__copyright__ = "Copyright © Stichting SciPost (SciPost Foundation)"
__license__ = "AGPL v3"
from .appraisal import QualificationForm, ReadinessForm
import datetime
from django import forms
from django.conf import settings
from django.db import transaction
from django.db.models import Q, Count
from django.forms.formsets import ORDERING_FIELD_NAME
from django.utils import timezone
from crispy_forms.helper import FormHelper
from crispy_forms.layout import Layout, Div, Field, ButtonHolder, Submit
from crispy_bootstrap5.bootstrap5 import FloatingField
from dal import autocomplete
from ..constants import (
REPORT_ACTION_CHOICES,
REPORT_REFUSAL_CHOICES,
REPORT_POST_EDREC,
REPORT_NORMAL,
STATUS_DRAFT,
STATUS_UNVETTED,
REPORT_ACTION_ACCEPT,
REPORT_ACTION_REFUSE,
PUT_TO_VOTING,
SUBMISSION_CYCLE_CHOICES,
CYCLE_UNDETERMINED,
CYCLE_DEFAULT,
CYCLE_SHORT,
CYCLE_DIRECT_REC,
EIC_REC_PUBLISH,
EIC_REC_MINOR_REVISION,
EIC_REC_MAJOR_REVISION,
EIC_REC_REJECT,
ALT_REC_CHOICES,
SUBMISSION_TIERS,
STATUS_VETTED,
DECISION_FIXED,
DEPRECATED,
)
from .. import exceptions, helpers
from ..helpers import to_ascii_only
from ..models import (
PreprintServer,
SubmissionAuthorProfile,
Submission,
RefereeInvitation,
Report,
EICRecommendation,
EditorialAssignment,
SubmissionTiering,
EditorialDecision,
PlagiarismAssessment,
iThenticateReport,
EditorialCommunication,
)
from ..regexes import CHEMRXIV_DOI_PATTERN
from colleges.models import Fellowship
from common.utils import Q_with_alternative_spellings
from journals.models import Journal, Publication
from journals.constants import (
PUBLISHABLE_OBJECT_TYPE_ARTICLE,
PUBLISHABLE_OBJECT_TYPE_CODEBASE,
PUBLISHABLE_OBJECT_TYPE_DATASET,
)
from mails.utils import DirectMailUtil
from ontology.models import AcademicField, Specialty, Topic
from preprints.helpers import get_new_scipost_identifier
from preprints.models import Preprint
from proceedings.models import Proceedings
from profiles.models import Profile
from scipost.services import DOICaller, ArxivCaller, FigshareCaller, OSFPreprintsCaller
from scipost.models import Contributor, Remark
import strings
import iThenticate
ARXIV_IDENTIFIER_PATTERN_NEW = r"^[0-9]{4,}\.[0-9]{4,5}v[0-9]{1,2}$"
FIGSHARE_IDENTIFIER_PATTERN = r"^[0-9]+\.v[0-9]{1,2}$"
OSFPREPRINTS_IDENTIFIER_PATTERN = r"^[a-z0-9]+$"
class PortalSubmissionSearchForm(forms.Form):
author = forms.CharField(max_length=100, required=False, label="Author(s)")
title = forms.CharField(max_length=100, required=False)
submitted_to = forms.ModelChoiceField(
queryset=Journal.objects.active(), required=False
)
identifier = forms.CharField(max_length=128, required=False)
proceedings = forms.ModelChoiceField(
queryset=Proceedings.objects.order_by("-submissions_close"), required=False
)
def __init__(self, *args, **kwargs):
self.acad_field_slug = kwargs.pop("acad_field_slug")
self.specialty_slug = kwargs.pop("specialty_slug")
self.reports_needed = kwargs.pop("reports_needed")
super().__init__(*args, **kwargs)
if self.acad_field_slug:
self.fields["submitted_to"].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(
Div(FloatingField("submitted_to"), css_class="col-lg-6"),
Div(FloatingField("identifier"), css_class="col-lg-6"),
css_class="row mb-0",
),
Div(
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 Submission objects fitting search criteria.
"""
submissions = Submission.objects.public_latest().unpublished()
if self.acad_field_slug and self.acad_field_slug != "all":
submissions = submissions.filter(acad_field__slug=self.acad_field_slug)
if self.specialty_slug and self.specialty_slug != "all":
submissions = submissions.filter(specialties__slug=self.specialty_slug)
if self.cleaned_data.get("submitted_to"):
submissions = submissions.filter(
submitted_to=self.cleaned_data.get("submitted_to")
)
if self.cleaned_data.get("proceedings"):
submissions = submissions.filter(
proceedings=self.cleaned_data.get("proceedings")
)
if self.cleaned_data.get("author"):
submissions = submissions.filter(
author_list__icontains=self.cleaned_data.get("author")
)
if self.cleaned_data.get("title"):
submissions = submissions.filter(
title__icontains=self.cleaned_data.get("title")
)
if self.cleaned_data.get("identifier"):
submissions = submissions.filter(
preprint__identifier_w_vn_nr__icontains=self.cleaned_data.get(
"identifier"
)
)
if self.reports_needed:
submissions = (
submissions.in_refereeing()
.open_for_reporting()
.reports_needed()
.order_by("submission_date")
)
return submissions
class SubmissionPoolSearchForm(forms.Form):
"""Filter a Submission queryset using basic search fields."""
submitted_to = forms.ModelChoiceField(
queryset=Journal.objects.active(), required=False
)
specialties = forms.ModelMultipleChoiceField(
queryset=Specialty.objects.all(),
widget=autocomplete.ModelSelect2Multiple(
url="/ontology/specialty-autocomplete", attrs={"data-html": True}
),
label="Specialties",
required=False,
)
proceedings = forms.ModelChoiceField(
queryset=Proceedings.objects.order_by("-submissions_close"), required=False
)
author = forms.CharField(max_length=100, required=False, label="Author(s)")
title = forms.CharField(max_length=512, required=False)
identifier = forms.CharField(max_length=128, required=False)
status = forms.ChoiceField(choices=())
editor_in_charge = forms.ModelChoiceField(
queryset=Fellowship.objects.active().select_related("contributor__user"),
required=False,
)
versions = forms.ChoiceField(
widget=forms.RadioSelect,
choices=(
("latest", "Latest submitted only"),
("any", "All versions"),
),
initial="latest",
)
search_set = forms.ChoiceField(
widget=forms.RadioSelect,
choices=(
("current", "Currently under consideration"),
(
"current_noawaitingresub",
"Currently under consideration\n(excluding awaiting resubmission)",
),
("historical", "All accessible history"),
),
initial="current",
)
ordering = forms.ChoiceField(
widget=forms.RadioSelect,
choices=(
(
"Submission date ",
(
("submission_recent", "most recent first"),
("submission_oldest", "oldest first"),
),
),
(
"Activity ",
(
("activity_recent", "most recent first"),
("activity_oldest", "oldest first"),
),
),
),
initial="submission_recent",
)
def __init__(self, *args, **kwargs):
request = kwargs.pop("request")
user = request.user
super().__init__(*args, **kwargs)
self.fields["status"].choices = self.get_status_choices(user)
if not user.contributor.is_ed_admin:
# restrict journals to those of Colleges of user's Fellowships
college_id_list = [
f.college.id for f in user.contributor.fellowships.active()
]
self.fields["submitted_to"].queryset = Journal.objects.filter(
college__in=college_id_list
)
self.helper = FormHelper()
self.helper.layout = Layout(
Div(
Div(FloatingField("submitted_to"), css_class="col-lg-6"),
Div(FloatingField("specialties"), css_class="col-lg-6"),
css_class="row mb-0",
),
Div(
Div(FloatingField("proceedings"), css_class="col-lg-6"),
css_class="row mb-0",
css_id="row_proceedings",
style="display: none",
),
Div(
Div(FloatingField("author"), css_class="col-lg-6"),
Div(FloatingField("title"), css_class="col-lg-6"),
css_class="row mb-0",
),
Div(
Div(FloatingField("identifier"), css_class="col-lg-3"),
Div(FloatingField("status"), css_class="col-lg-5"),
Div(
FloatingField("editor_in_charge"),
css_class="col-lg-4",
css_id="col_eic",
),
css_class="row mb-0",
),
Div(
Div(Field("versions"), css_class="col border"),
Div(Field("search_set"), css_class="col border"),
Div(Field("ordering"), css_class="col border"),
css_class="row mb-0",
),
)
def get_status_choices(self, user):
incoming = (
"Incoming",
(
(Submission.INCOMING, "Incoming: awaiting EdAdmin checks"),
(Submission.ADMISSION_FAILED, "Admission failed"),
(
Submission.ADMISSIBLE,
"Admissible; undergoing plagiarism checks",
),
(
"plagiarism_internal_failed_temporary",
"Failed internal plagiarism checks (temporary)",
),
(
"plagiarism_internal_failed_permanent",
"Failed internal plagiarism checks (permanent)",
),
(
"plagiarism_iThenticate_failed_temporary",
"Failed iThenticate plagiarism checks (temporary)",
),
(
"plagiarism_iThenticate_failed_permanent",
"Failed iThenticate plagiarism checks (permanent)",
),
),
)
preassignment = (
"Preassignment",
(
(Submission.PREASSIGNMENT, "In preassignment"),
(Submission.PREASSIGNMENT_FAILED, "preassignment failed"),
),
)
assignment = (
"Assignment",
(
(Submission.SEEKING_ASSIGNMENT, "Seeking editor assignment"),
("assignment_1", "... waiting for > 1 week"),
("assignment_2", "... waiting for > 2 weeks"),
("assignment_4", "... waiting for > 4 weeks"),
(
Submission.ASSIGNMENT_FAILED,
"Failed to find Editor-in-charge; manuscript rejected",
),
),
)
refereeing = (
"Refereeing",
(
(
Submission.REFEREEING_IN_PREPARATION,
"Refereeing in preparation (cycle choice needed)",
),
("in_refereeing", "In refereeing"),
("unvetted_reports", "... with unvetted Reports"),
("deadline_passed", "deadline passed, no recommendation yet"),
("refereeing_1", "Refereeing round ongoing for > 1 month"),
("refereeing_2", "Refereeing round ongoing for > 2 months"),
("refereeing_3", "Refereeing round ongoing for > 3 months"),
),
)
awaiting_resubmission = (
"Awaiting resubmission",
(
(
Submission.AWAITING_RESUBMISSION,
"Awaiting resubmission (minor or major revision requested)",
),
),
)
voting = (
"Voting",
(
("voting_prepare", "Voting in preparation"),
("voting_ongoing", "Voting ongoing"),
("voting_1", "... in voting for > 1 week"),
("voting_2", "... in voting for > 2 weeks"),
("voting_4", "... in voting for > 4 weeks"),
("nr_voted_for_gte_4", "At least 4 votes cast in favour of EiC rec"),
),
)
decided = (
"Decided",
(
(Submission.ACCEPTED_IN_TARGET, "Accepted in target Journal"),
(
Submission.ACCEPTED_IN_ALTERNATIVE_AWAITING_PUBOFFER_ACCEPTANCE,
"Accepted in other journal; awaiting puboffer acceptance",
),
(Submission.ACCEPTED_IN_ALTERNATIVE, "Accepted in alternative Journal"),
(Submission.REJECTED, "Rejected"),
(Submission.WITHDRAWN, "Withdrawn by the Authors"),
),
)
processed = (("Processed", ((Submission.PUBLISHED, "Published"),)),)
if user.contributor.is_ed_admin:
choices = (
("All", (("all", "All Submissions"),)),
incoming,
preassignment,
assignment,
refereeing,
awaiting_resubmission,
voting,
decided,
)
elif user.contributor.is_active_senior_fellow:
choices = (
("All", (("all", "All Submissions"),)),
preassignment,
assignment,
refereeing,
awaiting_resubmission,
voting,
decided,
)
else:
choices = (
("All", (("all", "All Submissions"),)),
assignment,
refereeing,
awaiting_resubmission,
voting,
decided,
)
return choices
def search_results(self, user):
"""
Return all Submission objects fitting search criteria.
