import hashlib
import json
import os
import random
import requests
import shutil
import string
import xml.etree.ElementTree as ET
from django.contrib.auth.decorators import login_required
from django.contrib.contenttypes.models import ContentType
from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
from django.core.urlresolvers import reverse
from django.conf import settings
from django.contrib import messages
from django.db import transaction
from django.http import Http404, HttpResponse
from django.utils import timezone
from django.shortcuts import get_object_or_404, render, redirect
from .exceptions import PaperNumberingError
from .helpers import paper_nr_string, issue_doi_label_from_doi_label
from .models import Journal, Issue, Publication, UnregisteredAuthor, Deposit, DOAJDeposit,\
GenericDOIDeposit
from .forms import FundingInfoForm, InitiatePublicationForm, ValidatePublicationForm,\
UnregisteredAuthorForm, CreateMetadataXMLForm, CitationListBibitemsForm,\
ReferenceFormSet
from .utils import JournalUtils
from comments.models import Comment
from funders.models import Funder
from submissions.models import Submission, Report
from scipost.models import Contributor
from production.constants import PROOFS_PUBLISHED
from production.models import ProductionEvent
from production.signals import notify_stream_status_change
from funders.forms import FunderSelectForm, GrantSelectForm
from scipost.forms import ConfirmationForm
from guardian.decorators import permission_required
############
# Journals
############
def journals(request):
'''Main landing page for Journals application.'''
context = {'journals': Journal.objects.order_by('name')}
return render(request, 'journals/journals.html', context)
def landing_page(request, doi_label):
journal = get_object_or_404(Journal, doi_label=doi_label)
current_issue = Issue.objects.published(
in_volume__in_journal=journal,
start_date__lte=timezone.now(),
until_date__gte=timezone.now()).order_by('-until_date').first()
latest_issue = Issue.objects.published(
in_volume__in_journal=journal,
until_date__lte=timezone.now()).order_by('-until_date').first()
prev_issue = None
if current_issue:
prev_issue = (Issue.objects.published(in_volume__in_journal=journal,
start_date__lt=current_issue.start_date)
.order_by('start_date').last())
context = {
'current_issue': current_issue,
'latest_issue': latest_issue,
'prev_issue': prev_issue,
'journal': journal
}
return render(request, 'journals/journal_landing_page.html', context)
def issues(request, doi_label):
journal = get_object_or_404(Journal, doi_label=doi_label)
issues = Issue.objects.published(in_volume__in_journal=journal).order_by('-until_date')
context = {
'issues': issues,
'journal': journal
}
return render(request, 'journals/journal_issues.html', context)
def recent(request, doi_label):
"""
Display page for the most recent 20 publications in SciPost Physics.
"""
journal = get_object_or_404(Journal, doi_label=doi_label)
recent_papers = Publication.objects.published(
in_issue__in_volume__in_journal=journal).order_by('-publication_date',
'-paper_nr')[:20]
context = {
'recent_papers': recent_papers,
'journal': journal,
}
return render(request, 'journals/journal_recent.html', context)
def accepted(request, doi_label):
"""
Display page for submissions to SciPost Physics which
have been accepted but are not yet published.
"""
journal = get_object_or_404(Journal, doi_label=doi_label)
accepted_SP_submissions = (Submission.objects.accepted()
.filter(submitted_to_journal=journal.name)
.order_by('-latest_activity'))
context = {
'accepted_SP_submissions': accepted_SP_submissions,
'journal': journal
}
return render(request, 'journals/journal_accepted.html', context)
def info_for_authors(request, doi_label):
journal = get_object_or_404(Journal, doi_label=doi_label)
context = {
'journal': journal
}
return render(request, 'journals/%s_info_for_authors.html' % doi_label, context)
def about(request, doi_label):
journal = get_object_or_404(Journal, doi_label=doi_label)
context = {
'journal': journal
}
return render(request, 'journals/%s_about.html' % doi_label, context)
def issue_detail(request, doi_label):
issue = Issue.objects.get_published(doi_label=doi_label)
journal = issue.in_volume.in_journal
papers = issue.publication_set.order_by('paper_nr')
next_issue = (Issue.objects.published(in_volume__in_journal=journal,
start_date__gt=issue.start_date)
.order_by('start_date').first())
prev_issue = (Issue.objects.published(in_volume__in_journal=journal,
start_date__lt=issue.start_date)
.order_by('start_date').last())
context = {
'issue': issue,
'prev_issue': prev_issue,
'next_issue': next_issue,
'papers': papers,
'journal': journal
}
return render(request, 'journals/journal_issue_detail.html', context)
#######################
# Publication process #
#######################
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def initiate_publication(request):
"""
Called by an Editorial Administrator.
Publish the manuscript after proofs have been accepted.
This method prefills a ValidatePublicationForm for further
processing (verification in validate_publication method).
