From 14cc9d01bd27b72496496fa1300dc909de060e5b Mon Sep 17 00:00:00 2001
From: Jorran de Wit <jorrandewit@outlook.com>
Date: Fri, 25 May 2018 17:11:14 +0200
Subject: [PATCH] Coi 2.
---
conflicts/admin.py | 9 +-
conflicts/apps.py | 4 +
conflicts/constants.py | 13 ++-
conflicts/management/__init__.py | 0
conflicts/management/commands/__init__.py | 0
.../commands/update_coi_via_arxiv.py | 34 +++++++
conflicts/migrations/0001_initial.py | 30 ++++++
.../migrations/0002_auto_20180525_1433.py | 34 +++++++
.../migrations/0003_auto_20180525_1438.py | 27 ++++++
..._conflictofinterest_related_submissions.py | 21 +++++
conflicts/models.py | 38 ++++++--
conflicts/services.py | 93 +++++++++++++++++++
conflicts/templatetags/__init__.py | 0
conflicts/templatetags/conflict_tags.py | 13 +++
conflicts/tests.py | 4 +
conflicts/views.py | 4 +
scipost/services.py | 2 +
submissions/managers.py | 4 +
.../0026_submission_needs_conflicts_update.py | 20 ++++
submissions/models.py | 3 +-
.../admin/submission_prescreening.html | 62 +++++++++++++
21 files changed, 405 insertions(+), 10 deletions(-)
create mode 100644 conflicts/management/__init__.py
create mode 100644 conflicts/management/commands/__init__.py
create mode 100644 conflicts/management/commands/update_coi_via_arxiv.py
create mode 100644 conflicts/migrations/0001_initial.py
create mode 100644 conflicts/migrations/0002_auto_20180525_1433.py
create mode 100644 conflicts/migrations/0003_auto_20180525_1438.py
create mode 100644 conflicts/migrations/0004_conflictofinterest_related_submissions.py
create mode 100644 conflicts/services.py
create mode 100644 conflicts/templatetags/__init__.py
create mode 100644 conflicts/templatetags/conflict_tags.py
create mode 100644 submissions/migrations/0026_submission_needs_conflicts_update.py
diff --git a/conflicts/admin.py b/conflicts/admin.py
index 8c38f3f3d..c36ef1606 100644
--- a/conflicts/admin.py
+++ b/conflicts/admin.py
@@ -1,3 +1,10 @@
+__copyright__ = "Copyright 2016-2018, Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
from django.contrib import admin
-# Register your models here.
+from .models import ConflictOfInterest
+
+
+admin.site.register(ConflictOfInterest)
diff --git a/conflicts/apps.py b/conflicts/apps.py
index 25d0ba12f..749dd0604 100644
--- a/conflicts/apps.py
+++ b/conflicts/apps.py
@@ -1,3 +1,7 @@
+__copyright__ = "Copyright 2016-2018, Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
from django.apps import AppConfig
diff --git a/conflicts/constants.py b/conflicts/constants.py
index 923e33295..7e27f64ad 100644
--- a/conflicts/constants.py
+++ b/conflicts/constants.py
@@ -1,7 +1,18 @@
+__copyright__ = "Copyright 2016-2018, Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
STATUS_UNVERIFIED, STATUS_VERIFIED = 'unverified', 'verified'
STATUS_DEPRECATED = 'deprecated'
-CONFLIC_OF_INTEREST_STATUSES = (
+CONFLICT_OF_INTEREST_STATUSES = (
(STATUS_UNVERIFIED, 'Unverified'),
(STATUS_VERIFIED, 'Verified by Admin'),
(STATUS_DEPRECATED, 'Deprecated'),
)
+
+
+TYPE_OTHER, TYPE_COAUTHOR = 'other', 'coauthor'
+CONFLICT_OF_INTEREST_TYPES = (
+ (TYPE_COAUTHOR, 'Co-authorship'),
+ (TYPE_OTHER, 'Other'),
+)
diff --git a/conflicts/management/__init__.py b/conflicts/management/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/conflicts/management/commands/__init__.py b/conflicts/management/commands/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/conflicts/management/commands/update_coi_via_arxiv.py b/conflicts/management/commands/update_coi_via_arxiv.py
new file mode 100644
index 000000000..259c7abd4
--- /dev/null
+++ b/conflicts/management/commands/update_coi_via_arxiv.py
@@ -0,0 +1,34 @@
+__copyright__ = "Copyright 2016-2018, Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
+from django.core.management.base import BaseCommand
+
+from scipost.models import Contributor
+from submissions.models import Submission
+
+from ...services import ArxivCaller
+
+
+class Command(BaseCommand):
+ """Update Conflict of Interests using arXiv API."""
