From 48b3fb750b6d248cdff86821781a9f1216149a65 Mon Sep 17 00:00:00 2001
From: "J.-S. Caux" <J.S.Caux@uva.nl>
Date: Sun, 19 Jul 2020 17:31:28 +0200
Subject: [PATCH] Full submission workflow reimplemented; ready to start
testing
---
preprints/factories.py | 1 -
preprints/helpers.py | 103 +++++--
...ve_preprint_scipost_preprint_identifier.py | 17 ++
preprints/models.py | 11 +-
.../scipost/personal_page/submissions.html | 2 +-
submissions/forms.py | 260 ++++++++++++------
.../submit_choose_preprint_server.html | 1 -
7 files changed, 274 insertions(+), 121 deletions(-)
create mode 100644 preprints/migrations/0011_remove_preprint_scipost_preprint_identifier.py
diff --git a/preprints/factories.py b/preprints/factories.py
index 70bd63418..da1fac394 100644
--- a/preprints/factories.py
+++ b/preprints/factories.py
@@ -21,7 +21,6 @@ class PreprintFactory(factory.django.DjangoModelFactory):
o.identifier_wo_vn_nr, o.vn_nr))
url = factory.lazy_attribute(lambda o: (
'https://arxiv.org/abs/%s' % o.identifier_wo_vn_nr))
- scipost_preprint_identifier = factory.Sequence(lambda n: Preprint.objects.count() + 1)
class Meta:
model = Preprint
diff --git a/preprints/helpers.py b/preprints/helpers.py
index 8c18ae956..78752a6f7 100644
--- a/preprints/helpers.py
+++ b/preprints/helpers.py
@@ -10,35 +10,84 @@ from submissions.models import Submission
from .models import Preprint
-def generate_new_scipost_identifier(old_preprint=None):
+def get_new_scipost_identifier(thread_hash=None):
"""
- Return an identifier for a new SciPost preprint series without version number.
+ Return an identifier for a new SciPost preprint (consistent with thread history).
- TODO: This method will explode as soon as it will be used similtaneously by two or more people.
+ A SciPost identifier is of the form [YYYY][MM]_[#####]v[vn_nr].
+
+ For an existing thread, different cases must be treated:
+
+ * All preprints in thread are SciPost preprints: the vn_nr is incremented.
+
+ * Previous preprints are all on an external preprint server: a brand new SciPost
+ identifier is generated; the vn_nr is put to [nr of previous subs in thread] + 1.
+
+ * Previous preprints mix SciPost and external identifiers: the SciPost identifier is
+ reused, putting the vn_nr to [nr of previous subs in thread] + 1.
"""
now = timezone.now()
- if isinstance(old_preprint, Submission):
- old_preprint = old_preprint.preprint
-
- if old_preprint:
- # Generate new version number of existing series.
- preprint_series = Preprint.objects.filter(
- scipost_preprint_identifier=old_preprint.scipost_preprint_identifier).values_list(
- 'vn_nr', flat=True)
- identifier = '{}v{}'.format(old_preprint.identifier_wo_vn_nr, max(preprint_series) + 1)
- return identifier, old_preprint.scipost_preprint_identifier
- else:
- # New series of Preprints.
