diff --git a/journals/migrations/0072_auto_20190922_1444.py b/journals/migrations/0072_auto_20190922_1444.py
new file mode 100644
index 0000000000000000000000000000000000000000..f1dc6557c4e159abd31892c1e30fd0688e06fac1
--- /dev/null
+++ b/journals/migrations/0072_auto_20190922_1444.py
@@ -0,0 +1,19 @@
+# Generated by Django 2.1.8 on 2019-09-22 12:44
+
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('journals', '0071_remove_publication_domain'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='publication',
+ name='doi_label',
+ field=models.CharField(db_index=True, max_length=200, unique=True, validators=[django.core.validators.RegexValidator('[a-zA-Z]+(.\\w+(.[0-9]+(.[0-9]{3,})?)?)?', 'Only valid DOI expressions are allowed: `[a-zA-Z]+(.\\w+(.[0-9]+(.[0-9]{3,})?)?)?`')]),
+ ),
+ ]
diff --git a/journals/models.py b/journals/models.py
index f881bfd1d3bbdebea17ed2235aa386d010fb1b87..5dfd5d6b69c3f6bb2ad0234397fb362d5d963cdb 100644
--- a/journals/models.py
+++ b/journals/models.py
@@ -1,760 +1,2 @@
__copyright__ = "Copyright © Stichting SciPost (SciPost Foundation)"
__license__ = "AGPL v3"
-
-
-import datetime
-from decimal import Decimal
-
-from django.contrib.contenttypes.fields import GenericForeignKey
-from django.contrib.contenttypes.models import ContentType
-from django.contrib.postgres.fields import JSONField
-from django.core.exceptions import ValidationError
-from django.db import models
-from django.db.models import Avg, Min, Sum, F
-from django.shortcuts import get_object_or_404
-from django.utils import timezone
-from django.urls import reverse
-
-from .behaviors import (
- doi_journal_validator, doi_volume_validator, doi_issue_validator, doi_publication_validator)
-from .constants import (
- STATUS_DRAFT, STATUS_PUBLICLY_OPEN, STATUS_PUBLISHED, ISSUE_STATUSES,
- PUBLICATION_PUBLISHED, CCBY4, CC_LICENSES, CC_LICENSES_URI, PUBLICATION_STATUSES,
- JOURNAL_STRUCTURE, ISSUES_AND_VOLUMES, ISSUES_ONLY)
-from .helpers import paper_nr_string
-from .managers import IssueQuerySet, PublicationQuerySet, JournalQuerySet
-
-from scipost.constants import SCIPOST_DISCIPLINES, SCIPOST_SUBJECT_AREAS, SCIPOST_APPROACHES
-from scipost.fields import ChoiceArrayField
-
-from proceedings.models import Proceedings
-
-
-################
-# Journals etc #
-################
-
-
-class PublicationAuthorsTable(models.Model):
- """
- PublicationAuthorsTable represents an author of a Publication.
-
- Fields:
- * publication
- * profile
- * affiliations: for this author/Publication (supersede profile.affiliations)
- * order: the ordinal position of this author in this Publication's list of authors.
- """
-
- publication = models.ForeignKey('journals.Publication', on_delete=models.CASCADE,
- related_name='authors')
- profile = models.ForeignKey('profiles.Profile', on_delete=models.PROTECT,
- blank=True, null=True)
- affiliations = models.ManyToManyField('organizations.Organization', blank=True)
- order = models.PositiveSmallIntegerField()
-
- class Meta:
- ordering = ('order',)
-
- def __str__(self):
- return str(self.profile)
-
- def save(self, *args, **kwargs):
- """Auto increment order number if not explicitly set."""
- if not self.order:
- self.order = self.publication.authors.count() + 1
- return super().save(*args, **kwargs)
-
- @property
- def is_registered(self):
- """Check if author is registered at SciPost."""
- return self.profile.contributor is not None
-
- @property
- def first_name(self):
- """Return first name of author."""
- return self.profile.first_name
-
- @property
- def last_name(self):
- """Return last name of author."""
- return self.profile.last_name
-
-
-class Journal(models.Model):
- """Journal is a container of Publications with a unique issn and doi_label.
-
- Publications may be categorized into issues or issues and volumes.
- """
-
- name = models.CharField(max_length=256, unique=True)
- name_abbrev = models.CharField(max_length=128, default='SciPost [abbrev]',
- help_text='Abbreviated name (for use in citations)')
- doi_label = models.CharField(max_length=200, unique=True, db_index=True,
- validators=[doi_journal_validator])
- issn = models.CharField(max_length=16, default='2542-4653', blank=True)
- active = models.BooleanField(default=True)
- structure = models.CharField(max_length=2,
- choices=JOURNAL_STRUCTURE, default=ISSUES_AND_VOLUMES)
- refereeing_period = models.DurationField(default=datetime.timedelta(days=28))
-
- objects = JournalQuerySet.as_manager()
-
- def __str__(self):
- return self.name
-
- def get_absolute_url(self):
- """Return Journal's homepage url."""
- return reverse('scipost:landing_page', args=(self.doi_label,))
-
- @property
- def doi_string(self):
- """Return DOI including the SciPost registrant prefix."""
- return '10.21468/' + self.doi_label
-
- @property
- def has_issues(self):
- return self.structure in (ISSUES_AND_VOLUMES, ISSUES_ONLY)
-
- @property
- def has_volumes(self):
- return self.structure in (ISSUES_AND_VOLUMES)
-
- def get_issues(self):
- if self.structure == ISSUES_AND_VOLUMES:
- return Issue.objects.filter(in_volume__in_journal=self).published()
- elif self.structure == ISSUES_ONLY:
- return self.issues.open_or_published()
- return Issue.objects.none()
-
- def get_latest_issue(self):
- """Get latest existing Issue in database irrespective of its status."""
- if self.structure == ISSUES_ONLY:
- return self.issues.order_by('-until_date').first()
- if self.structure == ISSUES_AND_VOLUMES:
- return Issue.objects.filter(in_volume__in_journal=self).order_by('-until_date').first()
- return None
-
- def get_latest_volume(self):
- """Get latest existing Volume in database irrespective of its status."""
- if self.structure == ISSUES_AND_VOLUMES:
- return self.volumes.order_by('-until_date').first()
- return None
-
- def get_publications(self):
- if self.structure == ISSUES_AND_VOLUMES:
- return Publication.objects.filter(in_issue__in_volume__in_journal=self)
- elif self.structure == ISSUES_ONLY:
- return Publication.objects.filter(in_issue__in_journal=self)
- return self.publications.all()
-
- def nr_publications(self, tier=None):
- publications = Publication.objects.filter(in_issue__in_volume__in_journal=self)
- if tier:
- publications = publications.filter(
- accepted_submission__eicrecommendations__recommendation=tier)
- return publications.count()
-
- def avg_processing_duration(self):
- duration = Publication.objects.filter(
- in_issue__in_volume__in_journal=self).aggregate(
- avg=Avg(F('publication_date') - F('submission_date')))['avg']
- if duration:
- return duration.total_seconds() / 86400
- return 0
-
- def citation_rate(self, tier=None):
- """Return the citation rate in units of nr citations per article per year."""
- publications = Publication.objects.filter(in_issue__in_volume__in_journal=self)
- if tier:
- publications = publications.filter(
- accepted_submission__eicrecommendations__recommendation=tier)
- ncites = 0
- deltat = 1 # to avoid division by zero
- for pub in publications:
- if pub.citedby and pub.latest_citedby_update:
- ncites += len(pub.citedby)
- deltat += (pub.latest_citedby_update.date() - pub.publication_date).days
- return (ncites * 365.25/deltat)
-
- def citedby_impact_factor(self, year):
- """Compute the impact factor for a given year YYYY, from Crossref cited-by data.