"""
latest = self.cleaned_data.get("versions") == "latest"
search_set = self.cleaned_data.get("search_set")
historical = search_set == "historical"
submissions = Submission.objects.in_pool(
user,
latest=latest,
historical=historical,
)
if not user.contributor.is_ed_admin:
submissions = submissions.stage_incoming_completed()
# if not user.contributor.is_active_senior_fellow:
# submissions = submissions.stage_preassignment_completed()
if search_set == "current_noawaitingresub":
submissions = submissions.exclude(status=Submission.AWAITING_RESUBMISSION)
if self.cleaned_data.get("specialties"):
submissions = submissions.filter(
specialties__in=self.cleaned_data.get("specialties")
)
if self.cleaned_data.get("submitted_to"):
submissions = submissions.filter(
submitted_to=self.cleaned_data.get("submitted_to")
)
if self.cleaned_data.get("proceedings"):
submissions = submissions.filter(
proceedings=self.cleaned_data.get("proceedings")
)
if self.cleaned_data.get("author"):
submissions = submissions.filter(
author_list__icontains=self.cleaned_data.get("author")
)
if self.cleaned_data.get("title"):
submissions = submissions.filter(
title__icontains=self.cleaned_data.get("title")
)
if self.cleaned_data.get("identifier"):
submissions = submissions.filter(
preprint__identifier_w_vn_nr__icontains=self.cleaned_data.get(
"identifier"
)
)
# filter by status
status = self.cleaned_data.get("status")
if status == "all":
pass
elif status == "plagiarism_internal_failed_temporary":
submissions = submissions.filter(
internal_plagiarism_assessment__status=PlagiarismAssessment.STATUS_FAILED_TEMPORARY,
)
elif status == "plagiarism_internal_failed_permanent":
submissions = submissions.filter(
internal_plagiarism_assessment__status=PlagiarismAssessment.STATUS_FAILED_PERMANENT,
)
elif status == "plagiarism_iThenticate_failed_temporary":
submissions = submissions.filter(
iThenticate_plagiarism_assessment__status=PlagiarismAssessment.STATUS_FAILED_TEMPORARY,
)
elif status == "plagiarism_iThenticate_failed_permanent":
submissions = submissions.filter(
iThenticate_plagiarism_assessment__status=PlagiarismAssessment.STATUS_FAILED_PERMANENT,
)
elif status == "assignment_1":
submissions = submissions.filter(
status=Submission.SEEKING_ASSIGNMENT,
submission_date__lt=timezone.now() - datetime.timedelta(days=7),
)
elif status == "assignment_2":
submissions = submissions.filter(
status=Submission.SEEKING_ASSIGNMENT,
submission_date__lt=timezone.now() - datetime.timedelta(days=14),
)
elif status == "assignment_4":
submissions = submissions.filter(
status=Submission.SEEKING_ASSIGNMENT,
submission_date__lt=timezone.now() - datetime.timedelta(days=28),
)
elif status == "in_refereeing":
submissions = submissions.in_refereeing()
elif status == "unvetted_reports":
reports_to_vet = Report.objects.awaiting_vetting()
id_list = [r.submission.id for r in reports_to_vet.all()]
submissions = submissions.filter(id__in=id_list)
elif status == "deadline_passed":
submissions = (
submissions.in_refereeing()
.filter(
reporting_deadline__lt=timezone.now(),
)
.exclude(eicrecommendations__isnull=False)
)
elif status == "refereeing_1":
submissions = (
submissions.filter(
referee_invitations__date_invited__lt=(
timezone.now() - datetime.timedelta(days=30)
)
)
.exclude(
referee_invitations__date_invited__lt=(
timezone.now() - datetime.timedelta(days=60)
)
)
.distinct()
.exclude(eicrecommendations__isnull=False)
)
elif status == "refereeing_2":
submissions = (
submissions.filter(
referee_invitations__date_invited__lt=(
timezone.now() - datetime.timedelta(days=60)
)
)
.exclude(
referee_invitations__date_invited__lt=(
timezone.now() - datetime.timedelta(days=90)
)
)
.distinct()
.exclude(eicrecommendations__isnull=False)
)
elif status == "refereeing_3":
submissions = (
submissions.filter(
referee_invitations__date_invited__lt=(
timezone.now() - datetime.timedelta(days=90)
)
)
.distinct()
.exclude(eicrecommendations__isnull=False)
)
elif status == "voting_prepare":
submissions = submissions.voting_in_preparation()
elif status == "voting_ongoing":
submissions = submissions.undergoing_voting()
elif status == "voting_1":
submissions = submissions.undergoing_voting(longer_than_days=7)
elif status == "voting_2":
submissions = submissions.undergoing_voting(longer_than_days=14)
elif status == "voting_4":
submissions = submissions.undergoing_voting(longer_than_days=28)
elif status == "nr_voted_for_gte_4":
ids_list = [
r.submission.id
for r in EICRecommendation.objects.put_to_voting()
.annotate(
nr_voted_for=Count("voted_for"),
)
.filter(nr_voted_for__gte=4)
]
submissions = submissions.undergoing_voting().filter(id__in=ids_list)
else: # if an actual unmodified status is used, just filter on that
submissions = submissions.filter(status=status)
# filter by EIC
if self.cleaned_data.get("editor_in_charge"):
submissions = submissions.filter(
editor_in_charge=self.cleaned_data.get("editor_in_charge").contributor
)
if self.cleaned_data.get("ordering") == "submission_oldest":
submissions = submissions.order_by("submission_date")
elif self.cleaned_data.get("ordering") == "activity_recent":
submissions = submissions.order_by("-latest_activity")
elif self.cleaned_data.get("ordering") == "activity_oldest":
submissions = submissions.order_by("latest_activity")
return submissions
class ReportSearchForm(forms.Form):
submission_title = forms.CharField(max_length=100, 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)
self.helper = FormHelper()
self.helper.layout = Layout(
Div(
Div(FloatingField("submission_title"), css_class="col-lg-6"),
),
)
def search_results(self):
reports = Report.objects.accepted()
if self.acad_field_slug and self.acad_field_slug != "all":
reports = reports.filter(submission__acad_field__slug=self.acad_field_slug)
if self.specialty_slug and self.specialty_slug != "all":
reports = reports.filter(
submission__specialties__slug=self.specialty_slug
)
if self.cleaned_data.get("submission_title"):
reports = reports.filter(
submission__title__icontains=self.cleaned_data.get("submission_title")
)
return reports
# Marked for deprecation
class SubmissionOldSearchForm(forms.Form):
"""Filter a Submission queryset using basic search fields."""
author = forms.CharField(max_length=100, required=False, label="Author(s)")
title = forms.CharField(max_length=100, required=False)
abstract = forms.CharField(max_length=1000, required=False)
def search_results(self):
"""Return all Submission objects according to search."""
return Submission.objects.public_latest().filter(
title__icontains=self.cleaned_data.get("title", ""),
author_list__icontains=self.cleaned_data.get("author", ""),
abstract__icontains=self.cleaned_data.get("abstract", ""),
)
######################################################################
#
# SubmissionForm prefill facilities. One class per integrated server.
#
######################################################################
# Checks
def check_resubmission_readiness(requested_by, submission):
"""
Check if submission can be resubmitted.
"""
if submission:
if submission.status == Submission.REJECTED:
# Explicitly give rejected status warning.
error_message = (
"This preprint has previously undergone refereeing "
"and has been rejected. Resubmission is only possible "
"if the manuscript has been substantially reworked into "
"a new submission with distinct identifier."
)
raise forms.ValidationError(error_message)
elif submission.open_for_resubmission:
# Check if verified author list contains current user.
if requested_by.contributor not in submission.authors.all():
error_message = (
"There exists a preprint with this identifier "
"but an earlier version number. Resubmission is only possible"
" if you are a registered author of this manuscript."
)
raise forms.ValidationError(error_message)
else:
# Submission has an inappropriate status for resubmission.
error_message = (
"There exists a preprint with this identifier "
"but an earlier version number, which is still undergoing "
"peer refereeing. "
"A resubmission can only be performed after request "
"from the Editor-in-charge. Please wait until the "
"closing of the previous refereeing round and "
"formulation of the Editorial Recommendation "
"before proceeding with a resubmission."
)
raise forms.ValidationError(error_message)
def check_identifier_is_unused(identifier):
# Check if identifier has already been used for submission
if Submission.objects.filter(preprint__identifier_w_vn_nr=identifier).exists():
error_message = "This preprint version has already been submitted to SciPost."
raise forms.ValidationError(error_message, code="duplicate")
def check_arxiv_identifier_w_vn_nr(identifier):
caller = ArxivCaller(identifier)
if caller.is_valid:
arxiv_data = caller.data
metadata = caller.metadata
else:
error_message = "A preprint associated to this identifier does not exist."
raise forms.ValidationError(error_message)
# Check if this paper has already been published (according to arXiv)
published_id = None
if "arxiv_doi" in arxiv_data:
published_id = arxiv_data["arxiv_doi"]
elif "arxiv_journal_ref" in arxiv_data:
published_id = arxiv_data["arxiv_journal_ref"]
if published_id:
error_message = (
"This paper has been published under DOI %(published_id)s. "
"It cannot be submitted again."
)
raise forms.ValidationError(
error_message, code="published", params={"published_id": published_id}
)
return arxiv_data, metadata, identifier
def check_chemrxiv_doi(doi):
"""
Call Crossref to get ChemRxiv preprint data.
"""
caller = DOICaller(doi)
if caller.is_valid:
data = caller.data
metadata = caller.data["crossref_data"]
else:
error_message = "A preprint associated to this DOI does not exist."
raise forms.ValidationError(error_message)
# Check if the type of this resource is indeed a preprint
if "subtype" in metadata:
if metadata["subtype"] != "preprint":
error_message = (
"This does not seem to be a preprint: the type "
"returned by Crossref on behalf of "
"%(preprint_server) is %(subtype). "
"Please contact techsupport."