- existing_identifier = Preprint.objects.filter(
- created__year=now.year, created__month=now.month).aggregate(
- identifier=Max('scipost_preprint_identifier'))['identifier']
- if not existing_identifier:
- existing_identifier = '1'
- else:
- existing_identifier = str(existing_identifier + 1)
-
- identifier = 'scipost_{year}{month}_{identifier}v1'.format(
- year=now.year, month=str(now.month).rjust(2, '0'),
- identifier=existing_identifier.rjust(5, '0'))
- return identifier, int(existing_identifier)
+ submissions_in_thread = Submission.objects.filter(thread_hash=thread_hash)
+
+ scipost_submissions_in_thread = submissions_in_thread.filter(
+ preprint__identifier_w_vn_nr__startswith='scipost')
+
+ # At least one previous submission on SciPost's preprint server
+ if len(scipost_submissions_in_thread) > 0:
+ identifier = '{}v{}'.format(
+ scipost_submissions_in_thread.first().identifier_wo_vn_nr,
+ str(len(scipost_submissions_in_thread) + 1))
+ return identifier
+
+ # No previous Submission, or no previous SciPost preprint in thread; new identifier
+ current_identifier_prefix = 'scipost_%s%s' % (now.year, str(now.month).rjust(2,'0'))
+ try:
+ next_identifier_nr = int(Preprint.objects.filter(
+ identifier_w_vn_nr__startswith=current_identifier_prefix
+ ).first().identifier_w_vn_nr.rpartition('v')[0].rpartition('_')[2]) + 1
+ except AttributeError:
+ next_identifier_nr = 1
+
+ identifier = 'scipost_{year}{month}_{identifier}v{vn_nr}'.format(
+ year=now.year, month=str(now.month).rjust(2, '0'),
+ identifier=str(next_identifier_nr).rjust(5, '0'),
+ vn_nr=str(len(submissions_in_thread) + 1)
+ )
+ return identifier
+
+
+# def generate_new_scipost_identifier_BUGGED(old_preprint=None):
+# """
+# Return an identifier for a new SciPost preprint series without version number.
+
+# TODO: This method will explode as soon as it will be used similtaneously by two or more people.
+# """
+# now = timezone.now()
+
+# if isinstance(old_preprint, Submission):
+# old_preprint = old_preprint.preprint
+
+# if old_preprint:
+# # Generate new version number of existing series.
+# # BUGGED! This fails to make scipost_preprint_identifier globally unique
+# # BUGGED! Instead, scipost_preprint_identifier can be repeated each month.
+# preprint_series = Preprint.objects.filter(
+# scipost_preprint_identifier=old_preprint.scipost_preprint_identifier).values_list(
+# 'vn_nr', flat=True)
+# identifier = '{}v{}'.format(old_preprint.identifier_wo_vn_nr, max(preprint_series) + 1)
+# return identifier, old_preprint.scipost_preprint_identifier
+# else:
+# # New series of Preprints.
+# existing_identifier = Preprint.objects.filter(
+# created__year=now.year, created__month=now.month).aggregate(
+# identifier=Max('scipost_preprint_identifier'))['identifier']
+# if not existing_identifier:
+# existing_identifier = '1'
+# else:
+# existing_identifier = str(existing_identifier + 1)
+
+# identifier = 'scipost_{year}{month}_{identifier}v1'.format(
+# year=now.year, month=str(now.month).rjust(2, '0'),
+# identifier=existing_identifier.rjust(5, '0'))
+# return identifier, int(existing_identifier)
diff --git a/preprints/migrations/0011_remove_preprint_scipost_preprint_identifier.py b/preprints/migrations/0011_remove_preprint_scipost_preprint_identifier.py
new file mode 100644
index 000000000..306529a65
--- /dev/null
+++ b/preprints/migrations/0011_remove_preprint_scipost_preprint_identifier.py
@@ -0,0 +1,17 @@
+# Generated by Django 2.2.11 on 2020-07-19 15:30
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('preprints', '0010_merge_20181207_1008'),
+ ]
+
+ operations = [
+ migrations.RemoveField(
+ model_name='preprint',
+ name='scipost_preprint_identifier',
+ ),
+ ]
diff --git a/preprints/models.py b/preprints/models.py
index 511278ef5..ead67904e 100644
--- a/preprints/models.py
+++ b/preprints/models.py
@@ -8,10 +8,10 @@ from django.http import Http404
class Preprint(models.Model):
- """A link with arXiv or standalone/SciPost-hosted preprint.
+ """
+ A preprint object, either at SciPost or with link to external preprint server.
