7 +21,7 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ~/.cache
-        key: reqs_${{ hashFiles('**/pyproject.toml') }}
+        key: reqs_${{ hashFiles('**/requirements.txt') }}
         restore-keys: reqs
     - run: |
         mkdir -p ~/.cache/downloads

addons/base/views.py

@@ -317,6 +317,9 @@ def get_authenticated_resource(resource_id):
     if resource.deleted:
         raise HTTPError(http_status.HTTP_410_GONE, message='Resource has been deleted.')
 
+    if getattr(resource, 'is_retracted', False):
+        raise HTTPError(http_status.HTTP_410_GONE, message='Resource has been retracted.')
+
     return resource
 
 

addons/boa/requirements.txt

@@ -0,0 +1,5 @@
+# Requirements for the boa add-on
+boa-api==0.1.14
+
+# Requirements for running asyncio in celery, using 3.4.1 for Python 3.6 compatibility
+asgiref==3.7.2

addons/box/requirements.txt

@@ -0,0 +1 @@
+boxsdk==3.9.2

addons/dataverse/requirements.txt

@@ -0,0 +1,3 @@
+# Allow for optional timeout parameter.
+# https://github.com/IQSS/dataverse-client-python/pull/27
+git+https://github.com/CenterForOpenScience/dataverse-client-python.git@2b3827578048e6df3818f82381c7ea9a2395e526 # branch is feature/dv-client-updates

addons/dropbox/requirements.txt

@@ -0,0 +1 @@
+dropbox==11.36.2

addons/github/requirements.txt

@@ -0,0 +1,3 @@
+cachecontrol==0.14.0
+github3.py==4.0.1
+uritemplate==4.1.1

addons/gitlab/requirements.txt

@@ -0,0 +1 @@
+python-gitlab==4.4.0

addons/mendeley/requirements.txt

@@ -0,0 +1,2 @@
+# up-to-date with mendeley's master + add folder support and future dep updates
+git+https://github.com/CenterForOpenScience/mendeley-python-sdk.git@be8a811fa6c3b105d9f5c656cabb6b1ba855ed5b # branch is feature/osf-dep-updates

addons/owncloud/requirements.txt

@@ -0,0 +1,2 @@
+# Requirements for the owncloud add-on
+pyocclient==0.6.0

addons/s3/requirements.txt

@@ -0,0 +1 @@
+boto3==1.34.60

addons/twofactor/requirements.txt

@@ -0,0 +1 @@
+pyotp==2.9.0

addons/wiki/requirements.txt

@@ -0,0 +1 @@
+pymongo==4.6.3

addons/zotero/requirements.txt

@@ -0,0 +1 @@
+Pyzotero==1.5.18

admin/base/urls.py

@@ -36,6 +36,7 @@
             re_path(r'^schema_responses/', include('admin.schema_responses.urls', namespace='schema_responses')),
             re_path(r'^registration_schemas/', include('admin.registration_schemas.urls', namespace='registration_schemas')),
             re_path(r'^cedar_metadata_templates/', include('admin.cedar.urls', namespace='cedar_metadata_templates')),
+            re_path(r'^notifications/', include('admin.notifications.urls', namespace='notifications')),
         ]),
     ),
 ]

admin/notifications/urls.py

@@ -0,0 +1,8 @@
+from django.urls import re_path
+from admin.notifications import views
+
+app_name = 'notifications'
+
+urlpatterns = [
+    re_path(r'^$', views.handle_duplicate_notifications, name='handle_duplicate_notifications'),
+]

admin/notifications/views.py

@@ -0,0 +1,54 @@
+from django.contrib.auth.decorators import user_passes_test
+from django.shortcuts import render, redirect
+from admin.base.utils import osf_staff_check
+from osf.models.notifications import NotificationSubscription
+from django.db.models import Count
+
+def delete_selected_notifications(selected_ids):
+    NotificationSubscription.objects.filter(id__in=selected_ids).delete()
+
+def detect_duplicate_notifications():
+    duplicates = (
+        NotificationSubscription.objects.values('user', 'node', 'event_name')
+        .annotate(count=Count('id'))
+        .filter(count__gt=1)
+    )
+
+    detailed_duplicates = []
+    for dup in duplicates:
+        notifications = NotificationSubscription.objects.filter(
+            user=dup['user'], node=dup['node'], event_name=dup['event_name']
+        ).order_by('created')
+
+        for notification in notifications:
+            detailed_duplicates.append({
+                'id': notification.id,
+                'user': notification.user,
+                'node': notification.node,
+                'event_name': notification.event_name,
+                'created': notification.created,
+                'count': dup['count']
+            })
+
+    return detailed_duplicates
+
+def process_duplicate_notifications(request):
+    detailed_duplicates = detect_duplicate_notifications()
+
+    if request.method == 'POST':
+        selected_ids = request.POST.getlist('selected_notifications')
+        delete_selected_notifications(selected_ids)
+        return detailed_duplicates, 'Selected duplicate notifications have been deleted.', True
+
+    return detailed_duplicates, '', False
+
+@user_passes_test(osf_staff_check)
+def handle_duplicate_notifications(request):
+    detailed_duplicates, message, is_post = process_duplicate_notifications(request)
+
+    context = {'duplicates': detailed_duplicates}
+    if is_post:
+        context['message'] = message
+        return redirect('notifications:handle_duplicate_notifications')
+
+    return render(request, 'notifications/handle_duplicate_notifications.html', context)

