__copyright__ = "Copyright 2016-2018, Stichting SciPost (SciPost Foundation)"
__license__ = "AGPL v3"
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.exceptions import PermissionDenied
from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
from django.core.urlresolvers import reverse, reverse_lazy
from django.conf import settings
from django.contrib import messages
from django.db import transaction
from django.db.models import Q
from django.http import Http404, HttpResponse
from django.utils import timezone
from django.utils.decorators import method_decorator
from django.views.generic.detail import DetailView
from django.views.generic.edit import UpdateView
from django.views.generic.list import ListView
from django.shortcuts import get_object_or_404, get_list_or_404, render, redirect
from .constants import STATUS_DRAFT, ISSUES_AND_VOLUMES, ISSUES_ONLY, INDIVIDUAL_PUBLCATIONS
from .exceptions import InvalidDOIError
from .models import Journal, Issue, Publication, Deposit, DOAJDeposit,\
GenericDOIDeposit, PublicationAuthorsTable, OrgPubFraction
from .forms import AbstractJATSForm, FundingInfoForm,\
UnregisteredAuthorForm, AuthorsTableOrganizationSelectForm,\
CreateMetadataXMLForm, CitationListBibitemsForm,\
ReferenceFormSet, CreateMetadataDOAJForm, DraftPublicationForm,\
PublicationGrantsForm, DraftPublicationApprovalForm, PublicationPublishForm,\
PublicationAuthorOrderingFormSet, OrgPubFractionsFormSet
from .mixins import PublicationMixin, ProdSupervisorPublicationPermissionMixin
from .utils import JournalUtils
from comments.models import Comment
from funders.forms import FunderSelectForm, GrantSelectForm
from funders.models import Grant
from mails.views import MailEditingSubView
from organizations.models import Organization
from submissions.constants import STATUS_PUBLISHED
from submissions.models import Submission, Report
from scipost.constants import SCIPOST_SUBJECT_AREAS
from scipost.forms import ConfirmationForm
from scipost.models import Contributor
from scipost.mixins import PermissionsMixin, RequestViewMixin, PaginationMixin
from guardian.decorators import permission_required
def doi_dispatch(request, journal_tag, part_1=None, part_2=None, part_3=None):
"""
Dispatch given DOI route to the appropriate view according to the Journal's settings.
journal_tag -- Part of the DOI right before the first period.
part_1 (optional) -- Part of the DOI after the first period.
part_2 (optional) -- Part of the DOI after the second period.
part_3 (optional) -- Part of the DOI after the third period.
"""
journal = get_object_or_404(Journal, doi_label=journal_tag)
if part_1 is None:
# This DOI refers to a Journal landing page.
return landing_page(request, journal_tag)
elif part_2 is None:
doi_label = '{0}.{1}'.format(journal_tag, part_1)
if journal.structure == INDIVIDUAL_PUBLCATIONS:
# Publication DOI for invidivual publication Journals.
return publication_detail(request, doi_label)
elif journal.structure == ISSUES_ONLY:
# Issue DOI for Issue only Journals.
return issue_detail(request, doi_label)
elif part_3 is None:
doi_label = '{0}.{1}.{2}'.format(journal_tag, part_1, part_2)
if journal.structure == ISSUES_AND_VOLUMES:
# Issue DOI for Issue+Volumes Journals.
# This should not happen. --> Where does this lead to even?
return issue_detail(request, doi_label)
elif journal.structure == ISSUES_ONLY:
# Publication DOI for Issue only Journals.
return publication_detail(request, doi_label)
else:
doi_label = '{0}.{1}.{2}.{3}'.format(journal_tag, part_1, part_2, part_3)
return publication_detail(request, doi_label)
# Invalid db configure
raise InvalidDOIError({
'journal_tag': journal_tag,
'part_1': part_1,
'part_2': part_2,
'part_3': part_3})
############
# Journals
############
def journals(request):
"""Main landing page for Journals application."""
context = {'journals': Journal.objects.order_by('name')}
return render(request, 'journals/journals.html', context)
class PublicationListView(PaginationMixin, ListView):
"""
Show Publications filtered per subject area.
