SciPost Code Repository

Skip to content
Snippets Groups Projects
forms.py 33.4 KiB
Newer Older
__copyright__ = "Copyright © Stichting SciPost (SciPost Foundation)"
import hashlib
import os
import random
import string
Jorran de Wit's avatar
Jorran de Wit committed
from datetime import datetime

from django import forms
from django.conf import settings
Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed
from django.db.models import Q, Max
from django.forms import BaseModelFormSet, modelformset_factory
from django.template import loader
from django.utils import timezone
from crispy_forms.helper import FormHelper
Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed
from crispy_forms.layout import Layout, Div, Field, ButtonHolder, Submit
from crispy_bootstrap5.bootstrap5 import FloatingField
from dal import autocomplete
from .constants import (
    STATUS_DRAFT,
    STATUS_PUBLICLY_OPEN,
    PUBLICATION_PREPUBLISHED,
    PUBLICATION_PUBLISHED,
)
Jorran de Wit's avatar
Jorran de Wit committed
from .exceptions import PaperNumberingError
from .models import (
    Issue,
    Publication,
    Reference,
    Volume,
    PublicationAuthorsTable,
    OrgPubFraction,
)
from .utils import JournalUtils

from common.utils import get_current_domain, jatsify_tags
from funders.models import Grant, Funder
Jorran de Wit's avatar
Jorran de Wit committed
from journals.models import Journal
Jorran de Wit's avatar
Jorran de Wit committed
from mails.utils import DirectMailUtil
from organizations.models import Organization
from proceedings.models import Proceedings
from production.constants import PROOFS_PUBLISHED
from production.models import ProductionEvent
from scipost.forms import RequestFormMixin
Jorran de Wit's avatar
Jorran de Wit committed
from scipost.services import DOICaller
from submissions.models import Submission
class PublicationSearchForm(forms.Form):
    """Simple search form to filter a Publication queryset."""

    author = forms.CharField(max_length=100, required=False, label="Author(s)")
    title = forms.CharField(max_length=100, required=False)
    doi_label = forms.CharField(max_length=100, required=False)
    journal = forms.ModelChoiceField(queryset=Journal.objects.all(), required=False)
    proceedings = forms.ModelChoiceField(
        queryset=Proceedings.objects.all(), required=False
    )

    def __init__(self, *args, **kwargs):
        self.acad_field_slug = kwargs.pop("acad_field_slug")
        self.specialty_slug = kwargs.pop("specialty_slug")
        super().__init__(*args, **kwargs)
        if self.acad_field_slug and self.acad_field_slug != "all":
            self.fields["journal"].queryset = Journal.objects.filter(
                college__acad_field__slug=self.acad_field_slug
            )
        self.helper = FormHelper()
        self.helper.layout = Layout(
            Div(
                Div(FloatingField("author"), css_class="col-lg-6"),
                Div(FloatingField("title"), css_class="col-lg-6"),
                css_class="row mb-0",
                Div(FloatingField("journal"), css_class="col-lg-6"),
                Div(FloatingField("doi_label"), css_class="col-lg-6"),
                css_class="row mb-0",
                Div(FloatingField("proceedings"), css_class="col-lg-6"),
                css_class="row mb-0",
                css_id="row_proceedings",
                style="display: none",
            ),
        )

    def search_results(self):
        """
        Return all public Publication objects fitting search criteria.
        """
        publications = Publication.objects.published()
        if self.acad_field_slug and self.acad_field_slug != "all":
            publications = publications.filter(acad_field__slug=self.acad_field_slug)
            if self.specialty_slug and self.specialty_slug != "all":
                publications = publications.filter(
                    specialties__slug=self.specialty_slug
                )
        if self.cleaned_data.get("author"):
            publications = publications.filter(
                author_list__icontains=self.cleaned_data.get("author")
            )
        if self.cleaned_data.get("title"):
            publications = publications.filter(
                title__icontains=self.cleaned_data.get("title")
        if self.cleaned_data.get("doi_label"):
            publications = publications.filter(
                doi_label__icontains=self.cleaned_data.get("doi_label")
            )
        if self.cleaned_data.get("journal"):
            publications = publications.for_journal(
                self.cleaned_data.get("journal").name
            )
            if self.cleaned_data.get("proceedings"):
                publications = publications.filter(
                    in_issue__proceedings=self.cleaned_data.get("proceedings")
class CitationListBibitemsForm(forms.ModelForm):
    latex_bibitems = forms.CharField(widget=forms.Textarea())

