From 4d279aca5e764e8d3b991d82d5fdbca303cb56a6 Mon Sep 17 00:00:00 2001
From: "J.-S. Caux" <J.S.Caux@uva.nl>
Date: Tue, 11 Jul 2017 09:27:55 +0200
Subject: [PATCH] General metadata improvements (Crossref, CLOCKSS)
---
journals/admin.py | 6 +-
journals/migrations/0031_clockssmetadata.py | 24 ++++++
journals/models.py | 13 ++++
.../templates/journals/manage_metadata.html | 7 +-
.../journals/publication_metadata_jats.xml | 22 ++++++
journals/urls/general.py | 3 +
journals/views.py | 74 ++++++++++++++-----
7 files changed, 128 insertions(+), 21 deletions(-)
create mode 100644 journals/migrations/0031_clockssmetadata.py
create mode 100644 journals/templates/journals/publication_metadata_jats.xml
diff --git a/journals/admin.py b/journals/admin.py
index 167b0f62e..59f964b20 100644
--- a/journals/admin.py
+++ b/journals/admin.py
@@ -1,7 +1,8 @@
from django.contrib import admin, messages
from django import forms
-from journals.models import UnregisteredAuthor, Journal, Volume, Issue, Publication, Deposit
+from journals.models import UnregisteredAuthor, Journal, Volume, Issue, Publication, \
+ Deposit, CLOCKSSmetadata
from scipost.models import Contributor
from submissions.models import Submission
@@ -79,3 +80,6 @@ class DepositAdmin(admin.ModelAdmin):
admin.site.register(Deposit, DepositAdmin)
+
+
+admin.site.register(CLOCKSSmetadata)
diff --git a/journals/migrations/0031_clockssmetadata.py b/journals/migrations/0031_clockssmetadata.py
new file mode 100644
index 000000000..e9f252ab1
--- /dev/null
+++ b/journals/migrations/0031_clockssmetadata.py
@@ -0,0 +1,24 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.3 on 2017-07-11 03:34
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('journals', '0030_auto_20170710_1051'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='CLOCKSSmetadata',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('metadata_xml_file_CLOCKSS', models.FileField(blank=True, max_length=512, null=True, upload_to='')),
+ ('publication', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='journals.Publication')),
+ ],
+ ),
+ ]
diff --git a/journals/models.py b/journals/models.py
index 3f5454a8f..e79ea87f0 100644
--- a/journals/models.py
+++ b/journals/models.py
@@ -236,3 +236,16 @@ class Deposit(models.Model):
def __str__(self):
return (self.deposition_date.strftime('%Y-%m-%D') +
' for 10.21468/' + self.publication.doi_label)
+
+class CLOCKSSmetadata(models.Model):
+ """
+ For the CLOCKSS archive, JATS formatted XML is produced.
+ """
+ publication = models.ForeignKey(Publication, on_delete=models.CASCADE)
+ metadata_xml_file_CLOCKSS = models.FileField(blank=True, null=True, max_length=512)
+
+ class Meta:
+ verbose_name = 'CLOCKSS metadata'
+
+ def __str__(self):
+ return ('CLOCKSS metadata for 10.21468/' + self.publication.doi_label)
diff --git a/journals/templates/journals/manage_metadata.html b/journals/templates/journals/manage_metadata.html
index 2d5ec8c24..839694a80 100644
--- a/journals/templates/journals/manage_metadata.html
+++ b/journals/templates/journals/manage_metadata.html
@@ -35,6 +35,7 @@ event: "focusin"
<th>Publication date</th>
<th>Latest metadata update</th>
<th>Latest successful Crossref deposit</th>
+ <th>CLOCKSS file exists?</th>
</tr>
</thead>
@@ -51,9 +52,10 @@ event: "focusin"
<td>No info available</td>
{% endif %}
<td>{{ publication|latest_successful_crossref_deposit }}</td>
+ <td>{% if publication.clockssmetadata_set.all.exists %}Yes{% else %}No{% endif %}</td>
</tr>
<tr id="collapse{{ publication.id }}" class="collapse" role="tabpanel" aria-labelledby="heading{{ publication.id }}" style="background-color: #fff;">
- <td colspan="4">
+ <td colspan="5">
<h3 class="ml-3">Actions</h3>
<ul>
<li>Mark the first author (currently: {% if publication.first_author %}{{ publication.first_author }} {% elif publication.first_author_unregistered %}{{ publication.first_author_unregistered }} (unregistered){% endif %})
