Author interface for ROR, CRediT, and ORCiD in submission workflow

docs/source/manager/submission/index.rst

@@ -24,8 +24,6 @@ This section allows you to control generic submission settings that affect how s
     - Any publication fees associated with submitting the paper.
 - Editors for Notification
     - This allows you to select which Editors are notified of new papers being submitted.
-- User Automatically Author
-    - If enabled the submission system assumes the user submitting the paper is also an author, they can be removed if required.
 - Competing Interests
     - This setting is deprecated in favour of the Submission Configurator version.
 - Submission Summary

docs/source/workflow/author.rst

@@ -70,7 +70,7 @@ Individual journals can add more fields to this page and they will be displayed
 
 Author Information
 ------------------
-On the Author Information page we can add the authors of our paper. One some journals the submitting user is added as an author automatically, on others you will have the option to add yourself as an author using a button. 
+On the Author Information page we can add the authors of our paper. The submitting user is added as an author automatically, but they can remove themselves and add other authors if needed.
 
 .. figure:: ../nstatic/no_authors.png
 

src/api/tests/test_oai.py

@@ -35,8 +35,9 @@ def setUpTestData(cls):
             date_published="1986-07-12T17:00:00.000+0200",
             authors=[cls.author],
         )
-        cls.author.add_credit('data-curation', cls.article)
-        cls.author.add_credit('writing-original-draft', cls.article)
+        cls.frozen_author = cls.author.frozen_author(cls.article)
+        cls.frozen_author.add_credit('data-curation')
+        cls.frozen_author.add_credit('writing-original-draft')
         cls.issue = helpers.create_issue(
             journal=cls.journal, vol=1, number=1,
             articles=[cls.article],
@@ -141,8 +142,7 @@ def test_get_record_jats(self):
         expected = GET_RECORD_DATA_JATS
         # Add a non correspondence author
         author_2 = helpers.create_author(self.journal, email="[email protected]")
-        self.article.authors.add(author_2)
-        self.article.snapshot_authors()
+        author_2.snapshot_as_author(self.article)
 
         setting_handler.save_setting(
             "general",

src/copyediting/tests.py

@@ -38,14 +38,14 @@ def setUpTestData(cls):
         )
         cls.active_article.title = 'Active Article'
         cls.active_article.save()
-        cls.active_article.authors.add(cls.author)
+        cls.author.snapshot_as_author(cls.active_article)
         cls.archived_article = helpers.create_article(
             journal=cls.journal_one,
         )
         cls.archived_article.stage = submission_models.STAGE_ARCHIVED
         cls.archived_article.title = 'Archived Article'
         cls.archived_article.save()
-        cls.archived_article.authors.add(cls.author)
+        cls.author.snapshot_as_author(cls.archived_article)
 
         cls.active_copyediting_task = models.CopyeditAssignment.objects.create(
             article=cls.active_article,
@@ -141,4 +141,4 @@ def test_active_article_review_task_200s(self):
         self.assertTrue(
             response.status_code,
             200,
-        )
+        )

src/core/example_settings.py

@@ -22,7 +22,7 @@
 
 # ORCID Settings
 ENABLE_ORCID = True
-ORCID_API_URL = 'http://pub.orcid.org/v1.2_rc7/'
+ORCID_API_URL = '' # Not needed any more. Requests are delegated to python-orcid.
 ORCID_URL = 'https://orcid.org/oauth/authorize'
 ORCID_TOKEN_URL = 'https://pub.orcid.org/oauth/token'
 ORCID_CLIENT_SECRET = ''

src/core/forms/__init__.py

@@ -26,6 +26,7 @@
     JournalSubmissionForm,
     LoginForm,
     NotificationForm,
+    OrcidAffiliationForm,
     OrganizationNameForm,
     PasswordResetForm,
     PressJournalAttrForm,

src/core/forms/forms.py

@@ -5,9 +5,11 @@
 
 import uuid
 import json
+import os
 
 from django import forms
 from django.db.models import Q
+from django.utils.datastructures import MultiValueDict
 from django.forms.fields import Field
 from django.utils import timezone
 from django.utils.translation import gettext_lazy as _
@@ -27,6 +29,7 @@
     JanewayTranslationModelForm,
     CaptchaForm,
     HTMLDateInput,
+    YesNoRadio,
 )
 from utils.logger import get_logger
 from submission import models as submission_models
@@ -966,6 +969,7 @@ class Meta:
         widgets = {
             'start': HTMLDateInput,
             'end': HTMLDateInput,
+            'is_primary': YesNoRadio,
         }
 