)
raise forms.ValidationError(
error_message,
code="wrong_subtype",
params={
"preprint_server": preprint_server.name,
"subtype": metadata["subtype"],
},
)
else:
raise forms.ValidationError(
"Crossref failed to return a subtype. Please contact techsupport.",
code="wrong_subtype",
)
# Explicitly add ChemRxiv as the preprint server:
data["preprint_server"] = PreprintServer.objects.get(name="ChemRxiv")
data["preprint_link"] = "https://doi.org/%s" % doi
# Build the identifier by stripping the DOI prefix:
identifier = doi
data["identifier_w_vn_nr"] = identifier
return data, metadata, identifier
def check_figshare_identifier_w_vn_nr(preprint_server, figshare_identifier_w_vn_nr):
"""
Call Figshare to retrieve submission prefill data and perform basic checks.
This method is defined outside of FigsharePrefillform in order to
also be callable by SubmissionForm.
"""
caller = FigshareCaller(preprint_server, figshare_identifier_w_vn_nr)
if caller.is_valid:
figshare_data = caller.data
metadata = caller.metadata
else:
error_message = "A preprint associated to this identifier does not exist."
raise forms.ValidationError(error_message)
# Check if the type of this resource is indeed a preprint
if "defined_type_name" in metadata:
if metadata["defined_type_name"] != "preprint":
error_message = (
"This does not seem to be a preprint: the type "
"returned by Figshare on behalf of "
"%(preprint_server) is %(defined_type_name)s. "
"Please contact techsupport."
)
raise forms.ValidationError(
error_message,
code="wrong_defined_type_name",
params={
"preprint_server": preprint_server.name,
"defined_type_name": metadata["defined_type_name"],
},
)
else:
raise forms.ValidationError(
"Figshare failed to return a defined_type_name. Please contact techsupport.",
code="wrong_defined_type_name",
)
# Check if this article has already been published (according to Figshare)
published_id = None
if "resource_doi" in metadata:
published_id = metadata["resource_doi"]
if published_id:
error_message = (
"This paper has been published under DOI %(published_id)s. "
"It cannot be submitted again."
)
raise forms.ValidationError(
error_message, code="published", params={"published_id": published_id}
)
identifier = preprint_server.name.lower() + "_" + figshare_identifier_w_vn_nr
return figshare_data, metadata, identifier
# DEPRECATED
def check_chemrxiv_figshare_identifier_w_vn_nr(chemrxiv_identifier_w_vn_nr):
"""
Call `check_figshare_identifier_w_vn_nr` but correct identifier
by substituting `chemrxiv` for `figshare`.
"""
data, metadata, identifier = check_figshare_identifier_w_vn_nr(
PreprintServer.objects.get(name="ChemRxiv"), chemrxiv_identifier_w_vn_nr
)
return data, metadata, identifier.replace("figshare", "chemrxiv")
def check_techrxiv_identifier_w_vn_nr(techrxiv_identifier_w_vn_nr):
"""
Call `check_figshare_identifier_w_vn_nr` but correct identifier
by substituting `techrxiv` for `figshare`.
"""
data, metadata, identifier = check_figshare_identifier_w_vn_nr(
PreprintServer.objects.get(name="TechRxiv"), techrxiv_identifier_w_vn_nr
)
return data, metadata, identifier.replace("figshare", "techrxiv")
def check_advance_identifier_w_vn_nr(advance_identifier_w_vn_nr):
"""
Call `check_figshare_identifier_w_vn_nr` but correct identifier
by substituting `advance` for `figshare`.
"""
data, metadata, identifier = check_figshare_identifier_w_vn_nr(
PreprintServer.objects.get(name="Advance"), advance_identifier_w_vn_nr
)
return data, metadata, identifier.replace("figshare", "advance")
def check_osfpreprints_identifier(preprint_server, osfpreprints_identifier):
"""
Call OSFPreprints to retrieve submission prefill data and perform basic checks.
This method is defined outside of FigsharePrefillform in order to
also be callable by SubmissionForm.
"""
caller = OSFPreprintsCaller(preprint_server, osfpreprints_identifier)
if caller.is_valid:
osfpreprints_data = caller.data
metadata = caller.metadata
else:
error_message = "A preprint associated to this identifier does not exist."
raise forms.ValidationError(error_message)
# Check if the type of this resource is indeed a preprint
if "type" in metadata:
if metadata["type"] != "preprints":
error_message = (
"This does not seem to be a preprint: the type "
"returned by OSFPreprints on behalf of "
"%(preprint_server) is %(type)s. "
"Please contact techsupport."
)
raise forms.ValidationError(
error_message,
code="wrong_type",
params={
"preprint_server": preprint_server.name,
"type": metadata["type"],
},
)
else:
raise forms.ValidationError(
"OSFPreprints failed to return a type. Please contact techsupport.",
code="wrong_type",
)
# TODO: Check if this article has already been published (according to OSFPreprints)
identifier = preprint_server.name.lower() + "_" + osfpreprints_identifier
return osfpreprints_data, metadata, identifier
def check_socarxiv_identifier(socarxiv_identifier):
"""
Call `check_osfpreprints_identifier_w_vn_nr` but correct identifier
by substituting `socarxiv` for `osfpreprints`.
"""
data, metadata, identifier = check_osfpreprints_identifier(
PreprintServer.objects.get(name="SocArXiv"), socarxiv_identifier
)
return data, metadata, identifier.replace("osfpreprints", "socarxiv")
class SubmissionPrefillForm(forms.Form):
"""
Base class for all SubmissionPrefillForms (one per integrated preprint server).
Based on kwargs `requested_by`, `journal_doi_label` and `thread_hash`,
this prepares initial data for SubmissionForm.
"""
def __init__(self, *args, **kwargs):
self.requested_by = kwargs.pop("requested_by")
self.journal = Journal.objects.get(doi_label=kwargs.pop("journal_doi_label"))
self.thread_hash = kwargs.pop("thread_hash")
if self.thread_hash:
# Resubmission
self.latest_submission = (
Submission.objects.filter(thread_hash=self.thread_hash)
.order_by("-submission_date", "-preprint")
.first()
)
else:
self.latest_submission = None
super().__init__(*args, **kwargs)
def is_resubmission(self):
return self.latest_submission is not None
def run_checks(self):
"""
Consistency checks on the prefill data.
"""
check_resubmission_readiness(self.requested_by, self.latest_submission)
def get_prefill_data(self):
form_data = {
"acad_field": self.journal.college.acad_field,
"submitted_to": self.journal,
}
if self.thread_hash:
form_data["thread_hash"] = self.thread_hash
form_data["is_resubmission_of"] = self.latest_submission.id
return form_data
class SciPostPrefillForm(SubmissionPrefillForm):
"""
Provide initial data for SubmissionForm (SciPost preprint server route).
"""
def is_valid(self):
"""
Accept an empty form as valid. Override Django BaseForm.is_valid
Django BaseForm method requires is_bound == True and not self.errors.
is_bound requires data is not None.
We thus override is_valid by cutting the is_bound == True out.
"""
return not self.errors
def get_prefill_data(self):
"""
Return initial form data originating from earlier Submission.
"""
form_data = super().get_prefill_data()
form_data["preprint_server"] = PreprintServer.objects.get(name="SciPost")
if self.is_resubmission():
form_data.update(
{
"title": self.latest_submission.title,
"abstract": self.latest_submission.abstract,
"author_list": self.latest_submission.author_list,
"acad_field": self.latest_submission.acad_field,
"specialties": [
s.id for s in self.latest_submission.specialties.all()
],
"approaches": self.latest_submission.approaches,
"referees_flagged": self.latest_submission.referees_flagged,
"referees_suggested": self.latest_submission.referees_suggested,
}
)
return form_data
class ArXivPrefillForm(SubmissionPrefillForm):
"""
Provide initial data for SubmissionForm (arXiv preprint server route).
This adds the `arxiv_identifier_w_vn_nr` field to those
from `SubmissionPrefillForm` base class.
"""
arxiv_identifier_w_vn_nr = forms.RegexField(
label="",
regex=ARXIV_IDENTIFIER_PATTERN_NEW,
strip=True,
error_messages={"invalid": strings.arxiv_query_invalid},
widget=forms.TextInput(),
)
def __init__(self, *args, **kwargs):
self.arxiv_data = {}
self.metadata = {}
super().__init__(*args, **kwargs)
def clean_arxiv_identifier_w_vn_nr(self):
"""
Do basic prechecks based on the arXiv ID only.
"""
identifier = self.cleaned_data.get("arxiv_identifier_w_vn_nr", None)
check_identifier_is_unused(identifier)
self.arxiv_data, self.metadata, identifier = check_arxiv_identifier_w_vn_nr(
identifier
)
return identifier
def get_prefill_data(self):
"""
Return dictionary to prefill `SubmissionForm`.
"""
form_data = super().get_prefill_data()
form_data.update(self.arxiv_data)
form_data["identifier_w_vn_nr"] = self.cleaned_data["arxiv_identifier_w_vn_nr"]
if self.is_resubmission():
form_data.update(
{
"approaches": self.latest_submission.approaches,
"referees_flagged": self.latest_submission.referees_flagged,
"referees_suggested": self.latest_submission.referees_suggested,
"acad_field": self.latest_submission.acad_field,
"specialties": [
s.id for s in self.latest_submission.specialties.all()
],
}
)
return form_data
class ChemRxivPrefillForm(SubmissionPrefillForm):
"""
Provide initial data for SubmissionForm from ChemRxiv
(metadata actually collected from Crossref API, not ChemRxiv).
This form is used by the ChemRxiv route (post-2021-07 style).
"""
chemrxiv_doi = forms.RegexField(
label="",
regex=CHEMRXIV_DOI_PATTERN,
strip=True,
error_messages={"invalid": "Invalid ChemRxiv DOI"},
widget=forms.TextInput(),
)
def __init__(self, *args, **kwargs):
self.crossref_data = {}
self.metadata = {}
super().__init__(*args, **kwargs)
def clean_chemrxiv_doi(self):
# To get the identifier, strip the DOI prefix
identifier = self.cleaned_data.get("chemrxiv_doi", None).partition("/")[2]
check_identifier_is_unused(identifier)
self.crossref_data, self.metadata, identifier = check_chemrxiv_doi(
self.cleaned_data["chemrxiv_doi"]
)
return identifier
def get_prefill_data(self):
"""
Return dictionary to prefill `SubmissionForm`.
"""
form_data = super().get_prefill_data()
form_data.update(self.crossref_data)
if self.is_resubmission():
form_data.update(
{
"approaches": self.latest_submission.approaches,
"referees_flagged": self.latest_submission.referees_flagged,
"referees_suggested": self.latest_submission.referees_suggested,
"acad_field": self.latest_submission.acad_field,
"specialties": [
s.id for s in self.latest_submission.specialties.all()
],
}
)
return form_data
class FigsharePrefillForm(SubmissionPrefillForm):
"""
Provide initial data for SubmissionForm from Figshare.