+
+ def add_arguments(self, parser):
+ parser.add_argument(
+ '--arxiv', action='store', default=0, type=str,
+ dest='arxiv', help='ArXiv id of Submission to force update of conflicts.')
+
+ def handle(self, *args, **options):
+ if options['arxiv']:
+ submissions = Submission.objects.filter(arxiv_identifier_w_vn_nr=options['arxiv'])
+ else:
+ submissions = Submission.objects.needs_conflicts_update()
+
+ for sub in submissions:
+ fellow_ids = sub.fellows.values_list('id', flat=True)
+ fellows = Contributor.objects.filter(fellowships__id__in=fellow_ids)
+ if 'entries' in sub.metadata:
+ caller = ArxivCaller(sub.metadata['entries'][0]['authors'])
+ caller.compare_to(fellows)
+ caller.add_to_db(sub)
+ Submission.objects.filter(id=sub.id).update(needs_conflicts_update=False)
diff --git a/conflicts/migrations/0001_initial.py b/conflicts/migrations/0001_initial.py
new file mode 100644
index 000000000..46182d027
--- /dev/null
+++ b/conflicts/migrations/0001_initial.py
@@ -0,0 +1,30 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.4 on 2018-05-25 07:52
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ initial = True
+
+ dependencies = [
+ ('scipost', '0014_auto_20180414_2218'),
+ ('journals', '0030_merge_20180519_2204'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='ConflictOfInterest',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('status', models.CharField(choices=[('unverified', 'Unverified'), ('verified', 'Verified by Admin'), ('deprecated', 'Deprecated')], default='unverified', max_length=16)),
+ ('type', models.CharField(choices=[('coauthor', 'Co-authorship'), ('other', 'Other')], default='other', max_length=16)),
+ ('origin', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='conflicts', to='scipost.Contributor')),
+ ('to_contributor', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='+', to='scipost.Contributor')),
+ ('to_unregistered', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='+', to='journals.UnregisteredAuthor')),
+ ],
+ ),
+ ]
diff --git a/conflicts/migrations/0002_auto_20180525_1433.py b/conflicts/migrations/0002_auto_20180525_1433.py
new file mode 100644
index 000000000..0337dd083
--- /dev/null
+++ b/conflicts/migrations/0002_auto_20180525_1433.py
@@ -0,0 +1,34 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.4 on 2018-05-25 12:33
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('conflicts', '0001_initial'),
+ ]
+
+ operations = [
+ migrations.RemoveField(
+ model_name='conflictofinterest',
+ name='to_unregistered',
+ ),
+ migrations.AddField(
+ model_name='conflictofinterest',
+ name='conflict_title',
+ field=models.CharField(blank=True, max_length=256),
+ ),
+ migrations.AddField(
+ model_name='conflictofinterest',
+ name='conflict_url',
+ field=models.URLField(blank=True),
+ ),
+ migrations.AddField(
+ model_name='conflictofinterest',
+ name='to_name',
+ field=models.CharField(blank=True, max_length=128),
+ ),
+ ]
diff --git a/conflicts/migrations/0003_auto_20180525_1438.py b/conflicts/migrations/0003_auto_20180525_1438.py
new file mode 100644
index 000000000..70026c687
--- /dev/null
+++ b/conflicts/migrations/0003_auto_20180525_1438.py
@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.4 on 2018-05-25 12:38
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('conflicts', '0002_auto_20180525_1433'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='conflictofinterest',
+ name='created',
+ field=models.DateTimeField(auto_now_add=True, default=django.utils.timezone.now),
+ preserve_default=False,
+ ),
+ migrations.AddField(
+ model_name='conflictofinterest',
+ name='modified',
+ field=models.DateTimeField(auto_now=True),
+ ),
+ ]
diff --git a/conflicts/migrations/0004_conflictofinterest_related_submissions.py b/conflicts/migrations/0004_conflictofinterest_related_submissions.py
new file mode 100644
index 000000000..cfaf39a93
--- /dev/null
+++ b/conflicts/migrations/0004_conflictofinterest_related_submissions.py
@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.4 on 2018-05-25 13:50
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('submissions', '0026_submission_needs_conflicts_update'),
+ ('conflicts', '0003_auto_20180525_1438'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='conflictofinterest',
+ name='related_submissions',
+ field=models.ManyToManyField(blank=True, related_name='conflicts', to='submissions.Submission'),
+ ),
+ ]
diff --git a/conflicts/models.py b/conflicts/models.py
index 2178ec6e8..380c54347 100644
--- a/conflicts/models.py
+++ b/conflicts/models.py
@@ -1,18 +1,42 @@
+__copyright__ = "Copyright 2016-2018, Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
+from django.core.exceptions import ValidationError
from django.db import models
-from .constants import CONFLIC_OF_INTEREST_STATUSES, STATUS_UNVERIFIED
+from .constants import (
+ CONFLICT_OF_INTEREST_STATUSES, STATUS_UNVERIFIED, CONFLICT_OF_INTEREST_TYPES, TYPE_OTHER)
class ConflictOfInterest(models.Model):
"""Conflict of Interest is a flagged relation between scientists."""