    class Meta:
        model = Publication
        fields = ()

    def __init__(self, *args, **kwargs):
Jorran de Wit's avatar
Jorran de Wit committed
        super().__init__(*args, **kwargs)
        self.fields["latex_bibitems"].widget.attrs.update(
            {"placeholder": "Paste the .tex bibitems here"}
        )
        entries_list = self.cleaned_data["latex_bibitems"]
        entries_list = re.sub(r"(?m)^\%.*\n?", "", entries_list)
        entries_list = entries_list.split("\doi{")
        for entry in entries_list[1:]:  # drop first bit before first \doi{
            dois.append(
                {
                    "key": "ref" + str(n_entry),
                    "doi": entry.partition("}")[0],
                }
    def save(self, *args, **kwargs):
        self.instance.metadata["citation_list"] = self.extract_dois()
        return super().save(*args, **kwargs)

class AbstractJATSForm(forms.ModelForm):
    abstract_jats = forms.CharField(
        widget=forms.Textarea(
            {
                "placeholder": "Paste the JATS abstract here (use pandoc to generate; see docs)"
            }
        )
    )

    class Meta:
        model = Publication
        fields = ()

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.fields["abstract_jats"].initial = self.instance.abstract_jats

    def save(self, *args, **kwargs):
        self.instance.abstract_jats = jatsify_tags(self.cleaned_data["abstract_jats"])
        return super().save(*args, **kwargs)


Jorran de Wit's avatar
Jorran de Wit committed
class FundingInfoForm(forms.ModelForm):
    funding_statement = forms.CharField(
        widget=forms.Textarea({"placeholder": "Paste the funding info statement here"})
    )
Jorran de Wit's avatar
Jorran de Wit committed
    class Meta:
        model = Publication
        fields = ()

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.fields["funding_statement"].initial = self.instance.metadata.get(
            "funding_statement"
        )
Jorran de Wit's avatar
Jorran de Wit committed
    def save(self, *args, **kwargs):
        self.instance.metadata["funding_statement"] = self.cleaned_data[
            "funding_statement"
        ]
Jorran de Wit's avatar
Jorran de Wit committed
        return super().save(*args, **kwargs)
class BasePublicationAuthorsTableFormSet(BaseModelFormSet):
    def save(self, *args, **kwargs):
        objects = super().save(*args, **kwargs)
        for form in self.ordered_forms:
            form.instance.order = form.cleaned_data["ORDER"]
            form.instance.save()
        return objects

PublicationAuthorOrderingFormSet = modelformset_factory(
    PublicationAuthorsTable,
    fields=(),
    can_order=True,
    extra=0,
    formset=BasePublicationAuthorsTableFormSet,
)
class AuthorsTableOrganizationSelectForm(forms.ModelForm):
Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed
    organization = forms.ModelChoiceField(
        queryset=Organization.objects.all(),
Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed
        widget=autocomplete.ModelSelect2(
            url="/organizations/organization-autocomplete", attrs={"data-html": True}
        ),

    class Meta:
        model = PublicationAuthorsTable
        fields = []


Jorran de Wit's avatar
Jorran de Wit committed
class CreateMetadataXMLForm(forms.ModelForm):
    class Meta:
        model = Publication
        fields = ["metadata_xml"]
    def __init__(self, *args, **kwargs):
        kwargs["initial"] = {"metadata_xml": self.new_xml(kwargs.get("instance"))}
        super().__init__(*args, **kwargs)

    def save(self, *args, **kwargs):
        self.instance.latest_metadata_update = timezone.now()
        return super().save(*args, **kwargs)

    def new_xml(self, publication):
        """
        Create new XML structure, return as a string.
        """
        # 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()
        funders = (
            Funder.objects.filter(grants__in=publication.grants.all())
            | publication.funders_generic.all()
        ).distinct()