This form is used by the ChemRxiv (pre-2021-07), TechRxiv and Advance routes.
"""
figshare_preprint_server = forms.ModelChoiceField(
queryset=PreprintServer.objects.filter(served_by__name="Figshare"),
widget=forms.HiddenInput(),
)
figshare_identifier_w_vn_nr = forms.RegexField(
label="",
regex=FIGSHARE_IDENTIFIER_PATTERN,
strip=True,
error_messages={"invalid": "Invalid Figshare identifier"},
widget=forms.TextInput(),
)
def __init__(self, *args, **kwargs):
self.figshare_data = {}
self.metadata = {}
self.identifier = None
super().__init__(*args, **kwargs)
def clean_figshare_identifier_w_vn_nr(self):
"""
Do basic prechecks based on the Figshare identifier.
"""
(
self.figshare_data,
self.metadata,
self.identifier,
) = check_figshare_identifier_w_vn_nr(
self.cleaned_data["figshare_preprint_server"],
self.cleaned_data["figshare_identifier_w_vn_nr"],
)
check_identifier_is_unused(self.identifier)
return self.cleaned_data["figshare_identifier_w_vn_nr"]
def get_prefill_data(self):
"""
Return dictionary to prefill `SubmissionForm`.
"""
form_data = super().get_prefill_data()
form_data.update(self.figshare_data)
if self.is_resubmission():
form_data.update(
{
"approaches": self.latest_submission.approaches,
"referees_flagged": self.latest_submission.referees_flagged,
"referees_suggested": self.latest_submission.referees_suggested,
"acad_field": self.latest_submission.acad_field,
"specialties": [
s.id for s in self.latest_submission.specialties.all()
],
}
)
return form_data
class OSFPreprintsPrefillForm(SubmissionPrefillForm):
"""
Provide initial data for SubmissionForm from OSFPreprints.
This form is used by the SocArXiv (and others) routes.
"""
osfpreprints_preprint_server = forms.ModelChoiceField(
queryset=PreprintServer.objects.filter(served_by__name="OSFPreprints"),
widget=forms.HiddenInput(),
)
osfpreprints_identifier = forms.RegexField(
label="",
regex=OSFPREPRINTS_IDENTIFIER_PATTERN,
strip=True,
error_messages={"invalid": "Invalid OSFPreprints identifier"},
widget=forms.TextInput(),
)
def __init__(self, *args, **kwargs):
self.osfpreprints_data = {}
self.metadata = {}
self.identifier = None
super().__init__(*args, **kwargs)
def clean_osfpreprints_identifier(self):
"""
Do basic prechecks based on the OSFPreprints identifier.
"""
(
self.osfpreprints_data,
self.metadata,
self.identifier,
) = check_osfpreprints_identifier(
self.cleaned_data["osfpreprints_preprint_server"],
self.cleaned_data["osfpreprints_identifier"],
)
check_identifier_is_unused(self.identifier)
return self.cleaned_data["osfpreprints_identifier"]
def get_prefill_data(self):
"""
Return dictionary to prefill `SubmissionForm`.
"""
form_data = super().get_prefill_data()
form_data.update(self.osfpreprints_data)
if self.is_resubmission():
form_data.update(
{
"approaches": self.latest_submission.approaches,
"referees_flagged": self.latest_submission.referees_flagged,
"referees_suggested": self.latest_submission.referees_suggested,
"acad_field": self.latest_submission.acad_field,
"specialties": [
s.id for s in self.latest_submission.specialties.all()
],
}
)
return form_data
###################
#
# Submission form
#
###################
class SubmissionForm(forms.ModelForm):
"""
Form to submit a new (re)Submission.
"""
specialties = forms.ModelMultipleChoiceField(
queryset=Specialty.objects.all(),
widget=autocomplete.ModelSelect2Multiple(
url="/ontology/specialty-autocomplete", attrs={"data-html": True}
),
label="Specialties",
help_text="Type to search, click to include",
)
topics = forms.ModelMultipleChoiceField(
queryset=Topic.objects.all(),
widget=autocomplete.ModelSelect2Multiple(
url="/ontology/topic-autocomplete",
attrs={"data-html": True},
forward=[
"specialties",
],
),
help_text="Type to search, click to include",
required=False,
)
followup_of = forms.ModelMultipleChoiceField(
queryset=Publication.objects.all(),
widget=autocomplete.ModelSelect2Multiple(
url="/journals/own-publication-autocomplete",
attrs={
"data-html": True,
"data-placeholder": "Optional",
},
),
required=False,
help_text="<strong>Does this Submission follow up on some of your earlier publications?<br>(for example: this Submission is a new codebase release for a previous Codebases publication)<br>If so, select them here.</strong><br><strong>This is NOT FOR SPECIFYING A RESUBMISSION: to resubmit a manuscript, choose the resubmission route after clicking the Submit button in the navbar.",
)
preprint_server = forms.ModelChoiceField(
queryset=PreprintServer.objects.all(), widget=forms.HiddenInput()
)
preprint_link = forms.URLField(widget=forms.HiddenInput())
identifier_w_vn_nr = forms.CharField(widget=forms.HiddenInput())
preprint_file = forms.FileField(
help_text=(
"Please submit the processed .pdf (not the source files; "
"these will only be required at the post-acceptance proofs stage)"
),
required=False,
)
class Meta:
model = Submission
fields = [
"is_resubmission_of",
"thread_hash",
"submitted_to",
"proceedings",
"acad_field",
"specialties",
"topics",
"approaches",
"title",
"author_list",
"abstract",
"followup_of",
"code_repository_url",
"data_repository_url",
"author_comments",
"list_of_changes",
"remarks_for_editors",
"referees_suggested",
"referees_flagged",
]
widgets = {
"submitted_to": forms.HiddenInput(),
"acad_field": forms.HiddenInput(),
"is_resubmission_of": forms.HiddenInput(),
"thread_hash": forms.HiddenInput(),
"code_repository_url": forms.TextInput(
attrs={"placeholder": "If applicable; please give the full URL"}
),
"data_repository_url": forms.TextInput(
attrs={"placeholder": "If applicable; please give the full URL"}
),
"remarks_for_editors": forms.Textarea(
attrs={
"placeholder": "Any private remarks (for the editors only)",
"rows": 5,
}
),
"referees_suggested": forms.Textarea(
attrs={
"placeholder": "Optional: names of suggested referees",
"rows": 5,
}
),
"referees_flagged": forms.Textarea(
attrs={
"placeholder": (
"Optional: names of referees whose reports "
"should be treated with caution (+ short reason)"
),
"rows": 5,
}
),
"author_comments": forms.Textarea(
attrs={
"placeholder": "Your resubmission letter (will be viewable online)"
}
),
"list_of_changes": forms.Textarea(
attrs={
"placeholder": (
"Give a point-by-point list of changes "
"(will be viewable online)"
)
}
),
}
def __init__(self, *args, **kwargs):
self.requested_by = kwargs.pop("requested_by")
self.submitted_to_journal = kwargs.pop("submitted_to_journal")
data = args[0] if len(args) > 1 else kwargs.get("data", {})
self.preprint_server = kwargs["initial"].get(
"preprint_server", None
) or PreprintServer.objects.get(id=data.get("preprint_server"))
self.thread_hash = kwargs["initial"].get("thread_hash", None) or data.get(
"thread_hash"
)
self.is_resubmission_of = kwargs["initial"].get(
"is_resubmission_of", None
) or data.get("is_resubmission_of")
self.preprint_data = {}
self.metadata = {} # container for possible external server-provided metadata
super().__init__(*args, **kwargs)
if self.preprint_server.name == "SciPost":
# SciPost identifier will be auto-generated
del self.fields["identifier_w_vn_nr"]
# Preprint will be linked directly from preprint file object
del self.fields["preprint_link"]
else:
# No need for a file upload if user is not using the SciPost preprint server.
del self.fields["preprint_file"]
if not self.is_resubmission():
del self.fields["is_resubmission_of"]
del self.fields["author_comments"]
del self.fields["list_of_changes"]
# Restrict choice of specialties to those of relevant AcademicField
if kwargs["initial"].get("acad_field", None):
self.fields["specialties"].widget.url = (
self.fields["specialties"].widget.url
+ "?acad_field_id="
+ str(kwargs["initial"].get("acad_field").id)
)
# Proceedings submission fields
if "Proc" not in self.submitted_to_journal.doi_label:
del self.fields["proceedings"]
else:
qs = self.fields["proceedings"].queryset.open_for_submission()
self.fields["proceedings"].queryset = qs
self.fields["proceedings"].empty_label = None
if not qs.exists():
del self.fields["proceedings"]
def is_resubmission(self):
return self.is_resubmission_of is not None
def clean(self, *args, **kwargs):
"""
Do all general checks for Submission.
"""
cleaned_data = super().clean(*args, **kwargs)
# SciPost preprints are auto-generated here.
if "identifier_w_vn_nr" not in cleaned_data:
cleaned_data["identifier_w_vn_nr"] = get_new_scipost_identifier(
thread_hash=self.thread_hash
)
if self.is_resubmission():
check_resubmission_readiness(
self.requested_by, cleaned_data["is_resubmission_of"]
)
self.clear_submission_object_types()
if "Proc" not in cleaned_data["submitted_to"].doi_label:
try:
del self.cleaned_data["proceedings"]
except KeyError:
# No proceedings returned to data
pass
return cleaned_data
def clear_submission_object_types(self):
"""
Check that the submitted material fits one of the Journal's options.
"""
submitted_types = []
if self.cleaned_data.get("preprint_file", None) or self.cleaned_data.get(
"preprint_link", None
):
submitted_types.append(PUBLISHABLE_OBJECT_TYPE_ARTICLE)
if self.cleaned_data.get("code_repository_url", None):
submitted_types.append(PUBLISHABLE_OBJECT_TYPE_CODEBASE)
if self.cleaned_data.get("data_repository_url", None):
submitted_types.append(PUBLISHABLE_OBJECT_TYPE_DATASET)
submitted_types.sort() # not needed here, but for future safety
submitted_types_code = " + ".join(submitted_types)
options = self.cleaned_data["submitted_to"].submission_object_types["options"]
if submitted_types_code not in options:
self.add_error(
None,
(
f"You are trying to submit document types: {submitted_types_code}, "
"but this Journal requires one of the following options: "
f"{', '.join(options)}"
),
)
def clean_author_list(self):
"""
Check if author list matches the Contributor submitting.
"""
author_list = self.cleaned_data["author_list"]
# Remove punctuation and convert to ASCII-only string.
clean_author_name = to_ascii_only(self.requested_by.last_name)
clean_author_list = to_ascii_only(author_list)
if not clean_author_name in clean_author_list:
error_message = (
"Your name does not match that of any of the authors. "
"You are not authorized to submit this preprint."
)
self.add_error("author_list", error_message)
return author_list
def clean_code_repository_url(self):
"""
Prevent having well-known servers in list.
"""
code_repository_url = self.cleaned_data["code_repository_url"]
if "arxiv.org" in str(code_repository_url).lower():
error_message = (
"ArXiv.org is not a code repository; "
"did you perhaps use the wrong form field?"