"""
initiate_publication_form = InitiatePublicationForm(request.POST or None)
if initiate_publication_form.is_valid():
submission = initiate_publication_form.cleaned_data['accepted_submission']
current_issue = initiate_publication_form.cleaned_data['to_be_issued_in']
# Determine next available paper number:
paper_nr = Publication.objects.filter(in_issue__in_volume=current_issue.in_volume).count()
paper_nr += 1
if paper_nr > 999:
raise PaperNumberingError(paper_nr)
# Build form data
doi_label = (
current_issue.in_volume.in_journal.name
+ '.' + str(current_issue.in_volume.number)
+ '.' + str(current_issue.number) + '.' + paper_nr_string(paper_nr)
)
doi_string = '10.21468/' + doi_label
BiBTeX_entry = (
'@Article{' + doi_label + ',\n'
'\ttitle={{' + submission.title + '}},\n'
'\tauthor={' + submission.author_list.replace(',', ' and') + '},\n'
'\tjournal={'
+ current_issue.in_volume.in_journal.get_abbreviation_citation()
+ '},\n'
'\tvolume={' + str(current_issue.in_volume.number) + '},\n'
'\tissue={' + str(current_issue.number) + '},\n'
'\tpages={' + paper_nr_string(paper_nr) + '},\n'
'\tyear={' + current_issue.until_date.strftime('%Y') + '},\n'
'\tpublisher={SciPost},\n'
'\tdoi={' + doi_string + '},\n'
'\turl={https://scipost.org/' + doi_string + '},\n'
'}\n'
)
initial = {
'accepted_submission': submission,
'in_issue': current_issue,
'paper_nr': paper_nr,
'discipline': submission.discipline,
'domain': submission.domain,
'subject_area': submission.subject_area,
'secondary_areas': submission.secondary_areas,
'title': submission.title,
'author_list': submission.author_list,
'abstract': submission.abstract,
'BiBTeX_entry': BiBTeX_entry,
'doi_label': doi_label,
'acceptance_date': submission.acceptance_date,
'submission_date': submission.submission_date,
'publication_date': timezone.now(),
}
validate_publication_form = ValidatePublicationForm(initial=initial)
context = {'validate_publication_form': validate_publication_form}
return render(request, 'journals/validate_publication.html', context)
context = {'initiate_publication_form': initiate_publication_form}
return render(request, 'journals/initiate_publication.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def validate_publication(request):
"""
This creates a Publication instance from the ValidatePublicationForm,
pre-filled by the initiate_publication method above.
"""
# TODO: move from uploads to Journal folder
# TODO: create metadata
# TODO: set DOI, register with Crossref
# TODO: add funding info
context = {}
validate_publication_form = ValidatePublicationForm(request.POST or None,
request.FILES or None)
if validate_publication_form.is_valid():
publication = validate_publication_form.save()
# Fill in remaining data
submission = publication.accepted_submission
publication.authors.add(*submission.authors.all())
if publication.first_author:
publication.authors.add(publication.first_author)
if publication.first_author_unregistered:
publication.authors_unregistered.add(publication.first_author_unregistered)
publication.authors_claims.add(*submission.authors_claims.all())
publication.authors_false_claims.add(*submission.authors_false_claims.all())
# Add Institutions to the publication
for author in publication.authors.all():
for current_affiliation in author.affiliations.active():
publication.institutions.add(current_affiliation.institution)
# Save the beast
publication.save()
# Move file to final location
initial_path = publication.pdf_file.path
new_dir = (settings.MEDIA_ROOT + publication.in_issue.path + '/'
+ publication.get_paper_nr())
new_path = new_dir + '/' + publication.doi_label.replace('.', '_') + '.pdf'
os.makedirs(new_dir)
os.rename(initial_path, new_path)
publication.pdf_file.name = new_path
publication.save()
# Mark the submission as having been published:
submission.published_as = publication
submission.status = 'published'
submission.save()
# Update ProductionStream
if hasattr(submission, 'production_stream'):
stream = submission.production_stream
stream.status = PROOFS_PUBLISHED
stream.save()
if request.user.production_user:
prodevent = ProductionEvent(
stream=stream,
event='status',
comments=' published the manuscript.',
noted_by=request.user.production_user
)
prodevent.save()
notify_stream_status_change(request.user, stream, False)
# TODO: Create a Commentary Page
# Email authors
JournalUtils.load({'publication': publication})
JournalUtils.send_authors_paper_published_email()
# Add SubmissionEvents
submission.add_general_event('The Submission has been published as %s.'
% publication.doi_label)
messages.success(request, 'The publication has been validated.')
return redirect(publication.get_absolute_url())
else:
context['errormessage'] = 'The form was invalid.'
context['validate_publication_form'] = validate_publication_form
return render(request, 'journals/validate_publication.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def manage_metadata(request, issue_doi_label=None, doi_label=None):
issues = Issue.objects.all().order_by('-until_date')
publications = Publication.objects.all()
if doi_label:
issue_doi_label = issue_doi_label_from_doi_label(doi_label)
if issue_doi_label:
publications = publications.filter(in_issue__doi_label=issue_doi_label)
publications = publications.order_by('-publication_date', '-paper_nr')
associate_grant_form = GrantSelectForm()
associate_generic_funder_form = FunderSelectForm()
context = {
'issues': issues,
'issue_doi_label': issue_doi_label,
'publications': publications,
'associate_grant_form': associate_grant_form,
'associate_generic_funder_form': associate_generic_funder_form,
}
return render(request, 'journals/manage_metadata.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def mark_first_author(request, publication_id, contributor_id):
publication = get_object_or_404(Publication, id=publication_id)
contributor = get_object_or_404(Contributor, id=contributor_id)
publication.first_author = contributor
publication.first_author_unregistered = None
publication.save()
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': publication.doi_label}))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def mark_first_author_unregistered(request, publication_id, unregistered_author_id):
publication = get_object_or_404(Publication, id=publication_id)
unregistered_author = get_object_or_404(UnregisteredAuthor, id=unregistered_author_id)
publication.first_author = None
publication.first_author_unregistered = unregistered_author
publication.save()
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': publication.doi_label}))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def add_author(request, publication_id, contributor_id=None, unregistered_author_id=None):
"""
If not all authors are registered Contributors or if they have not
all claimed authorship, this method allows editorial administrators
to associated them to the publication.
