Merge pull request #3128 from BirkbeckCTP/2817-register-issue-journal…

…-dois

Adds support for Issue and Journal DOIs to Crossref Integration

docs/source/manager/articlesissues/index.rst

@@ -84,6 +84,9 @@ To create an issue select *Create Issue* in the top right and in the modal that
 
     New issue form
 
+- Issue DOI
+    - Issues can have a DOI, which will be registered with all of its articles in crossref. If you are using Janeway's autoregistration (recommended) or if you are not interested on registering DOIs for issues, you can leave this field blank.
+
 Issue Articles
 ~~~~~~~~~~~~~~
 You can manage the article associated with a given issue by selecting the *View* option, the data of the issue will be displayed along with a list of articles grouped by section.

docs/source/manager/identifiers/index.rst

@@ -100,10 +100,28 @@ DOI Display Suffix
     Text to append to DOIs -- also used to generate DOI URLs
 
 DOI Pattern
-    The pattern for auto-generating DOIs. Defaults to using the journal code and article ID (e.g. orbit.123):
+    The pattern for auto-generating DOIs. Defaults to using the journal code and article ID (e.g. ``orbit.123``):
 
         ``{{ article.journal.code }}.{{ article.pk }}``
 
+Title DOI
+    The DOI (not in URL format) registered for this journal (e.g. ``10.001/my-journal``). It is included on all deposits for this journal. It must be registered ahead of time.
+
+    It is mandatory for a journal to have a DOI registered **only** when an ISSN is not available for a journal, as Crossref requires at least one unique identifier for every journal.
+
+    However, even if your journal has an ISSN, Crossref still recommends registering a DOI for your journal. We recommend using your journal code as the DOI. For example, with the prefix of ``10.0001`` and the journal code of ``abcd``, you could set the journal DOI to ``10.0001/abcd``.
+
+Issue DOI Pattern
+    Janeway supports minting DOIs for journal issues automatically. With this setting, you can define the pattern used to generate the issue-level DOI that will be used for registration.
+
+    With the default pattern, an issue with ID ``1`` (and prefix ``10.0001``, and journal code ``abcd``) will have a generated DOI of ``10.0001/abcd.issue.1``.
+
+    A collection with an ID of ``2`` would have a generated DOI of ``10.0001/abcd.collection.2``.
+
+Auto-register issue-level DOIs
+    When enabled, issues will have a DOI assigned and registered as soon as the first article in the issue is scheduled for publication. If an issue DOI has not been entered manually, Janeway will use the pattern defined in the setting above to generate one automatically.
+
+
 Crosscheck Settings
 -------------------
 Janeway also has support for Crosscheck (also called Similarity Check), which is provided by iThenticate. You can # for an account via Crossref and this will allow you to send submitted manuscripts for originality checking.

src/core/logic.py

@@ -390,7 +390,7 @@ def get_settings_to_edit(display_group, journal):
         xref_settings = [
             'use_crossref', 'crossref_test', 'crossref_username', 'crossref_password', 'crossref_email',
             'crossref_name', 'crossref_prefix', 'crossref_registrant', 'doi_display_prefix', 'doi_display_suffix',
-            'doi_pattern', 'doi_manager_action_maximum_size',
+            'doi_pattern', 'doi_manager_action_maximum_size', 'title_doi', 'issue_doi_pattern', 'register_issue_dois'
         ]
 
         settings = process_setting_list(xref_settings, 'Identifiers', journal)

src/events/logic.py

@@ -208,7 +208,11 @@ class Events:
     # raised when proofing is complete
     ON_PROOFING_COMPLETE = 'on_proofing_complete'
 
-    #kwargs: request, article
+    # kwargs: article, issue, user
+    # raised when an article is assigned to an issue
+    ON_ARTICLE_ASSIGNED_TO_ISSUE = 'on_article_assigned_to_issue'
+
+    # kwargs: request, article
     # raised when an article is marked as published
     ON_ARTICLE_PUBLISHED = 'on_article_published'
 

src/events/registration.py

@@ -7,6 +7,7 @@
 from utils import transactional_emails, workflow_tasks
 from events import logic as event_logic
 from journal import logic as journal_logic
+from identifiers import logic as id_logic
 
 # wire up event notifications
 
@@ -181,3 +182,8 @@
 # N.B. this is critical to the operation of the task framework. It automatically tears down tasks that have registered
 # for event listeners
 event_logic.Events.register_for_event('destroy_tasks', core_models.Task.destroyer)
+
+event_logic.Events.register_for_event(
+    event_logic.Events.ON_ARTICLE_ASSIGNED_TO_ISSUE,
+    id_logic.on_article_assign_to_issue,
+)

src/identifiers/logic.py

@@ -311,12 +311,17 @@ def create_crossref_journal_context(
     ISSN_override=None,
     publication_title=None
 ):
-    return {
+    journal_data = {
         'title': publication_title or journal.name,
         'journal_issn': ISSN_override or journal.issn,
         'print_issn': journal.print_issn,
         'press': journal.press,
     }
+    if journal.doi:
+        journal_data["doi"] = journal.doi
+        journal_data["url"] = journal.site_url()
+
+    return journal_data
 
 def create_crossref_article_context(article, identifier=None):