"""
queryset = Publication.objects.published()
paginate_by = 10
def get_queryset(self):
qs = super().get_queryset()
if self.request.GET.get('journal'):
qs = qs.for_journal(self.request.GET['journal'])
if self.request.GET.get('issue'):
try:
issue = int(self.request.GET['issue'])
except ValueError:
issue = None
if issue:
qs = qs.filter(in_issue__id=issue)
if self.request.GET.get('subject'):
qs = qs.for_subject(self.request.GET['subject'])
if self.request.GET.get('orderby') == 'citations':
qs = qs.order_by('-number_of_citations')
else:
qs = qs.order_by('-publication_date', '-paper_nr')
return qs
def get_context_data(self, **kwargs):
context = super().get_context_data(**kwargs)
context['recent_issues'] = Issue.objects.published().order_by('-start_date')[:5]
context['subject_areas'] = (('', 'Show all'),) + SCIPOST_SUBJECT_AREAS[0][1]
return context
def landing_page(request, doi_label):
"""Journal details page.
The landing page of a Journal lists either the latest and the current issue of a Journal
of paginates the individual Publications.
"""
journal = get_object_or_404(Journal, doi_label=doi_label)
context = {
'journal': journal,
'most_cited': Publication.objects.for_journal(journal.name).published().most_cited(5),
'latest_publications': Publication.objects.for_journal(journal.name).published()[:5],
'accepted_submissions': Submission.objects.accepted().filter(
submitted_to_journal=journal.name).order_by('-latest_activity'),
}
return render(request, 'journals/journal_landing_page.html', context)
class IssuesView(DetailView):
"""
List all Issues sorted per Journal.
"""
queryset = Journal.objects.has_issues()
slug_field = slug_url_kwarg = 'doi_label'
template_name = 'journals/journal_issues.html'
def redirect_to_about(request, doi_label):
journal = get_object_or_404(Journal, doi_label=doi_label)
return redirect(
reverse('journal:about', kwargs={'doi_label': journal.doi_label}), permanent=True)
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 = get_object_or_404(Issue.objects.published(), doi_label=doi_label)
journal = issue.in_volume.in_journal
papers = issue.publications.published().order_by('paper_nr')
next_issue = Issue.objects.published().filter(
in_volume__in_journal=journal, start_date__gt=issue.start_date
).order_by('start_date').first()
prev_issue = Issue.objects.published().filter(
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 #
#######################
class PublicationGrantsView(PermissionsMixin, UpdateView):
"""
Add/update grants associated to a Publication.
"""
permission_required = 'scipost.can_draft_publication'
queryset = Publication.objects.drafts()
slug_field = slug_url_kwarg = 'doi_label'
form_class = PublicationGrantsForm
template_name = 'journals/grants_form.html'
class PublicationGrantsRemovalView(PermissionsMixin, DetailView):
"""
Remove grant associated to a Publication.
"""
permission_required = 'scipost.can_draft_publication'
queryset = Publication.objects.drafts()
slug_field = slug_url_kwarg = 'doi_label'
def get(self, request, *args, **kwargs):
super().get(request, *args, **kwargs)
grant = get_object_or_404(Grant, id=kwargs.get('grant_id'))
self.object.grants.remove(grant)
return redirect(reverse('journals:update_grants', args=(self.object.doi_label,)))
@permission_required('scipost.can_publish_accepted_submission', raise_exception=True)
def publication_authors_ordering(request, doi_label):
publication = get_object_or_404(Publication, doi_label=doi_label)
formset = PublicationAuthorOrderingFormSet(
request.POST or None, queryset=publication.authors.order_by('order'))
if formset.is_valid():
formset.save()
messages.success(request, 'Author ordering updated')
return redirect(publication.get_absolute_url())
context = {
'formset': formset,
'publication': publication,
}
return render(request, 'journals/publication_authors_form.html', context)
class DraftPublicationUpdateView(PermissionsMixin, UpdateView):
"""
Any Production Officer or Administrator can draft a new publication without publishing here.
The actual publishing is done lin a later stadium, after the draft has been finished.
