diff --git a/SciPost_v1/settings/base.py b/SciPost_v1/settings/base.py
index 0ca208465dd5f4706ee6a3421d8bb91d4eee9e0c..62c8ff2aa6d133346ce7476f8fcb4e83617fbba7 100644
--- a/SciPost_v1/settings/base.py
+++ b/SciPost_v1/settings/base.py
@@ -313,3 +313,42 @@ AUTH_PASSWORD_VALIDATORS = [
]
CSRF_FAILURE_VIEW = 'scipost.views.csrf_failure'
+
+# Logging
+LOGGING = {
+ 'version': 1,
+ 'disable_existing_loggers': False,
+ 'formatters': {
+ 'verbose': {
+ 'format': '[%(asctime)s] %(levelname)s | %(message)s'
+ },
+ },
+ 'handlers': {
+ 'scipost_file_arxiv': {
+ 'level': 'INFO',
+ 'class': 'logging.FileHandler',
+ 'filename': '/path/to/logs/arxiv.log',
+ 'formatter': 'verbose',
+ },
+ 'scipost_file_doi': {
+ 'level': 'INFO',
+ 'class': 'logging.FileHandler',
+ 'filename': '/path/to/logs/doi.log',
+ 'formatter': 'verbose',
+ },
+ },
+ 'loggers': {
+ 'scipost.services.arxiv': {
+ 'handlers': ['scipost_file_arxiv'],
+ 'level': 'INFO',
+ 'propagate': True,
+ 'formatter': 'simple',
+ },
+ 'scipost.services.doi': {
+ 'handlers': ['scipost_file_doi'],
+ 'level': 'INFO',
+ 'propagate': True,
+ 'formatter': 'simple',
+ },
+ },
+}
diff --git a/SciPost_v1/settings/local_JSC.py b/SciPost_v1/settings/local_JSC.py
index f4dcbe1891cd9a9b8ba42739749f2528e168a2f0..843fea24255bb1b2521b3144f4d0f173eb79d460 100644
--- a/SciPost_v1/settings/local_JSC.py
+++ b/SciPost_v1/settings/local_JSC.py
@@ -11,3 +11,7 @@ WEBPACK_LOADER['DEFAULT']['BUNDLE_DIR_NAME'] =\
MAILCHIMP_API_USER = get_secret("MAILCHIMP_API_USER")
MAILCHIMP_API_KEY = get_secret("MAILCHIMP_API_KEY")
+
+# Logging
+LOGGING['handlers']['scipost_file_arxiv']['filename'] = '/Users/jscaux/Sites/SciPost.org/scipost_v1/local_files/logs/arxiv.log'
+LOGGING['handlers']['scipost_file_doi']['filename'] = '/Users/jscaux/Sites/SciPost.org/scipost_v1/local_files/logs/doi.log'
diff --git a/SciPost_v1/settings/local_jorran.py b/SciPost_v1/settings/local_jorran.py
index cd2ed99b46436673da26e9b69da2ec69da258b0d..b458216b2d898d444ce1e586d892d86c76c97410 100644
--- a/SciPost_v1/settings/local_jorran.py
+++ b/SciPost_v1/settings/local_jorran.py
@@ -26,3 +26,7 @@ DATABASES['default']['PORT'] = '5433'
# iThenticate
ITHENTICATE_USERNAME = get_secret('ITHENTICATE_USERNAME')
ITHENTICATE_PASSWORD = get_secret('ITHENTICATE_PASSWORD')
+
+# Logging
+LOGGING['handlers']['scipost_file_arxiv']['filename'] = '/Users/jorranwit/Develop/SciPost/SciPost_v1/logs/arxiv.log'
+LOGGING['handlers']['scipost_file_doi']['filename'] = '/Users/jorranwit/Develop/SciPost/SciPost_v1/logs/doi.log'
diff --git a/SciPost_v1/settings/production.py b/SciPost_v1/settings/production.py
index ffba29aff8e844946a5124210c21372395a849c5..4d6bb7a6c1f88119eebe06c08b530fb341c53450 100644
--- a/SciPost_v1/settings/production.py
+++ b/SciPost_v1/settings/production.py
@@ -44,3 +44,7 @@ MAILCHIMP_API_KEY = get_secret("MAILCHIMP_API_KEY")
# iThenticate
ITHENTICATE_USERNAME = get_secret('ITHENTICATE_USERNAME')
ITHENTICATE_PASSWORD = get_secret('ITHENTICATE_PASSWORD')
+
+# Logging
+LOGGING['handlers']['scipost_file_arxiv']['filename'] = '/home/scipost/webapps/scipost/logs/arxiv.log'