     template_context = {
@@ -625,3 +630,28 @@ def register_preprint_doi(request, crossref_enabled, identifier):
             util_models.LogEntry.add_entry('Submission', "Deposited {0}. Status: {1}".format(token, status), 'Info',
                                            target=identifier.article)
             logger.info("Status of {} in {}: {}".format(token, identifier.identifier, status))
+
+
+def generate_issue_doi_from_logic(issue):
+    doi_prefix = setting_handler.get_setting(
+        'Identifiers', 'crossref_prefix', issue.journal).value
+    doi_suffix = render_template.get_requestless_content(
+        {'issue': issue},
+        issue.journal,
+        'issue_doi_pattern',
+        group_name='Identifiers')
+    return '{0}/{1}'.format(doi_prefix, doi_suffix)
+
+
+def auto_assign_issue_doi(issue):
+    auto_assign_enabled = setting_handler.get_setting(
+        'Identifiers', 'use_crossref', issue.journal,
+        default=True,
+    ).processed_value
+    if auto_assign_enabled and not issue.doi:
+        issue.doi = generate_issue_doi_from_logic(issue)
+        issue.save()
+
+
+def on_article_assign_to_issue(article, issue, user):
+    auto_assign_issue_doi(issue)

src/identifiers/tests/test_logic.py

@@ -1,23 +1,25 @@
 import datetime
+from io import BytesIO, StringIO
+import json
+import mock
 import pytz
+import os
+
 
 from django.test import TestCase
 from django.conf import settings
 from django.utils import timezone
 
 from identifiers import logic, models
 from core.models import SettingGroup
+from journal import logic as journal_logic
 from submission import models as submission_models
 from utils.testing import helpers
 from utils.setting_handler import save_setting
 from utils.shared import clear_cache
 from lxml import etree
 from bs4 import BeautifulSoup
 import requests
-from io import BytesIO, StringIO
-import os
-import json
-
 class TestLogic(TestCase):
 
     @classmethod
@@ -353,6 +355,72 @@ def test_conference_deposit_xml_document_has_basically_correct_components(self):
         # There should be two conference papers (articles)
         self.assertEqual(2, len(soup.find_all('conference_paper')))
 
+    def test_issue_doi_deposited_correctly(self):
+        template = 'common/identifiers/crossref_doi_batch.xml'
+        issue = self.article_one.issue
+        issue.doi = issue_doi = "10.0001/issue"
+        issue.save()
+        identifier = self.article_one.get_doi_object
+        clear_cache()
+
+        template_context = logic.create_crossref_doi_batch_context(
+            self.article_one.journal,
+            {identifier},
+        )
+        deposit = logic.render_to_string(template, template_context)
+
+        soup = BeautifulSoup(deposit, 'lxml')
+        # There should be one doi_batch
+        issue_soup = soup.find('journal_issue')
+        found = False
+        if issue_soup:
+            issue_doi_soup = issue_soup.find("doi_data")
+            if issue_doi_soup:
+                self.assertEqual(issue_doi_soup.find("doi").string, issue_doi)
+                self.assertEqual(issue_doi_soup.find("resource").string, issue.url)
+                found = True
+        if not found:
+            raise AssertionError("No Issue DOI found on article deposit")
+
+    def test_journal_doi_deposited_correctly(self):
+        template = 'common/identifiers/crossref_doi_batch.xml'
+        issue = self.article_one.issue
+        journal_doi = "10.0001/journal"
+        save_setting('Identifiers', 'title_doi', issue.journal, journal_doi)
+        identifier = self.article_one.get_doi_object
+        clear_cache()
+
+        template_context = logic.create_crossref_doi_batch_context(
+            self.article_one.journal,
+            {identifier},
+        )
+        deposit = logic.render_to_string(template, template_context)
+
+        soup = BeautifulSoup(deposit, 'lxml')
+        # There should be one doi_batch
+        journal_soup = soup.find('journal_metadata')
+        found = False
+        if journal_soup:
+            doi_soup = journal_soup.find("doi_data")
+            if doi_soup:
+                self.assertEqual(doi_soup.find("doi").string, journal_doi)
+                self.assertEqual(
+                    doi_soup.find("resource").string, issue.journal.site_url())
+                found = True
+        if not found:
+            raise AssertionError("No Issue DOI found on article deposit")
+
+    def test_issue_doi_auto_assigned(self):
+        issue = helpers.create_issue(self.journal_one, vol=99, number=99)
+        self.request.POST = {"assign_issue": issue.pk}
+        mock_messages = mock.patch('journal.logic.messages').start()
+        mock_messages.messages = mock.MagicMock()
+        save_setting('Identifiers', 'register_issue_dois', self.journal_one, '')
+        from events import registration # Forces events to load into memory
+        journal_logic.handle_assign_issue(self.request, self.article_one, issue)
+        issue.refresh_from_db()
+        self.assertTrue(issue.doi)
+
     def test_check_crossref_settings(self):
 
         # Missing settings

src/journal/issue_forms.py

@@ -29,7 +29,7 @@ class Meta:
         fields = (