admin/preprints/forms.py

@@ -1,9 +1,33 @@
 from django import forms
 
 from osf.models import Preprint
-
+from osf.utils.workflows import ReviewStates
 
 class ChangeProviderForm(forms.ModelForm):
     class Meta:
         model = Preprint
         fields = ('provider',)
+
+
+class MachineStateForm(forms.ModelForm):
+    class Meta:
+        model = Preprint
+        fields = ('machine_state',)
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        if not self.instance.is_public:
+            self.fields['machine_state'].widget.attrs['disabled'] = 'disabled'
+        else:
+            if self.instance.machine_state == ReviewStates.INITIAL.db_name:
+                self.fields['machine_state'].choices = [
+                    (ReviewStates.INITIAL.value, ReviewStates.INITIAL.value),
+                    (ReviewStates.PENDING.value, ReviewStates.PENDING.value),
+                ]
+            else:
+                # Disabled Option you are on
+                self.fields['machine_state'].widget.attrs['disabled'] = 'disabled'
+                self.fields['machine_state'].choices = [
+                    (self.instance.machine_state.title(), self.instance.machine_state)
+                ]

admin/preprints/urls.py

@@ -10,6 +10,8 @@
     re_path(r'^known_ham$', views.PreprintKnownHamList.as_view(), name='known-ham'),
     re_path(r'^withdrawal_requests$', views.PreprintWithdrawalRequestList.as_view(), name='withdrawal-requests'),
     re_path(r'^(?P<guid>[a-z0-9]+)/$', views.PreprintView.as_view(), name='preprint'),
+    re_path(r'^(?P<guid>[a-z0-9]+)/change_provider/$', views.PreprintProviderChangeView.as_view(), name='preprint-provider'),
+    re_path(r'^(?P<guid>[a-z0-9]+)/machine_state/$', views.PreprintMachineStateView.as_view(), name='preprint-machine-state'),
     re_path(r'^(?P<guid>[a-z0-9]+)/reindex_share_preprint/$', views.PreprintReindexShare.as_view(),
         name='reindex-share-preprint'),
     re_path(r'^(?P<guid>[a-z0-9]+)/remove_user/(?P<user_id>[a-z0-9]+)/$', views.PreprintRemoveContributorView.as_view(),

admin/preprints/views.py

@@ -15,7 +15,7 @@
 from admin.base.views import GuidView
 from admin.base.forms import GuidForm
 from admin.nodes.views import NodeRemoveContributorView
-from admin.preprints.forms import ChangeProviderForm
+from admin.preprints.forms import ChangeProviderForm, MachineStateForm
 
 from api.share.utils import update_share
 
@@ -62,6 +62,21 @@ class PreprintView(PreprintMixin, GuidView):
     """
     template_name = 'preprints/preprint.html'
     permission_required = ('osf.view_preprint', 'osf.change_preprint',)
+
+    def get_context_data(self, **kwargs):
+        preprint = self.get_object()
+        return super().get_context_data(**{
+            'preprint': preprint,
+            'SPAM_STATUS': SpamStatus,
+            'change_provider_form': ChangeProviderForm(instance=preprint),
+            'change_machine_state_form': MachineStateForm(instance=preprint),
+        }, **kwargs)
+
+
+class PreprintProviderChangeView(PreprintMixin, GuidView):
+    """ Allows authorized users to view preprint info and change a preprint's provider.
+    """
+    permission_required = ('osf.view_preprint', 'osf.change_preprint',)
     form_class = ChangeProviderForm
 
     def post(self, request, *args, **kwargs):
@@ -79,13 +94,26 @@ def post(self, request, *args, **kwargs):
 
         return redirect(self.get_success_url())
 
-    def get_context_data(self, **kwargs):
+
+class PreprintMachineStateView(PreprintMixin, GuidView):
+    """ Allows authorized users to view preprint info and change a preprint's machine_state.
+    """
+    permission_required = ('osf.view_preprint', 'osf.change_preprint',)
+    form_class = MachineStateForm
+
+    def post(self, request, *args, **kwargs):
         preprint = self.get_object()
-        return super().get_context_data(**{
-            'preprint': preprint,
-            'SPAM_STATUS': SpamStatus,
-            'form': ChangeProviderForm(instance=preprint),
-        }, **kwargs)
+        new_machine_state = request.POST.get('machine_state')
+        if new_machine_state and preprint.machine_state != new_machine_state:
+            preprint.machine_state = new_machine_state
+            try:
+                preprint.save()
+            except Exception as e:
+                messages.error(self.request, e.message)
+
+            preprint.refresh_from_db()
+
+        return redirect(self.get_success_url())
 