@@ -87,8 +89,9 @@ event: "focusin"
<li><a href="{% url 'journals:create_metadata_xml' publication.doi_label %}">(re)create metadata</a></li>
<li><a href="{% url 'journals:metadata_xml_deposit' publication.doi_label 'test' %}">Test metadata deposit (via Crossref test server)</a></li>
<li><a href="{% url 'journals:metadata_xml_deposit' publication.doi_label 'deposit' %}">Deposit the metadata to Crossref</a></li>
+ <li><a href="{% url 'journals:produce_CLOCKSS_metadata_file' doi_label=publication.doi_label %}">Produce CLOCKSS metadata file</a></li>
</ul>
- <h3 class="ml-3">Deposits</h3>
+ <h3 class="ml-3">Crossref Deposits</h3>
<table class="ml-5">
<thead class="thead-default">
<th>Timestamp</th>
diff --git a/journals/templates/journals/publication_metadata_jats.xml b/journals/templates/journals/publication_metadata_jats.xml
new file mode 100644
index 000000000..6f97e3fb7
--- /dev/null
+++ b/journals/templates/journals/publication_metadata_jats.xml
@@ -0,0 +1,22 @@
+<article dtd-version="1.1d3">
+<front>
+<journal-meta>
+<publisher>
+<publisher-name>SciPost</publisher-name>
+</publisher>
+<issn>{{ publication.in_issue.in_volume.in_journal.issn }}</issn>
+</journal-meta>
+<article-meta>
+<title-group>
+<article-title>{{ publication.title }}</article-title>
+</title-group>
+<article-id pub-id-type="doi">{{ publication.doi_string }}</article-id>
+<volume>{{ publication.in_issue.in_volume.number }}</volume>
+<issue>{{ publication.in_issue.number }}</issue>
+<pub-date publication-format="epub" date-type="pub" iso-8601-date="{{ publication.publication_date|date:'Y-m-d' }}">
+<day>{{ publication.publication_date|date:'d' }}</day>
+<month>{{ publication.publication_date|date:'m' }}</month>
+<year>{{ publication.publication_date|date:'Y' }}</year>
+</pub-date></article-meta>
+</front>
+</article>
diff --git a/journals/urls/general.py b/journals/urls/general.py
index 3fd938879..b9ca2cef6 100644
--- a/journals/urls/general.py
+++ b/journals/urls/general.py
@@ -55,6 +55,9 @@ urlpatterns = [
url(r'^mark_deposit_success/(?P<deposit_id>[0-9]+)/(?P<success>[0-1])$',
journals_views.mark_deposit_success,
name='mark_deposit_success'),
+ url(r'^produce_CLOCKSS_metadata_file/(?P<doi_label>[a-zA-Z]+.[0-9]+.[0-9]+.[0-9]{3,})$',
+ journals_views.produce_CLOCKSS_metadata_file,
+ name='produce_CLOCKSS_metadata_file'),
url(r'^harvest_citedby_list/$',
journals_views.harvest_citedby_list,
name='harvest_citedby_list'),
diff --git a/journals/views.py b/journals/views.py
index 4eb5a6810..b4c25fbbf 100644
--- a/journals/views.py
+++ b/journals/views.py
@@ -11,6 +11,8 @@ from django.conf import settings
from django.contrib import messages
from django.utils import timezone
from django.shortcuts import get_object_or_404, render, redirect
+from django.template import Template, Context
+from django.template.loader import get_template
from django.db import transaction
from django.http import HttpResponse
@@ -21,7 +23,7 @@ from .forms import FundingInfoForm, InitiatePublicationForm, ValidatePublication
UnregisteredAuthorForm, CreateMetadataXMLForm, CitationListBibitemsForm
from .utils import JournalUtils
-from journals.models import Publication, Deposit
+from journals.models import Publication, Deposit, CLOCKSSmetadata
from submissions.models import Submission
from scipost.models import Contributor
@@ -475,7 +477,7 @@ def create_metadata_xml(request, doi_label):
'<abbrev_title>'
+ publication.in_issue.in_volume.in_journal.get_abbreviation_citation() +
'</abbrev_title>\n'
- '<issn>' + publication.in_issue.in_volume.in_journal.issn + '</issn>\n'
+ '<issn media_type=\'electronic\'>' + publication.in_issue.in_volume.in_journal.issn + '</issn>\n'
'<doi_data>\n'
'<doi>' + publication.in_issue.in_volume.in_journal.doi_string + '</doi>\n'
'<resource>https://scipost.org/'
@@ -548,6 +550,7 @@ def create_metadata_xml(request, doi_label):
+ publication.doi_string + '/pdf</resource>\n'
'</item></collection>\n'