        # Render from template
        template = loader.get_template("xml/publication_crossref.html")
        context = {
            "domain": get_current_domain(),
            "publication": publication,
            "doi_batch_id": doi_batch_id,
            "deposit_email": settings.CROSSREF_DEPOSIT_EMAIL,
            "funders": funders,
        }
        return template.render(context)

Jorran de Wit's avatar
Jorran de Wit committed

class CreateMetadataDOAJForm(forms.ModelForm):
    class Meta:
        model = Publication
        fields = ["metadata_DOAJ"]

    def __init__(self, *args, **kwargs):
        self.request = kwargs.pop("request")
        kwargs["initial"] = {"metadata_DOAJ": self.generate(kwargs.get("instance"))}
        super().__init__(*args, **kwargs)

    def generate(self, publication):
        issn = str(publication.get_journal().issn)
            "bibjson": {
                "author": [{"name": publication.author_list}],
                "title": publication.title,
                "abstract": publication.abstract,
                "year": publication.publication_date.strftime("%Y"),
                "month": publication.publication_date.strftime("%m"),
                "identifier": [
                    {"type": "eissn", "id": issn},
                    {"type": "doi", "id": publication.doi_string},
                        "url": self.request.build_absolute_uri(
                            publication.get_absolute_url()
                        ),
                        "type": "fulltext",
                "journal": {
                    "start_page": publication.get_paper_nr(),
Jorran de Wit's avatar
Jorran de Wit committed
        if publication.in_issue:
            if publication.in_issue.in_volume:
                md["bibjson"]["journal"]["volume"] = str(
                    publication.in_issue.in_volume.number
                )
            md["bibjson"]["journal"]["number"] = str(publication.in_issue.number)
Jorran de Wit's avatar
Jorran de Wit committed
class BaseReferenceFormSet(BaseModelFormSet):
    """
    BaseReferenceFormSet is used to help fill the Reference list for Publications

    It is required to add the required keyword argument `publication` to this FormSet.
    """
Jorran de Wit's avatar
Jorran de Wit committed
    initial_references = []

    def __init__(self, *args, **kwargs):
        self.publication = kwargs.pop("publication")
        extra = kwargs.pop("extra")
        self.extra = int(extra if extra else "0")
        kwargs["form_kwargs"] = {"publication": self.publication}
Jorran de Wit's avatar
Jorran de Wit committed
        super().__init__(*args, **kwargs)

    def prefill(self):
        citations = self.publication.metadata.get("citation_list", [])
Jorran de Wit's avatar
Jorran de Wit committed

        for cite in citations:
            caller = DOICaller(cite["doi"])
Jorran de Wit's avatar
Jorran de Wit committed

            if caller.is_valid:
                # Authors
                author_list = []
                for author in caller._crossref_data["author"][:3]:
Jorran de Wit's avatar
Jorran de Wit committed
                    try:
                        author_list.append(
                            "{}. {}".format(author["given"][0], author["family"])
                        )
Jorran de Wit's avatar
Jorran de Wit committed
                    except KeyError:
                        author_list.append(author["name"])
Jorran de Wit's avatar
Jorran de Wit committed

Jorran de Wit's avatar
Jorran de Wit committed
                if len(author_list) > 2:
                    authors = ", ".join(author_list[:-1])
                    authors += " and " + author_list[-1]
Jorran de Wit's avatar
Jorran de Wit committed
                else:
                    authors = " and ".join(author_list)
Jorran de Wit's avatar
Jorran de Wit committed

                # Citation
                citation = "<em>{}</em> {} <b>{}</b>, {} ({})".format(
                    caller.data["title"],
                    caller.data["journal"],
                    caller.data["volume"],
                    caller.data["pages"],
                    datetime.strptime(caller.data["pub_date"], "%Y-%m-%d").year,
                )

                self.initial_references.append(
                    {
                        "reference_number": cite["key"][3:],
                        "authors": authors,
                        "citation": citation,
                        "identifier": cite["doi"],
                        "link": "https://doi.org/{}".format(cite["doi"]),
                    }
                )
Jorran de Wit's avatar
Jorran de Wit committed
            else:
                self.initial_references.append(
                    {
                        "reference_number": cite["key"][3:],
                        "identifier": cite["doi"],
                        "link": "https://doi.org/{}".format(cite["doi"]),
                    }
                )
Jorran de Wit's avatar
Jorran de Wit committed