 
 class PreprintSearchView(PermissionRequiredMixin, FormView):

admin/templates/base.html

@@ -311,6 +311,9 @@
           {% if perms.osf.change_maintenancestate %}
             <li><a href="{% url 'maintenance:display' %}"><i class='fa fa-link'></i> <span>Maintenance Alerts</span></a></li>
           {% endif %}
+          {% if perms.osf.view_notification %}
+            <li><a href="{% url 'notifications:handle_duplicate_notifications' %}"><i class='fa fa-link'></i><span>Duplicate Notifications</span> </a></li>
+          {% endif %}
           </ul><!-- /.sidebar-menu -->
         </section>
         <!-- /.sidebar -->

admin/templates/notifications/handle_duplicate_notifications.html

@@ -0,0 +1,54 @@
+{% extends "base.html" %}
+{% load render_bundle from webpack_loader %}
+{% load static %}
+
+{% block title %}
+    <title>Duplicate Notifications</title>
+{% endblock title %}
+
+{% block content %}
+    <h2>Duplicate Notifications</h2>
+
+    {% if message %}
+        <div class="alert alert-success">
+            {{ message }}
+        </div>
+    {% endif %}
+
+    {% if duplicates %}
+        <form method="post">
+            {% csrf_token %}
+            <table class="table table-striped table-hover table-responsive">
+                <thead>
+                    <tr>
+                        <th>Select</th>
+                        <th>User</th>
+                        <th>Node</th>
+                        <th>Event Name</th>
+                        <th>Created</th>
+                        <th>Count</th>
+                    </tr>
+                </thead>
+                <tbody>
+                {% for notification in duplicates %}
+                    <tr>
+                        <td><input type="checkbox" name="selected_notifications" value="{{ notification.id }}"></td>
+                        <td>{{ notification.user }}</td>
+                        <td>{{ notification.node }}</td>
+                        <td>{{ notification.event_name }}</td>
+                        <td>{{ notification.created }}</td>
+                        <td>{{ notification.count }}</td>
+                    </tr>
+                {% empty %}
+                    <tr>
+                        <td colspan="6">No duplicate notifications found!</td>
+                    </tr>
+                {% endfor %}
+                </tbody>
+            </table>
+            <button type="submit" class="btn btn-danger">Delete Selected</button>
+        </form>
+    {% else %}
+        <p>No duplicate notifications found.</p>
+    {% endif %}
+{% endblock content %}

admin/templates/preprints/machine_state.html

@@ -0,0 +1,22 @@
+{% load node_extras %}
+<tr>
+    <td>Machine State</td>
+    <td>
+        <h4 >{{ preprint.machine_state }}</h4>
+        <h4 >{{ preprint.state }}</h4>
+        {% if perms.osf.change_preprint %}
+            <a class="btn btn-link" role="button" data-toggle="collapse" href="#collapseChangeMachineState">
+                Change preprint machine_state
+            </a>
+            <div class="collapse" id="collapseChangeMachineState">
+                <div class="well">
+                    <form action="{% url 'preprints:preprint-machine-state' guid=preprint.guid %}" method="post">
+                        {% csrf_token %}
+                        {{ change_machine_state_form.as_p }}
+                        <input class="btn-btn-primary" type="submit" value="Submit" />
+                    </form>
+                </div>
+            </div>
+        {% endif %}
+    </td>
+</tr>

admin/templates/preprints/preprint.html

@@ -74,10 +74,6 @@ <h2>Preprint: <b>{{ preprint.title }}</b> <a href="{{ preprint.absolute_url }}">
                         <td>Published</td>
                         <td>{{ preprint.is_published }}</td>
                     </tr>
-                    <tr>
-                        <td>Machine State</td>
-                        <td>{{ preprint.machine_state }}</td>
-                    </tr>
                     {%  if preprint.is_published %}
                         <tr>
                             <td>Date Published</td>
@@ -104,6 +100,7 @@ <h2>Preprint: <b>{{ preprint.title }}</b> <a href="{{ preprint.absolute_url }}">
                         </tr>
                     {% endif %}
                     {% include "preprints/provider.html" with preprint=preprint %}
+                    {% include "preprints/machine_state.html" with preprint=preprint %}
                     <tr>
                         <td>Subjects</td>
                         <td>

admin/templates/preprints/provider.html

@@ -9,9 +9,9 @@
             </a>
             <div class="collapse" id="collapseChangeProvider">
                 <div class="well">
-                    <form action="{% url 'preprints:preprint' guid=preprint.guid %}" method="post">
+                    <form action="{% url 'preprints:preprint-provider' guid=preprint.guid %}" method="post">
                         {% csrf_token %}
-                        {{ form.as_p }}
+                        {{ change_provider_form.as_p }}
                         <input class="btn-btn-primary" type="submit" value="Submit" />
                     </form>
                 </div>