status = models.CharField(
- max_length=16, choices=CONFLIC_OF_INTEREST_STATUSES, default=STATUS_UNVERIFIED)
- origin = models.ForeignKey('scipost.Contributor')
- to_contributor = models.ForeignKey('scipost.Contributor', blank=True, null=True)
- to_unregistered = models.ForeignKey('journals.UnregisteredAuthor', blank=True, null=True)
+ max_length=16, choices=CONFLICT_OF_INTEREST_STATUSES, default=STATUS_UNVERIFIED)
+ origin = models.ForeignKey('scipost.Contributor', related_name='conflicts')
+ to_contributor = models.ForeignKey(
+ 'scipost.Contributor', blank=True, null=True, related_name='+')
+ to_name = models.CharField(max_length=128, blank=True)
+ type = models.CharField(
+ max_length=16, choices=CONFLICT_OF_INTEREST_TYPES, default=TYPE_OTHER)
+
+ # Meta
+ conflict_url = models.URLField(blank=True)
+ conflict_title = models.CharField(max_length=256, blank=True)
+ related_submissions = models.ManyToManyField(
+ 'submissions.Submission', blank=True, related_name='conflicts')
+ created = models.DateTimeField(auto_now_add=True)
+ modified = models.DateTimeField(auto_now=True)
+
+ def __str__(self):
+ _str = '{} {}'.format(self.get_type_display(), self.origin)
+ if self.conflict_title:
+ _str += ' on {}...'.format(self.conflict_title[:20])
+ return _str
def clean(self):
+ """Check if Conflict of Interest is complete."""
if not self.to_contributor and not self.to_unregistered:
- raise NotImplementedError('Choose something...')
- raise NotImplementedError('Fine.')
+ raise ValidationError(
+ 'Conflict of Interest must be related to Contributor or UnregisteredAuthor.')
diff --git a/conflicts/services.py b/conflicts/services.py
new file mode 100644
index 000000000..dcbee9f3a
--- /dev/null
+++ b/conflicts/services.py
@@ -0,0 +1,93 @@
+__copyright__ = "Copyright 2016-2018, Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
+# Module for making external api calls as needed in the submissions cycle
+import feedparser
+import logging
+
+from scipost.models import Contributor
+
+from .constants import TYPE_COAUTHOR
+from .models import ConflictOfInterest
+
+logger = logging.getLogger('scipost.conflicts.arxiv')
+
+
+class ArxivCaller:
+ """ArXiv Caller will help retrieve author data from arXiv API."""
+
+ query_base_url = 'https://export.arxiv.org/api/query?search_query={query}'
+
+ def __init__(self, author_list):
+ """Init ArXivCaller with list `author_list` as per Submission meta data."""
+ self.author_query = ''
+ self.conflicts = []
+
+ last_names = []
+ for author in author_list:
+ # Gather author data to do conflict-of-interest queries with
+ last_names.append(author['name'].split()[-1])
+ self.author_query = '+OR+'.join(last_names)
+
+ logger.info('Update from ArXiv for author list [{0}]'.format(author_list[:30]))
+
+ def compare_to(self, contributors_list):
+ """Add list of Contributors to compare the `author_list` with."""