        # Add prefill information to the form
        if not self.initial_extra:
            self.initial_extra = self.initial_references
        else:
            self.initial_extra.extend(self.initial_references)
        self.extra += len(self.initial_extra)
Jorran de Wit's avatar
Jorran de Wit committed


class ReferenceForm(forms.ModelForm):
    class Meta:
        model = Reference
        fields = [
            "reference_number",
            "authors",
            "citation",
            "identifier",
            "link",
Jorran de Wit's avatar
Jorran de Wit committed
        ]

    def __init__(self, *args, **kwargs):
        self.publication = kwargs.pop("publication")
Jorran de Wit's avatar
Jorran de Wit committed
        super().__init__(*args, **kwargs)

    def save(self, *args, **kwargs):
        self.instance.publication = self.publication
        super().save(*args, **kwargs)


ReferenceFormSet = modelformset_factory(
    Reference, formset=BaseReferenceFormSet, form=ReferenceForm, can_delete=True
)
Jorran de Wit's avatar
Jorran de Wit committed


class DraftPublicationForm(forms.ModelForm):
Jorran de Wit's avatar
Jorran de Wit committed
    """
    This Form is used by the Production Supervisors to create a new Publication object
    and prefill all data. It is only able to create a `draft` version of a Publication object.
    """
Jorran de Wit's avatar
Jorran de Wit committed
    class Meta:
        model = Publication
        fields = [
Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed
            "pubtype",
            "doi_label",
            "pdf_file",
            "in_issue",
            "paper_nr",
Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed
            "paper_nr_suffix",
            "title",
            "author_list",
            "abstract",
            "acad_field",
            "specialties",
            "approaches",
            "cc_license",
            "submission_date",
            "acceptance_date",
            "publication_date",
        ]

    def __init__(
        self, data=None, identifier_w_vn_nr=None, issue_id=None, *args, **kwargs
    ):
Jorran de Wit's avatar
Jorran de Wit committed
        # Use separate instance to be able to prefill the form without any existing Publication
        self.submission = None
        self.issue = None
Jorran de Wit's avatar
Jorran de Wit committed
        self.to_journal = None
        if identifier_w_vn_nr:
            try:
                self.submission = Submission.objects.accepted().get(
                    preprint__identifier_w_vn_nr=identifier_w_vn_nr
                )
            except Submission.DoesNotExist:
                self.submission = None
Jorran de Wit's avatar
Jorran de Wit committed

        # Check if the Submission is related to a Journal with individual Publications only
        if self.submission:
            try:
                self.to_journal = Journal.objects.has_individual_publications().get(
                    name=self.submission.editorial_decision.for_journal.name
                )
Jorran de Wit's avatar
Jorran de Wit committed
            except Journal.DoesNotExist:
                self.to_journal = None

        # If the Journal is not for individual publications, choose a Issue for Publication
        if issue_id and not self.to_journal:
            try:
                self.issue = self.get_possible_issues().get(id=issue_id)
            except Issue.DoesNotExist:
                self.issue = None

Jorran de Wit's avatar
Jorran de Wit committed
        super().__init__(data, *args, **kwargs)
Jorran de Wit's avatar
Jorran de Wit committed

        if kwargs.get("instance") or self.issue or self.to_journal:
Jorran de Wit's avatar
Jorran de Wit committed
            # When updating: fix in_issue, because many fields are directly related to the issue.
            del self.fields["in_issue"]
Jorran de Wit's avatar
Jorran de Wit committed
            self.prefill_fields()
        else:
            self.fields["in_issue"].queryset = self.get_possible_issues()
Jorran de Wit's avatar
Jorran de Wit committed
            self.delete_secondary_fields()