)
self.add_error("code_repository_url", error_message)
return code_repository_url
def clean_data_repository_url(self):
"""
Prevent having well-known servers in list.
"""
data_repository_url = self.cleaned_data["data_repository_url"]
if "arxiv.org" in str(data_repository_url).lower():
error_message = (
"ArXiv.org is not a data repository; "
"did you perhaps use the wrong form field?"
)
self.add_error("data_repository_url", error_message)
return data_repository_url
def clean_identifier_w_vn_nr(self):
identifier = self.cleaned_data.get("identifier_w_vn_nr", None)
check_identifier_is_unused(identifier)
if self.preprint_server.name == "arXiv":
(
self.preprint_data,
self.metadata,
identifier,
) = check_arxiv_identifier_w_vn_nr(identifier)
elif self.preprint_server.name == "ChemRxiv":
self.preprint_data, self.metadata, identifier = check_chemrxiv_doi(
identifier
)
elif self.preprint_server.name == "TechRxiv":
(
self.preprint_data,
self.metadata,
identifier,
) = check_techrxiv_identifier_w_vn_nr(identifier.replace("techrxiv_", ""))
elif self.preprint_server.name == "Advance":
(
self.preprint_data,
self.metadata,
identifier,
) = check_advance_identifier_w_vn_nr(identifier.replace("advance_", ""))
elif self.preprint_server.name == "SocArXiv":
self.preprint_data, self.metadata, identifier = check_socarxiv_identifier(
identifier.replace("socarxiv_", "")
)
else:
error_message = (
"Check method not implemented for preprint server: %s. "
"Please contact techsupport."
) % self.preprint_server
self.add_error("identifier_w_vn_nr", error_message)
return identifier
@transaction.atomic
def save(self):
"""
Create the new Submission and Preprint instances.
"""
submission = super().save(commit=False)
submission.submitted_by = self.requested_by.contributor
submission.reporting_deadline = (
# give 8 days for Admission, Preassignment and Assignment stages
timezone.now()
+ datetime.timedelta(days=8)
+ self.cleaned_data["submitted_to"].refereeing_period
)
# Save identifiers
url = ""
if self.cleaned_data.get("preprint_link", None):
url = self.cleaned_data["preprint_link"]
preprint, __ = Preprint.objects.get_or_create(
identifier_w_vn_nr=self.cleaned_data["identifier_w_vn_nr"],
url=url,
_file=self.cleaned_data.get("preprint_file", None),
)
# Save metadata directly from preprint server call without possible user interception
submission.metadata = self.metadata
submission.preprint = preprint
submission.save()
# Try to match the submitting author's last name to a position from the author list.
try:
submitting_author_order = list(
map(
lambda x: self.requested_by.contributor.profile.last_name
in x.strip(),
submission.author_list.split(","),
)
).index(True)
except ValueError:
# Otherwise, assume the submitting author is the first author.
submitting_author_order = 1
# Add the submitter's AuthorProfile:
author_profile = SubmissionAuthorProfile(
submission=submission,
profile=self.requested_by.contributor.profile,
order=submitting_author_order,
)
author_profile.save()
submission.author_profiles.add(author_profile)
# Explicitly handle specialties (otherwise they are not saved)
submission.specialties.set(self.cleaned_data["specialties"])
if self.is_resubmission():
self.process_resubmission(submission)
# Gather first known author and Fellows.
submission.authors.add(self.requested_by.contributor)
self.set_fellowship(submission)
# Return latest version of the Submission. It could be outdated by now.
submission.refresh_from_db()
return submission
def process_resubmission(self, submission):
"""
Update all fields for new and old Submission and EditorialAssignments.
-- submission: the new version of the Submission series.
"""
if not submission.is_resubmission_of:
raise Submission.DoesNotExist
previous_submission = submission.is_resubmission_of
# Close last submission
Submission.objects.filter(id=previous_submission.id).update(
open_for_reporting=False, status=Submission.RESUBMITTED
)
# Copy Topics
submission.topics.add(*previous_submission.topics.all())
# Open for comments (reports: opened upon cycle choice) and copy EIC info
Submission.objects.filter(id=submission.id).update(
open_for_commenting=True,
open_for_reporting=False,
visible_public=previous_submission.visible_public,
visible_pool=True,
refereeing_cycle=CYCLE_UNDETERMINED,
editor_in_charge=previous_submission.editor_in_charge,
status=Submission.REFEREEING_IN_PREPARATION,
)
# Add author(s) (claim) fields
submission.authors.add(*previous_submission.authors.all())
submission.authors_claims.add(*previous_submission.authors_claims.all())
submission.authors_false_claims.add(
*previous_submission.authors_false_claims.all()
)
# Create new EditorialAssigment for the current Editor-in-Charge
EditorialAssignment.objects.create(
submission=submission,
to=previous_submission.editor_in_charge,
status=EditorialAssignment.STATUS_ACCEPTED,
)
def set_fellowship(self, submission):
"""
Set the default set of (guest) Fellows for this Submission.
"""
qs = Fellowship.objects.active()
if submission.proceedings:
# Add only Proceedings-related Fellowships
fellows = qs.filter(
proceedings=submission.proceedings
).return_active_for_submission(submission)
submission.fellows.set(fellows)
else:
fellows = (
qs.regular_or_senior()
.filter(
college=submission.submitted_to.college,
contributor__profile__specialties__in=submission.specialties.all(),
)
.return_active_for_submission(submission)
)
submission.fellows.set(fellows)
class SubmissionReportsForm(forms.ModelForm):
"""Update refereeing pdf for Submission."""
class Meta:
model = Submission
fields = ["pdf_refereeing_pack"]
class PreassignEditorsForm(forms.ModelForm):
"""Preassign editors during Submission preassignment."""
assign = forms.BooleanField(required=False)
to = forms.ModelChoiceField(
queryset=Contributor.objects.none(), required=True, widget=forms.HiddenInput()
)
class Meta:
model = EditorialAssignment
fields = ("to",)
def __init__(self, *args, **kwargs):
self.submission = kwargs.pop("submission")
super().__init__(*args, **kwargs)
self.fields["to"].queryset = Contributor.objects.filter(
fellowships__in=self.submission.fellows.all()
)
self.fields["assign"].initial = self.instance.id is not None
def save(self, commit=True):
"""Create/get unordered EditorialAssignments or delete existing if needed."""
if self.cleaned_data["assign"]:
# Create/save
self.instance, __ = EditorialAssignment.objects.get_or_create(
submission=self.submission, to=self.cleaned_data["to"]
)
elif self.instance.id is not None:
# Delete if exists
if self.instance.status == Submission.PREASSIGNED:
self.instance.delete()
return self.instance
def get_fellow(self):
"""Get fellow either via initial data or instance."""
if self.instance.id is not None:
return self.instance.to
return self.initial.get("to", None)
class BasePreassignEditorsFormSet(forms.BaseModelFormSet):
"""Pre-assign editors during Submission preassignment."""
def __init__(self, *args, **kwargs):
self.submission = kwargs.pop("submission")
super().__init__(*args, **kwargs)
self.queryset = self.submission.editorial_assignments.order_by(
"invitation_order"
)
# Prefill form fields and create unassigned rows for unassigned fellows.
assigned_fellows = self.submission.fellows.filter(
contributor__editorial_assignments__in=self.queryset
)
unassigned_fellows = self.submission.fellows.exclude(
contributor__editorial_assignments__in=self.queryset
)
possible_assignments = [
{ORDERING_FIELD_NAME: -1} for fellow in assigned_fellows
]
for fellow in unassigned_fellows:
possible_assignments.append(
{
"submission": self.submission,
"to": fellow.contributor,
ORDERING_FIELD_NAME: -1,
}
)
self.initial = possible_assignments
self.extra += len(unassigned_fellows)
def add_fields(self, form, index):
"""Force hidden input for ORDER field."""
super().add_fields(form, index)
if ORDERING_FIELD_NAME in form.fields:
form.fields[ORDERING_FIELD_NAME].widget = forms.HiddenInput()
def get_form_kwargs(self, index):
"""Add submission to form arguments."""
kwargs = super().get_form_kwargs(index)
kwargs["submission"] = self.submission
return kwargs
def save(self, commit=True):
"""Save each form and order EditorialAssignments."""
objects = super().save(commit=False)
objects = []
count = 0
for form in self.ordered_forms:
ed_assignment = form.save()
if ed_assignment.id is None:
continue
count += 1
EditorialAssignment.objects.filter(id=ed_assignment.id).update(
invitation_order=count
)
objects.append(ed_assignment)
return objects
PreassignEditorsFormSet = forms.modelformset_factory(
EditorialAssignment,
can_order=True,
extra=0,
formset=BasePreassignEditorsFormSet,
form=PreassignEditorsForm,
)
class SubmissionReassignmentForm(forms.ModelForm):
"""Process reassignment of EIC for Submission."""
new_editor = forms.ModelChoiceField(
queryset=Contributor.objects.none(), required=True
)
email_old_eic = forms.BooleanField(
required=False,
initial=True,
help_text="Whether the previous EiC should be informed",
)
class Meta:
model = Submission
fields = ()
def __init__(self, *args, **kwargs):
"""Add related submission as argument."""
self.submission = kwargs.pop("submission")
super().__init__(*args, **kwargs)
self.fields["new_editor"].queryset = Contributor.objects.filter(
fellowships__in=self.submission.fellows.all()
).exclude(id=self.submission.editor_in_charge.id)
def save(self):
"""Update old/create new Assignment and send mails."""
old_editor = self.submission.editor_in_charge
old_assignment = (
self.submission.editorial_assignments.ongoing()
.filter(to=old_editor)
.first()
)
if old_assignment:
EditorialAssignment.objects.filter(id=old_assignment.id).update(
status=EditorialAssignment.STATUS_REPLACED
)
# Update Submission and update/create Editorial Assignments
now = timezone.now()
assignment = EditorialAssignment.objects.create(
submission=self.submission,
to=self.cleaned_data["new_editor"],
status=EditorialAssignment.STATUS_ACCEPTED,
date_invited=now,
date_answered=now,
)
self.submission.editor_in_charge = self.cleaned_data["new_editor"]
self.submission.save()
# Email old and new editor
if old_assignment and self.cleaned_data["email_old_eic"]:
mail_sender = DirectMailUtil(
"fellows/email_fellow_replaced_by_other", assignment=old_assignment
)
mail_sender.send_mail()
mail_sender = DirectMailUtil(
"fellows/email_fellow_assigned_submission", assignment=assignment
)
mail_sender.send_mail()
class SubmissionTargetJournalForm(forms.ModelForm):
"""Change the target journal for the Submission."""
class Meta:
model = Submission
fields = [
"submitted_to",
]
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.fields["submitted_to"].queryset = Journal.objects.active()
self.helper = FormHelper()
self.helper.layout = Layout(
FloatingField("submitted_to"),
ButtonHolder(Submit("submit", "Update", css_class="btn btn-danger")),
)
class SubmissionTargetProceedingsForm(forms.ModelForm):
"""Change the target Proceedings for the Submission."""
class Meta:
model = Submission
fields = ["proceedings"]
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.fields["proceedings"].queryset = Proceedings.objects.order_by(
"-submissions_close"
)
self.fields["proceedings"].help_text = None
self.helper = FormHelper()
self.helper.layout = Layout(
FloatingField("proceedings"),
ButtonHolder(Submit("submit", "Update", css_class="btn btn-danger")),
)
class SubmissionPreprintFileForm(forms.ModelForm):
"""Change the submitted pdf for the Submission."""
class Meta:
model = Preprint
fields = ["_file"]
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.helper = FormHelper()
self.helper.layout = Layout(
Field("_file"),
ButtonHolder(Submit("submit", "Update", css_class="btn btn-danger")),
)
class SubmissionPreassignmentForm(forms.ModelForm):
"""Processing decision for preassignment of Submission."""