- If the instance is a SciPost preprint, the `_file` and `scipost_preprint_identifier` fields
- should be filled. Otherwise, these fields should be left blank.
+ If the instance is a SciPost preprint, the `_file` field should be filled.
"""
# (arXiv) identifiers with/without version number
@@ -20,10 +20,7 @@ class Preprint(models.Model):
vn_nr = models.PositiveSmallIntegerField(verbose_name='Version number', default=1)
url = models.URLField(blank=True)
- # SciPost-preprints only
- scipost_preprint_identifier = models.PositiveIntegerField(
- verbose_name='SciPost preprint ID',
- null=True, blank=True, help_text='Unique identifier for SciPost standalone preprints')
+ # SciPost preprints only
_file = models.FileField(
verbose_name='Preprint file', help_text='Preprint file for SciPost standalone preprints',
upload_to='UPLOADS/PREPRINTS/%Y/%m/', max_length=200, blank=True)
diff --git a/scipost/templates/partials/scipost/personal_page/submissions.html b/scipost/templates/partials/scipost/personal_page/submissions.html
index 1248fa733..10dad4e86 100644
--- a/scipost/templates/partials/scipost/personal_page/submissions.html
+++ b/scipost/templates/partials/scipost/personal_page/submissions.html
@@ -31,7 +31,7 @@
<p class="card-text mt-1">
<ul>
{% if sub.open_for_resubmission %}
- <li><a href="{% url 'submissions:submit_choose_journal' discipline=sub.discipline thread_hash=sub.thread_hash %}"><i class="fa fa-arrow-right"></i> resubmit</a></li>
+ <li><a href="{% url 'submissions:submit_choose_journal' discipline=sub.discipline %}?thread_hash={{ sub.thread_hash }}"><i class="fa fa-arrow-right"></i> resubmit</a></li>
{% endif %}
{% if sub.under_consideration %}
{% if sub.editor_in_charge %}
diff --git a/submissions/forms.py b/submissions/forms.py
index ff7d69de4..5ec6f0865 100644
--- a/submissions/forms.py
+++ b/submissions/forms.py
@@ -38,7 +38,7 @@ from colleges.models import Fellowship
from common.utils import Q_with_alternative_spellings
from journals.models import Journal
from mails.utils import DirectMailUtil
-from preprints.helpers import generate_new_scipost_identifier
+from preprints.helpers import get_new_scipost_identifier
from preprints.models import Preprint
from profiles.models import Profile
from scipost.constants import SCIPOST_SUBJECT_AREAS
@@ -337,6 +337,70 @@ class SubmissionService:
#
######################################################################
+# Checks
+
+def check_resubmission_readiness(requested_by, submission):
+ """
+ Check if submission can be resubmitted.
+ """
+ if submission:
+ if submission.status == STATUS_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 metadata, identifier
+
class SubmissionPrefillForm(forms.Form):
"""
@@ -367,38 +431,7 @@ class SubmissionPrefillForm(forms.Form):
"""
Consistency checks on the prefill data.
"""
- self._check_resubmission_readiness()
-
- def _check_resubmission_readiness(self):
- """
- Check if previous submitted versions (if any) can be resubmitted.
- """
- if self.latest_submission:
- if self.latest_submission.status == STATUS_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 self.latest_submission.open_for_resubmission:
- # Check if verified author list contains current user.
- if self.requested_by.contributor not in self.latest_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 not an appropriate 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)
+ check_resubmission_readiness(self.requested_by, self.latest_submission)
def get_prefill_data(self):
return {}
@@ -471,31 +504,35 @@ class ArXivPrefillForm(SubmissionPrefillForm):
"""
identifier = self.cleaned_data.get('arxiv_identifier_w_vn_nr', None)
- caller = ArxivCaller(identifier)
- if caller.is_valid:
- self.arxiv_data = caller.data
- self.metadata = caller.metadata
- else:
- error_message = 'A preprint associated to this identifier does not exist.'