    def get_possible_issues(self):
Jorran de Wit's avatar
Jorran de Wit committed
        issues = Issue.objects.filter(until_date__gte=timezone.now())
        if self.submission:
                issues.for_journal(self.submission.submitted_to.name)
                | issues.for_journal(
                    self.submission.editorial_decision.for_journal.name
                )
Jorran de Wit's avatar
Jorran de Wit committed
        return issues
Jorran de Wit's avatar
Jorran de Wit committed
    def delete_secondary_fields(self):
        """
        Delete fields from the self.fields dictionary. Later on, this submitted sparse form can
        be used to prefill these secondary fields.
        """
Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed
        del self.fields["pubtype"]
        del self.fields["doi_label"]
        del self.fields["pdf_file"]
        del self.fields["paper_nr"]
Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed
        del self.fields["paper_nr_suffix"]
        del self.fields["title"]
        del self.fields["author_list"]
        del self.fields["abstract"]
        del self.fields["acad_field"]
        del self.fields["specialties"]
        del self.fields["approaches"]
        del self.fields["cc_license"]
        del self.fields["submission_date"]
        del self.fields["acceptance_date"]
        del self.fields["publication_date"]
Jorran de Wit's avatar
Jorran de Wit committed
    def clean(self):
        data = super().clean()
        if not self.instance.id:
            if self.submission:
                self.instance.accepted_submission = self.submission
            if self.issue:
                self.instance.in_issue = self.issue
            if self.to_journal:
                self.instance.in_journal = self.to_journal
        return data

Jorran de Wit's avatar
Jorran de Wit committed
    def save(self, *args, **kwargs):
        """
        Save the Publication object always as a draft and prefill the Publication with
        related Submission data only when appending the Publication.
        """
        do_prefill = False
        if not self.instance.id:
            do_prefill = True
Jorran de Wit's avatar
Jorran de Wit committed
        super().save(*args, **kwargs)
Jorran de Wit's avatar
Jorran de Wit committed
        if do_prefill:
            self.first_time_fill()
        return self.instance

    def first_time_fill(self):
        """
        Take over fields from related Submission object. This can only be done after
        the Publication object has been added to the database due to m2m relations.
        """
        self.instance.status = STATUS_DRAFT

        if self.submission:
            # Copy all existing author and non-author relations to Publication
            for submission_author in self.submission.authors.all():
                PublicationAuthorsTable.objects.create(
                    publication=self.instance, profile=submission_author.profile
                )
            self.instance.topics.add(*self.submission.topics.all())
Jorran de Wit's avatar
Jorran de Wit committed

    def prefill_fields(self):
        if self.submission:
            self.fields["title"].initial = self.submission.title
            self.fields["author_list"].initial = self.submission.author_list
            self.fields["abstract"].initial = self.submission.abstract
            self.fields["acad_field"].initial = self.submission.acad_field.id
            self.fields["specialties"].initial = [
                s.id for s in self.submission.specialties.all()
            ]
            self.fields["approaches"].initial = self.submission.approaches
            self.fields[
                "submission_date"
            ].initial = self.submission.original_submission_date
            self.fields["acceptance_date"].initial = self.submission.acceptance_date
            self.fields["publication_date"].initial = timezone.now()
Jorran de Wit's avatar
Jorran de Wit committed
        # Fill data for Publications grouped by Issues (or Issue+Volume).
        if hasattr(self.instance, "in_issue") and self.instance.in_issue:
Jorran de Wit's avatar
Jorran de Wit committed
            self.issue = self.instance.in_issue
        if self.issue:
            self.prefill_with_issue(self.issue)

        # Fill data for Publications ungrouped; directly linked to a Journal.
        if hasattr(self.instance, "in_journal") and self.instance.in_journal:
Jorran de Wit's avatar
Jorran de Wit committed
            self.to_journal = self.instance.in_issue
        if self.to_journal:
            self.prefill_with_journal(self.to_journal)
Jorran de Wit's avatar
Jorran de Wit committed

    def prefill_with_issue(self, issue):
        # Determine next available paper number:
Jorran de Wit's avatar
Jorran de Wit committed
        if issue.in_volume:
            # Issue/Volume
            paper_nr = (
                Publication.objects.filter(in_issue__in_volume=issue.in_volume).count()
                + 1
            )
Jorran de Wit's avatar
Jorran de Wit committed
        elif issue.in_journal:
            # Issue only
            paper_nr = Publication.objects.filter(in_issue=issue).count() + 1
Jorran de Wit's avatar
Jorran de Wit committed
        if paper_nr > 999:
            raise PaperNumberingError(paper_nr)
Jorran de Wit's avatar
Jorran de Wit committed

