views.py

__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_PUBLICATIONS
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_PUBLICATIONS:
            # 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)

        # The third option: a `Issue and Volume Journal DOI` would lead to a "volume detail page",
        # but that does not exist. Redirect to the Journal landing page instead.
        return landing_page(request, journal_tag)
    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.
            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 = {
        'subject_areas': SCIPOST_SUBJECT_AREAS,
        '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_journal or issue.in_volume.in_journal

    papers = issue.publications.published().order_by('paper_nr')
    next_issue = Issue.objects.published().filter(start_date__gt=issue.start_date).filter(
        Q(in_volume__in_journal=journal) | Q(in_journal=journal),
        ).distinct().order_by('start_date').first()
    prev_issue = Issue.objects.published().filter(start_date__lt=issue.start_date).filter(
        Q(in_volume__in_journal=journal) | Q(in_journal=journal)
        ).distinct().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}))


@permission_required('scipost.can_manage_ontology', return_403=True)
def publication_add_topic(request, doi_label):
    """
    Add a predefined Topic to an existing Publication object.
    This also adds the Topic to all authors' Profiles.
    """
    publication = get_object_or_404(Publication, doi_label=doi_label)
    select_topic_form = SelectTopicForm(request.POST or None)
    if select_topic_form.is_valid():
        publication.topics.add(select_topic_form.cleaned_data['topic'])
        publication.save()


@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

    # Create OrgPubFraction objects from existing organization links
    for org in publication.get_organizations():
        pubfrac, created = OrgPubFraction.objects.get_or_create(
            publication=publication, organization=org)

    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) |