Merge branch 'master' into 3478-submission_summary

Signed-off-by: Andy Byers <[email protected]>

requirements.txt

@@ -57,7 +57,7 @@ requests==2.31.0
 six==1.14.0
 sqlparse==0.4.4
 swapper==1.3.0
-tqdm==4.65.0
+tqdm==4.66.3
 ua-parser==0.16.1
 # See #3736
 urllib3<2

src/copyediting/models.py

@@ -51,7 +51,11 @@ class CopyeditAssignment(models.Model):
     date_decided = models.DateTimeField(null=True, blank=True)
 
     files_for_copyediting = models.ManyToManyField('core.File', related_name='files_for_copyediting')
-    copyeditor_files = models.ManyToManyField('core.File', blank=True)
+    copyeditor_files = models.ManyToManyField(
+        'core.File',
+        blank=True,
+        related_name='copyeditor_files',
+    )
     copyeditor_completed = models.DateTimeField(blank=True, null=True)
 
     copyedit_reopened = models.DateTimeField(blank=True, null=True)

src/core/migrations/0096_update_review_ack_email.py

@@ -0,0 +1,36 @@
+# Generated by Django 4.2 on 2024-07-17 09:52
+
+from django.db import migrations
+from utils import migration_utils
+
+OLD_VALUE_ONE = 'Dear {{ review_assignment.editor.first_name }}, <br><br>This is a notification that the reviewer status on "{{ article.safe_title }}" in {{ article.journal.name }} has been updated.  You can view more information on the journal site: {{ review_in_review_url }}  <br><br>All best wishes, <br>{{ request.user.signature }}'
+OLD_VALUE_TWO = 'Dear {{ review_assignment.editor.full_name }}, <br/><br/>This is a notification that the reviewer status on "{{ article.safe_title }}" in {{ article.journal.name }} has been updated.  You can view more information on the journal site: {{ review_in_review_url }}  <br/><br/>Regards,'
+OLD_VALUE_THREE = 'Dear {{ review_assignment.editor.full_name }}, <br/><br/>This is a notification that the reviewer status on "{{ article.safe_title }}" in {{ article.journal.name }} has been updated.  You can view more information on the journal site: {{ review_in_review_url }}  <br/><br/>Regards, <br/>{{ request.user.signature }}'
+OLD_VALUE_FOUR = 'Dear {{ review_assignment.editor.full_name }}, <br><br>This is a notification that the reviewer status on "{{ article.safe_title }}" in {{ article.journal.name }} has been updated.  You can view more information on the journal website at: {{ review_in_review_url }}  <br><br>Best wishes,<br> <br>{{ request.user.signature }}'
+OLD_VALUE_FIVE = 'Dear {{ review_assignment.editor.full_name }}, <br><br>This is a notification that the reviewer status on "{{ article.safe_title }}" in {{ article.journal.name }} has been updated.  You can view more information on the journal site: {{ review_in_review_url }}  <br><br>Regards, <br>{{ request.user.signature }}'
+OLD_VALUE_SIX = 'Dear {{ review_assignment.editor.full_name }}, <br><br>This is a notification that the reviewer status on "{{ article.safe_title }}" in {{ article.journal.name }} has been updated.  You can view more information on the journal site: {{ review_in_review_url }}  <br><br>Regards,'
+NEW_VALUE = "<p>Dear {{ review_assignment.editor.full_name }},</p><p>{{ review_assignment.reviewer.full_name }} has completed their review of \"{{ review_assignment.article.title }}\"{% if review_assignment.decision %} with this recommendation: {{ review_assignment.get_decision_display }}{% endif %}.</p><p>You can view more information on the journal site: {% journal_url 'review_view_review' review_assignment.article.pk review_assignment.pk %}</p><p>Regards,</p>"
+
+
+def replace_review_completed_ack(apps, schema_editor):
+    migration_utils.update_default_setting_values(
+        apps,
+        setting_name='review_complete_acknowledgement',
+        group_name='email',
+        values_to_replace=[OLD_VALUE_ONE, OLD_VALUE_TWO, OLD_VALUE_THREE, OLD_VALUE_FOUR, OLD_VALUE_FIVE, OLD_VALUE_SIX],
+        replacement_value=NEW_VALUE,
+    )
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('core', '0095_auto_20240605_1024'),
+    ]
+
+    operations = [
+        migrations.RunPython(
+            replace_review_completed_ack,
+            reverse_code=migrations.RunPython.noop,
+        ),
+    ]

src/core/models.py

@@ -8,6 +8,7 @@
 import statistics
 import json
 from datetime import timedelta
+from django.utils.html import format_html
 import pytz
 from hijack.signals import hijack_started, hijack_ended
 import warnings
@@ -32,7 +33,7 @@
 from django.dispatch import receiver
 from django.urls import reverse
 from django.utils.functional import cached_property
-from django.template.defaultfilters import linebreaksbr
+from django.template.defaultfilters import date
 import swapper
 
 from core import files, validators
@@ -1225,6 +1226,15 @@ def unlink_files(self):
     def __str__(self):
         return "{0} ({1})".format(self.id, self.label)
 