        self.fields["paper_nr"].initial = str(paper_nr)
Jorran de Wit's avatar
Jorran de Wit committed
        if issue.in_volume:
            doi_label = "{journal}.{vol}.{issue}.{paper}".format(
                journal=issue.in_volume.in_journal.doi_label,
Jorran de Wit's avatar
Jorran de Wit committed
                vol=issue.in_volume.number,
                issue=issue.number,
                paper=str(paper_nr).rjust(3, "0"),
            )
Jorran de Wit's avatar
Jorran de Wit committed
        elif issue.in_journal:
            doi_label = "{journal}.{issue}.{paper}".format(
                journal=issue.in_journal.doi_label,
Jorran de Wit's avatar
Jorran de Wit committed
                issue=issue.number,
                paper=str(paper_nr).rjust(3, "0"),
            )
        self.fields["doi_label"].initial = doi_label
        doi_string = "10.21468/{doi}".format(doi=doi_label)
Jorran de Wit's avatar
Jorran de Wit committed

Jorran de Wit's avatar
Jorran de Wit committed
    def prefill_with_journal(self, journal):
        # Determine next available paper number:
Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed
        #paper_nr = journal.publications.count() + 1
        paper_nr = (journal.publications.aggregate(Max("paper_nr"))["paper_nr__max"] or 0) + 1
        self.fields["paper_nr"].initial = str(paper_nr)
        doi_label = "{journal}.{paper}".format(
            journal=journal.doi_label, paper=paper_nr
        )
        self.fields["doi_label"].initial = doi_label
Jorran de Wit's avatar
Jorran de Wit committed

Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed

class DraftAccompanyingPublicationForm(forms.Form):
    anchor = forms.ModelChoiceField(
        queryset=Publication.objects.all(),
        widget=forms.HiddenInput(),
    )
    title = forms.CharField(max_length=300)
    abstract = forms.CharField(widget=forms.Textarea())
    doi_label_suffix = forms.CharField(max_length=128)

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.helper = FormHelper()
        self.helper.layout = Layout(
            Field("anchor"),
            FloatingField("title"),
            Field("abstract"),
            FloatingField("doi_label_suffix"),
            ButtonHolder(Submit("submit", "Submit", css_class="btn btn-primary")),
        )

    def save(self, *args, **kwargs):
        anchor = self.cleaned_data["anchor"]
        # Create a new Publication based on the anchor data
        companion = Publication(
            accepted_submission=anchor.accepted_submission,
            in_issue=anchor.in_issue,
            in_journal=anchor.in_journal,
            paper_nr=anchor.paper_nr,
            paper_nr_suffix=self.cleaned_data["doi_label_suffix"],
            status=STATUS_DRAFT,
            title=self.cleaned_data["title"],
            author_list=anchor.author_list,
            abstract=self.cleaned_data["abstract"],
            acad_field=anchor.acad_field,
            approaches=anchor.approaches,
            doi_label=f"{anchor.doi_label}-{self.cleaned_data['doi_label_suffix']}",
            submission_date=anchor.submission_date,
            acceptance_date=anchor.acceptance_date,
            publication_date=anchor.publication_date,
Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed
        companion.save()
        # Handle ManyToMany fields
        companion.specialties.add(*anchor.specialties.all())
        companion.topics.add(*anchor.topics.all())
        companion.grants.add(*anchor.grants.all())
        companion.funders_generic.add(*anchor.funders_generic.all())

        # Add authors, using anchor info
        for author in anchor.authors.all():
            pat = PublicationAuthorsTable.objects.create(
                publication=companion,
                profile=author.profile,
                order=author.order,
            )
            pat.affiliations.add(*author.affiliations.all())

        # Add References, using anchor info
        for reference in anchor.references.all():
            Reference.objects.create(
                reference_number=reference.reference_number,
                publication=companion,
                authors=reference.authors,
                citation=reference.citation,
                identifier=reference.identifier,
                link=reference.link,
            )