-
- This is defined as the total number of citations in year YYYY
- for all papers published in years YYYY-1 and YYYY-2, divided
- by the number of papers published in year YYYY.
- """
- publications = self.get_publications().filter(
- models.Q(publication_date__year=int(year)-1) |
- models.Q(publication_date__year=int(year)-2))
- nrpub = publications.count()
- if nrpub == 0:
- return 0
- ncites = 0
- for pub in publications:
- if pub.citedby and pub.latest_citedby_update:
- for citation in pub.citedby:
- if citation['year'] == year:
- ncites += 1
- return ncites / nrpub
-
-
-class Volume(models.Model):
- """
- A Volume belongs to a specific Journal, and is a container for
- either (multiple) Issue(s) or Publication(s).
- """
- in_journal = models.ForeignKey(
- 'journals.Journal', limit_choices_to={'structure': ISSUES_AND_VOLUMES},
- on_delete=models.CASCADE)
- number = models.PositiveSmallIntegerField()
- start_date = models.DateField(default=timezone.now)
- until_date = models.DateField(default=timezone.now)
- doi_label = models.CharField(max_length=200, unique=True, db_index=True,
- validators=[doi_volume_validator])
-
- class Meta:
- default_related_name = 'volumes'
- ordering = ('-until_date',)
- unique_together = ('number', 'in_journal')
-
- def __str__(self):
- return str(self.in_journal) + ' Vol. ' + str(self.number)
-
- def clean(self):
- """Check if the Volume is assigned to a valid Journal."""
- if not self.in_journal.has_volumes:
- raise ValidationError({
- 'in_journal': ValidationError('This journal does not allow for the use of Volumes',
- code='invalid'),
- })
-
- @property
- def doi_string(self):
- return '10.21468/' + self.doi_label
-
- def is_current(self):
- today = timezone.now().date()
- return self.start_date <= today and self.until_date >= today
-
- def nr_publications(self, tier=None):
- publications = Publication.objects.filter(in_issue__in_volume=self)
- if tier:
- publications = publications.filter(
- accepted_submission__eicrecommendations__recommendation=tier)
- return publications.count()
-
- def avg_processing_duration(self):
- duration = Publication.objects.filter(
- in_issue__in_volume=self).aggregate(
- avg=Avg(F('publication_date') - F('submission_date')))['avg']
- if duration:
- return duration.total_seconds() / 86400
- return 0
-
- def citation_rate(self, tier=None):
- """Returns the citation rate in units of nr citations per article per year."""
- publications = Publication.objects.filter(in_issue__in_volume=self)
- if tier:
- publications = publications.filter(
- accepted_submission__eicrecommendations__recommendation=tier)
- ncites = 0
- deltat = 1 # to avoid division by zero
- for pub in publications:
- if pub.citedby and pub.latest_citedby_update:
- ncites += len(pub.citedby)
- deltat += (pub.latest_citedby_update.date() - pub.publication_date).days
- return (ncites * 365.25 / deltat)
-
-
-class Issue(models.Model):
- """
- An Issue is related to a specific Journal, either indirectly via a Volume
- container, or directly. It is a container for multiple Publications.
- """
- in_journal = models.ForeignKey(
- 'journals.Journal', on_delete=models.CASCADE, null=True, blank=True,
- limit_choices_to={'structure': ISSUES_ONLY},
- help_text='Assign either a Volume or Journal to the Issue')
- in_volume = models.ForeignKey(
- 'journals.Volume', on_delete=models.CASCADE, null=True, blank=True,
- help_text='Assign either a Volume or Journal to the Issue')
- number = models.PositiveIntegerField()
- slug = models.SlugField()
- start_date = models.DateField(default=timezone.now)
- until_date = models.DateField(default=timezone.now)
- status = models.CharField(max_length=20, choices=ISSUE_STATUSES, default=STATUS_PUBLISHED)
- doi_label = models.CharField(max_length=200, unique=True, db_index=True,
- validators=[doi_issue_validator])
-
- # absolute path on filesystem: (JOURNALS_DIR)/journal/vol/issue/
- path = models.CharField(max_length=200)
-
- objects = IssueQuerySet.as_manager()
-
- class Meta:
- default_related_name = 'issues'
- ordering = ('-until_date',)
- unique_together = ('number', 'in_volume')
-
- def __str__(self):
- text = self.issue_string
- if hasattr(self, 'proceedings'):
- return text
- text += ' (%s)' % self.period_as_string
- if self.status == STATUS_DRAFT:
- text += ' (In draft)'
- return text
-
- def clean(self):
- """Check if either a Journal or Volume is assigned to the Issue."""
- if not (self.in_journal or self.in_volume):
- raise ValidationError({
- 'in_journal': ValidationError('Either assign a Journal or Volume to this Issue',
- code='required'),
- 'in_volume': ValidationError('Either assign a Journal or Volume to this Issue',
- code='required'),
- })
- if self.in_journal and not self.in_journal.has_issues:
- raise ValidationError({
- 'in_journal': ValidationError('This journal does not allow for the use of Issues',
- code='invalid'),
- })
-
- def get_absolute_url(self):
- return reverse('scipost:issue_detail', args=[self.doi_label])
-
- @property
- def doi_string(self):
- return '10.21468/' + self.doi_label
-
- @property
- def issue_string(self):
- if self.in_volume:
- return '%s issue %s' % (self.in_volume, self.number)
- elif self.status == STATUS_PUBLICLY_OPEN:
- try:
- return '%s (open): %s (%s)' % (self.in_journal,
- self.proceedings.event_name, self.number)
- except Proceedings.DoesNotExist:
- pass
- return '%s (open): %s' % (self.in_journal, self.number)
- return '%s issue %s' % (self.in_journal, self.number)
-
- @property
- def short_str(self):
- if self.in_volume:
- return 'Vol. %s issue %s' % (self.in_volume.number, self.number)
- return 'Issue %s' % self.doi_label.rpartition('.')[2]
-
- @property
- def period_as_string(self):
- if self.start_date.month == self.until_date.month:
- return '%s %s' % (self.until_date.strftime('%B'), self.until_date.strftime('%Y'))
- return '%s - %s' % (self.start_date.strftime('%B'), self.until_date.strftime('%B %Y'))
-
- def get_journal(self):
- if self.in_journal:
- return self.in_journal
- return self.in_volume.in_journal
-
- def is_current(self):
- today = timezone.now().date()
- return self.start_date <= today and self.until_date >= today
-
- def nr_publications(self, tier=None):
- publications = Publication.objects.filter(in_issue=self)
- if tier:
- publications = publications.filter(
- accepted_submission__eicrecommendations__recommendation=tier)
- return publications.count()
-
- def avg_processing_duration(self):
- duration = Publication.objects.filter(
- in_issue=self).aggregate(
- avg=Avg(F('publication_date') - F('submission_date')))['avg']
- if duration:
- return duration.total_seconds() / 86400
- return 0
-
- def citation_rate(self, tier=None):
- """Return the citation rate in units of nr citations per article per year."""
- publications = Publication.objects.filter(in_issue=self)
- if tier:
- publications = publications.filter(
- accepted_submission__eicrecommendations__recommendation=tier)
- ncites = 0
- deltat = 1 # to avoid division by zero
- for pub in publications:
- if pub.citedby and pub.latest_citedby_update:
- ncites += len(pub.citedby)
- deltat += (pub.latest_citedby_update.date() - pub.publication_date).days
- return (ncites * 365.25 / deltat)
-
-
-class Publication(models.Model):
- """A Publication is an object directly related to an accepted Submission.
-
- It contains metadata, the actual publication file, author data, etc. etc.
- It may be directly related to a Journal or to an Issue.