- raise forms.ValidationError(error_message)
+ 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')
-
- # Check if this paper has already been published (according to arXiv)
- published_id = None
- if 'arxiv_doi' in self.arxiv_data:
- published_id = self.arxiv_data['arxiv_doi']
- elif 'arxiv_journal_ref' in self.arxiv_data:
- published_id = self.arxiv_data['arxiv_journal_ref']
+ self.metadata, identifier = check_arxiv_identifier_w_vn_nr(identifier)
- 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})
+ # caller = ArxivCaller(identifier)
+ # if caller.is_valid:
+ # self.arxiv_data = caller.data
+ # self.metadata = caller.metadata
+ # else:
+ # error_message = 'A preprint associated to this identifier does not exist.'
+ # raise forms.ValidationError(error_message)
+
+ # # 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')
+
+ # # Check if this paper has already been published (according to arXiv)
+ # published_id = None
+ # if 'arxiv_doi' in self.arxiv_data:
+ # published_id = self.arxiv_data['arxiv_doi']
+ # elif 'arxiv_journal_ref' in self.arxiv_data:
+ # published_id = self.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 identifier
def get_prefill_data(self):
@@ -583,6 +620,9 @@ class SubmissionForm(forms.ModelForm):
self.requested_by = kwargs.pop('requested_by')
self.preprint_server = kwargs.pop('preprint_server')
self.thread_hash = kwargs['initial'].get('thread_hash', None)
+
+ self.metadata = {} # container for possible external server-provided metadata
+
# print("form args:\n", args)
# print("form kwargs:\n", kwargs)
# print("is_resubmission: %s" % self.is_resubmission())
@@ -657,17 +697,22 @@ class SubmissionForm(forms.ModelForm):
cleaned_data = super().clean(*args, **kwargs)
# SciPost preprints are auto-generated here.
- self.scipost_identifier = None
+ # self.scipost_identifier = None
if 'identifier_w_vn_nr' not in cleaned_data:
- self.service.identifier, self.scipost_identifier = generate_new_scipost_identifier(
- cleaned_data.get('is_resubmission_of', None))
- # Also copy to the form data
- self.cleaned_data['identifier_w_vn_nr'] = self.service.identifier
+ # self.scipost_identifier = generate_new_scipost_identifier(
+ # cleaned_data.get('is_resubmission_of', None))
+ # # Also copy to the form data
+ # self.cleaned_data['identifier_w_vn_nr'] = self.service.identifier
+ self.cleaned_data['identifier_w_vn_nr'] = get_new_scipost_identifier(
+ thread_hash=self.thread_hash)
# Run checks again to clean any possible human intervention and run checks again
# with possibly newly generated identifier.
- self.service.run_checks()
- self.service.identifier_matches_regex(cleaned_data['submitted_to'].doi_label)
+ # self.service.run_checks()
+ # self.service.identifier_matches_regex(cleaned_data['submitted_to'].doi_label)
+
+ if self.is_resubmission():
+ check_resubmission_readiness(self.requested_by, cleaned_data['is_resubmission_of'])
if 'Proc' not in self.cleaned_data['submitted_to'].doi_label:
try:
@@ -693,6 +738,15 @@ class SubmissionForm(forms.ModelForm):
self.add_error('author_list', error_message)
return author_list
+ 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 == 'arXiv':
+ self.metadata, identifier = check_arxiv_identifier_w_vn_nr(identifier)
+ return identifier
+
def clean_submission_type(self):
"""
Validate Submission type for the SciPost Physics journal.
@@ -703,24 +757,6 @@ class SubmissionForm(forms.ModelForm):
self.add_error('submission_type', 'Please specify the submission type.')
return submission_type
- def set_pool(self, submission):
- """
- Set the default set of (guest) Fellows for this Submission.