"""
permission_required = 'scipost.can_draft_publication'
queryset = Publication.objects.unpublished()
slug_url_kwarg = 'identifier_w_vn_nr'
slug_field = 'accepted_submission__preprint__identifier_w_vn_nr'
form_class = DraftPublicationForm
template_name = 'journals/publication_form.html'
def get_object(self, queryset=None):
try:
publication = Publication.objects.get(
accepted_submission__preprint__identifier_w_vn_nr=self.kwargs.get(
'preprint__identifier_w_vn_nr'))
except Publication.DoesNotExist:
if Submission.objects.accepted().filter(preprint__identifier_w_vn_nr=self.kwargs.get(
'identifier_w_vn_nr')).exists():
return None
raise Http404('No accepted Submission found')
if publication.status == STATUS_DRAFT:
return publication
if self.request.user.has_perm('scipost.can_publish_accepted_submission'):
return publication
raise Http404('Found Publication is not in draft')
def get_form_kwargs(self):
kwargs = super().get_form_kwargs()
kwargs['identifier_w_vn_nr'] = self.kwargs.get('identifier_w_vn_nr')
kwargs['issue_id'] = self.request.GET.get('issue')
return kwargs
class DraftPublicationApprovalView(PermissionsMixin, UpdateView):
permission_required = 'scipost.can_draft_publication'
queryset = Publication.objects.drafts()
slug_field = slug_url_kwarg = 'doi_label'
form_class = DraftPublicationApprovalForm
template_name = 'journals/publication_approval_form.html'
@method_decorator(transaction.atomic, name='dispatch')
class PublicationPublishView(PermissionsMixin, RequestViewMixin, UpdateView):
permission_required = 'scipost.can_publish_accepted_submission'
queryset = Publication.objects.unpublished()
slug_field = slug_url_kwarg = 'doi_label'
form_class = PublicationPublishForm
template_name = 'journals/publication_publish_form.html'
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def manage_metadata(request, doi_label=None, issue_doi_label=None, journal_doi_label=None):
journal = None
journals = Journal.objects.all()
issue = None
if doi_label:
publications = get_list_or_404(Publication, doi_label=doi_label)
journal = publications[0].get_journal()
elif issue_doi_label:
issue = get_object_or_404(Issue, doi_label=issue_doi_label)
if issue.in_volume:
journal = issue.in_volume.in_journal
else:
journal = issue.in_journal
publications = issue.publications.all()
elif journal_doi_label:
journal = get_object_or_404(Journal, doi_label=journal_doi_label)
publications = Publication.objects.for_journal(journal.name)
else:
# Limit the amount of Publications to still an idiot size
publications = Publication.objects.all()[:50]
# Speeds up operations by reducing the number of queries
if not isinstance(publications, list):
publications = publications.prefetch_related(
'authors', 'funders_generic', 'deposit_set', 'doajdeposit_set')
associate_grant_form = GrantSelectForm()
associate_generic_funder_form = FunderSelectForm()
context = {
'journal': journal,
'journals': journals,
'issue_doi_label': issue_doi_label,
'journal_doi_label': journal_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_draft_publication', return_403=True)
@transaction.atomic
def add_author(request, doi_label, 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, doi_label=doi_label)
if not publication.is_draft and not request.user.has_perm('can_publish_accepted_submission'):
raise Http404('You do not have permission to edit this non-draft Publication')
if contributor_id:
contributor = get_object_or_404(Contributor, id=contributor_id)
PublicationAuthorsTable.objects.create(contributor=contributor, publication=publication)
publication.save()
messages.success(request, 'Added {} as an author.'.format(contributor))
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': publication.doi_label}))
contributors_found = None
form = UnregisteredAuthorForm(request.POST or request.GET or None)
if request.POST and form.is_valid():
unregistered_author = form.save()
PublicationAuthorsTable.objects.create(
publication=publication,
unregistered_author=unregistered_author)
messages.success(request, 'Added {} as an unregistered author.'.format(
unregistered_author
))
return redirect(reverse('journals:add_author',
kwargs={'doi_label': publication.doi_label}))
elif form.is_valid():
contributors_found = Contributor.objects.filter(
user__last_name__icontains=form.cleaned_data['last_name'])
context = {
'publication': publication,
'contributors_found': contributors_found,
'form': form,
}
return render(request, 'journals/add_author.html', context)
class AuthorAffiliationView(PublicationMixin, PermissionsMixin, DetailView):
"""
Handle the author affiliations for a Publication.
"""
permission_required = 'scipost.can_draft_publication'
template_name = 'journals/author_affiliations.html'
def get_context_data(self, **kwargs):
context = super().get_context_data(**kwargs)
context['add_affiliation_form'] = AuthorsTableOrganizationSelectForm()
return context
@permission_required('scipost.can_draft_publication', return_403=True)
@transaction.atomic
def add_affiliation(request, doi_label, pk):
"""
Adds an affiliation to a PublicationAuthorsTable.