- """
-
- # Publication data
- accepted_submission = models.OneToOneField('submissions.Submission', on_delete=models.CASCADE,
- related_name='publication')
- in_issue = models.ForeignKey(
- 'journals.Issue', on_delete=models.CASCADE, null=True, blank=True,
- help_text='Assign either an Issue or Journal to the Publication')
- in_journal = models.ForeignKey(
- 'journals.Journal', on_delete=models.CASCADE, null=True, blank=True,
- help_text='Assign either an Issue or Journal to the Publication')
- paper_nr = models.PositiveSmallIntegerField()
- status = models.CharField(max_length=8,
- choices=PUBLICATION_STATUSES, default=STATUS_DRAFT)
-
- # Core fields
- title = models.CharField(max_length=300)
- author_list = models.CharField(max_length=10000, verbose_name="author list")
- abstract = models.TextField()
- abstract_jats = models.TextField(blank=True, default='',
- help_text='JATS version of abstract for Crossref deposit')
- pdf_file = models.FileField(upload_to='UPLOADS/PUBLICATIONS/%Y/%m/', max_length=200)
- discipline = models.CharField(max_length=20, choices=SCIPOST_DISCIPLINES, default='physics')
- subject_area = models.CharField(max_length=10, choices=SCIPOST_SUBJECT_AREAS,
- verbose_name='Primary subject area', default='Phys:QP')
- secondary_areas = ChoiceArrayField(
- models.CharField(max_length=10, choices=SCIPOST_SUBJECT_AREAS), blank=True, null=True)
- approaches = ChoiceArrayField(
- models.CharField(max_length=24, choices=SCIPOST_APPROACHES),
- blank=True, null=True, verbose_name='approach(es) [optional]')
-
- # Authors
- authors_claims = models.ManyToManyField('scipost.Contributor', blank=True,
- related_name='claimed_publications')
- authors_false_claims = models.ManyToManyField('scipost.Contributor', blank=True,
- related_name='false_claimed_publications')
-
- cc_license = models.CharField(max_length=32, choices=CC_LICENSES, default=CCBY4)
-
- # Funders
- grants = models.ManyToManyField('funders.Grant', blank=True)
- funders_generic = models.ManyToManyField('funders.Funder', blank=True) # not linked to a grant
- pubfractions_confirmed_by_authors = models.BooleanField(default=False)
-
- # Metadata
- metadata = JSONField(default=dict, blank=True, null=True)
- metadata_xml = models.TextField(blank=True) # for Crossref deposit
- metadata_DOAJ = JSONField(default=dict, blank=True, null=True)
- doi_label = models.CharField(max_length=200, unique=True, db_index=True,
- validators=[doi_publication_validator])
- BiBTeX_entry = models.TextField(blank=True)
- doideposit_needs_updating = models.BooleanField(default=False)
- citedby = JSONField(default=dict, blank=True, null=True)
- number_of_citations = models.PositiveIntegerField(default=0)
-
- # Topics for semantic linking
- topics = models.ManyToManyField('ontology.Topic', blank=True)
-
- # Date fields
- submission_date = models.DateField(verbose_name='submission date')
- acceptance_date = models.DateField(verbose_name='acceptance date')
- publication_date = models.DateField(verbose_name='publication date')
- latest_citedby_update = models.DateTimeField(null=True, blank=True)
- latest_metadata_update = models.DateTimeField(blank=True, null=True)
- latest_activity = models.DateTimeField(auto_now=True) # Needs `auto_now` as its not explicity updated anywhere?
-
- objects = PublicationQuerySet.as_manager()
-
- class Meta:
- default_related_name = 'publications'
- ordering = ('-publication_date', '-paper_nr')
-
- def __str__(self):
- return '{cite}, {title} by {authors}, {date}'.format(
- cite=self.citation,
- title=self.title[:30],
- authors=self.author_list[:30],
- date=self.publication_date.strftime('%Y-%m-%d'))
-
- def clean(self):
- """Check if either a valid Journal or Issue is assigned to the Publication."""
- if not (self.in_journal or self.in_issue):
- raise ValidationError({
- 'in_journal': ValidationError(
- 'Either assign a Journal or Issue to this Publication', code='required'),
- 'in_issue': ValidationError(
- 'Either assign a Journal or Issue to this Publication', code='required'),
- })
- if self.in_journal and self.in_issue:
- # Assigning both a Journal and an Issue will screw up the database
- raise ValidationError({
- 'in_journal': ValidationError(
- 'Either assign only a Journal or Issue to this Publication', code='invalid'),
- 'in_issue': ValidationError(
- 'Either assign only a Journal or Issue to this Publication', code='invalid'),
- })
- if self.in_issue and not self.get_journal().has_issues:
- # Assigning both a Journal and an Issue will screw up the database
- raise ValidationError({
- 'in_issue': ValidationError(
- 'This journal does not allow the use of Issues',
- code='invalid'),
- })
- if self.in_journal and self.get_journal().has_issues:
- # Assigning both a Journal and an Issue will screw up the database
- raise ValidationError({
- 'in_journal': ValidationError(
- 'This journal does not allow the use of individual Publications',
- code='invalid'),
- })
-
- def get_absolute_url(self):
- return reverse('scipost:publication_detail', args=(self.doi_label,))
-
- def get_cc_license_URI(self):
- for (key, val) in CC_LICENSES_URI:
- if key == self.cc_license:
- return val
- raise KeyError
-
- def get_all_affiliations(self):
- """
- Returns all author affiliations.
- """
- from organizations.models import Organization
- return Organization.objects.filter(
- publicationauthorstable__publication=self
- ).annotate(order=Min('publicationauthorstable__order')).order_by('order')
-
- def get_all_funders(self):
- from funders.models import Funder
- return Funder.objects.filter(
- models.Q(grants__publications=self) | models.Q(publications=self)).distinct()
-
- def get_organizations(self):
- """
- Returns a queryset of all Organizations which are associated to this Publication,
- through being in author affiliations, funders or generic funders.
- """
- from organizations.models import Organization
- return Organization.objects.filter(
- models.Q(publicationauthorstable__publication=self) |
- models.Q(funder__grants__publications=self) |
- models.Q(funder__publications=self)).distinct()
-
- @property
- def doi_string(self):
- return '10.21468/' + self.doi_label
-
- @property
- def is_draft(self):
- return self.status == STATUS_DRAFT
-
- @property
- def is_published(self):
- if self.status != PUBLICATION_PUBLISHED:
- return False
-
- if self.in_issue:
- return self.in_issue.status == STATUS_PUBLISHED
- elif self.in_journal:
- return self.in_journal.active
- return False
-
- @property
- def has_xml_metadata(self):
- return self.metadata_xml != ''
-
- @property
- def has_bibtex_entry(self):
- return self.BiBTeX_entry != ''
-
- @property
- def has_citation_list(self):
- return 'citation_list' in self.metadata and len(self.metadata['citation_list']) > 0
-
- @property
- def has_funding_statement(self):
- return 'funding_statement' in self.metadata and self.metadata['funding_statement']
-
- @property
- def pubfractions_sum_to_1(self):
- """ Checks that the support fractions sum up to one. """
- return self.pubfractions.aggregate(Sum('fraction'))['fraction__sum'] == 1
-
- @property
- def citation(self):
- """Return Publication name in the preferred citation format."""