PASS, FAIL = "pass", "fail"
CHOICES = (
(PASS, "Pass preassignment. Proceed to the Pool."),
(FAIL, "Fail preassignment."),
)
decision = forms.ChoiceField(
widget=forms.RadioSelect, choices=CHOICES, required=False
)
message_for_authors = forms.CharField(
required=False, widget=forms.Textarea({"placeholder": "Message for authors"})
)
remark_for_pool = forms.CharField(
required=False, widget=forms.Textarea({"placeholder": "Remark for the pool"})
)
class Meta:
model = Submission
fields = ()
def __init__(self, *args, **kwargs):
"""Add related submission as argument."""
self.submission = kwargs.pop("submission")
self.current_user = kwargs.pop("current_user")
super().__init__(*args, **kwargs)
def clean(self):
"""Check if Submission has right status."""
data = super().clean()
if self.instance.status != Submission.PREASSIGNMENT:
self.add_error(None, "This Submission is currently not in preassignment.")
if data["decision"] == self.PASS:
if not self.instance.fellows.exists():
self.add_error(
None, "Please add at least one fellow to the pool first."
)
if not self.instance.editorial_assignments.exists():
self.add_error(None, "Please complete the pre-assignments form first.")
return data
@transaction.atomic
def save(self):
"""Update Submission status."""
if self.cleaned_data["decision"] == self.PASS:
Submission.objects.filter(id=self.instance.id).update(
status=Submission.SEEKING_ASSIGNMENT,
visible_pool=True,
visible_public=False,
)
self.instance.add_general_event("Submission passed preassignment.")
elif self.cleaned_data["decision"] == self.FAIL:
EditorialAssignment.objects.filter(
submission=self.instance
).invited().update(status=EditorialAssignment.STATUS_DEPRECATED)
Submission.objects.filter(id=self.instance.id).update(
status=Submission.PREASSIGNMENT_FAILED,
visible_pool=False,
visible_public=False,
)
self.instance.add_general_event("Submission failed preassignment.")
mail_sender = DirectMailUtil(
"preassignment_failed",
instance=self.instance,
message_for_authors=self.cleaned_data["message_for_authors"],
header_template="submissions/admin/preassignment_failed.html",
)
mail_sender.send_mail()
if self.cleaned_data["message_for_authors"]:
Remark.objects.create(
submission=self.instance,
contributor=self.current_user.contributor,
remark=self.cleaned_data["message_for_authors"],
)
if self.cleaned_data["remark_for_pool"]:
Remark.objects.create(
submission=self.instance,
contributor=self.current_user.contributor,
remark=self.cleaned_data["remark_for_pool"],
)
class WithdrawSubmissionForm(forms.Form):
"""
A submitting author has the right to withdraw the manuscript.
"""
confirm = forms.ChoiceField(
widget=forms.RadioSelect,
choices=((True, "Confirm"), (False, "Abort")),
label="",
)
def __init__(self, *args, **kwargs):
"""Add related submission as argument."""
self.submission = kwargs.pop("submission")
super().__init__(*args, **kwargs)
def is_confirmed(self):
return self.cleaned_data.get("confirm") in (True, "True")
def save(self):
if self.is_confirmed():
# Update submission (current + any previous versions)
Submission.objects.filter(id=self.submission.id).update(
visible_public=False,
visible_pool=False,
open_for_commenting=False,
open_for_reporting=False,
status=Submission.WITHDRAWN,
latest_activity=timezone.now(),
)
self.submission.get_other_versions().update(visible_public=False)
# Update all assignments
EditorialAssignment.objects.filter(
submission=self.submission
).need_response().update(status=EditorialAssignment.STATUS_DEPRECATED)
EditorialAssignment.objects.filter(
submission=self.submission
).accepted().update(status=EditorialAssignment.STATUS_COMPLETED)
# Deprecate any outstanding recommendations
if EICRecommendation.objects.filter(submission=self.submission).exists():
EICRecommendation.objects.filter(
submission=self.submission
).active().update(status=DEPRECATED)
# Update editorial decision
if EditorialDecision.objects.filter(submission=self.submission).exists():
decision = EditorialDecision.objects.filter(
submission=self.submission
).latest_version()
decision.status = EditorialDecision.PUBOFFER_REFUSED_BY_AUTHORS
decision.save()
# Delete any production stream
if hasattr(self.submission, "production_stream"):
self.submission.production_stream.delete()
self.submission.refresh_from_db()
return self.submission
######################
# Editorial workflow #
######################
class EditorialAssignmentForm(forms.ModelForm):
"""Create and/or process new EditorialAssignment for Submission."""
DECISION_CHOICES = (("accept", "Accept"), ("decline", "Decline"))
CYCLE_CHOICES = (
(CYCLE_DEFAULT, "Normal refereeing cycle"),
(CYCLE_DIRECT_REC, "Directly formulate Editorial Recommendation for rejection"),
)
decision = forms.ChoiceField(
widget=forms.RadioSelect,
choices=DECISION_CHOICES,
label="Are you willing to take charge of this Submission?",
)
refereeing_cycle = forms.ChoiceField(
widget=forms.RadioSelect, choices=CYCLE_CHOICES, initial=CYCLE_DEFAULT
)
refusal_reason = forms.ChoiceField(choices=EditorialAssignment.REFUSAL_REASONS)
class Meta:
model = EditorialAssignment
fields = () # Don't use the default fields options because of the ordering of fields.
def __init__(self, *args, **kwargs):
"""Add related submission as argument."""
self.submission = kwargs.pop("submission")
self.request = kwargs.pop("request")
super().__init__(*args, **kwargs)
if not self.instance.id:
del self.fields["decision"]
del self.fields["refusal_reason"]
def has_accepted_invite(self):
"""Check if invite is accepted or if voluntered to become EIC."""
return (
"decision" not in self.cleaned_data
or self.cleaned_data["decision"] == "accept"
)
def is_normal_cycle(self):
"""Check if normal refereeing cycle is chosen."""
return self.cleaned_data["refereeing_cycle"] == CYCLE_DEFAULT
def save(self, commit=True):
"""Save Submission to EditorialAssignment."""
self.instance.submission = self.submission
self.instance.date_answered = timezone.now()
self.instance.to = self.request.user.contributor
assignment = super().save() # Save already, in case it's a new recommendation.
if self.has_accepted_invite():
# Update related Submission.
if self.is_normal_cycle():
# Default Refereeing process
deadline = (
timezone.now()
+ self.instance.submission.submitted_to.refereeing_period
)
# Update related Submission.
Submission.objects.filter(id=self.submission.id).update(
refereeing_cycle=CYCLE_DEFAULT,
status=Submission.IN_REFEREEING,
editor_in_charge=self.request.user.contributor,
reporting_deadline=deadline,
open_for_reporting=True,
open_for_commenting=True,
visible_public=True,
latest_activity=timezone.now(),
)
# Refresh the instance
self.instance.submission = Submission.objects.get(id=self.submission.id)
else:
# Direct editorial recommendation
visible_public = False
if self.instance.submission.is_resubmission_of:
visible_public = (
self.instance.submission.is_resubmission_of.visible_public
)
Submission.objects.filter(id=self.submission.id).update(
refereeing_cycle=CYCLE_DIRECT_REC,
status=Submission.REFEREEING_CLOSED,
editor_in_charge=self.request.user.contributor,
reporting_deadline=timezone.now(),
open_for_reporting=False,
open_for_commenting=True,
visible_public=visible_public,
latest_activity=timezone.now(),
)
# Refresh the instance
self.instance.submission = Submission.objects.get(id=self.submission.id)
# Implicitly or explicity accept the assignment and deprecate others.
assignment.status = EditorialAssignment.STATUS_ACCEPTED
# Update all other 'open' invitations
EditorialAssignment.objects.filter(
submission=self.submission
).need_response().exclude(id=assignment.id).update(
status=EditorialAssignment.STATUS_DEPRECATED,
)
else:
assignment.status = EditorialAssignment.STATUS_DECLINED
assignment.refusal_reason = self.cleaned_data["refusal_reason"]
assignment.save() # Save again to register acceptance
return assignment
class RefereeSearchForm(forms.Form):
last_name = forms.CharField(
widget=forms.TextInput(
{"placeholder": "Search for a referee in the SciPost Profiles database"}
)
)
def search(self):
query = Q_with_alternative_spellings(
last_name__icontains=self.cleaned_data["last_name"]
)
return (
Profile.objects.filter(query)
.exclude(contributor__user__is_superuser=True)
.exclude(contributor__user__is_staff=True)
)
class ConsiderRefereeInvitationForm(forms.Form):
accept = forms.ChoiceField(
widget=forms.RadioSelect,
choices=((True, "Accept"), (False, "Decline")),
label="Are you willing to referee this Submission?",
)
refusal_reason = forms.ChoiceField(
choices=EditorialAssignment.REFUSAL_REASONS, required=False
)
class SetRefereeingDeadlineForm(forms.Form):
deadline = forms.DateField(
label="",
widget=forms.SelectDateWidget(
years=[timezone.now().year + i for i in range(2)],
empty_label=("Year", "Month", "Day"),
),
)
def clean_deadline(self):
if not (self.cleaned_data.get("deadline") >= timezone.now().date()):
self.add_error("deadline", "Please choose a future date!")
return self.cleaned_data.get("deadline")
class VotingEligibilityForm(forms.ModelForm):
"""Assign Fellows to vote for EICRecommendation and open its status for voting."""
eligible_fellows = forms.ModelMultipleChoiceField(
queryset=Contributor.objects.none(),
widget=forms.CheckboxSelectMultiple(),
required=True,
label="Eligible for voting",
)
class Meta:
model = EICRecommendation
fields = ()
def __init__(self, *args, **kwargs):
"""Get queryset of Contributors eligible for voting."""