"""
table = get_object_or_404(PublicationAuthorsTable, pk=pk)
form = AuthorsTableOrganizationSelectForm(request.POST or None)
if form.is_valid():
table.affiliations.add(form.cleaned_data['organization'])
table.save()
return redirect(reverse('journals:author_affiliations',
kwargs={'doi_label': doi_label}))
context = {'table': table, 'add_affiliation_form': form}
return render(request, 'journals/author_affiliation_add.html', context)
@permission_required('scipost.can_draft_publication', return_403=True)
@transaction.atomic
def remove_affiliation(request, doi_label, pk, organization_id):
"""
Remove an affiliation in a PublicationAuthorsTable.
"""
table = get_object_or_404(PublicationAuthorsTable, pk=pk)
org = get_object_or_404(Organization, pk=organization_id)
table.affiliations.remove(org)
table.save()
return redirect(reverse('journals:author_affiliations',
kwargs={'doi_label': doi_label}))
@permission_required('scipost.can_draft_publication', 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)
if not publication.is_draft and not request.user.has_perm('scipost.can_publish_accepted_submission'):
raise Http404('You do not have permission to edit this non-draft Publication')
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)
class CitationUpdateView(PublicationMixin, ProdSupervisorPublicationPermissionMixin, UpdateView):
"""
Populates the citation_list dictionary entry in the metadata field in a Publication instance.
"""
form_class = CitationListBibitemsForm
template_name = 'journals/create_citation_list_metadata.html'
def get_success_url(self):
return reverse_lazy('journals:create_citation_list_metadata',
kwargs={'doi_label': self.object.doi_label})
class AbstractJATSUpdateView(PublicationMixin, ProdSupervisorPublicationPermissionMixin, UpdateView):
"""
Add or update the JATS version of the abstract.
This should be produced separately using pandoc.
"""
form_class = AbstractJATSForm
template_name = 'journals/create_abstract_jats.html'
def get_success_url(self):
return reverse_lazy('journals:manage_metadata',
kwargs={'doi_label': self.object.doi_label})
class FundingInfoView(PublicationMixin, ProdSupervisorPublicationPermissionMixin, UpdateView):
"""
Add/update funding statement to the xml_metadata
"""
form_class = FundingInfoForm
template_name = 'journals/create_funding_info_metadata.html'
def get_success_url(self):
return reverse_lazy('journals:manage_metadata',
kwargs={'doi_label': self.object.doi_label})
@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.doideposit_needs_updating = True
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}))
class CreateMetadataXMLView(PublicationMixin,
ProdSupervisorPublicationPermissionMixin,
UpdateView):
"""
To be called by an EdAdmin (or Production Supervisor) after the authors,
author ordering, affiliations, 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.
"""
form_class = CreateMetadataXMLForm
template_name = 'journals/create_metadata_xml.html'
def get_success_url(self):
return reverse_lazy('journals:manage_metadata',
kwargs={'doi_label': self.object.doi_label})
@permission_required('scipost.can_draft_publication', 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 not publication.is_draft and not request.user.has_perm('scipost.can_publish_accepted_submission'):
raise Http404('You do not have permission to access this non-draft Publication')
if not request.user.has_perm('scipost.can_publish_accepted_submission') and option != 'test':
raise PermissionDenied('You do not have permission to do real Crossref deposits')
if publication.metadata_xml is None:
messages.warning(
request,
'This publication has no metadata. Produce it first before saving it.')
return redirect(reverse('journals:create_metadata_xml',
kwargs={'doi_label': publication.doi_label}))
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]
# Find Crossref xml files
path = ''
if publication.in_issue:
path += '{issue_path}/{paper_nr}/{doi_label}_Crossref'.format(
issue_path=publication.in_issue.path,
paper_nr=publication.get_paper_nr(),
doi_label=publication.doi_label.replace('.', '_'))
if publication.in_journal:
path += 'SCIPOST_JOURNALS/{journal_name}/{paper_nr}/{doi_label}_Crossref'.format(
journal_name=publication.in_journal.name,
paper_nr=publication.get_paper_nr(),
doi_label=publication.doi_label.replace('.', '_'))
os.makedirs(settings.MEDIA_ROOT + path, exist_ok=True)
path_wo_timestamp = path + '.xml'
path += '_{timestamp}.xml'.format(timestamp=timestamp)
valid = True
response_headers = None
response_text = None
if os.path.isfile(settings.MEDIA_ROOT + path):
# Deposit already done before.
valid = False
else:
# New deposit, go for it.
if option == 'deposit' and not settings.DEBUG:
# CAUTION: Real deposit only on production!
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
f = open(settings.MEDIA_ROOT + path, 'w', encoding='utf-8')
f.write(publication.metadata_xml)
f.close()
# Update Crossref timestamp-free file to latest deposit
shutil.copyfile(settings.MEDIA_ROOT + path,
settings.MEDIA_ROOT + path_wo_timestamp)
deposit.metadata_xml_file = path
deposit.save()
publication.latest_crossref_deposit = timezone.now()
publication.save()
context = {
'option': option,
'publication': publication,
'response_headers': response_headers,
'response_text': response_text,
'valid': valid,
}
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)
form = CreateMetadataDOAJForm(request.POST or None, instance=publication, request=request)
if form.is_valid():
form.save()
messages.success(request, '<h3>%s</h3>Successfully produced metadata DOAJ.'
% publication.doi_label)
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': doi_label}))
context = {
'publication': publication,
'form': form
}
return render(request, 'journals/metadata_doaj_create.html', context)
@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',
kwargs={'doi_label': doi_label}))
#timestamp = publication.metadata_xml.partition('<timestamp>')[2].partition('</timestamp>')[0]
timestamp = timezone.now().strftime('%Y%m%d%H%M%S')
# Find DOAJ json files
path = ''
if publication.in_issue:
path += '{issue_path}/{paper_nr}/{doi_label}_DOAJ'.format(
issue_path=publication.in_issue.path,
paper_nr=publication.get_paper_nr(),
doi_label=publication.doi_label.replace('.', '_'))
elif publication.in_journal:
path += 'SCIPOST_JOURNALS/{journal_name}/{paper_nr}/{doi_label}_DOAJ'.format(
journal_name=publication.in_journal.name,
paper_nr=publication.get_paper_nr(),
doi_label=publication.doi_label.replace('.', '_'))
os.makedirs(settings.MEDIA_ROOT + path, exist_ok=True)
path_wo_timestamp = path + '.json'
path += '_{timestamp}.json'.format(timestamp=timestamp)
if os.path.isfile(settings.MEDIA_ROOT + 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
f = open(settings.MEDIA_ROOT + path, 'w')
f.write(json.dumps(publication.metadata_DOAJ))
f.close()
# Copy file
shutil.copyfile(settings.MEDIA_ROOT + path,
settings.MEDIA_ROOT + path_wo_timestamp)
# Save the database entry
deposit.metadata_DOAJ_file = path
deposit.save()
messages.success(request, '<h3>%s</h3>Successful deposit of metadata DOAJ.'
% publication.doi_label)
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': publication.doi_label}))
@login_required
def allocate_orgpubfractions(request, doi_label):
"""
Set the relative support obtained from Organizations
for the research contained in a Publication.
This view is accessible to EdAdmin as well as to the corresponding author
of the Publication.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
if not request.user.is_authenticated:
raise Http404
elif not (request.user == publication.accepted_submission.submitted_by.user or
request.user.has_perm('scipost.can_publish_accepted_submission')):
raise Http404
if not publication.pubfractions.all().exists():
# Create new OrgPubFraction objects from existing data, spreading weight evenly
for org in publication.get_organizations():
pubfrac = OrgPubFraction(publication=publication,
organization=org, fraction=0)
pubfrac.save()
formset = OrgPubFractionsFormSet(request.POST or None,
queryset=publication.pubfractions.all())
if formset.is_valid():
formset.save()
if request.user == publication.accepted_submission.submitted_by.user:
publication.pubfractions_confirmed_by_authors = True
publication.save()
messages.success(request, 'Funding fractions successfully allocated.')
return redirect(publication.get_absolute_url())
context = {
'publication': publication,
'formset': formset,
}
return render(request, 'journals/allocate_orgpubfractions.html', context)
@login_required
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
def request_pubfrac_check(request, doi_label):
"""
This view is used by EdAdmin to request confirmation of the OrgPubFractions
for a given Publication.