- if self.in_issue and self.in_issue.in_volume:
- return '{journal} {volume}, {paper_nr} ({year})'.format(
- journal=self.in_issue.in_volume.in_journal.name_abbrev,
- volume=self.in_issue.in_volume.number,
- paper_nr=self.get_paper_nr(),
- year=self.publication_date.strftime('%Y'))
- elif self.in_issue and self.in_issue.in_journal:
- return '{journal} {issue}, {paper_nr} ({year})'.format(
- journal=self.in_issue.in_journal.name_abbrev,
- issue=self.in_issue.number,
- paper_nr=self.get_paper_nr(),
- year=self.publication_date.strftime('%Y'))
- elif self.in_journal:
- return '{journal} {paper_nr} ({year})'.format(
- journal=self.in_journal.name_abbrev,
- paper_nr=self.paper_nr,
- year=self.publication_date.strftime('%Y'))
- return '{paper_nr} ({year})'.format(
- paper_nr=self.paper_nr,
- year=self.publication_date.strftime('%Y'))
-
- def get_cc_license_URI(self):
- for (key, val) in CC_LICENSES_URI:
- if key == self.cc_license:
- return val
- raise KeyError
-
- def get_all_funders(self):
- from funders.models import Funder
- return Funder.objects.filter(
- models.Q(grants__publications=self) | models.Q(publications=self)).distinct()
-
- def get_journal(self):
- if self.in_journal:
- return self.in_journal
- elif self.in_issue.in_journal:
- return self.in_issue.in_journal
- return self.in_issue.in_volume.in_journal
-
- def journal_issn(self):
- return self.get_journal().issn
-
- def get_paper_nr(self):
- if self.in_journal:
- return self.paper_nr
- return paper_nr_string(self.paper_nr)
-
- def citation_rate(self):
- """Returns the citation rate in units of nr citations per article per year."""
- if self.citedby and self.latest_citedby_update:
- ncites = len(self.citedby)
- deltat = (self.latest_citedby_update.date() - self.publication_date).days
- return (ncites * 365.25 / deltat)
- else:
- return 0
-
- def get_similar_publications(self):
- """Return 4 Publications with same subject area."""
- return Publication.objects.published().filter(
- subject_area=self.subject_area).exclude(id=self.id)[:4]
-
- def get_issue_related_publications(self):
- """Return 4 Publications within same Issue."""
- return Publication.objects.published().filter(
- in_issue=self.in_issue).exclude(id=self.id)[:4]
-
-
-class Reference(models.Model):
- """A Refence is a reference used in a specific Publication."""
- reference_number = models.IntegerField()
- publication = models.ForeignKey('journals.Publication', on_delete=models.CASCADE)
-
- authors = models.CharField(max_length=1028)
- citation = models.CharField(max_length=1028, blank=True)
- identifier = models.CharField(blank=True, max_length=128)
- link = models.URLField(blank=True)
-
- class Meta:
- unique_together = ('reference_number', 'publication')
- ordering = ['reference_number']
- default_related_name = 'references'
-
- def __str__(self):
- return '[{}] {}, {}'.format(self.reference_number, self.authors[:30], self.citation[:30])
-
-
-class OrgPubFraction(models.Model):
- """
- Associates a fraction of the funding credit for a given publication to an Organization,
- to help answer the question: who funded this research?
-
- Fractions for a given publication should sum up to one.
-
- This data is used to compile publicly-displayed information on Organizations
- as well as to set suggested contributions from Partners.
-
- To be set (ideally) during production phase, based on information provided by the authors.
- """
- organization = models.ForeignKey('organizations.Organization', on_delete=models.CASCADE,
- related_name='pubfractions', blank=True, null=True)
- publication = models.ForeignKey('journals.Publication', on_delete=models.CASCADE,
- related_name='pubfractions')
- fraction = models.DecimalField(max_digits=4, decimal_places=3, default=Decimal('0.000'))
-
- class Meta:
- unique_together = (('organization', 'publication'),)
-
-
-class Deposit(models.Model):
- """
- Each time a Crossref deposit is made for a Publication,
- a Deposit object instance is created containing the Publication's
- current version of the metadata_xml field.
- All deposit history is thus contained here.
- """
- publication = models.ForeignKey(Publication, on_delete=models.CASCADE)
- timestamp = models.CharField(max_length=40)
- doi_batch_id = models.CharField(max_length=40)
- metadata_xml = models.TextField(blank=True)
- metadata_xml_file = models.FileField(blank=True, null=True, max_length=512)
- deposition_date = models.DateTimeField(blank=True, null=True)
- response_text = models.TextField(blank=True)
- deposit_successful = models.NullBooleanField(default=None)
-
- class Meta:
- ordering = ['-timestamp']
-
- def __str__(self):
- _str = ''
- if self.deposition_date:
- _str += '%s for ' % self.deposition_date.strftime('%Y-%m-%D')
- return _str + self.publication.doi_label
-
-
-class DOAJDeposit(models.Model):
- """
- For the Directory of Open Access Journals.
- """
- publication = models.ForeignKey(Publication, on_delete=models.CASCADE)
- timestamp = models.CharField(max_length=40)
- metadata_DOAJ = JSONField()
- metadata_DOAJ_file = models.FileField(blank=True, null=True, max_length=512)
- deposition_date = models.DateTimeField(blank=True, null=True)
- response_text = models.TextField(blank=True, null=True)
- deposit_successful = models.NullBooleanField(default=None)
-
- class Meta:
- verbose_name = 'DOAJ deposit'
-
- def __str__(self):
- return ('DOAJ deposit for ' + self.publication.doi_label)
-
-
-class GenericDOIDeposit(models.Model):
- """
- Instances of this class represent Crossref deposits for non-publication
- objects such as Reports, Comments etc.
- """
- content_type = models.ForeignKey(ContentType, on_delete=models.CASCADE)
- object_id = models.PositiveIntegerField()
- content_object = GenericForeignKey()
- timestamp = models.CharField(max_length=40, default='')
- doi_batch_id = models.CharField(max_length=40, default='')
- metadata_xml = models.TextField(blank=True, null=True)
- deposition_date = models.DateTimeField(blank=True, null=True)
- response = models.TextField(blank=True, null=True)
- deposit_successful = models.NullBooleanField(default=None)
-
- class Meta:
- ordering = ['-timestamp']
-
- def __str__(self):
- return 'GenericDOIDeposit for %s %s' % (self.content_type, str(self.content_object))
diff --git a/journals/models/__init__.py b/journals/models/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..72e45349d61fe2bf68326259565c1bc287d93d58
--- /dev/null
+++ b/journals/models/__init__.py
@@ -0,0 +1,9 @@
+__copyright__ = "Copyright © Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
+from .journal import Journal
+from .volume import Volume
+from .issue import Issue
+from .publication import PublicationAuthorsTable, Publication, Reference, OrgPubFraction
+from .deposits import Deposit, DOAJDeposit, GenericDOIDeposit
diff --git a/journals/models/deposits.py b/journals/models/deposits.py
new file mode 100644
index 0000000000000000000000000000000000000000..914a0f5bb2ce108c667b02454a5c702c585e2036
--- /dev/null
+++ b/journals/models/deposits.py
@@ -0,0 +1,77 @@
+__copyright__ = "Copyright © Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
+from django.contrib.contenttypes.fields import GenericForeignKey
+from django.contrib.contenttypes.models import ContentType
+from django.contrib.postgres.fields import JSONField
+from django.db import models
+
+from journals.models import Publication
+
+
+class Deposit(models.Model):
+ """
+ Each time a Crossref deposit is made for a Publication,
+ a Deposit object instance is created containing the Publication's
+ current version of the metadata_xml field.
+ All deposit history is thus contained here.