             'issue_title', 'volume', 'issue', 'date', 'issue_description',
             'short_description', 'cover_image', 'large_image', 'issue_type',
-            'code',
+            'code', 'doi',
         )
 
 

src/journal/logic.py

@@ -18,6 +18,7 @@
 from django.conf import settings
 from django.shortcuts import redirect, get_object_or_404
 from django.urls import reverse
+from django.utils.translation import ugettext_lazy as _
 from django.template.loader import get_template
 from django.core.validators import validate_email, ValidationError
 from django.utils.timezone import make_aware
@@ -202,19 +203,30 @@ def handle_new_issue(request):
     return [form, 'issue', new_issue]
 
 
-def handle_assign_issue(request, article, issues):
-    try:
-        issue_to_assign = journal_models.Issue.objects.get(pk=request.POST.get('assign_issue', None))
-
-        if issue_to_assign in issues:
-            issue_to_assign.articles.add(article)
-            issue_to_assign.save()
-            messages.add_message(request, messages.SUCCESS, 'Article assigned to issue.')
-        else:
-
-            messages.add_message(request, messages.WARNING, 'Issue not in this journals issue list.')
-    except journal_models.Issue.DoesNotExist:
-        messages.add_message(request, messages.WARNING, 'Issue does no exist.')
+def handle_assign_issue(request, article, issue):
+    added = False
+    if not article.section:
+        messages.add_message(
+            request,
+            messages.WARNING,
+            _('Articles without a section cannot be added to an issue.'),
+        )
+    elif issue not in article.journal.issues:
+        messages.add_message(
+            request, messages.WARNING, 'Issue not in this journal’s issue list.')
+    else:
+        issue.articles.add(article)
+        issue.save()
+        messages.add_message(
+            request, messages.SUCCESS, 'Article assigned to issue.')
+        event_logic.Events.raise_event(
+            event_logic.Events.ON_ARTICLE_ASSIGNED_TO_ISSUE,
+            article=article,
+            issue=issue,
+            user=request.user,
+        )
+        added = True
+    return added
 
 
 def handle_unassign_issue(request, article, issues):
@@ -224,12 +236,12 @@ def handle_unassign_issue(request, article, issues):
         if issue_to_unassign in issues:
             issue_to_unassign.articles.remove(article)
             issue_to_unassign.save()
-            messages.add_message(request, messages.SUCCESS, 'Article unassigned from Issue.')
+            messages.add_message(request, messages.SUCCESS, 'Article unassigned from issue.')
         else:
 
-            messages.add_message(request, messages.WARNING, 'Issue not in this journals issue list.')
+            messages.add_message(request, messages.WARNING, 'Issue not in this journal’s issue list.')
     except journal_models.Issue.DoesNotExist:
-        messages.add_message(request, messages.WARNING, 'Issue does no exist.')
+        messages.add_message(request, messages.WARNING, 'Issue does not exist.')
 
 
 def handle_set_pubdate(request, article):

src/journal/migrations/0053_issue_doi.py

@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.29 on 2022-09-08 14:28
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('journal', '0052_issue_display_title'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='issue',
+            name='doi',
+            field=models.CharField(blank=True, help_text='The DOI (not URL) to be registered for the issue when registering articles that are part of this issue. If you have enabled issue autoregistration in your settings, this field should not be entered manually.', max_length=255, null=True, verbose_name='DOI'),
+        ),
+    ]

src/journal/models.py

@@ -34,7 +34,7 @@
 from press import models as press_models
 from submission import models as submission_models
 from utils import setting_handler, logic, install, shared
-from utils.function_cache import cache
+from utils.function_cache import cache, mutable_cached_property
 from utils.logger import get_logger
 
 logger = get_logger(__name__)
@@ -265,6 +265,14 @@ def publisher(self, value):
     def issn(self):
         return setting_handler.get_setting('general', 'journal_issn', self, default=True).value
 
+    @mutable_cached_property
+    def doi(self):
+        return setting_handler.get_setting('Identifiers', 'title_doi', self, default=True).value or None
+
+    @doi.setter
+    def doi(self, value):
+        setting_handler.save_setting('Identifiers', 'title_doi', self, value)
+
     @property
     @cache(120)
     def print_issn(self):
@@ -567,6 +575,17 @@ class Issue(AbstractLastModifiedModel):
             " url for this issue. e.g: 'winter-special-issue'."
         ),
     )
+    doi = models.CharField(
+        max_length=255,
+        blank=True,
+        null=True,
+        verbose_name='DOI',
+        help_text='The DOI (not URL) to be registered for the issue when registering '
+                  'articles that are part of this issue. If you have enabled issue '
+                  'autoregistration in your settings, this field should not be '
+                  'entered manually.',
+        )
+
 
     @property
     def hero_image_url(self):