        # Add PubFractions
        for pubfrac in anchor.pubfractions.all():
            OrgPubFraction.objects.create(
                organization=pubfrac.organization,
                publication=companion,
                fraction=pubfrac.fraction,
            )

        return companion
Jorran de Wit's avatar
Jorran de Wit committed


class DraftPublicationApprovalForm(forms.ModelForm):
Jorran de Wit's avatar
Jorran de Wit committed
    class Meta:
        model = Publication
Jorran de Wit's avatar
Jorran de Wit committed
        fields = ()

    def save(self, commit=True):
        self.instance.status = PUBLICATION_PREPUBLISHED
        if commit:
            self.instance.save()
            mail_sender = DirectMailUtil("publication_ready", instance=self.instance)
Jorran de Wit's avatar
Jorran de Wit committed
            mail_sender.send_mail()
Jorran de Wit's avatar
Jorran de Wit committed
        return self.instance


class PublicationGrantsForm(forms.ModelForm):
    grant = forms.ModelChoiceField(queryset=Grant.objects.none())

    class Meta:
        model = Publication
        fields = []

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.fields["grant"].queryset = Grant.objects.exclude(
            id__in=self.instance.grants.values_list("id", flat=True)
        )
Jorran de Wit's avatar
Jorran de Wit committed

    def save(self, commit=True):
        if commit:
            self.instance.grants.add(self.cleaned_data["grant"])
Jorran de Wit's avatar
Jorran de Wit committed
        return self.instance


class PublicationPublishForm(RequestFormMixin, forms.ModelForm):
    class Meta:
        model = Publication
        fields = []

    def move_pdf(self):
Jorran de Wit's avatar
Jorran de Wit committed
        """
        To keep the Publication pdfs organized we move the pdfs to their own folder
        organized by journal and optional issue folder.
        """
Jean-Sébastien Caux's avatar
Jean-Sébastien Caux committed
        if self.instance.pdf_file:
            initial_path = self.instance.pdf_file.path
            new_dir = ""
            if self.instance.in_issue:
                new_dir += self.instance.in_issue.path
            elif self.instance.in_journal:
                new_dir += "SCIPOST_JOURNALS/{name}".format(
                    name=self.instance.in_journal.doi_label
                )
            new_dir += "/{paper_nr}".format(paper_nr=self.instance.get_paper_nr())
            os.makedirs(settings.MEDIA_ROOT + new_dir, exist_ok=True)
            new_dir += "/{doi}.pdf".format(doi=self.instance.doi_label.replace(".", "_"))
            os.rename(initial_path, settings.MEDIA_ROOT + new_dir)
            self.instance.pdf_file.name = new_dir
Jorran de Wit's avatar
Jorran de Wit committed

        self.instance.status = PUBLICATION_PUBLISHED
        self.instance.save()

    def update_submission(self):
        # Mark the submission as having been published:
        submission = self.instance.accepted_submission
        submission.published_as = self.instance
        submission.status = submission.PUBLISHED
        submission.save()

        # Add SubmissionEvents
        submission.add_general_event(
            "The Submission has been published as %s." % self.instance.doi_label
        )

    def update_stream(self):
        # Update ProductionStream
        submission = self.instance.accepted_submission
        if hasattr(submission, "production_stream"):
            stream = submission.production_stream
            stream.status = PROOFS_PUBLISHED
            stream.save()
            if self.request.user.production_user:
                prodevent = ProductionEvent(
                    stream=stream,
                    event="status",
                    comments=" published the manuscript.",
                    noted_by=self.request.user.production_user,
                )
                prodevent.save()

    def save(self, commit=True):
        if commit:
            self.move_pdf()
            self.update_submission()
            self.update_stream()

            # Email authors
            JournalUtils.load({"publication": self.instance})
            JournalUtils.send_authors_paper_published_email()
        return self.instance
class VolumeForm(forms.ModelForm):
    """
    Add or Update a Volume instance which is directly related to either a Journal.
    """

    class Meta:
        model = Volume
        fields = (
            "in_journal",
            "start_date",
            "until_date",
            "doi_label",
        )