+LOGGING['handlers']['scipost_file_doi']['filename'] = '/home/scipost/webapps/scipost/logs/doi.log'
diff --git a/journals/migrations/0003_auto_20180117_2323.py b/journals/migrations/0003_auto_20180117_2323.py
new file mode 100644
index 0000000000000000000000000000000000000000..5020b0dab1564a5cd8d66e0949cf841480621828
--- /dev/null
+++ b/journals/migrations/0003_auto_20180117_2323.py
@@ -0,0 +1,37 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.4 on 2018-01-17 22:23
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('journals', '0002_auto_20171229_1435'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='deposit',
+ name='doi_batch_id',
+ field=models.CharField(max_length=40),
+ ),
+ migrations.AlterField(
+ model_name='deposit',
+ name='metadata_xml',
+ field=models.TextField(blank=True, default=''),
+ preserve_default=False,
+ ),
+ migrations.AlterField(
+ model_name='deposit',
+ name='response_text',
+ field=models.TextField(blank=True, default=''),
+ preserve_default=False,
+ ),
+ migrations.AlterField(
+ model_name='deposit',
+ name='timestamp',
+ field=models.CharField(max_length=40),
+ ),
+ ]
diff --git a/journals/models.py b/journals/models.py
index 9ffed4c252f4da7890dd28034a3bfd1e81831c33..ad42c6973258bbf8f70bf7905ac98985593925a2 100644
--- a/journals/models.py
+++ b/journals/models.py
@@ -226,20 +226,22 @@ class Deposit(models.Model):
All deposit history is thus contained here.
"""
publication = models.ForeignKey(Publication, on_delete=models.CASCADE)
- timestamp = models.CharField(max_length=40, default='')
- doi_batch_id = models.CharField(max_length=40, default='')
- metadata_xml = models.TextField(blank=True, null=True)
+ 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, null=True)
+ response_text = models.TextField(blank=True)
deposit_successful = models.NullBooleanField(default=None)
class Meta:
ordering = ['-timestamp']
def __str__(self):
- return (self.deposition_date.strftime('%Y-%m-%D') +
- ' for ' + self.publication.doi_label)
+ _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):
diff --git a/journals/views.py b/journals/views.py
index ae5562dfd3e6e727cb706c789c15da175f215b32..81ebaebce9d3cb16d9cca586d195158d00c8aafc 100644
--- a/journals/views.py
+++ b/journals/views.py
@@ -3,13 +3,13 @@ import json
import os
import random
import requests
+import shutil
import string
import xml.etree.ElementTree as ET
from django.contrib.auth.decorators import login_required
from django.contrib.contenttypes.models import ContentType
from django.core.urlresolvers import reverse
-from django.core.files.base import ContentFile
from django.conf import settings
from django.contrib import messages
from django.http import Http404
@@ -719,6 +719,11 @@ def metadata_xml_deposit(request, doi_label, option='test'):
Makes use of the python requests module.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
+
+ if publication.metadata_xml is None:
+ errormessage = 'This publication has no metadata. Produce it first before saving it.'