+ for contributor in contributors_list:
+ # For each fellow found, so a query with the authors to check for conflicts
+ search_query = 'au:({fellow}+AND+({authors}))'.format(
+ fellow=contributor.user.last_name, authors=self.author_query)
+ queryurl = self.query_base_url.format(query=search_query)
+ queryurl += '&sortBy=submittedDate&sortOrder=descending&max_results=5'
+ queryurl = queryurl.replace(' ', '+') # Fallback for some last names with spaces
+
+ # Call the API
+ response_content = feedparser.parse(queryurl)
+ valid = False
+ logger.info('GET [{contributor}] [request] | {url}'.format(
+ contributor=contributor.user.last_name, url=queryurl))
+ if self._search_result_present(response_content):
+ valid = True
+ self.conflicts.append({
+ 'from': contributor,
+ 'results': response_content
+ })
+ logger.info('{result} | {response}.'.format(
+ result='Found results' if valid else 'No results',
+ response=response_content))
+ return
+
+ def _search_result_present(self, data):
+ if len(data.get('entries', [])) > 0:
+ return 'title' in data['entries'][0]
+ return False
+
+ def add_to_db(self, submission=None):
+ """Add found conflicts to database as unverfied co-author conflicts."""
+ logger.info('Pushing {} query results to database.'.format(len(self.conflicts)))
+
+ count = 0
+ for conflict in self.conflicts:
+ # Loop all separate queries
+ for result in conflict['results']['entries']:
+ # Read all results in one query
+ for author in result['authors']:
+ # Try to find an registered Contributor first.
+ contributor = Contributor.objects.active().filter(
+ user__first_name__istartswith=author['name'][0], # Only use first letter due to database inconsistency
+ user__last_name__iendswith=author['name'].split(' ')[-1]).first()
+
+ coi, new = ConflictOfInterest.objects.get_or_create(
+ origin=conflict['from'],
+ to_contributor=contributor,
+ to_name=author['name'],
+ conflict_url=result['link'].replace('http:', 'https:'),
+ defaults={
+ 'conflict_title': result['title'],
+ 'type': TYPE_COAUTHOR})
+ if submission:
+ coi.related_submissions.add(submission)
+ if new:
+ count += 1
+ logger.info('{} new conflicts added.'.format(count))
diff --git a/conflicts/templatetags/__init__.py b/conflicts/templatetags/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/conflicts/templatetags/conflict_tags.py b/conflicts/templatetags/conflict_tags.py
new file mode 100644
index 000000000..01c2a5bc7
--- /dev/null
+++ b/conflicts/templatetags/conflict_tags.py
@@ -0,0 +1,13 @@
+__copyright__ = "Copyright 2016-2018, Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
+from django import template
+
+register = template.Library()
+
+
+@register.filter
+def filter_for_contributor(qs, contributor):
+ """Filter ConflictOfInterest query for specific Contributor."""
+ return qs.filter(origin=contributor)
diff --git a/conflicts/tests.py b/conflicts/tests.py
index 7ce503c2d..9135c42ab 100644
--- a/conflicts/tests.py
+++ b/conflicts/tests.py
@@ -1,3 +1,7 @@
+__copyright__ = "Copyright 2016-2018, Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
from django.test import TestCase
# Create your tests here.
diff --git a/conflicts/views.py b/conflicts/views.py
index 91ea44a21..3dcbaf4f5 100644
--- a/conflicts/views.py
+++ b/conflicts/views.py
@@ -1,3 +1,7 @@
+__copyright__ = "Copyright 2016-2018, Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
from django.shortcuts import render
# Create your views here.
diff --git a/scipost/services.py b/scipost/services.py
index 1d3f8b975..dfb01269e 100644
--- a/scipost/services.py
+++ b/scipost/services.py
@@ -98,6 +98,8 @@ class DOICaller:
class ArxivCaller:
+ """ArXiv Caller will help retrieve Submission data from arXiv API."""
+
query_base_url = 'https://export.arxiv.org/api/query?id_list=%s'
def __init__(self, identifier):
diff --git a/submissions/managers.py b/submissions/managers.py
index c7632ce37..91b6d4e65 100644
--- a/submissions/managers.py
+++ b/submissions/managers.py
@@ -192,6 +192,10 @@ class SubmissionQuerySet(models.QuerySet):
"""Return Submission that allow for commenting."""
return self.filter(open_for_commenting=True)
+ def needs_conflicts_update(self):
+ """Return set of Submissions that need an ConflictOfInterest update."""