This is important for the Crossref metadata, in which all authors must appear.
"""
publication = get_object_or_404(Publication, id=publication_id)
if contributor_id:
contributor = get_object_or_404(Contributor, id=contributor_id)
publication.authors.add(contributor)
publication.save()
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': publication.doi_label}))
if request.method == 'POST':
form = UnregisteredAuthorForm(request.POST)
if form.is_valid():
contributors_found = Contributor.objects.filter(
user__last_name__icontains=form.cleaned_data['last_name'])
unregistered_authors_found = UnregisteredAuthor.objects.filter(
last_name__icontains=form.cleaned_data['last_name'])
new_unreg_author_form = UnregisteredAuthorForm(
initial={'first_name': form.cleaned_data['first_name'],
'last_name': form.cleaned_data['last_name'], })
else:
errormessage = 'Please fill in the form properly'
return render(request, 'scipost/error.html', context={'errormessage': errormessage})
else:
form = UnregisteredAuthorForm()
contributors_found = None
unregistered_authors_found = None
new_unreg_author_form = UnregisteredAuthorForm()
context = {'publication': publication,
'contributors_found': contributors_found,
'unregistered_authors_found': unregistered_authors_found,
'form': form,
'new_unreg_author_form': new_unreg_author_form, }
return render(request, 'journals/add_author.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def add_unregistered_author(request, publication_id, unregistered_author_id):
publication = get_object_or_404(Publication, id=publication_id)
unregistered_author = get_object_or_404(UnregisteredAuthor, id=unregistered_author_id)
publication.authors_unregistered.add(unregistered_author)
publication.save()
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': publication.doi_label}))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def add_new_unreg_author(request, publication_id):
publication = get_object_or_404(Publication, id=publication_id)
if request.method == 'POST':
new_unreg_author_form = UnregisteredAuthorForm(request.POST)
if new_unreg_author_form.is_valid():
new_unreg_author = new_unreg_author_form.save()
publication.authors_unregistered.add(new_unreg_author)
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': publication.doi_label}))
raise Http404
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def create_citation_list_metadata(request, doi_label):
"""
Called by an Editorial Administrator.
This populates the citation_list dictionary entry
in the metadata field in a Publication instance.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
if request.method == 'POST':
bibitems_form = CitationListBibitemsForm(request.POST, request.FILES)
if bibitems_form.is_valid():
publication.metadata['citation_list'] = bibitems_form.extract_dois()
publication.save()
bibitems_form = CitationListBibitemsForm()
context = {
'publication': publication,
'bibitems_form': bibitems_form,
}
if request.method == 'POST':
context['citation_list'] = publication.metadata['citation_list']
return render(request, 'journals/create_citation_list_metadata.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def update_references(request, doi_label):
"""
Update the References for a certain Publication.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
references = publication.references.all()
formset = ReferenceFormSet(request.POST or None, queryset=references, publication=publication,
extra=request.GET.get('extra'))
if request.GET.get('prefill'):
formset.prefill()
if formset.is_valid():
formset.save()
messages.success(request, 'References saved')
return redirect(publication.get_absolute_url())
context = {
'publication': publication,
'formset': formset,
}
return render(request, 'journals/update_references.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def create_funding_info_metadata(request, doi_label):
"""
Called by an Editorial Administrator.
This populates the funding_info dictionary entry
in the metadata field in a Publication instance.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
funding_info_form = FundingInfoForm(request.POST or None)
if funding_info_form.is_valid():
publication.metadata['funding_statement'] = funding_info_form.cleaned_data[
'funding_statement']
publication.save()
try:
initial = {'funding_statement': publication.metadata['funding_statement']}
funding_statement = initial['funding_statement']
except KeyError:
initial = {'funding_statement': ''}
funding_statement = ''
context = {'publication': publication,
'funding_info_form': FundingInfoForm(initial=initial),
'funding_statement': funding_statement}
return render(request, 'journals/create_funding_info_metadata.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def add_associated_grant(request, doi_label):
"""
Called by an Editorial Administrator.
This associates a grant from the database to this publication.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
grant_select_form = GrantSelectForm(request.POST or None)
if grant_select_form.is_valid():
publication.grants.add(grant_select_form.cleaned_data['grant'])
publication.save()
messages.success(request, 'Grant added to publication %s' % str(publication))
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': publication.doi_label}))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def add_generic_funder(request, doi_label):
"""
Called by an Editorial Administrator.
This associates a funder (generic, not via grant) from the database to this publication.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
funder_select_form = FunderSelectForm(request.POST or None)
if funder_select_form.is_valid():
publication.funders_generic.add(funder_select_form.cleaned_data['funder'])
publication.save()
messages.success(request, 'Generic funder added to publication %s' % str(publication))
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': doi_label}))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def create_metadata_xml(request, doi_label):
"""
To be called by an EdAdmin after the citation_list,
funding_info entries have been filled.
Populates the metadata_xml field of a Publication instance.