super().__init__(*args, **kwargs)
# If there exists a previous recommendation, include previous voting Fellows:
prev_elig_id = []
for prev_rec in self.instance.submission.eicrecommendations.all():
prev_elig_id += [fellow.id for fellow in prev_rec.eligible_to_vote.all()]
eligible = (
Contributor.objects.filter(fellowships__pool=self.instance.submission)
.filter(
Q(EIC=self.instance.submission)
| Q(profile__specialties__in=self.instance.submission.specialties.all())
| Q(pk__in=prev_elig_id)
)
.order_by("user__last_name")
.distinct()
)
self.fields["eligible_fellows"].queryset = eligible
def save(self, commit=True):
"""Update EICRecommendation status and save its voters."""
self.instance.eligible_to_vote.set(self.cleaned_data["eligible_fellows"])
self.instance.status = PUT_TO_VOTING
if commit:
self.instance.save()
self.instance.submission.touch()
self.instance.voted_for.add(self.instance.submission.editor_in_charge)
return self.instance
def get_eligible_fellows(self):
return self.fields["eligible_fellows"].queryset
############
# Reports:
############
class ReportPDFForm(forms.ModelForm):
class Meta:
model = Report
fields = ["pdf_report"]
class ReportForm(forms.ModelForm):
"""Write Report form."""
report_type = REPORT_NORMAL
class Meta:
model = Report
fields = [
"qualification",
"strengths",
"weaknesses",
"report",
"requested_changes",
"validity",
"significance",
"originality",
"clarity",
"formatting",
"grammar",
"recommendation",
"remarks_for_editors",
"file_attachment",
"anonymous",
]
def __init__(self, *args, **kwargs):
if kwargs.get("instance"):
if kwargs["instance"].is_followup_report:
# Prefill data from latest report in the series
latest_report = kwargs["instance"].latest_report_from_thread()
kwargs.update(
{
"initial": {
"qualification": latest_report.qualification,
"anonymous": latest_report.anonymous,
}
}
)
self.submission = kwargs.pop("submission")
super().__init__(*args, **kwargs)
self.fields["strengths"].widget.attrs.update(
{
"placeholder": (
"Give a point-by-point "
"(numbered 1-, 2-, ...) list of the paper's strengths"
),
"rows": 10,
"cols": 100,
}
)
self.fields["weaknesses"].widget.attrs.update(
{
"placeholder": (
"Give a point-by-point "
"(numbered 1-, 2-, ...) list of the paper's weaknesses"
),
"rows": 10,
"cols": 100,
}
)
self.fields["report"].widget.attrs.update(
{
"placeholder": "Your general remarks. Are this Journal's acceptance criteria met? Would you recommend publication in another Journal instead?",
"rows": 10,
"cols": 100,
}
)
self.fields["requested_changes"].widget.attrs.update(
{
"placeholder": "Give a numbered (1-, 2-, ...) list of specifically requested changes",
"cols": 100,
}
)
self.fields[
"file_attachment"
].label = "File attachment (2MB limit; for a figure or similar - please avoid annotated pdfs)"
# Required fields on submission; optional on save as draft
if "save_submit" in self.data:
required_fields = ["report", "recommendation"]
else:
required_fields = []
required_fields_label = ["report", "recommendation"]
for field in required_fields:
self.fields[field].required = True
# Let user know the field is required!
for field in required_fields_label:
self.fields[field].label += " *"
if self.submission.eicrecommendations.active().exists():
# An active EICRecommendation is already formulated. This Report will be flagged.
self.report_type = REPORT_POST_EDREC
def save(self):
"""
Update meta data if ModelForm is submitted (non-draft).
Possibly overwrite the default status if user asks for saving as draft.
"""
report = super().save(commit=False)
report.report_type = self.report_type
report.submission = self.submission
report.date_submitted = timezone.now()
# Save with right status asked by user
if "save_draft" in self.data:
report.status = STATUS_DRAFT
elif "save_submit" in self.data:
report.status = STATUS_UNVETTED
# Update invitation and report meta data if exist
updated_invitations = self.submission.referee_invitations.filter(
referee=report.author
).update(fulfilled=True)
if updated_invitations > 0:
report.invited = True
# Check if report author if the report is being flagged on the submission
if self.submission.referees_flagged:
if report.author.user.last_name in self.submission.referees_flagged:
report.flagged = True
report.save()
return report
class VetReportForm(forms.Form):
action_option = forms.ChoiceField(
widget=forms.RadioSelect,
choices=REPORT_ACTION_CHOICES,
required=True,
label="Action",
)
refusal_reason = forms.ChoiceField(choices=REPORT_REFUSAL_CHOICES, required=False)
email_response_field = forms.CharField(
widget=forms.Textarea(), label="Justification (optional)", required=False
)
def __init__(self, *args, **kwargs):
self.report = kwargs.pop("report", None)
super().__init__(*args, **kwargs)
self.fields["email_response_field"].widget.attrs.update(
{
"placeholder": (
"Optional: give a textual justification "
"(will be included in the email to the Report's author)"
),
"rows": 5,
}
)
def clean_refusal_reason(self):
"""Require a refusal reason if report is rejected."""
reason = self.cleaned_data["refusal_reason"]
if self.cleaned_data["action_option"] == REPORT_ACTION_REFUSE:
if not reason:
self.add_error(
"refusal_reason", "A reason must be given to refuse a report."
)
return reason
def process_vetting(self, current_contributor):
"""Set the right report status and update submission fields if needed."""
report = self.report
if self.cleaned_data["action_option"] == REPORT_ACTION_ACCEPT:
# Accept the report as is
Report.objects.filter(id=report.id).update(
status=STATUS_VETTED,
vetted_by=current_contributor,
)
report.submission.touch()
elif self.cleaned_data["action_option"] == REPORT_ACTION_REFUSE:
# The report is rejected
Report.objects.filter(id=report.id).update(
status=self.cleaned_data["refusal_reason"],
)
else:
raise exceptions.InvalidReportVettingValue(
self.cleaned_data["action_option"]
)
report.refresh_from_db()
return report
###################
# Communications #
###################
class EditorialCommunicationForm(forms.ModelForm):
class Meta:
model = EditorialCommunication
fields = ("text",)
widgets = {
"text": forms.Textarea(
attrs={"rows": 5, "placeholder": "Write your message in this box."}
),
}
######################
# EIC Recommendation #
######################
class EICRecommendationForm(forms.ModelForm):
"""Formulate an EICRecommendation."""
DAYS_TO_VOTE = 7
assignment = None
earlier_recommendations = []
tier = forms.ChoiceField(
widget=forms.RadioSelect, choices=SUBMISSION_TIERS, required=False
)
class Meta:
model = EICRecommendation
fields = [
"for_journal",
"recommendation",
"tier",
"remarks_for_authors",
"requested_changes",
"remarks_for_editorial_college",
]
widgets = {
"remarks_for_authors": forms.Textarea(
{
"placeholder": (
"Your remarks for the authors. If you recommend to accept or reject, will"
" only be seen after the college vote concludes."
),
"rows": 10,
}
),
"requested_changes": forms.Textarea(
{
"placeholder": (
"If you request revisions, give a numbered (1-, 2-, ...)"
" list of specifically requested changes"
),
}
),
"remarks_for_editorial_college": forms.Textarea(
{
"placeholder": (
"If you recommend to accept or reject the manuscript, the Editorial College"
" will vote. Summarize the reasons for your recommendation. Focus especially"
" on the aspects that do not directly follow from the referee reports."
),
}
),
}
def __init__(self, *args, **kwargs):
"""Accept two additional kwargs.
-- submission: The Submission to formulate an EICRecommendation for.
-- reformulate (bool): Reformulate the currently available EICRecommendations.
"""
self.submission = kwargs.pop("submission")
self.reformulate = kwargs.pop("reformulate", False)
self.load_earlier_recommendations()
if self.reformulate:
latest_recommendation = self.earlier_recommendations.first()
if latest_recommendation:
kwargs["initial"] = {
"for_journal": latest_recommendation.for_journal,
"recommendation": latest_recommendation.recommendation,
}
super().__init__(*args, **kwargs)
for_journal_qs = Journal.objects.active().filter(
# The journals which can be recommended for are those falling under
# the responsibility of the College of the journal submitted to
college=self.submission.submitted_to.college
)
if self.submission.submitted_to.name.partition(" ")[0] == "SciPost":
# Submitted to a SciPost journal, so Selections is accessible
for_journal_qs = for_journal_qs | Journal.objects.filter(
name="SciPost Selections"
)
self.fields["for_journal"].queryset = for_journal_qs
if self.submission.submitted_to.name.partition(" ")[0] == "SciPost":
# Submitted to a SciPost journal, so Core and Selections are accessible
self.fields["for_journal"].help_text = (
"Please be aware of all the points below!"
"<ul><li>SciPost Selections: means article in field flagship journal "
"(SciPost Physics, Astronomy, Biology, Chemistry...) "
"with extended abstract published separately in SciPost Selections. "
"Only choose this for "
"an <em>exceptionally</em> good submission to a flagship journal.</li>"
"<li>A submission to a flaghip which does not meet the latter's "
"tough expectations and criteria can be recommended for publication "
"in the field's Core journal (if it exists).</li>"
"<li>Conversely, an extremely good submission to a field's Core journal can be "
"recommended for publication in the field's flagship, provided "
"it fulfils the latter's expectations and criteria.</li>"
"</ul>"
)
self.fields["recommendation"].help_text = (
"Selecting any of the three Publish choices means that you recommend publication.<br>"
"Which one you choose simply indicates your ballpark evaluation of the "
"submission's quality and has no further consequence on the publication."
)
self.load_assignment()
def clean(self):
cleaned_data = super().clean()
if cleaned_data["recommendation"] == EIC_REC_PUBLISH:
if not cleaned_data["for_journal"]:
raise forms.ValidationError(
"If you recommend Publish, please specify for which Journal."
)
if cleaned_data["tier"] == "":
raise forms.ValidationError(
"If you recommend Publish, please also provide a Tier."
)
if (
cleaned_data["recommendation"] in (EIC_REC_PUBLISH, EIC_REC_REJECT)
and len(cleaned_data["remarks_for_editorial_college"]) < 10
):
raise forms.ValidationError(
"You must substantiate your recommendation to accept or reject the manuscript."
)
def save(self):
# If the cycle hadn't been chosen, set it to the DirectCycle
if not self.submission.refereeing_cycle:
self.submission.refereeing_cycle = CYCLE_DIRECT_REC
self.submission.save()
recommendation = super().save(commit=False)
recommendation.submission = self.submission
recommendation.voting_deadline += datetime.timedelta(
days=self.DAYS_TO_VOTE
) # Test this
recommendation.version = len(self.earlier_recommendations) + 1
# Delete any previous tierings (irrespective of new/updated recommendation):
SubmissionTiering.objects.filter(
submission=self.submission, fellow=self.submission.editor_in_charge
).delete()
if self.reformulate:
event_text = (
"The Editorial Recommendation has been reformulated for Journal {}: {}."
)
else:
event_text = (
"An Editorial Recommendation has been formulated for Journal {}: {}."