- """
- qs = Fellowship.objects.active()
- fellows = qs.regular().filter(
- contributor__profile__discipline=submission.discipline).filter(
- Q(contributor__profile__expertises__contains=[submission.subject_area]) |
- Q(contributor__profile__expertises__overlap=submission.secondary_areas)
- ).return_active_for_submission(submission)
- submission.fellows.set(fellows)
-
- if submission.proceedings:
- # Add Guest Fellowships if the Submission is a Proceedings manuscript
- guest_fellows = qs.guests().filter(
- proceedings=submission.proceedings).return_active_for_submission(submission)
- submission.fellows.add(*guest_fellows)
-
@transaction.atomic
def save(self):
"""
@@ -736,16 +772,16 @@ class SubmissionForm(forms.ModelForm):
identifier_wo_vn_nr=identifiers[0],
vn_nr=identifiers[2],
url=self.cleaned_data.get('arxiv_link', ''),
- scipost_preprint_identifier=self.scipost_identifier,
+ # scipost_preprint_identifier=self.scipost_identifier,
_file=self.cleaned_data.get('preprint_file', None), )
# Save metadata directly from ArXiv call without possible user interception
- submission.metadata = self.service.metadata
+ submission.metadata = self.metadata
submission.preprint = preprint
submission.save()
if self.is_resubmission():
- self.service.process_resubmission_procedure(submission)
+ self.process_resubmission(submission)
# Gather first known author and Fellows.
submission.authors.add(self.requested_by.contributor)
@@ -755,6 +791,62 @@ class SubmissionForm(forms.ModelForm):
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(
+ is_current=False, open_for_reporting=False, status=STATUS_RESUBMITTED)
+
+ # Copy Topics
+ submission.topics.add(*previous_submission.topics.all())
+
+ # Open for comment and reporting and copy EIC info
+ Submission.objects.filter(id=submission.id).update(
+ open_for_reporting=True,
+ open_for_commenting=True,
+ visible_pool=True,
+ refereeing_cycle=CYCLE_UNDETERMINED,
+ editor_in_charge=previous_submission.editor_in_charge,
+ status=STATUS_EIC_ASSIGNED)
+
+ # 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=STATUS_ACCEPTED)
+
+ def set_pool(self, submission):
+ """
+ Set the default set of (guest) Fellows for this Submission.
+ """
+ qs = Fellowship.objects.active()
+ fellows = qs.regular().filter(
+ contributor__profile__discipline=submission.discipline).filter(
+ Q(contributor__profile__expertises__contains=[submission.subject_area]) |
+ Q(contributor__profile__expertises__overlap=submission.secondary_areas)
+ ).return_active_for_submission(submission)
+ submission.fellows.set(fellows)
+
+ if submission.proceedings:
+ # Add Guest Fellowships if the Submission is a Proceedings manuscript
+ guest_fellows = qs.guests().filter(
+ proceedings=submission.proceedings).return_active_for_submission(submission)
+ submission.fellows.add(*guest_fellows)
+
class SubmissionReportsForm(forms.ModelForm):
"""Update refereeing pdf for Submission."""
diff --git a/submissions/templates/submissions/submit_choose_preprint_server.html b/submissions/templates/submissions/submit_choose_preprint_server.html
index 2c3a16c21..2d8e3f1c8 100644
--- a/submissions/templates/submissions/submit_choose_preprint_server.html
+++ b/submissions/templates/submissions/submit_choose_preprint_server.html
@@ -49,7 +49,6 @@
</div>
<div class="card-body">
{% if server.name == 'SciPost' %}
- <a class="btn btn-success text-white" role="button" href="{% url 'submissions:submit_manuscript_scipost' journal_doi_label=journal.doi_label %}{% if thread_hash %}?thread_hash={{ thread_hash }}{% endif %}"><i class="fa fa-arrow-right"></i> Go to the SciPost submission form</a>
<form action="{% url 'submissions:submit_manuscript_scipost' journal_doi_label=journal.doi_label %}" method="get">
{{ scipost_prefill_form }}
{% if thread_hash %}
--
GitLab