The contents can then be sent to Crossref for registration.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
create_metadata_xml_form = CreateMetadataXMLForm(request.POST or None, instance=publication)
if create_metadata_xml_form.is_valid():
create_metadata_xml_form.save()
messages.success(request, 'Metadata XML saved')
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': doi_label}))
# create a doi_batch_id
salt = ""
for i in range(5):
salt = salt + random.choice(string.ascii_letters)
salt = salt.encode('utf8')
idsalt = publication.title[:10]
idsalt = idsalt.encode('utf8')
doi_batch_id = hashlib.sha1(salt+idsalt).hexdigest()
initial = {'metadata_xml': ''}
initial['metadata_xml'] += (
'<?xml version="1.0" encoding="UTF-8"?>\n'
'<doi_batch version="4.4.0" xmlns="http://www.crossref.org/schema/4.4.0" '
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" '
'xmlns:fr="http://www.crossref.org/fundref.xsd" '
'xsi:schemaLocation="http://www.crossref.org/schema/4.4.0 '
'http://www.crossref.org/shema/deposit/crossref4.4.0.xsd" '
'xmlns:ai="http://www.crossref.org/AccessIndicators.xsd">\n'
'<head>\n'
'<doi_batch_id>' + str(doi_batch_id) + '</doi_batch_id>\n'
'<timestamp>' + timezone.now().strftime('%Y%m%d%H%M%S') + '</timestamp>\n'
'<depositor>\n'
'<depositor_name>scipost</depositor_name>\n'
'<email_address>' + settings.CROSSREF_DEPOSIT_EMAIL + '</email_address>\n'
'</depositor>\n'
'<registrant>scipost</registrant>\n'
'</head>\n'
'<body>\n'
'<journal>\n'
'<journal_metadata>\n'
'<full_title>' + publication.in_issue.in_volume.in_journal.get_name_display()
+ '</full_title>\n'
'<abbrev_title>'
+ publication.in_issue.in_volume.in_journal.get_abbreviation_citation() +
'</abbrev_title>\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/'
+ publication.in_issue.in_volume.in_journal.doi_string + '</resource>\n'
'</doi_data>\n'
'</journal_metadata>\n'
'<journal_issue>\n'
'<publication_date media_type=\'online\'>\n'
'<year>' + publication.publication_date.strftime('%Y') + '</year>\n'
'</publication_date>\n'
'<journal_volume>\n'
'<volume>' + str(publication.in_issue.in_volume.number) + '</volume>\n'
'</journal_volume>\n'
'<issue>' + str(publication.in_issue.number) + '</issue>\n'
'</journal_issue>\n'
'<journal_article publication_type=\'full_text\'>\n'
'<titles><title>' + publication.title + '</title></titles>\n'
'<contributors>\n'
)
# Precondition: all authors MUST be listed in authors field of publication instance,
# this to be checked by EdAdmin before publishing.
for author in publication.authors.all():
if author == publication.first_author:
initial['metadata_xml'] += (
'<person_name sequence=\'first\' contributor_role=\'author\'> '
'<given_name>' + author.user.first_name + '</given_name> '
'<surname>' + author.user.last_name + '</surname> '
)
else:
initial['metadata_xml'] += (
'<person_name sequence=\'additional\' contributor_role=\'author\'> '
'<given_name>' + author.user.first_name + '</given_name> '
'<surname>' + author.user.last_name + '</surname> '
)
if author.orcid_id:
initial['metadata_xml'] += '<ORCID>http://orcid.org/' + author.orcid_id + '</ORCID>'
initial['metadata_xml'] += '</person_name>\n'
for author_unreg in publication.authors_unregistered.all():
if author_unreg == publication.first_author_unregistered:
initial['metadata_xml'] += (
'<person_name sequence=\'first\' contributor_role=\'author\'> '
'<given_name>' + author_unreg.first_name + '</given_name> '
'<surname>' + author_unreg.last_name + '</surname> '
)
else:
initial['metadata_xml'] += (
'<person_name sequence=\'additional\' contributor_role=\'author\'> '
'<given_name>' + author_unreg.first_name + '</given_name> '
'<surname>' + author_unreg.last_name + '</surname> '
)
initial['metadata_xml'] += '</person_name>\n'
initial['metadata_xml'] += '</contributors>\n'
initial['metadata_xml'] += (
'<publication_date media_type=\'online\'>\n'
'<month>' + publication.publication_date.strftime('%m') + '</month>'
'<day>' + publication.publication_date.strftime('%d') + '</day>'
'<year>' + publication.publication_date.strftime('%Y') + '</year>'
'</publication_date>\n'
'<publisher_item><item_number item_number_type="article_number">'
+ paper_nr_string(publication.paper_nr) +
'</item_number></publisher_item>\n'
'<crossmark>\n'
'<crossmark_policy>10.21468/SciPost.CrossmarkPolicy</crossmark_policy>\n'
'<crossmark_domains>\n'
'<crossmark_domain><domain>scipost.org</domain></crossmark_domain>\n'
'</crossmark_domains>\n'
'<crossmark_domain_exclusive>false</crossmark_domain_exclusive>\n'
)
funders = (Funder.objects.filter(grant__in=publication.grants.all())
| publication.funders_generic.all()).distinct()
nr_funders = funders.count()
initial['metadata_xml'] += '<custom_metadata>\n'
if nr_funders > 0:
initial['metadata_xml'] += '<fr:program name="fundref">\n'
for funder in funders:
if nr_funders > 1:
initial['metadata_xml'] += '<fr:assertion name="fundgroup">\n'
initial['metadata_xml'] += (
'<fr:assertion name="funder_name">' + funder.name + '\n'
'<fr:assertion name="funder_identifier">'
+ funder.identifier + '</fr:assertion>\n'
'</fr:assertion>\n')
for grant in publication.grants.all():
if grant.funder == funder:
initial['metadata_xml'] += (
'<fr:assertion name="award_number">'
+ grant.number + '</fr:assertion>\n')
if nr_funders > 1:
initial['metadata_xml'] += '</fr:assertion>\n'
initial['metadata_xml'] += '</fr:program>\n'
initial['metadata_xml'] += (
'<ai:program name="AccessIndicators">\n'
'<ai:license_ref>' + publication.get_cc_license_URI() +
'</ai:license_ref>\n'
'</ai:program>\n'
)
initial['metadata_xml'] += '</custom_metadata>\n'
initial['metadata_xml'] += (
'</crossmark>\n'
'<archive_locations><archive name="CLOCKSS"></archive></archive_locations>\n'
'<doi_data>\n'
'<doi>' + publication.doi_string + '</doi>\n'
'<resource>https://scipost.org/' + publication.doi_string + '</resource>\n'
'<collection property="crawler-based">\n'
'<item crawler="iParadigms">\n'
'<resource>https://scipost.org/'
+ publication.doi_string + '/pdf</resource>\n'
'</item></collection>\n'
'<collection property="text-mining">\n'
'<item><resource mime_type="application/pdf">'
'https://scipost.org/' + publication.doi_string + '/pdf</resource></item>\n'
'</collection>'
'</doi_data>\n'
)
try:
if publication.metadata['citation_list']:
initial['metadata_xml'] += '<citation_list>\n'
for ref in publication.metadata['citation_list']:
initial['metadata_xml'] += (
'<citation key="' + ref['key'] + '">'
'<doi>' + ref['doi'] + '</doi>'
'</citation>\n'
)
initial['metadata_xml'] += '</citation_list>\n'
except KeyError:
pass
initial['metadata_xml'] += (
'</journal_article>\n'
'</journal>\n'
)
initial['metadata_xml'] += '</body>\n</doi_batch>'
publication.latest_metadata_update = timezone.now()
publication.save()
context = {
'publication': publication,
'create_metadata_xml_form': CreateMetadataXMLForm(initial=initial, instance=publication),
}
return render(request, 'journals/create_metadata_xml.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def metadata_xml_deposit(request, doi_label, option='test'):
"""
Crossref metadata deposit.
If test==True, test the metadata_xml using the Crossref test server.
Makes use of the python requests module.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
if publication.metadata_xml is None:
errormessage = 'This publication has no metadata. Produce it first before saving it.'
return render(request, 'scipost/error.html', context={'errormessage': errormessage})
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('.', '_')
+ '_Crossref_' + timestamp + '.xml')
if os.path.isfile(path):
errormessage = 'The metadata file for this metadata timestamp already exists'
return render(request, 'scipost/error.html', context={'errormessage': errormessage})
if option == 'deposit' and not settings.DEBUG:
# CAUTION: Real deposit only on production (non-debug-mode)
url = 'http://doi.crossref.org/servlet/deposit'
else:
url = 'http://test.crossref.org/servlet/deposit'
# First perform the actual deposit to Crossref
params = {
'operation': 'doMDUpload',
'login_id': settings.CROSSREF_LOGIN_ID,
'login_passwd': settings.CROSSREF_LOGIN_PASSWORD,
}
files = {
'fname': ('metadata.xml', publication.metadata_xml.encode('utf-8'), 'multipart/form-data')
}
r = requests.post(url, params=params, files=files)
response_headers = r.headers
response_text = r.text
# Then create the associated Deposit object (saving the metadata to a file)
if option == 'deposit':
deposit = Deposit(publication=publication, timestamp=timestamp, doi_batch_id=doi_batch_id,
metadata_xml=publication.metadata_xml, deposition_date=timezone.now())
deposit.response_text = r.text
# Save the filename with timestamp
path_with_timestamp = '{issue}/{paper}/{doi}_Crossref_{timestamp}.xml'.format(
issue=publication.in_issue.path,
paper=publication.get_paper_nr(),
doi=publication.doi_label.replace('.', '_'),
timestamp=timestamp)
f = open(settings.MEDIA_ROOT + path_with_timestamp, 'w', encoding='utf-8')
f.write(publication.metadata_xml)
f.close()
# Copy file
path_without_timestamp = '{issue}/{paper}/{doi}_Crossref.xml'.format(
issue=publication.in_issue.path,
paper=publication.get_paper_nr(),
doi=publication.doi_label.replace('.', '_'))
shutil.copyfile(settings.MEDIA_ROOT + path_with_timestamp,
settings.MEDIA_ROOT + path_without_timestamp)
deposit.metadata_xml_file = path_with_timestamp
deposit.save()
publication.latest_crossref_deposit = timezone.now()
publication.save()
context = {
'option': option,
'publication': publication,
'response_headers': response_headers,
'response_text': response_text,
}
return render(request, 'journals/metadata_xml_deposit.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def mark_deposit_success(request, deposit_id, success):
deposit = get_object_or_404(Deposit, pk=deposit_id)
if success == '1':
deposit.deposit_successful = True
elif success == '0':
deposit.deposit_successful = False
deposit.save()
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': deposit.publication.doi_label}))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def produce_metadata_DOAJ(request, doi_label):
publication = get_object_or_404(Publication, doi_label=doi_label)
JournalUtils.load({'request': request, 'publication': publication})
publication.metadata_DOAJ = JournalUtils.generate_metadata_DOAJ()
publication.save()
messages.success(request, '<h3>%s</h3>Successfully produced metadata DOAJ.'
% publication.doi_label)
return redirect(reverse('journals:manage_metadata'))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def metadata_DOAJ_deposit(request, doi_label):
"""
DOAJ metadata deposit.