'</doi_data>\n'
+ '<pages><first_page>' + publication.paper_nr + '</first_page></pages>\n'
)
try:
if publication.metadata['citation_list']:
@@ -608,22 +611,30 @@ def metadata_xml_deposit(request, doi_label, option='test'):
response_headers = r.headers
response_text = r.text
- # Then, if deposit, create the associated Deposit object (saving the metadata to a file)
- content = ContentFile(publication.metadata_xml)
- timestamp = (publication.metadata_xml.partition(
- '<timestamp>'))[2].partition('</timestamp>')[0]
- doi_batch_id = (publication.metadata_xml.partition(
- '<doi_batch_id>'))[2].partition('</doi_batch_id>')[0]
- path = (settings.MEDIA_ROOT + publication.in_issue.path + '/'
- + publication.get_paper_nr() + '/' + publication.doi_label.replace('.', '_')
- + '_' + timestamp + '.xml')
- deposit = Deposit(publication=publication, timestamp=timestamp, doi_batch_id=doi_batch_id,
- metadata_xml=publication.metadata_xml, deposition_date=timezone.now())
- deposit.metadata_xml_file.save(path, content)
- deposit.response_text = r.text
- deposit.save()
- publication.latest_crossref_deposit = timezone.now()
- publication.save()
+ # Then create the associated Deposit object (saving the metadata to a file)
+ if option == 'deposit':
+ content = ContentFile(publication.metadata_xml)
+ timestamp = (publication.metadata_xml.partition(
+ '<timestamp>'))[2].partition('</timestamp>')[0]
+ doi_batch_id = (publication.metadata_xml.partition(
+ '<doi_batch_id>'))[2].partition('</doi_batch_id>')[0]
+ path = (settings.MEDIA_ROOT + publication.in_issue.path + '/'
+ + publication.get_paper_nr() + '/' + publication.doi_label.replace('.', '_')
+ + '_' + timestamp + '.xml')
+ deposit = Deposit(publication=publication, timestamp=timestamp, doi_batch_id=doi_batch_id,
+ metadata_xml=publication.metadata_xml, deposition_date=timezone.now())
+ deposit.metadata_xml_file.save(path, content)
+ deposit.response_text = r.text
+ deposit.save()
+ publication.latest_crossref_deposit = timezone.now()
+ publication.save()
+ # Save a copy to the filename without timestamp
+ path1 = (settings.MEDIA_ROOT + publication.in_issue.path + '/'
+ + publication.get_paper_nr() + '/' + publication.doi_label.replace('.', '_')
+ + '.xml')
+ f = open(path1, 'w')
+ f.write(xml)
+ f.close()
context = {
'option': option,
@@ -645,6 +656,33 @@ def mark_deposit_success(request, deposit_id, success):
return redirect(reverse('journals:manage_metadata'))
+@permission_required('scipost.can_publish_accepted_submission', return_403=True)
+def produce_CLOCKSS_metadata_file(request, doi_label):
+ publication = get_object_or_404(Publication, doi_label=doi_label)
+ context = Context({'publication': publication,})
+ xml = get_template('journals/publication_metadata_jats.xml').render(context)
+ content = ContentFile(xml)
+ timestamp = (publication.metadata_xml.partition(
+ '<timestamp>'))[2].partition('</timestamp>')[0]
+ path = (settings.MEDIA_ROOT + publication.in_issue.path + '/'
+ + publication.get_paper_nr() + '/' + publication.doi_label.replace('.', '_')
+ + '_CLOCKSS_' + timestamp + '.xml')
+ if os.path.isfile(path):
+ errormessage = 'The CLOCKSS metadata file for this metadata timestamp already exists'
+ return render(request, 'scipost/error.html', context={'errormessage': errormessage})
+ clockssmeta = CLOCKSSmetadata(publication=publication)
+ clockssmeta.metadata_xml_file_CLOCKSS.save(path, content)
+ clockssmeta.save()
+ # Save a copy to the filename without timestamp
+ path1 = (settings.MEDIA_ROOT + publication.in_issue.path + '/'
+ + publication.get_paper_nr() + '/' + publication.doi_label.replace('.', '_')
+ + '_CLOCKSS.xml')
+ f = open(path1, 'w')
+ f.write(xml)
+ f.close()
+ return redirect(reverse('journals:manage_metadata'))
+
+
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def harvest_citedby_list(request):
publications = Publication.objects.order_by('-publication_date')
--
GitLab