+    def detail(self):
+        return format_html(
+            '{} galley linked to <a href="#file_{}">file {}: {}</a>',
+            self.label,
+            self.file.pk,
+            self.file.pk,
+            self.file.original_filename,
+        )
+
     def render(self, recover=False):
         return files.render_xml(
             self.file, self.article,

src/core/templatetags/dates.py

@@ -0,0 +1,30 @@
+from django import template
+from django.utils import timezone
+
+
+register = template.Library()
+
+@register.simple_tag
+def offset_date(days=0, input_type="date"):
+    """
+    Get a string representing today's date or the now datetime,
+    with an offset of X days.
+    :param days: number of days from now that the date should be set
+    :param date: date or datetime-local
+
+    Usage:
+
+    <input
+      id="due"
+      name="due"
+      type="{{ input_type }}"
+      value="{% offset_date days=3 input_type=input_type %}">
+
+    See admin.core.widgets.soon_date_buttons for a use case.
+
+    """
+    due = timezone.now() + timezone.timedelta(days=days)
+    if input_type == "date":
+        return due.strftime("%Y-%m-%d")
+    elif input_type == "datetime-local":
+        return due.strftime("%Y-%m-%dT%H:%M")

src/core/templatetags/uuid.py

@@ -0,0 +1,8 @@
+from django import template
+from uuid import uuid4
+
+register = template.Library()
+
+@register.simple_tag
+def get_uuid4():
+    return f'u{str(uuid4())}'

src/journal/views.py

@@ -2646,7 +2646,7 @@ def serve_article_pdf(request, identifier_type, identifier):
         identifier,
     )
 
-    if not article_object and not article_object.is_published:
+    if not article_object or not article_object.is_published:
         raise Http404
 
     pdf = article_object.pdfs.first()

src/repository/migrations/0044_alter_repositoryfield_help_text.py

@@ -0,0 +1,31 @@
+# Generated by Django 4.2 on 2024-06-26 10:12
+
+from django.db import migrations, models
+from django.template.defaultfilters import striptags
+
+
+def strip_html_tags_from_repo_field_help_text(apps, schema_editor):
+    RepositoryField = apps.get_model('repository', 'RepositoryField')
+
+    for field in RepositoryField.objects.all():
+        field.help_text = striptags(field.help_text)
+        field.save()
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('repository', '0043_auto_20240402_1256'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='repositoryfield',
+            name='help_text',
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.RunPython(
+            strip_html_tags_from_repo_field_help_text,
+            reverse_code=migrations.RunPython.noop,
+        )
+    ]

src/repository/models.py

@@ -356,7 +356,10 @@ class RepositoryField(models.Model):
     )
     required = models.BooleanField(default=True)
     order = models.IntegerField()
-    help_text = models.TextField(blank=True, null=True)
+    help_text = models.TextField(
+        blank=True,
+        null=True,
+    )
     display = models.BooleanField(
         default=False,
         help_text='Whether or not display this field in the article page',

src/review/tests.py

@@ -275,6 +275,50 @@ def test_csv_doesnt_create_duplicate_assignments(self):
             self.review_assignment_complete,
         )
 