+ """
+ publication = models.ForeignKey(Publication, on_delete=models.CASCADE)
+ timestamp = models.CharField(max_length=40)
+ doi_batch_id = models.CharField(max_length=40)
+ metadata_xml = models.TextField(blank=True)
+ metadata_xml_file = models.FileField(blank=True, null=True, max_length=512)
+ deposition_date = models.DateTimeField(blank=True, null=True)
+ response_text = models.TextField(blank=True)
+ deposit_successful = models.NullBooleanField(default=None)
+
+ class Meta:
+ ordering = ['-timestamp']
+
+ def __str__(self):
+ _str = ''
+ if self.deposition_date:
+ _str += '%s for ' % self.deposition_date.strftime('%Y-%m-%D')
+ return _str + self.publication.doi_label
+
+
+class DOAJDeposit(models.Model):
+ """
+ For the Directory of Open Access Journals.
+ """
+ publication = models.ForeignKey(Publication, on_delete=models.CASCADE)
+ timestamp = models.CharField(max_length=40)
+ metadata_DOAJ = JSONField()
+ metadata_DOAJ_file = models.FileField(blank=True, null=True, max_length=512)
+ deposition_date = models.DateTimeField(blank=True, null=True)
+ response_text = models.TextField(blank=True, null=True)
+ deposit_successful = models.NullBooleanField(default=None)
+
+ class Meta:
+ verbose_name = 'DOAJ deposit'
+
+ def __str__(self):
+ return ('DOAJ deposit for ' + self.publication.doi_label)
+
+
+class GenericDOIDeposit(models.Model):
+ """
+ Instances of this class represent Crossref deposits for non-publication
+ objects such as Reports, Comments etc.
+ """
+ content_type = models.ForeignKey(ContentType, on_delete=models.CASCADE)
+ object_id = models.PositiveIntegerField()
+ content_object = GenericForeignKey()
+ timestamp = models.CharField(max_length=40, default='')
+ doi_batch_id = models.CharField(max_length=40, default='')
+ metadata_xml = models.TextField(blank=True, null=True)
+ deposition_date = models.DateTimeField(blank=True, null=True)
+ response = models.TextField(blank=True, null=True)
+ deposit_successful = models.NullBooleanField(default=None)
+
+ class Meta:
+ ordering = ['-timestamp']
+
+ def __str__(self):
+ return 'GenericDOIDeposit for %s %s' % (self.content_type, str(self.content_object))
diff --git a/journals/models/issue.py b/journals/models/issue.py
new file mode 100644
index 0000000000000000000000000000000000000000..7e8eda8f6553a4b3c5511b2d61b2ea4717c97fc0
--- /dev/null
+++ b/journals/models/issue.py
@@ -0,0 +1,145 @@
+__copyright__ = "Copyright © Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
+from django.core.exceptions import ValidationError
+from django.db import models
+from django.db.models import Avg, F
+from django.utils import timezone
+from django.urls import reverse
+
+from proceedings.models import Proceedings
+
+from ..behaviors import doi_issue_validator
+from ..constants import ISSUES_ONLY, ISSUE_STATUSES, STATUS_DRAFT, STATUS_PUBLISHED,\
+ STATUS_PUBLICLY_OPEN
+from ..managers import IssueQuerySet
+
+
+
+class Issue(models.Model):
+ """
+ An Issue is related to a specific Journal, either indirectly via a Volume
+ container, or directly. It is a container for multiple Publications.
+ """
+ in_journal = models.ForeignKey(
+ 'journals.Journal', on_delete=models.CASCADE, null=True, blank=True,
+ limit_choices_to={'structure': ISSUES_ONLY},
+ help_text='Assign either a Volume or Journal to the Issue')
+ in_volume = models.ForeignKey(
+ 'journals.Volume', on_delete=models.CASCADE, null=True, blank=True,
+ help_text='Assign either a Volume or Journal to the Issue')
+ number = models.PositiveIntegerField()
+ slug = models.SlugField()
+ start_date = models.DateField(default=timezone.now)
+ until_date = models.DateField(default=timezone.now)
+ status = models.CharField(max_length=20, choices=ISSUE_STATUSES, default=STATUS_PUBLISHED)
+ doi_label = models.CharField(max_length=200, unique=True, db_index=True,
+ validators=[doi_issue_validator])
+
+ # absolute path on filesystem: (JOURNALS_DIR)/journal/vol/issue/
+ path = models.CharField(max_length=200)
+
+ objects = IssueQuerySet.as_manager()
+
+ class Meta:
+ default_related_name = 'issues'
+ ordering = ('-until_date',)
+ unique_together = ('number', 'in_volume')
+
+ def __str__(self):
+ text = self.issue_string
+ if hasattr(self, 'proceedings'):
+ return text
+ text += ' (%s)' % self.period_as_string
+ if self.status == STATUS_DRAFT:
+ text += ' (In draft)'
+ return text
+
+ def clean(self):
+ """Check if either a Journal or Volume is assigned to the Issue."""
+ if not (self.in_journal or self.in_volume):
+ raise ValidationError({
+ 'in_journal': ValidationError('Either assign a Journal or Volume to this Issue',
+ code='required'),
+ 'in_volume': ValidationError('Either assign a Journal or Volume to this Issue',
+ code='required'),
+ })
+ if self.in_journal and not self.in_journal.has_issues:
+ raise ValidationError({
+ 'in_journal': ValidationError('This journal does not allow for the use of Issues',
+ code='invalid'),
+ })
+
+ def get_absolute_url(self):
+ return reverse('scipost:issue_detail', args=[self.doi_label])
+
+ @property
+ def doi_string(self):
+ return '10.21468/' + self.doi_label
+
+ @property
+ def issue_string(self):
+ if self.in_volume:
+ return '%s issue %s' % (self.in_volume, self.number)
+ elif self.status == STATUS_PUBLICLY_OPEN:
+ try:
+ return '%s (open): %s (%s)' % (self.in_journal,
+ self.proceedings.event_name, self.number)
+ except Proceedings.DoesNotExist:
+ pass
+ return '%s (open): %s' % (self.in_journal, self.number)
+ return '%s issue %s' % (self.in_journal, self.number)
+
+ @property
+ def short_str(self):
+ if self.in_volume:
+ return 'Vol. %s issue %s' % (self.in_volume.number, self.number)
+ return 'Issue %s' % self.doi_label.rpartition('.')[2]
+
+ @property
+ def period_as_string(self):
+ if self.start_date.month == self.until_date.month:
+ return '%s %s' % (self.until_date.strftime('%B'), self.until_date.strftime('%Y'))
+ return '%s - %s' % (self.start_date.strftime('%B'), self.until_date.strftime('%B %Y'))
+
+ def get_journal(self):
+ if self.in_journal:
+ return self.in_journal
+ return self.in_volume.in_journal
+
+ def is_current(self):
+ today = timezone.now().date()
+ return self.start_date <= today and self.until_date >= today
+
+ def nr_publications(self, tier=None):
+ from journals.models import Publication
+ publications = Publication.objects.filter(in_issue=self)
+ if tier:
+ publications = publications.filter(
+ accepted_submission__eicrecommendations__recommendation=tier)
+ return publications.count()
+
+ def avg_processing_duration(self):
+ from journals.models import Publication
+ duration = Publication.objects.filter(
+ in_issue=self).aggregate(
+ avg=Avg(F('publication_date') - F('submission_date')))['avg']
+ if duration:
+ return duration.total_seconds() / 86400
+ return 0
+
+ def citation_rate(self, tier=None):
+ """Return the citation rate in units of nr citations per article per year."""