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        if not self.instance.id:
            del self.fields["doi_label"]

    def save(self):
        if self.instance.id:
            # Use regular save method if updating existing instance.
            return super().save()

        # Obtain next number, path and DOI if creating new Issue.
        volume = super().save(commit=False)
        volume.number = volume.in_journal.volumes.count() + 1
        volume.doi_label = "{}.{}".format(volume.in_journal.doi_label, volume.number)
        volume.save()
        return volume


class IssueForm(forms.ModelForm):
    """
    Add or Update an Issue instance which is directly related to either a Journal or a Volume.
    """

    class Meta:
        model = Issue
        fields = (
            "in_journal",
            "in_volume",
            "start_date",
            "until_date",
            "status",
            "doi_label",
        )

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        if not self.instance.id:
            del self.fields["doi_label"]

    def save(self):
        if self.instance.id:
            # Use regular save method if updating existing instance.
            return super().save()

        # Obtain next number, path and DOI if creating new Issue.
        issue = super().save(commit=False)
        journal = issue.get_journal()
        path = settings.JOURNALS_DIR
        if journal.has_volumes:
            volume = journal.volumes.first()
            number = volume.issues.count() + 1
            doi = "{}.{}.{}".format(journal.doi_label, volume.number, number)
            path += "/{}/{}/{}".format(journal.doi_label, volume.number, number)
            if self.cleaned_data["status"] == STATUS_PUBLICLY_OPEN:
                # Temporary park this issue with a number generated from the timestamp
                # This is useful for e.g. Proceedings, which only get their final
                # number when published (not when they are made publicly open for submission).
                # The format is [YYYY][MM][3-digit code]
                # where the next-available 3-digit code is found
                number_check = 1000 * int(timezone.now().strftime("%Y%m"))
                number = (
                    number_check
                    + journal.issues.filter(number__gt=number_check).count()
                    + 1
                )
            else:
                number = journal.issues.count() + 1
            doi = "{}.{}".format(journal.doi_label, number)
            path += "/{}/{}".format(journal.doi_label, number)
        issue.number = number
        issue.slug = str(number)
        issue.doi_label = doi
        issue.path = path
        issue.save()
        return issue


class SetOrgPubFractionForm(forms.ModelForm):
    class Meta:
        model = OrgPubFraction
        fields = ["organization", "publication", "fraction"]

    def __init__(self, *args, **kwargs):
        super(SetOrgPubFractionForm, self).__init__(*args, **kwargs)
        if self.instance.id:
            self.fields["organization"].disabled = True
            self.fields["publication"].widget = forms.HiddenInput()


class BaseOrgPubFractionsFormSet(BaseModelFormSet):
    def clean(self):
        """
        Checks that the fractions add up to one.
        """
        norm = 0
        for form in self.forms:
Jorran de Wit's avatar
Jorran de Wit committed
            form.is_valid()
            norm += 1000 * form.cleaned_data.get("fraction", 0)
        if norm != 1000:
            raise forms.ValidationError(
                f"The fractions do not add up to one! Getting {norm} / 1000"
            )
OrgPubFractionsFormSet = modelformset_factory(
    OrgPubFraction,
    fields=("publication", "organization", "fraction"),
    formset=BaseOrgPubFractionsFormSet,
    form=SetOrgPubFractionForm,
    extra=0,
)
    q = forms.CharField(max_length=32, label="Search (by title, author names)")
    action_url_base_kwargs = forms.JSONField(required=False)
    action_target_element_id = forms.CharField()

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.helper = FormHelper()
        self.helper.layout = Layout(
            FloatingField("q", autocomplete="off"),
            Field("action_url_name", type="hidden"),
            Field("action_url_base_kwargs", type="hidden"),
            Field("action_target_element_id", type="hidden"),
        if self.cleaned_data["q"]:
            publications = Publication.objects.filter(
                Q(title__icontains=self.cleaned_data["q"])
                | Q(author_list__icontains=self.cleaned_data["q"])
                | Q(doi_label__icontains=self.cleaned_data["q"])
            ).distinct()
            return publications
        else:
            return Publication.objects.none()