)
if recommendation.recommendation in [
EIC_REC_MINOR_REVISION,
EIC_REC_MAJOR_REVISION,
]:
# Minor/Major revision: return to Author; ask to resubmit
recommendation.status = DECISION_FIXED
Submission.objects.filter(id=self.submission.id).update(
open_for_reporting=False,
open_for_commenting=False,
reporting_deadline=timezone.now(),
status=Submission.AWAITING_RESUBMISSION,
)
if self.assignment:
# The EIC has fulfilled this editorial assignment.
self.assignment.status = EditorialAssignment.STATUS_COMPLETED
self.assignment.save()
# Add SubmissionEvents for both Author and EIC
self.submission.add_general_event(
event_text.format(
str(recommendation.for_journal),
recommendation.get_recommendation_display(),
)
)
elif recommendation.recommendation in [
EIC_REC_PUBLISH,
EIC_REC_REJECT,
]:
# if rec is to publish, specify the tiering (deleting old ones first):
if recommendation.recommendation == EIC_REC_PUBLISH:
tiering = SubmissionTiering(
submission=self.submission,
fellow=self.submission.editor_in_charge,
for_journal=recommendation.for_journal,
tier=self.cleaned_data["tier"],
)
tiering.save()
# set correct status for Submission
Submission.objects.filter(id=self.submission.id).update(
open_for_reporting=False,
open_for_commenting=False,
reporting_deadline=timezone.now(),
status=Submission.VOTING_IN_PREPARATION,
)
# Add SubmissionEvent for EIC only
self.submission.add_event_for_eic(
event_text.format(
str(recommendation.for_journal),
recommendation.get_recommendation_display(),
)
)
else:
raise exceptions.InvalidRecommendationError(recommendation.recommendation)
if self.earlier_recommendations:
self.earlier_recommendations.update(active=False, status=DEPRECATED)
# All reports already submitted are now formulated *after* eic rec formulation
Report.objects.filter(
submission__eicrecommendations__in=self.earlier_recommendations
).update(report_type=REPORT_NORMAL)
recommendation.save()
# The EIC should vote in favour of their own recommendation
# This should be done after the recommendation is saved, so that the
# id is determined for use in the ManyToMany relation.
# Tiering has already been created above, and no special objects are required
# in the event of submission rejection.
recommendation.voted_for.add(self.submission.editor_in_charge)
recommendation.save()
return recommendation
def revision_requested(self):
return self.instance.recommendation in [
EIC_REC_MINOR_REVISION,
EIC_REC_MAJOR_REVISION,
]
def has_assignment(self):
return self.assignment is not None
def load_assignment(self):
# Find EditorialAssignment for Submission
try:
self.assignment = self.submission.editorial_assignments.accepted().get(
to=self.submission.editor_in_charge
)
return True
except EditorialAssignment.DoesNotExist:
return False
def load_earlier_recommendations(self):
"""Load and save EICRecommendations related to Submission of the instance."""
self.earlier_recommendations = self.submission.eicrecommendations.all()
###############
# Vote form #
###############
class RecommendationVoteForm(forms.Form):
"""Cast vote on EICRecommendation form."""
vote = forms.ChoiceField(
widget=forms.RadioSelect,
choices=[("agree", "Agree"), ("disagree", "Disagree"), ("abstain", "Abstain")],
)
tier = forms.ChoiceField(
widget=forms.RadioSelect, choices=SUBMISSION_TIERS, required=False
)
alternative_for_journal = forms.ModelChoiceField(
label="Alternative recommendation: for which Journal?",
widget=forms.Select,
queryset=Journal.objects.active(),
required=False,
)
alternative_recommendation = forms.ChoiceField(
label="Which action do you recommend?",
widget=forms.Select,
choices=ALT_REC_CHOICES,
required=False,
)
remark = forms.CharField(
widget=forms.Textarea(
attrs={
"rows": 3,
"cols": 30,
"placeholder": "Any further remark you want to add? (optional)",
}
),
label="",
required=False,
)
def clean(self):
cleaned_data = super().clean()
if cleaned_data["vote"] == "disagree" and (
cleaned_data["alternative_for_journal"] is None
or cleaned_data["alternative_recommendation"] == ""
):
raise forms.ValidationError(
"If you disagree, you must provide an alternative recommendation "
"(by filling both the for journal and recommendation fields)."
)
class EditorialDecisionForm(forms.ModelForm):
"""For EdAdmin to fix the outcome on a Submission, after voting is completed."""
class Meta:
model = EditorialDecision
fields = [
"submission",
"for_journal",
"decision",
"taken_on",
"remarks_for_authors",
"remarks_for_editorial_college",
"status",
]
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
if "submission" in self.initial:
self.fields["submission"].queryset = Submission.objects.filter(
pk=self.initial["submission"],
)
self.fields["submission"].disabled = True
self.fields["remarks_for_authors"].widget.attrs.update(
{"placeholder": "[will be seen by authors and Fellows]"}
)
self.fields["remarks_for_editorial_college"].widget.attrs.update(
{"placeholder": "[will only be seen by Fellows]"}
)
def clean(self):
cleaned_data = super().clean()
if (
cleaned_data["decision"] == EIC_REC_REJECT
and cleaned_data["status"] == EditorialDecision.AWAITING_PUBOFFER_ACCEPTANCE
):
raise forms.ValidationError(
"If the decision is to reject, the status cannot be "
"Awaiting author acceptance of publication offer."
)
def save(self):
decision = super().save(commit=False)
if not self.instance.id: # a new object is created
if self.cleaned_data["submission"].editorialdecision_set.all().exists():
decision.version = (
self.cleaned_data["submission"]
.editorialdecision_set.all()
.latest_version()
.version
+ 1
)
decision.save()
return decision
class RestartRefereeingForm(forms.Form):
"""
For EdAdmin to restart the latest refereeing round.
"""
confirm = forms.ChoiceField(
widget=forms.RadioSelect,
choices=((True, "Confirm"), (False, "Abort")),
label="",
)
def __init__(self, *args, **kwargs):
"""Add related submission as argument."""
self.submission = kwargs.pop("submission")
super().__init__(*args, **kwargs)
def is_confirmed(self):
return self.cleaned_data.get("confirm") in (True, "True")
def save(self):
if self.is_confirmed():
Submission.objects.filter(id=self.submission.id).update(
status=Submission.REFEREEING_IN_PREPARATION,
refereeing_cycle=CYCLE_UNDETERMINED,
acceptance_date=None,
latest_activity=timezone.now(),
)
self.submission.editorial_assignments.filter(
to=self.submission.editor_in_charge,
status=EditorialAssignment.STATUS_COMPLETED,
).update(status=EditorialAssignment.STATUS_ACCEPTED)
self.submission.eicrecommendations.active().update(status=DEPRECATED)
self.submission.editorialdecision_set.update(
status=EditorialDecision.DEPRECATED
)
# Delete any production stream
if hasattr(self.submission, "production_stream"):
self.submission.production_stream.delete()
self.submission.refresh_from_db()
return self.submission
class SubmissionCycleChoiceForm(forms.ModelForm):
"""
For the EIC to take a decision on the Submission's cycle. Used for resubmissions only.
"""
referees_reinvite = forms.ModelMultipleChoiceField(
queryset=RefereeInvitation.objects.none(),
widget=forms.CheckboxSelectMultiple({"checked": "checked"}),
required=False,
label="Reinvite referees",
)
class Meta:
model = Submission
fields = ("refereeing_cycle",)
widgets = {"refereeing_cycle": forms.RadioSelect}
def __init__(self, *args, **kwargs):
"""Update choices and queryset."""
super().__init__(*args, **kwargs)
self.fields["refereeing_cycle"].choices = SUBMISSION_CYCLE_CHOICES
other_submissions = self.instance.other_versions.all()
if other_submissions:
self.fields[
"referees_reinvite"
].queryset = RefereeInvitation.objects.filter(
submission__in=other_submissions
).distinct()
def save(self):
"""
If the cycle is for a normal or short refereeing round, open the sub for reporting.
"""
if self.cleaned_data["refereeing_cycle"] in [CYCLE_DEFAULT, CYCLE_SHORT]:
self.instance.open_for_reporting = True
return super().save()
class iThenticateReportForm(forms.ModelForm):
class Meta:
model = iThenticateReport
fields = []
def __init__(self, submission, *args, **kwargs):
self.submission = submission
super().__init__(*args, **kwargs)
if kwargs.get("files", {}).get("file"):
# Add file field if file data is coming in!
self.fields["file"] = forms.FileField()
def clean(self):
cleaned_data = super().clean()
doc_id = self.instance.doc_id
if not doc_id and not self.fields.get("file"):
try:
# cleaned_data['document'] = helpers.retrieve_pdf_from_arxiv(
# self.submission.preprint.identifier_w_vn_nr)
cleaned_data["document"] = self.submission.preprint.get_document()
except exceptions.PreprintDocumentNotFoundError:
self.add_error(
None, "Preprint document not found. Please upload the pdf manually."
)
self.fields[
"file"
] = forms.FileField() # Add this field now it's needed
elif not doc_id and cleaned_data.get("file"):
cleaned_data["document"] = cleaned_data["file"].read()
elif doc_id:
self.document_id = doc_id
# Login client to append login-check to form
self.client = self.get_client()
if not self.client:
return None
# Document (id) is found
if cleaned_data.get("document"):
self.document = cleaned_data["document"]
self.response = self.call_ithenticate()
if hasattr(self, "response") and self.response:
return cleaned_data
# Don't return anything as someone submitted invalid data for the form at this point!
return None
def save(self, *args, **kwargs):
data = self.response
report, created = iThenticateReport.objects.get_or_create(doc_id=data["id"])
if not created:
try:
iThenticateReport.objects.filter(doc_id=data["id"]).update(
uploaded_time=data["uploaded_time"],
processed_time=data["processed_time"],
percent_match=data["percent_match"],
part_id=data.get("parts", [{}])[0].get("id"),
)
except KeyError:
pass
else:
report.save()
Submission.objects.filter(id=self.submission.id).update(
iThenticate_plagiarism_report=report
)
return report
def call_ithenticate(self):
if hasattr(self, "document_id"):
# Update iThenticate status
return self.update_status()
elif hasattr(self, "document"):
# Upload iThenticate document first time
return self.upload_document()
def get_client(self):
client = iThenticate.API.Client(
settings.ITHENTICATE_USERNAME, settings.ITHENTICATE_PASSWORD
)
if client.login():
return client
self.add_error(None, "Failed to login to iThenticate.")
return None
def update_status(self):
client = self.client
response = client.documents.get(self.document_id)
if response["status"] == 200:
return response.get("data")[0].get("documents")[0]
self.add_error(
None, "Updating failed. iThenticate didn't return valid data [1]"
)
for msg in client.messages:
self.add_error(None, msg)
return None
def upload_document(self):
from ..plagiarism import iThenticate
plagiarism = iThenticate()
data = plagiarism.upload_submission(self.document, self.submission)
# Give feedback to the user
if not data:
self.add_error(
None, "Updating failed. iThenticate didn't return valid data [3]"
)
for msg in plagiarism.get_messages():
self.add_error(None, msg)
return None
return data