+ from journals.models import Publication
+ publications = Publication.objects.filter(in_issue=self)
+ if tier:
+ publications = publications.filter(
+ accepted_submission__eicrecommendations__recommendation=tier)
+ ncites = 0
+ deltat = 1 # to avoid division by zero
+ for pub in publications:
+ if pub.citedby and pub.latest_citedby_update:
+ ncites += len(pub.citedby)
+ deltat += (pub.latest_citedby_update.date() - pub.publication_date).days
+ return (ncites * 365.25 / deltat)
diff --git a/journals/models/journal.py b/journals/models/journal.py
new file mode 100644
index 0000000000000000000000000000000000000000..b297bac92f8c15a8a353c46e4522f9e3122e27d5
--- /dev/null
+++ b/journals/models/journal.py
@@ -0,0 +1,137 @@
+__copyright__ = "Copyright © Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
+import datetime
+
+from django.db import models
+from django.db.models import Avg, F
+from django.urls import reverse
+
+from ..behaviors import doi_journal_validator
+from ..constants import JOURNAL_STRUCTURE, ISSUES_AND_VOLUMES, ISSUES_ONLY
+from ..managers import JournalQuerySet
+
+
+class Journal(models.Model):
+ """Journal is a container of Publications with a unique issn and doi_label.
+
+ Publications may be categorized into issues or issues and volumes.
+ """
+
+ name = models.CharField(max_length=256, unique=True)
+ name_abbrev = models.CharField(max_length=128, default='SciPost [abbrev]',
+ help_text='Abbreviated name (for use in citations)')
+ doi_label = models.CharField(max_length=200, unique=True, db_index=True,
+ validators=[doi_journal_validator])
+ issn = models.CharField(max_length=16, default='2542-4653', blank=True)
+ active = models.BooleanField(default=True)
+ structure = models.CharField(max_length=2,
+ choices=JOURNAL_STRUCTURE, default=ISSUES_AND_VOLUMES)
+ refereeing_period = models.DurationField(default=datetime.timedelta(days=28))
+
+ objects = JournalQuerySet.as_manager()
+
+ def __str__(self):
+ return self.name
+
+ def get_absolute_url(self):
+ """Return Journal's homepage url."""
+ return reverse('scipost:landing_page', args=(self.doi_label,))
+
+ @property
+ def doi_string(self):
+ """Return DOI including the SciPost registrant prefix."""
+ return '10.21468/' + self.doi_label
+
+ @property
+ def has_issues(self):
+ return self.structure in (ISSUES_AND_VOLUMES, ISSUES_ONLY)
+
+ @property
+ def has_volumes(self):
+ return self.structure in (ISSUES_AND_VOLUMES)
+
+ def get_issues(self):
+ from journals.models import Issue
+ if self.structure == ISSUES_AND_VOLUMES:
+ return Issue.objects.filter(in_volume__in_journal=self).published()
+ elif self.structure == ISSUES_ONLY:
+ return self.issues.open_or_published()
+ return Issue.objects.none()
+
+ def get_latest_issue(self):
+ """Get latest existing Issue in database irrespective of its status."""
+ from journals.models import Issue
+ if self.structure == ISSUES_ONLY:
+ return self.issues.order_by('-until_date').first()
+ if self.structure == ISSUES_AND_VOLUMES:
+ return Issue.objects.filter(in_volume__in_journal=self).order_by('-until_date').first()
+ return None
+
+ def get_latest_volume(self):
+ """Get latest existing Volume in database irrespective of its status."""
+ if self.structure == ISSUES_AND_VOLUMES:
+ return self.volumes.order_by('-until_date').first()
+ return None
+
+ def get_publications(self):
+ from journals.models import Publication
+ if self.structure == ISSUES_AND_VOLUMES:
+ return Publication.objects.filter(in_issue__in_volume__in_journal=self)
+ elif self.structure == ISSUES_ONLY:
+ return Publication.objects.filter(in_issue__in_journal=self)
+ return self.publications.all()
+
+ def nr_publications(self, tier=None):
+ from journals.models import Publication
+ publications = Publication.objects.filter(in_issue__in_volume__in_journal=self)
+ if tier:
+ publications = publications.filter(
+ accepted_submission__eicrecommendations__recommendation=tier)
+ return publications.count()
+
+ def avg_processing_duration(self):
+ from journals.models import Publication
+ duration = Publication.objects.filter(
+ in_issue__in_volume__in_journal=self).aggregate(
+ avg=Avg(F('publication_date') - F('submission_date')))['avg']
+ if duration:
+ return duration.total_seconds() / 86400
+ return 0
+
+ def citation_rate(self, tier=None):
+ """Return the citation rate in units of nr citations per article per year."""
+ from journals.models import Publication
+ publications = Publication.objects.filter(in_issue__in_volume__in_journal=self)
+ if tier:
+ publications = publications.filter(
+ accepted_submission__eicrecommendations__recommendation=tier)
+ ncites = 0
+ deltat = 1 # to avoid division by zero
+ for pub in publications:
+ if pub.citedby and pub.latest_citedby_update:
+ ncites += len(pub.citedby)
+ deltat += (pub.latest_citedby_update.date() - pub.publication_date).days
+ return (ncites * 365.25/deltat)
+
+ def citedby_impact_factor(self, year):
+ """Compute the impact factor for a given year YYYY, from Crossref cited-by data.
+
+ This is defined as the total number of citations in year YYYY
+ for all papers published in years YYYY-1 and YYYY-2, divided
+ by the number of papers published in year YYYY.
+ """
+ publications = self.get_publications().filter(
+ models.Q(publication_date__year=int(year)-1) |
+ models.Q(publication_date__year=int(year)-2))
+ nrpub = publications.count()
+ if nrpub == 0:
+ return 0
+ ncites = 0
+ for pub in publications:
+ if pub.citedby and pub.latest_citedby_update:
+ for citation in pub.citedby:
+ if citation['year'] == year:
+ ncites += 1
+ return ncites / nrpub
diff --git a/journals/models/publication.py b/journals/models/publication.py
new file mode 100644
index 0000000000000000000000000000000000000000..0e6439a99d7c7b8e585e0652379c74ae02f31a44
--- /dev/null
+++ b/journals/models/publication.py
@@ -0,0 +1,368 @@
+__copyright__ = "Copyright © Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
+from decimal import Decimal
+
+from django.contrib.postgres.fields import JSONField
+from django.core.exceptions import ValidationError
+from django.db import models
+from django.db.models import Min, Sum
+from django.urls import reverse
+
+from ..behaviors import doi_publication_validator
+from ..constants import (STATUS_DRAFT, STATUS_PUBLISHED,
+ PUBLICATION_PUBLISHED, CCBY4, CC_LICENSES, CC_LICENSES_URI, PUBLICATION_STATUSES)
+from ..helpers import paper_nr_string
+from ..managers import PublicationQuerySet
+
+from scipost.constants import SCIPOST_DISCIPLINES, SCIPOST_SUBJECT_AREAS, SCIPOST_APPROACHES
+from scipost.fields import ChoiceArrayField
+
+
+class PublicationAuthorsTable(models.Model):
+ """
+ PublicationAuthorsTable represents an author of a Publication.
+
+ Fields:
+ * publication
+ * profile
+ * affiliations: for this author/Publication (supersede profile.affiliations)
+ * order: the ordinal position of this author in this Publication's list of authors.
+ """
+
+ publication = models.ForeignKey('journals.Publication', on_delete=models.CASCADE,
+ related_name='authors')
+ profile = models.ForeignKey('profiles.Profile', on_delete=models.PROTECT,
+ blank=True, null=True)
+ affiliations = models.ManyToManyField('organizations.Organization', blank=True)
+ order = models.PositiveSmallIntegerField()
+
+ class Meta:
+ ordering = ('order',)
+
+ def __str__(self):
+ return str(self.profile)
+
+ def save(self, *args, **kwargs):
+ """Auto increment order number if not explicitly set."""
+ if not self.order:
+ self.order = self.publication.authors.count() + 1
+ return super().save(*args, **kwargs)
+
+ @property
+ def is_registered(self):
+ """Check if author is registered at SciPost."""
+ return self.profile.contributor is not None
+
+ @property
+ def first_name(self):
+ """Return first name of author."""