     def __init__(self, *args, **kwargs):
@@ -975,14 +979,15 @@ def __init__(self, *args, **kwargs):
 
     def clean(self):
         cleaned_data = super().clean()
-        query = Q(account=self.account, organization=self.organization)
-        for key, value in cleaned_data.items():
-            query &= Q((key, value))
-        if self._meta.model.objects.filter(query).exists():
-            self.add_error(
-                None,
-                "An affiliation with matching details already exists."
-            )
+        if not self.instance.pk:
+            query = Q(account=self.account, organization=self.organization)
+            for key, value in cleaned_data.items():
+                query &= Q((key, value))
+            if self._meta.model.objects.filter(query).exists():
+                self.add_error(
+                    None,
+                    "An affiliation with matching details already exists."
+                )
         return cleaned_data
 
     def save(self, commit=True):
@@ -994,6 +999,76 @@ def save(self, commit=True):
         return affiliation
 
 
+class OrcidAffiliationForm(forms.ModelForm):
+    """
+    A form for creating ControlledAffiliation objects
+    from ORCID data.
+    """
+
+    class Meta:
+        model = models.ControlledAffiliation
+        fields = '__all__'
+
+    def __init__(
+        self,
+        orcid_affiliation,
+        tzinfo=timezone.get_current_timezone(),
+        data=None,
+        *args,
+        **kwargs,
+    ):
+        if not data:
+            data = MultiValueDict()
+
+        # The `get` methods below are used together with `or`
+        # defensively because of the data population in the API.
+        # It can have keys pointing to None values like:
+        # {"year": {"value": 2019}, "month": None}
+
+        data['title'] = orcid_affiliation.get('role-title', '') or ''
+        data['department'] = orcid_affiliation.get('department-name', '') or ''
+
+        org = None
+        orcid_org = orcid_affiliation.get('organization', {}) or {}
+        disamb_org = orcid_org.get('disambiguated-organization', {}) or {}
+        disamb_id = disamb_org.get('disambiguated-organization-identifier', '') or ''
+        if disamb_id.startswith('https://ror.org/'):
+            ror_id = os.path.split(disamb_id)[-1]
+            try:
+                org = models.Organization.objects.get(ror_id=ror_id)
+            except models.Organization.DoesNotExist:
+                pass
+        if not org:
+            address = orcid_org.get('address', {}) or {}
+            org, _created = models.Organization.get_or_create_without_ror(
+                institution=orcid_org.get('name', '') or '',
+                country=address.get('country', '') or '',
+                account=data.get('account'),
+                frozen_author=data.get('frozen_author'),
+                preprint_author=data.get('preprint_author'),
+            )
+        data['organization'] = org
+
+        orcid_start = orcid_affiliation.get('start-date', {}) or {}
+        if orcid_start:
+            data['start'] = timezone.datetime(
+                int((orcid_start.get('year', {}) or {}).get('value', 1)),
+                int((orcid_start.get('month', {}) or {}).get('value', 1)),
+                int((orcid_start.get('day', {}) or {}).get('value', 1)),
+                tzinfo=tzinfo,
+            )
+        orcid_end = orcid_affiliation.get('end-date', {}) or {}
+        if orcid_end:
+            data['end'] = timezone.datetime(
+                int((orcid_end.get('year', {}) or {}).get('value', 1)),
+                int((orcid_end.get('month', {}) or {}).get('value', 1)),
+                int((orcid_end.get('day', {}) or {}).get('value', 1)),
+                tzinfo=tzinfo,
+            )
+
+        super().__init__(data=data, *args, **kwargs)
+
+
 class ConfirmDeleteForm(forms.Form):
     """
     A generic form for use on confirm-delete pages

src/core/include_urls.py

@@ -129,7 +129,7 @@
     re_path(r'^manager/user/(?P<user_id>\d+)/edit/$', core_views.user_edit, name='core_user_edit'),
     re_path(r'^manager/user/(?P<user_id>\d+)/history/$', core_views.user_history, name='core_user_history'),
 
-    ## Affiliations
+    # Affiliations
     re_path(
         r'^profile/organization/search/$',
         core_views.OrganizationListView.as_view(),
@@ -155,6 +155,11 @@
         core_views.affiliation_update,
         name='core_affiliation_update'
     ),
+    re_path(
+        r'^profile/affiliation/update-from-orcid/(?P<how_many>primary|all)/$',
+        core_views.affiliation_update_from_orcid,
+        name='core_affiliation_update_from_orcid'
+    ),
     re_path(
         r'^profile/affiliation/(?P<affiliation_id>\d+)/delete/$',
         core_views.affiliation_delete,
@@ -322,7 +327,8 @@
                 "Failed to import urls for plugin %s: %s", plugin.name, error,
             )
         except Exception as error:
-            logger.error("Error loading plugin %s", block.name)
+            print("Error loading plugin %s", plugin.name)
+            logger.error("Error loading plugin %s", plugin.name)
             logger.exception(error)
 