Makes use of the python requests module.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
if not publication.metadata_DOAJ:
messages.warning(request, '<h3>%s</h3>Failed: please first produce '
'DOAJ metadata before depositing.' % publication.doi_label)
return redirect(reverse('journals:manage_metadata'))
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('.', '_')
+ '_DOAJ_' + timestamp + '.json')
if os.path.isfile(path):
errormessage = 'The metadata file for this metadata timestamp already exists'
return render(request, 'scipost/error.html', context={'errormessage': errormessage})
url = 'https://doaj.org/api/v1/articles'
params = {
'api_key': settings.DOAJ_API_KEY,
}
try:
r = requests.post(url, params=params, json=publication.metadata_DOAJ)
r.raise_for_status()
except requests.exceptions.HTTPError:
messages.warning(request, '<h3>%s</h3>Failed: Post went wrong, response text: %s' % (
publication.doi_label, r.text))
# Then create the associated Deposit object (saving the metadata to a file)
deposit = DOAJDeposit(publication=publication, timestamp=timestamp,
metadata_DOAJ=publication.metadata_DOAJ, deposition_date=timezone.now())
deposit.response_text = r.text
# Save a copy to the filename with and without timestamp
path_with_timestamp = '{issue}/{paper}/{doi}_DOAJ_{timestamp}.json'.format(
issue=publication.in_issue.path,
paper=publication.get_paper_nr(),
doi=publication.doi_label.replace('.', '_'),
timestamp=timestamp)
f = open(settings.MEDIA_ROOT + path_with_timestamp, 'w')
f.write(json.dumps(publication.metadata_DOAJ))
f.close()
# Copy file
path_without_timestamp = '{issue}/{paper}/{doi}_DOAJ.json'.format(
issue=publication.in_issue.path,
paper=publication.get_paper_nr(),
doi=publication.doi_label.replace('.', '_'))
shutil.copyfile(settings.MEDIA_ROOT + path_with_timestamp,
settings.MEDIA_ROOT + path_without_timestamp)
# Save the database entry
deposit.metadata_DOAJ_file = path_with_timestamp
deposit.save()
messages.success(request, '<h3>%s</h3>Successfull deposit of metadata DOAJ.'
% publication.doi_label)
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': publication.doi_label}))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def mark_doaj_deposit_success(request, deposit_id, success):
deposit = get_object_or_404(DOAJDeposit, pk=deposit_id)
if success == '1':
deposit.deposit_successful = True
elif success == '0':
deposit.deposit_successful = False
deposit.save()
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': deposit.publication.doi_label}))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def harvest_citedby_list(request):
publications = Publication.objects.order_by('-publication_date')
context = {
'publications': publications
}
return render(request, 'journals/harvest_citedby_list.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def harvest_citedby_links(request, doi_label):
publication = get_object_or_404(Publication, doi_label=doi_label)
# create a doi_batch_id
salt = ""
for i in range(5):
salt = salt + random.choice(string.ascii_letters)
salt = salt.encode('utf8')
idsalt = publication.title[:10]
idsalt = idsalt.encode('utf8')
doi_batch_id = hashlib.sha1(salt+idsalt).hexdigest()
query_xml = ('<?xml version = "1.0" encoding="UTF-8"?>'
'<query_batch version="2.0" xmlns = "http://www.crossref.org/qschema/2.0"'
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"'
'xsi:schemaLocation="http://www.crossref.org/qschema/2.0 '
'http://www.crossref.org/qschema/crossref_query_input2.0.xsd">'
'<head>'
'<email_address>' + settings.CROSSREF_DEPOSIT_EMAIL + '</email_address>'
'<doi_batch_id>' + str(doi_batch_id) + '</doi_batch_id>'
'</head>'
'<body>'
'<fl_query alert="false">'
'<doi>' + publication.doi_string + '</doi>'
'</fl_query>'
'</body>'
'</query_batch>')
url = 'http://doi.crossref.org/servlet/getForwardLinks'
params = {'usr': settings.CROSSREF_LOGIN_ID,
'pwd': settings.CROSSREF_LOGIN_PASSWORD,
'qdata': query_xml,
'doi': publication.doi_string, }
r = requests.post(url, params=params)
if r.status_code == 401:
messages.warning(request, ('<h3>Crossref credentials are invalid.</h3>'
'Please contact the SciPost Admin.'))
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': doi_label}))
response_headers = r.headers
response_text = r.text
response_deserialized = ET.fromstring(r.text)
prefix = '{http://www.crossref.org/qrschema/2.0}'
citations = []
for link in response_deserialized.iter(prefix + 'forward_link'):
doi = link.find(prefix + 'journal_cite').find(prefix + 'doi').text
article_title = link.find(prefix + 'journal_cite').find(prefix + 'article_title').text
try:
journal_abbreviation = link.find(prefix + 'journal_cite').find(
prefix + 'journal_abbreviation').text
except:
journal_abbreviation = None
try:
volume = link.find(prefix + 'journal_cite').find(prefix + 'volume').text
except AttributeError:
volume = None
try:
first_page = link.find(prefix + 'journal_cite').find(prefix + 'first_page').text
except:
first_page = None
try:
item_number = link.find(prefix + 'journal_cite').find(prefix + 'item_number').text
except:
item_number = None
multiauthors = False
for author in link.find(prefix + 'journal_cite').find(
prefix + 'contributors').iter(prefix + 'contributor'):
if author.get('sequence') == 'first':
first_author_given_name = author.find(prefix + 'given_name').text
first_author_surname = author.find(prefix + 'surname').text
else:
multiauthors = True
year = link.find(prefix + 'journal_cite').find(prefix + 'year').text
citations.append({'doi': doi,
'article_title': article_title,
'journal_abbreviation': journal_abbreviation,
'first_author_given_name': first_author_given_name,
'first_author_surname': first_author_surname,
'multiauthors': multiauthors,
'volume': volume,
'first_page': first_page,
'item_number': item_number,
'year': year, })
publication.citedby = citations
publication.latest_citedby_update = timezone.now()
publication.save()
context = {
'publication': publication,
'response_headers': response_headers,
'response_text': response_text,
'response_deserialized': response_deserialized,
'citations': citations,
}
return render(request, 'journals/harvest_citedby_links.html', context)
@login_required
def sign_existing_report(request, report_id):
"""
Allows the author of a Report, originally submitted anonymously,
to sign the Report.