+ return self.filter(needs_conflicts_update=True)
+
class SubmissionEventQuerySet(models.QuerySet):
def for_author(self):
diff --git a/submissions/migrations/0026_submission_needs_conflicts_update.py b/submissions/migrations/0026_submission_needs_conflicts_update.py
new file mode 100644
index 000000000..7bf7d57d4
--- /dev/null
+++ b/submissions/migrations/0026_submission_needs_conflicts_update.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.4 on 2018-05-25 12:44
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('submissions', '0025_auto_20180520_1430'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='submission',
+ name='needs_conflicts_update',
+ field=models.BooleanField(default=True),
+ ),
+ ]
diff --git a/submissions/models.py b/submissions/models.py
index 3211a217d..3eba5ff28 100644
--- a/submissions/models.py
+++ b/submissions/models.py
@@ -104,7 +104,8 @@ class Submission(models.Model):
# Comments can be added to a Submission
comments = GenericRelation('comments.Comment', related_query_name='submissions')
- # iThenticate Reports
+ # iThenticate and conflicts
+ needs_conflicts_update = models.BooleanField(default=True)
plagiarism_report = models.OneToOneField('submissions.iThenticateReport',
on_delete=models.SET_NULL,
null=True, blank=True,
diff --git a/submissions/templates/submissions/admin/submission_prescreening.html b/submissions/templates/submissions/admin/submission_prescreening.html
index 8ebe8e61d..27e3507cc 100644
--- a/submissions/templates/submissions/admin/submission_prescreening.html
+++ b/submissions/templates/submissions/admin/submission_prescreening.html
@@ -2,6 +2,7 @@
{% load bootstrap %}
{% load scipost_extras %}
+{% load conflict_tags %}
{% block pagetitle %}: pre-screening ({{ submission.arxiv_identifier_w_vn_nr }}){% endblock pagetitle %}
@@ -69,6 +70,67 @@
<p>No Plagiarism Report found. <a href="{% url 'submissions:plagiarism' submission.arxiv_identifier_w_vn_nr %}">Run plagiarism check</a>.</p>
{% endif %}
+ <h3>Editorial Pre-assignments</h3>
+ <div>
+
+ {% if submission.needs_conflicts_update %}
+ <p>
+ <i class="fa fa-clock-o text-danger" aria-hidden="true"></i>
+ <span class="text-muted">Conflict of interest awaiting update. <a href="mailto:techsupport@scipost.org">Contact techsupport</a> if this is not automatically resolved soon.</span>
+ </p>
+ {% else %}
+ <p>
+ <i class="fa fa-check-circle text-success" aria-hidden="true"></i>
+ <span class="text-muted">Conflict of interest updated.</span>
+ <br><br>
+
+ Select Fellows that are eligable to become editor-in-charge and sort them in prefered order of invitation. Every [time], the next selected Fellow in line will be invited until an editor is assigned.
+ </p>
+
+ <table class="table">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Fellow</th>
+ <th>Possible conflicts</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for fellow in submission.fellows.all %}
+ <tr>
+ <td>
+ <a href="javascript:;"><i class="fa fa-bars" aria-hidden="true"></i></a>
+ <input type="checkbox" class="ml-2">
+ </td>
+ <td>{{ fellow.contributor }}</td>
+ <td>
+ {% for conflict in submission.conflicts.all|filter_for_contributor:fellow.contributor %}
+ <div class="my-1">
+ <a href="{{ conflict.conflict_url }}" target="_blank">{{ conflict.conflict_title }}</a>
+ <br>
+ In conflict with: {{ conflict.to_name }}
+ <br>
+ {% if conflict.status == 'unverified' %}
+ <i class="fa fa-question-circle text-warning" aria-hidden="true"></i>
+ {% elif conflict.status == 'verified' %}
+ <i class="fa fa-check-circle text-success" aria-hidden="true"></i>
+ {% endif %}
+ {{ conflict.get_status_display }}: {{ conflict.get_type_display }}.
+
+
+ <br>
+ </div>
+ {% empty %}
+ <em><i class="fa fa-check text-success" aria-hidden="true"></i> No conflicts found</em>
+ {% endfor %}
+ </td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ {% endif %}
+ </div>
+
<h3>Take decision on pre-screening</h3>
<form method="post">
{% csrf_token %}
--
GitLab