+ return self.profile.first_name
+
+ @property
+ def last_name(self):
+ """Return last name of author."""
+ return self.profile.last_name
+
+
+
+class Publication(models.Model):
+ """A Publication is an object directly related to an accepted Submission.
+
+ It contains metadata, the actual publication file, author data, etc. etc.
+ It may be directly related to a Journal or to an Issue.
+ """
+
+ # Publication data
+ accepted_submission = models.OneToOneField('submissions.Submission', on_delete=models.CASCADE,
+ related_name='publication')
+ in_issue = models.ForeignKey(
+ 'journals.Issue', on_delete=models.CASCADE, null=True, blank=True,
+ help_text='Assign either an Issue or Journal to the Publication')
+ in_journal = models.ForeignKey(
+ 'journals.Journal', on_delete=models.CASCADE, null=True, blank=True,
+ help_text='Assign either an Issue or Journal to the Publication')
+ paper_nr = models.PositiveSmallIntegerField()
+ status = models.CharField(max_length=8,
+ choices=PUBLICATION_STATUSES, default=STATUS_DRAFT)
+
+ # Core fields
+ title = models.CharField(max_length=300)
+ author_list = models.CharField(max_length=10000, verbose_name="author list")
+ abstract = models.TextField()
+ abstract_jats = models.TextField(blank=True, default='',
+ help_text='JATS version of abstract for Crossref deposit')
+ pdf_file = models.FileField(upload_to='UPLOADS/PUBLICATIONS/%Y/%m/', max_length=200)
+ discipline = models.CharField(max_length=20, choices=SCIPOST_DISCIPLINES, default='physics')
+ subject_area = models.CharField(max_length=10, choices=SCIPOST_SUBJECT_AREAS,
+ verbose_name='Primary subject area', default='Phys:QP')
+ secondary_areas = ChoiceArrayField(
+ models.CharField(max_length=10, choices=SCIPOST_SUBJECT_AREAS), blank=True, null=True)
+ approaches = ChoiceArrayField(
+ models.CharField(max_length=24, choices=SCIPOST_APPROACHES),
+ blank=True, null=True, verbose_name='approach(es) [optional]')
+
+ # Authors
+ authors_claims = models.ManyToManyField('scipost.Contributor', blank=True,
+ related_name='claimed_publications')
+ authors_false_claims = models.ManyToManyField('scipost.Contributor', blank=True,
+ related_name='false_claimed_publications')
+
+ cc_license = models.CharField(max_length=32, choices=CC_LICENSES, default=CCBY4)
+
+ # Funders
+ grants = models.ManyToManyField('funders.Grant', blank=True)
+ funders_generic = models.ManyToManyField('funders.Funder', blank=True) # not linked to a grant
+ pubfractions_confirmed_by_authors = models.BooleanField(default=False)
+
+ # Metadata
+ metadata = JSONField(default=dict, blank=True, null=True)
+ metadata_xml = models.TextField(blank=True) # for Crossref deposit
+ metadata_DOAJ = JSONField(default=dict, blank=True, null=True)
+ doi_label = models.CharField(max_length=200, unique=True, db_index=True,
+ validators=[doi_publication_validator])
+ BiBTeX_entry = models.TextField(blank=True)
+ doideposit_needs_updating = models.BooleanField(default=False)
+ citedby = JSONField(default=dict, blank=True, null=True)
+ number_of_citations = models.PositiveIntegerField(default=0)
+
+ # Topics for semantic linking
+ topics = models.ManyToManyField('ontology.Topic', blank=True)
+
+ # Date fields
+ submission_date = models.DateField(verbose_name='submission date')
+ acceptance_date = models.DateField(verbose_name='acceptance date')
+ publication_date = models.DateField(verbose_name='publication date')
+ latest_citedby_update = models.DateTimeField(null=True, blank=True)
+ latest_metadata_update = models.DateTimeField(blank=True, null=True)
+ latest_activity = models.DateTimeField(auto_now=True) # Needs `auto_now` as its not explicity updated anywhere?
+
+ objects = PublicationQuerySet.as_manager()
+
+ class Meta:
+ default_related_name = 'publications'
+ ordering = ('-publication_date', '-paper_nr')
+
+ def __str__(self):
+ return '{cite}, {title} by {authors}, {date}'.format(
+ cite=self.citation,
+ title=self.title[:30],
+ authors=self.author_list[:30],
+ date=self.publication_date.strftime('%Y-%m-%d'))
+
+ def clean(self):
+ """Check if either a valid Journal or Issue is assigned to the Publication."""
+ if not (self.in_journal or self.in_issue):
+ raise ValidationError({
+ 'in_journal': ValidationError(
+ 'Either assign a Journal or Issue to this Publication', code='required'),
+ 'in_issue': ValidationError(
+ 'Either assign a Journal or Issue to this Publication', code='required'),
+ })
+ if self.in_journal and self.in_issue:
+ # Assigning both a Journal and an Issue will screw up the database
+ raise ValidationError({
+ 'in_journal': ValidationError(
+ 'Either assign only a Journal or Issue to this Publication', code='invalid'),
+ 'in_issue': ValidationError(
+ 'Either assign only a Journal or Issue to this Publication', code='invalid'),
+ })
+ if self.in_issue and not self.get_journal().has_issues:
+ # Assigning both a Journal and an Issue will screw up the database
+ raise ValidationError({
+ 'in_issue': ValidationError(
+ 'This journal does not allow the use of Issues',
+ code='invalid'),
+ })
+ if self.in_journal and self.get_journal().has_issues:
+ # Assigning both a Journal and an Issue will screw up the database
+ raise ValidationError({
+ 'in_journal': ValidationError(
+ 'This journal does not allow the use of individual Publications',
+ code='invalid'),
+ })
+
+ def get_absolute_url(self):
+ return reverse('scipost:publication_detail', args=(self.doi_label,))
+
+ def get_cc_license_URI(self):
+ for (key, val) in CC_LICENSES_URI:
+ if key == self.cc_license:
+ return val
+ raise KeyError
+
+ def get_all_affiliations(self):
+ """
+ Returns all author affiliations.
+ """
+ from organizations.models import Organization
+ return Organization.objects.filter(
+ publicationauthorstable__publication=self
+ ).annotate(order=Min('publicationauthorstable__order')).order_by('order')
+
+ def get_all_funders(self):
+ from funders.models import Funder
+ return Funder.objects.filter(
+ models.Q(grants__publications=self) | models.Q(publications=self)).distinct()
+
+ def get_organizations(self):
+ """
+ Returns a queryset of all Organizations which are associated to this Publication,
+ through being in author affiliations, funders or generic funders.
+ """
+ from organizations.models import Organization
+ return Organization.objects.filter(
+ models.Q(publicationauthorstable__publication=self) |
+ models.Q(funder__grants__publications=self) |
+ models.Q(funder__publications=self)).distinct()
+
+ @property
+ def doi_string(self):
+ return '10.21468/' + self.doi_label
+
+ @property
+ def is_draft(self):
+ return self.status == STATUS_DRAFT
+
+ @property
+ def is_published(self):
+ if self.status != PUBLICATION_PUBLISHED:
+ return False
+
+ if self.in_issue:
+ return self.in_issue.status == STATUS_PUBLISHED
+ elif self.in_journal:
+ return self.in_journal.active
+ return False
+
+ @property
+ def has_xml_metadata(self):
+ return self.metadata_xml != ''
+
+ @property
+ def has_bibtex_entry(self):
+ return self.BiBTeX_entry != ''
+
+ @property
+ def has_citation_list(self):
+ return 'citation_list' in self.metadata and len(self.metadata['citation_list']) > 0
+
+ @property
+ def has_funding_statement(self):
+ return 'funding_statement' in self.metadata and self.metadata['funding_statement']
+
+ @property
+ def pubfractions_sum_to_1(self):
+ """ Checks that the support fractions sum up to one. """
+ return self.pubfractions.aggregate(Sum('fraction'))['fraction__sum'] == 1
+
+ @property
+ def citation(self):
+ """Return Publication name in the preferred citation format."""