+    def test_incomplete_reviews(self):
+        args = {'owner': self.regular_user,
+                'title': 'Test Article',
+                'stage': submission_models.STAGE_UNDER_REVIEW,}
+        article1 = helpers.create_article(self.journal_one, **args)
+
+        article1.correspondence_author = self.regular_user
+        article1.save()
+
+        round =  review_models.ReviewRound.objects.create(article=article1,
+                                                          round_number=1,)
+
+        assignment = helpers.create_review_assignment(
+                                        journal=self.journal_one,
+                                        article=article1,
+                                        is_complete=False,
+                                        review_round=round,
+                                        reviewer=self.regular_user,
+                                    )
+        assignment.decision = None
+        assignment.save()
+
+        self.client.force_login(self.editor)
+        decline_url = reverse('review_decision',
+                              kwargs={'article_id': article1.pk,
+                                      'decision': 'decline'})
+        response = self.client.get(decline_url,
+                                   SERVER_NAME=self.journal_one.domain,)
+        msg = "The following incomplete reviews will be marked as withdrawn"
+        self.assertContains(response, msg)
+
+        data = {'cc': [''],
+                'bcc': [''],
+                'subject': ['Article Declined'],
+                'body': ['Article Declined'],
+                'attachments': [''],
+                'skip': ['skip']}
+        response = self.client.post(decline_url,
+                                    data,
+                                    SERVER_NAME=self.journal_one.domain,)
+        review_set = article1.reviewassignment_set.all()
+        self.assertEqual(review_set.filter(is_complete=True).count(), 1)
+        self.assertEqual(review_set.filter(is_complete=False).count(), 0)
+
     def test_completed_reviews_shared_setting(self):
         # setup data
         article_with_completed_reviews = helpers.create_article(

src/static/admin/js/check_all.js

@@ -1,3 +1,5 @@
+// Deprecated. Use select_all.html instead.
+
  $("#checkall").click(function () {
      $('input:checkbox').not(this).prop('checked', this.checked);
- });
+ });

src/static/common/css/common.css

@@ -298,3 +298,32 @@ article .list-romanupper {
     padding: 15px;
     margin-top: 15px;
 }
+
+/* Styling for skip to main content link */
+.skip-container {
+    position: relative;
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    height: 0;
+    overflow: hidden;
+}
+
+.skip-to-content,
+.skip-to-nav {
+    position: absolute;
+    left: -999px;
+}
+
+.skip-to-content:focus,
+.skip-to-nav:focus {
+    position: relative;
+    left: 0;
+    margin-block-start: 10px;
+    margin-block-end: 10px;
+}
+
+.skip-container:focus-within {
+    height: auto;
+    overflow: visible;
+}

src/submission/models.py

@@ -1514,6 +1514,10 @@ def decline_article(self):
         self.date_declined = timezone.now()
         self.date_accepted = None
         self.stage = STAGE_REJECTED
+
+        self.incomplete_reviews().update(decision=RD.DECISION_WITHDRAWN.value,
+                                         date_complete=timezone.now(),
+                                         is_complete=True,)
         self.save()
 
     def undo_review_decision(self):
@@ -1831,6 +1835,11 @@ def hidden_completed_reviews(self):
             decision='withdrawn',
         )
 
+    def incomplete_reviews(self):
+        return self.reviewassignment_set.filter(is_complete=False,
+                                                date_declined__isnull=True,
+                                                decision__isnull=True)
+
     def ms_and_figure_files(self):
         return chain(self.manuscript_files.all(), self.data_figure_files.all())
 

src/templates/admin/core/widgets/select_all.html

@@ -0,0 +1,44 @@
+{% comment %}
+Easily select or deselect all the checkboxes for a given field.
+
+Make sure to wrap this widget and the checkboxes in fieldset.
+
+Usage:
+
+<fieldset>
+    <legend>Which colours?</legend>
+    {% include "admin/core/widgets/select_all.html" %}
+    <input id="red" name="red" type="checkbox"><label for="red">Red</label>
+    <input id="blue" name="blue" type="checkbox"><label for="blue">Blue</label>
+</fieldset>
+
+{% endcomment %}
+
+{% load uuid %}
+
+{% get_uuid4 as pid %}
+
+<div id="{{ pid }}" style="button-group">
+    <button class="button selectall" type="button">
+        <span class="fa fa-check"></span>
+        Select all
+    </button>
+    <button class="button deselectall" type="button">
+        <span class="fa fa-close"></span>
+        Deselect all
+    </button>
+</div>
+<script defer type="module">
+    function toggleInputsInFieldset(event) {
+        const checked = event.currentTarget.classList.contains('selectall');
+        const fieldset = event.currentTarget.closest('fieldset');
+        const checkboxes = fieldset.querySelectorAll('input[type="checkbox"]');
+        Array.from(checkboxes).forEach(checkbox => {
+          checkbox.checked = checked;
+        });
+    }
+    const selectAll = document.querySelector('#{{ pid }} .selectall');
+    selectAll.addEventListener('click', toggleInputsInFieldset);
+    const deselectAll = document.querySelector('#{{ pid }} .deselectall');
+    deselectAll.addEventListener('click', toggleInputsInFieldset);
+</script>