This occurs post-publication, after all the affiliations and funders have
been confirmed.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
mail_request = MailEditingSubView(
request, mail_code='authors/request_pubfrac_check', instance=publication)
if mail_request.is_valid():
messages.success(request, 'The corresponding author has been emailed.')
mail_request.send()
return redirect(reverse('journals:manage_metadata',
kwargs={'doi_label': publication.doi_label}))
else:
return mail_request.return_render()
@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'):
citation = {}
# Cited in Journal, Book, or whatever you want to be cited in.
link_el = link[0]
# The only required field in Crossref: doi.
citation['doi'] = link_el.find(prefix + 'doi').text
if link_el.find(prefix + 'article_title') is not None:
citation['article_title'] = link_el.find(prefix + 'article_title').text
if link_el.find(prefix + 'journal_abbreviation') is not None:
citation['journal_abbreviation'] = link_el.find(prefix + 'journal_abbreviation').text
if link_el.find(prefix + 'volume') is not None:
citation['volume'] = link_el.find(prefix + 'volume').text
if link_el.find(prefix + 'first_page') is not None:
citation['first_page'] = link_el.find(prefix + 'first_page').text
if link_el.find(prefix + 'item_number') is not None:
citation['item_number'] = link_el.find(prefix + 'item_number').text
if link_el.find(prefix + 'year') is not None:
citation['year'] = link_el.find(prefix + 'year').text
if link_el.find(prefix + 'issn') is not None:
citation['issn'] = link_el.find(prefix + 'issn').text
if link_el.find(prefix + 'isbn') is not None:
citation['isbn'] = link_el.find(prefix + 'isbn').text
multiauthors = False
for author in link_el.find(prefix + 'contributors').iter(prefix + 'contributor'):
if author.get('sequence') == 'first':
citation['first_author_given_name'] = author.find(prefix + 'given_name').text
citation['first_author_surname'] = author.find(prefix + 'surname').text
else:
multiauthors = True
citation['multiauthors'] = multiauthors
citations.append(citation)
# Update Publication object
publication.citedby = citations
publication.number_of_citations = len(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()
needing_update = request.GET.get('needing_update')
if needing_update == 'True':
reports = reports.filter(
Q(needs_doi=None) |
Q(needs_doi=True, doideposit_needs_updating=True)).filter(
submission__status=STATUS_PUBLISHED)
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()
_object.refresh_from_db()
# 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__preprint__identifier_wo_vn_nr=_object.submission.preprint.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):
"""
The actual Publication detail page. This is visible for everyone if published or
visible for Production Supervisors and Administrators if in draft.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
if not publication.is_published and not request.user.has_perm('scipost.can_draft_publication'):
raise Http404('Publication is not publicly visible')
context = {
'publication': publication,
'journal': publication.get_journal(),
}
return render(request, 'journals/publication_detail.html', context)
def publication_detail_pdf(request, doi_label):
"""
The actual Publication pdf. This is visible for everyone if published or
visible for Production Supervisors and Administrators if in draft.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
if not publication.is_published and not request.user.has_perm('scipost.can_draft_publication'):
raise Http404('Publication is not publicly visible')
response = HttpResponse(publication.pdf_file.read(), content_type='application/pdf')
response['Content-Disposition'] = ('filename='
+ publication.doi_label.replace('.', '_') + '.pdf')
return response
######################
# Feed DOIs to arXiv #
######################
def arxiv_doi_feed(request, doi_label):
"""
This method provides arXiv with the doi and journal ref of the 100 most recent
publications in the journal specified by doi_label.
"""
journal = get_object_or_404(Journal, doi_label=doi_label)
feedxml = ('<preprint xmlns="http://arxiv.org/doi_feed" '
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" '
'identifier="SciPost.org ' + doi_label + ' arXiv.org DOI feed" '
'version="DOI SnappyFeed v1.0" '
'xsi:schemaLocation="http://arxiv.org/doi_feed '
'http://arxiv.org/schemas/doi_feed.xsd">')
now = timezone.now()
feedxml += '<date year="%s" month="%s" day="%s" />' % (now.strftime('%Y'),
now.strftime('%m'), now.strftime('%d'))
publications = Publication.objects.filter(
in_issue__in_volume__in_journal=journal).order_by('-publication_date')[:100]
for publication in publications:
feedxml += ('\n<article preprint_id="%s" doi="%s" journal_ref="%s" />' % (
publication.accepted_submission.preprint.identifier_wo_vn_nr, publication.doi_string,
publication.citation))
feedxml += '\n</preprint>'
return HttpResponse(feedxml, content_type='text/xml')