+ if self.in_issue and self.in_issue.in_volume:
+ return '{journal} {volume}, {paper_nr} ({year})'.format(
+ journal=self.in_issue.in_volume.in_journal.name_abbrev,
+ volume=self.in_issue.in_volume.number,
+ paper_nr=self.get_paper_nr(),
+ year=self.publication_date.strftime('%Y'))
+ elif self.in_issue and self.in_issue.in_journal:
+ return '{journal} {issue}, {paper_nr} ({year})'.format(
+ journal=self.in_issue.in_journal.name_abbrev,
+ issue=self.in_issue.number,
+ paper_nr=self.get_paper_nr(),
+ year=self.publication_date.strftime('%Y'))
+ elif self.in_journal:
+ return '{journal} {paper_nr} ({year})'.format(
+ journal=self.in_journal.name_abbrev,
+ paper_nr=self.paper_nr,
+ year=self.publication_date.strftime('%Y'))
+ return '{paper_nr} ({year})'.format(
+ paper_nr=self.paper_nr,
+ year=self.publication_date.strftime('%Y'))
+
+ def get_cc_license_URI(self):
+ for (key, val) in CC_LICENSES_URI:
+ if key == self.cc_license:
+ return val
+ raise KeyError
+
+ def get_all_funders(self):
+ from funders.models import Funder
+ return Funder.objects.filter(
+ models.Q(grants__publications=self) | models.Q(publications=self)).distinct()
+
+ def get_journal(self):
+ if self.in_journal:
+ return self.in_journal
+ elif self.in_issue.in_journal:
+ return self.in_issue.in_journal
+ return self.in_issue.in_volume.in_journal
+
+ def journal_issn(self):
+ return self.get_journal().issn
+
+ def get_paper_nr(self):
+ if self.in_journal:
+ return self.paper_nr
+ return paper_nr_string(self.paper_nr)
+
+ def citation_rate(self):
+ """Returns the citation rate in units of nr citations per article per year."""
+ if self.citedby and self.latest_citedby_update:
+ ncites = len(self.citedby)
+ deltat = (self.latest_citedby_update.date() - self.publication_date).days
+ return (ncites * 365.25 / deltat)
+ else:
+ return 0
+
+ def get_similar_publications(self):
+ """Return 4 Publications with same subject area."""
+ return Publication.objects.published().filter(
+ subject_area=self.subject_area).exclude(id=self.id)[:4]
+
+ def get_issue_related_publications(self):
+ """Return 4 Publications within same Issue."""
+ return Publication.objects.published().filter(
+ in_issue=self.in_issue).exclude(id=self.id)[:4]
+
+
+class Reference(models.Model):
+ """A Refence is a reference used in a specific Publication."""
+ reference_number = models.IntegerField()
+ publication = models.ForeignKey('journals.Publication', on_delete=models.CASCADE)
+
+ authors = models.CharField(max_length=1028)
+ citation = models.CharField(max_length=1028, blank=True)
+ identifier = models.CharField(blank=True, max_length=128)
+ link = models.URLField(blank=True)
+
+ class Meta:
+ unique_together = ('reference_number', 'publication')
+ ordering = ['reference_number']
+ default_related_name = 'references'
+
+ def __str__(self):
+ return '[{}] {}, {}'.format(self.reference_number, self.authors[:30], self.citation[:30])
+
+
+class OrgPubFraction(models.Model):
+ """
+ Associates a fraction of the funding credit for a given publication to an Organization,
+ to help answer the question: who funded this research?
+
+ Fractions for a given publication should sum up to one.
+
+ This data is used to compile publicly-displayed information on Organizations
+ as well as to set suggested contributions from Partners.
+
+ To be set (ideally) during production phase, based on information provided by the authors.
+ """
+ organization = models.ForeignKey('organizations.Organization', on_delete=models.CASCADE,
+ related_name='pubfractions', blank=True, null=True)
+ publication = models.ForeignKey('journals.Publication', on_delete=models.CASCADE,
+ related_name='pubfractions')
+ fraction = models.DecimalField(max_digits=4, decimal_places=3, default=Decimal('0.000'))
+
+ class Meta:
+ unique_together = (('organization', 'publication'),)
diff --git a/journals/models/volume.py b/journals/models/volume.py
new file mode 100644
index 0000000000000000000000000000000000000000..df1500e1d0b0f0675fb8390324bfdc7b5f2242ad
--- /dev/null
+++ b/journals/models/volume.py
@@ -0,0 +1,82 @@
+__copyright__ = "Copyright © Stichting SciPost (SciPost Foundation)"
+__license__ = "AGPL v3"
+
+
+from django.core.exceptions import ValidationError
+from django.db import models
+from django.db.models import Avg, F
+from django.utils import timezone
+
+from ..behaviors import doi_volume_validator
+from ..constants import ISSUES_AND_VOLUMES
+
+
+class Volume(models.Model):
+ """
+ A Volume belongs to a specific Journal, and is a container for
+ either (multiple) Issue(s) or Publication(s).
+ """
+ in_journal = models.ForeignKey(
+ 'journals.Journal', limit_choices_to={'structure': ISSUES_AND_VOLUMES},
+ on_delete=models.CASCADE)
+ number = models.PositiveSmallIntegerField()
+ start_date = models.DateField(default=timezone.now)
+ until_date = models.DateField(default=timezone.now)
+ doi_label = models.CharField(max_length=200, unique=True, db_index=True,
+ validators=[doi_volume_validator])
+
+ class Meta:
+ default_related_name = 'volumes'
+ ordering = ('-until_date',)
+ unique_together = ('number', 'in_journal')
+
+ def __str__(self):
+ return str(self.in_journal) + ' Vol. ' + str(self.number)
+
+ def clean(self):
+ """Check if the Volume is assigned to a valid Journal."""
+ if not self.in_journal.has_volumes:
+ raise ValidationError({
+ 'in_journal': ValidationError('This journal does not allow for the use of Volumes',
+ code='invalid'),
+ })
+
+ @property
+ def doi_string(self):
+ return '10.21468/' + self.doi_label
+
+ def is_current(self):
+ today = timezone.now().date()
+ return self.start_date <= today and self.until_date >= today
+
+ def nr_publications(self, tier=None):
+ from journals.models import Publication
+ publications = Publication.objects.filter(in_issue__in_volume=self)
+ if tier:
+ publications = publications.filter(
+ accepted_submission__eicrecommendations__recommendation=tier)
+ return publications.count()
+
+ def avg_processing_duration(self):
+ from journals.models import Publication
+ duration = Publication.objects.filter(
+ in_issue__in_volume=self).aggregate(
+ avg=Avg(F('publication_date') - F('submission_date')))['avg']
+ if duration:
+ return duration.total_seconds() / 86400
+ return 0
+
+ def citation_rate(self, tier=None):
+ """Returns the citation rate in units of nr citations per article per year."""
+ from journals.models import Publication
+ publications = Publication.objects.filter(in_issue__in_volume=self)
+ if tier:
+ publications = publications.filter(
+ accepted_submission__eicrecommendations__recommendation=tier)
+ ncites = 0
+ deltat = 1 # to avoid division by zero
+ for pub in publications:
+ if pub.citedby and pub.latest_citedby_update:
+ ncites += len(pub.citedby)
+ deltat += (pub.latest_citedby_update.date() - pub.publication_date).days
+ return (ncites * 365.25 / deltat)