 # load the notification plugins

src/core/logic.py

@@ -24,7 +24,7 @@
 from django.utils import timezone
 from django.utils.translation import get_language, gettext_lazy as _
 
-from core import models, files, plugin_installed_apps
+from core import forms, models, files, plugin_installed_apps
 from utils.function_cache import cache
 from review import models as review_models
 from utils import render_template, notify_helpers, setting_handler
@@ -293,9 +293,6 @@ def get_settings_to_edit(display_group, journal, user):
              'object': setting_handler.get_setting('general', 'editors_for_notification', journal),
              'choices': journal.editor_pks()
              },
-            {'name': 'user_automatically_author',
-             'object': setting_handler.get_setting('general', 'user_automatically_author', journal),
-             },
             {'name': 'submission_summary',
              'object': setting_handler.get_setting('general', 'submission_summary', journal),
              },
@@ -1032,3 +1029,19 @@ def filter_articles_to_editor_assigned(request, articles):
     )
     assignment_article_pks = [assignment.article.pk for assignment in assignments]
     return articles.filter(pk__in=assignment_article_pks)
+
+
+def create_organization_name(request):
+    form = forms.OrganizationNameForm(request.POST)
+    if form.is_valid():
+        organization_name = form.save()
+        organization = models.Organization.objects.create()
+        organization_name.custom_label_for = organization
+        organization_name.save()
+        messages.add_message(
+            request,
+            messages.SUCCESS,
+            _("Custom organization created: %(organization)s")
+                % {"organization": organization_name},
+        )
+        return organization_name

src/core/migrations/0104_location_organization_affiliation.py

@@ -55,7 +55,7 @@ class Migration(migrations.Migration):
                 ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
                 ('title', models.CharField(blank=True, max_length=300, verbose_name='Title, position, or role')),
                 ('department', models.CharField(blank=True, max_length=300, verbose_name='Department, unit, or team')),
-                ('is_primary', models.BooleanField(default=False, help_text='Each account can have one primary affiliation')),
+                ('is_primary', models.BooleanField(default=False, help_text='Each author or user can have one primary affiliation')),
                 ('start', models.DateField(blank=True, null=True, verbose_name='Start date')),
                 ('end', models.DateField(blank=True, null=True, help_text='Leave empty for a current affiliation', verbose_name='End date')),
                 ('account', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
@@ -64,7 +64,7 @@ class Migration(migrations.Migration):
                 ('preprint_author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='repository.preprintauthor')),
             ],
             options={
-                'ordering': ['is_primary', '-pk'],
+                'ordering': ['-is_primary', '-pk'],
             },
         ),
         migrations.AddConstraint(

src/core/migrations/0107_alter_controlledaffiliation_options_and_more.py

@@ -0,0 +1,21 @@
+# Generated by Django 4.2.20 on 2025-05-01 14:14
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('core', '0106_remove_account_country_affiliation_organization'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='controlledaffiliation',
+            options={'ordering': ['-is_primary', '-end', '-start', '-pk']},
+        ),
+        migrations.AlterModelOptions(
+            name='organization',
+            options={},
+        ),
+    ]

src/core/model_utils.py

@@ -6,6 +6,7 @@
 __license__ = "AGPL v3"
 __maintainer__ = "Birkbeck Centre for Technology and Publishing"
 from contextlib import contextmanager
+from hashlib import md5
 from io import BytesIO
 import re
 import sys
@@ -912,3 +913,15 @@ def create(self, **kwargs):
     def filter(self, *args, **kwargs):
         kwargs = self._remap_old_affiliation_lookups(kwargs)
         return super().filter(*args, **kwargs)
+
+
+def generate_dummy_email(details):
+    """
+    :param details: a dict whose keys and values will serve as the hash seed
+    :type details: dict
+    """
+    seed = ''.join([str(key) + str(val) for key, val in details.items()])
+    hashed = md5(str(seed).encode("utf-8")).hexdigest()
+    # Avoid validation bug where two @@ symbols are used in the email
+    domain = settings.DUMMY_EMAIL_DOMAIN.replace('@', '')
+    return "{0}@{1}".format(hashed, domain)