"""
report = get_object_or_404(Report, pk=report_id)
if report.author != request.user.contributor:
errormessage = 'Only the author of this Report can change its anonymity status'
return render(request, 'scipost/error.html', context={'errormessage': errormessage})
form = ConfirmationForm(request.POST or None)
if form.is_valid():
if form.cleaned_data['confirm'] == 'True':
report.anonymous = False
report.doideposit_needs_updating = True
report.save()
messages.success(request, 'Your Report is now publicly signed.')
else:
messages.error(request, 'Report signing operation cancelled.')
return redirect(reverse('scipost:personal_page'))
context = {'report': report, 'form': form}
return render(request, 'journals/sign_existing_report.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def manage_report_metadata(request):
"""
This page offers Editorial Administrators tools for managing
the metadata of Reports.
"""
reports = Report.objects.all()
paginator = Paginator(reports, 25)
page = request.GET.get('page')
try:
reports = paginator.page(page)
except PageNotAnInteger:
reports = paginator.page(1)
except EmptyPage:
reports = paginator.page(paginator.num_pages)
context = {
'reports': reports,
}
return render(request, 'journals/manage_report_metadata.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def manage_comment_metadata(request):
"""
This page offers Editorial Administrators tools for managing
the metadata of Comments.
"""
comments = Comment.objects.all()
context = {
'comments': comments,
}
return render(request, 'journals/manage_comment_metadata.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def mark_report_doi_needed(request, report_id, needed):
report = get_object_or_404(Report, pk=report_id)
if needed == '1':
report.needs_doi = True
elif needed == '0':
report.needs_doi = False
report.save()
return redirect(reverse('journals:manage_report_metadata'))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def mark_comment_doi_needed(request, comment_id, needed):
comment = get_object_or_404(Comment, pk=comment_id)
if needed == '1':
comment.needs_doi = True
elif needed == '0':
comment.needs_doi = False
comment.save()
return redirect(reverse('journals:manage_comment_metadata'))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
@transaction.atomic
def generic_metadata_xml_deposit(request, **kwargs):
"""
This method creates the metadata for non-Publication objects
such as Reports and Comments, and deposits the metadata to
Crossref.
If there exists a relation to a SciPost-published object,
the deposit uses Crossref's peer review content type.
Otherwise the deposit is done as a dataset.
"""
type_of_object = kwargs['type_of_object']
object_id = int(kwargs['object_id'])
if type_of_object == 'report':
_object = get_object_or_404(Report, id=object_id)
elif type_of_object == 'comment':
_object = get_object_or_404(Comment, id=object_id)
relation_to_published = _object.relation_to_published
if not _object.doi_label:
_object.create_doi_label()
# create a doi_batch_id
salt = ""
for i in range(5):
salt = salt + random.choice(string.ascii_letters)
salt = salt.encode('utf8')
idsalt = str(_object)[:10]
idsalt = idsalt.encode('utf8')
timestamp = timezone.now().strftime('%Y%m%d%H%M%S')
doi_batch_id = hashlib.sha1(salt+idsalt).hexdigest()
metadata_xml = (
'<?xml version="1.0" encoding="UTF-8"?>\n'
'<doi_batch version="4.4.1" xmlns="http://www.crossref.org/schema/4.4.1" '
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" '
'xsi:schemaLocation="http://www.crossref.org/schema/4.4.1 '
'http://www.crossref.org/shema/deposit/crossref4.4.1.xsd">\n'
'<head>\n'
'<doi_batch_id>' + str(doi_batch_id) + '</doi_batch_id>\n'
'<timestamp>' + timestamp + '</timestamp>\n'
'<depositor>\n'
'<depositor_name>scipost</depositor_name>\n'
'<email_address>' + settings.CROSSREF_DEPOSIT_EMAIL + '</email_address>\n'
'</depositor>\n'
'<registrant>scipost</registrant>\n'
'</head>\n'
)
if relation_to_published:
metadata_xml += (
'<body>\n'
'<peer_review stage="' + relation_to_published['stage'] + '">\n'
'<contributors>'
)
if _object.anonymous:
metadata_xml += (
'<anonymous sequence="first" contributor_role="'
+ relation_to_published['contributor_role'] + '"/>'
)
else:
metadata_xml += (
'<person_name sequence="first" contributor_role="'
+ relation_to_published['contributor_role'] + '">'
'<given_name>' + _object.author.user.first_name + '</given_name>'
'<surname>' + _object.author.user.last_name + '</surname>'
'</person_name>\n'
)
if isinstance(_object, Publication):
url_to_declare = 'https://scipost.org{}'.format(_object.get_absolute_url())
else:
url_to_declare = 'https://scipost.org/{}'.format(_object.doi_label)
metadata_xml += (
'</contributors>\n'
'<titles><title>' + relation_to_published['title'] + '</title></titles>\n'
'<review_date>'
'<month>' + _object.date_submitted.strftime('%m') + '</month>'
'<day>' + _object.date_submitted.strftime('%d') + '</day>'
'<year>' + _object.date_submitted.strftime('%Y') + '</year>'
'</review_date>\n'
'<program xmlns="http://www.crossref.org/relations.xsd">\n'
'<related_item>'
'<description>' + relation_to_published['title'] + '</description>\n'
'<inter_work_relation relationship-type="isReviewOf" identifier-type="doi">'
+ relation_to_published['isReviewOfDOI'] + '</inter_work_relation></related_item>\n'
'</program>'
'<doi_data><doi>' + _object.doi_string + '</doi>\n'
'<resource>' + url_to_declare +
'</resource></doi_data>\n'
'</peer_review>\n'
'</body>\n'
'</doi_batch>\n'
)
else:
metadata_xml += (
'<body>\n'
'<database>\n'
'<database_metadata language="en">\n'
'<titles><title>SciPost Reports and Comments</title></titles>\n'
'</database_metadata>\n'
'<dataset dataset_type="collection">\n'
'<doi_data><doi>' + _object.doi_string + '</doi>\n'
'<resource>https://scipost.org' + _object.get_absolute_url() +
'</resource></doi_data>\n'
'</dataset></database>\n'
'</body></doi_batch>'
)
if not settings.CROSSREF_DEBUG:
# CAUTION: Debug is False, production goes for real deposit!!!
url = 'http://doi.crossref.org/servlet/deposit'
else:
url = 'http://test.crossref.org/servlet/deposit'
params = {
'operation': 'doMDUpload',
'login_id': settings.CROSSREF_LOGIN_ID,
'login_passwd': settings.CROSSREF_LOGIN_PASSWORD,
}
files = {'fname': ('metadata.xml', metadata_xml, 'multipart/form-data')}
r = requests.post(url, params=params, files=files)
deposit = GenericDOIDeposit(content_type=ContentType.objects.get_for_model(_object),
object_id=object_id,
content_object=_object,
timestamp=timestamp,
doi_batch_id=doi_batch_id,
metadata_xml=metadata_xml,
deposition_date=timezone.now(),
response=r.text)
deposit.save()
context = {
'response_headers': r.headers,
'response_text': r.text,
}
return render(request, 'journals/generic_metadata_xml_deposit.html', context)
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def mark_generic_deposit_success(request, deposit_id, success):
deposit = get_object_or_404(GenericDOIDeposit, pk=deposit_id)
if success == '1':
deposit.deposit_successful = True
deposit.content_object.doideposit_needs_updating = False
deposit.content_object.save()
elif success == '0':
deposit.deposit_successful = False
deposit.save()
if deposit.content_type.name == 'report':
return redirect(reverse('journals:manage_report_metadata'))
else:
return redirect(reverse('journals:manage_comment_metadata'))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def email_object_made_citable(request, **kwargs):
"""
This method sends an email to the author of a Report or a Comment,
to notify that the object has been made citable (doi registered).
"""
type_of_object = kwargs['type_of_object']
object_id = int(kwargs['object_id'])
if type_of_object == 'report':
_object = get_object_or_404(Report, id=object_id)
redirect_to = reverse('journals:manage_report_metadata')
publication_citation=None
publication_doi=None
try:
publication=Publication.objects.get(
accepted_submission__arxiv_identifier_wo_vn_nr=_object.submission.arxiv_identifier_wo_vn_nr)
publication_citation = publication.citation()
publication_doi = publication.doi_string
except Publication.DoesNotExist:
pass
elif type_of_object == 'comment':
_object = get_object_or_404(Comment, id=object_id)
redirect_to = reverse('journals:manage_comment_metadata')
else:
raise Http404
if not _object.doi_label:
messages.warning(request, 'This object does not have a DOI yet.')
return redirect(redirect_to)
if type_of_object == 'report':
JournalUtils.load({'report': _object,
'publication_citation': publication_citation,
'publication_doi': publication_doi})
JournalUtils.email_report_made_citable()
else:
JournalUtils.load({'comment': _object, })
JournalUtils.email_comment_made_citable()
messages.success(request, 'Email sent')
return redirect(redirect_to)
###########
# Viewing #
###########
def report_detail(request, doi_label):
report = get_object_or_404(Report.objects.accepted(), doi_label=doi_label)
return redirect(report.get_absolute_url())
def comment_detail(request, doi_label):
comment = get_object_or_404(Comment.objects.vetted().regular_comments(), doi_label=doi_label)
return redirect(comment.get_absolute_url())
def author_reply_detail(request, doi_label):
comment = get_object_or_404(Comment.objects.vetted().author_replies(), doi_label=doi_label)
return redirect(comment.get_absolute_url())
def publication_detail(request, doi_label):
publication = Publication.objects.get_published(doi_label=doi_label)
journal = publication.in_issue.in_volume.in_journal
context = {
'publication': publication,
'journal': journal
}
return render(request, 'journals/publication_detail.html', context)
def publication_detail_pdf(request, doi_label):
publication = Publication.objects.get_published(doi_label=doi_label)
response = HttpResponse(publication.pdf_file.read(), content_type='application/pdf')
response['Content-Disposition'] = ('filename='
+ publication.doi_label.replace('.', '_') + '.pdf')
return response