+ return render(request, 'scipost/error.html', context={'errormessage': errormessage})
+
timestamp = (publication.metadata_xml.partition(
'<timestamp>'))[2].partition('</timestamp>')[0]
doi_batch_id = (publication.metadata_xml.partition(
@@ -726,46 +731,58 @@ def metadata_xml_deposit(request, doi_label, option='test'):
path = (settings.MEDIA_ROOT + publication.in_issue.path + '/'
+ publication.get_paper_nr() + '/' + publication.doi_label.replace('.', '_')
+ '_Crossref_' + timestamp + '.xml')
+
if os.path.isfile(path):
errormessage = 'The metadata file for this metadata timestamp already exists'
return render(request, 'scipost/error.html', context={'errormessage': errormessage})
+
if option == 'deposit' and not settings.DEBUG:
# CAUTION: Real deposit only on production (non-debug-mode)
url = 'http://doi.crossref.org/servlet/deposit'
else:
url = 'http://test.crossref.org/servlet/deposit'
- if publication.metadata_xml is None:
- errormessage = 'This publication has no metadata. Produce it first before saving it.'
- return render(request, 'scipost/error.html', context={'errormessage': errormessage})
# First perform the actual deposit to Crossref
params = {
'operation': 'doMDUpload',
'login_id': settings.CROSSREF_LOGIN_ID,
'login_passwd': settings.CROSSREF_LOGIN_PASSWORD,
}
- files = {'fname': ('metadata.xml', publication.metadata_xml, 'multipart/form-data')}
+ files = {
+ 'fname': ('metadata.xml', publication.metadata_xml.encode('utf-8'), 'multipart/form-data')
+ }
r = requests.post(url, params=params, files=files)
response_headers = r.headers
response_text = r.text
# Then create the associated Deposit object (saving the metadata to a file)
if option == 'deposit':
- content = ContentFile(publication.metadata_xml)
deposit = Deposit(publication=publication, timestamp=timestamp, doi_batch_id=doi_batch_id,
metadata_xml=publication.metadata_xml, deposition_date=timezone.now())
- deposit.metadata_xml_file.save(path, content)
deposit.response_text = r.text
+
+ # Save the filename with timestamp
+ path_with_timestamp = '{issue}/{paper}/{doi}_Crossref_{timestamp}.xml'.format(
+ issue=publication.in_issue.path,
+ paper=publication.get_paper_nr(),
+ doi=publication.doi_label.replace('.', '_'),
+ timestamp=timestamp)
+ f = open(settings.MEDIA_ROOT + path_with_timestamp, 'w')
+ f.write(publication.metadata_xml)
+ f.close()
+
+ # Copy file
+ path_without_timestamp = '{issue}/{paper}/{doi}_Crossref.xml'.format(
+ issue=publication.in_issue.path,
+ paper=publication.get_paper_nr(),
+ doi=publication.doi_label.replace('.', '_'))
+ shutil.copyfile(settings.MEDIA_ROOT + path_with_timestamp,
+ settings.MEDIA_ROOT + path_without_timestamp)
+
+ deposit.metadata_xml_file = path_with_timestamp
deposit.save()
publication.latest_crossref_deposit = timezone.now()
publication.save()
- # Save a copy to the filename without timestamp
- path1 = (settings.MEDIA_ROOT + publication.in_issue.path + '/'
- + publication.get_paper_nr() + '/' + publication.doi_label.replace('.', '_')
- + '_Crossref.xml')
- f = open(path1, 'w')
- f.write(publication.metadata_xml)
- f.close()
context = {
'option': option,
@@ -807,6 +824,7 @@ def metadata_DOAJ_deposit(request, doi_label):
Makes use of the python requests module.
"""
publication = get_object_or_404(Publication, doi_label=doi_label)
+
if not publication.metadata_DOAJ:
messages.warning(request, '<h3>%s</h3>Failed: please first produce '
'DOAJ metadata before depositing.' % publication.doi_label)
@@ -820,8 +838,8 @@ def metadata_DOAJ_deposit(request, doi_label):
if os.path.isfile(path):
errormessage = 'The metadata file for this metadata timestamp already exists'
return render(request, 'scipost/error.html', context={'errormessage': errormessage})
- url = 'https://doaj.org/api/v1/articles'
+ url = 'https://doaj.org/api/v1/articles'
params = {
'api_key': settings.DOAJ_API_KEY,
}
@@ -833,21 +851,32 @@ def metadata_DOAJ_deposit(request, doi_label):
publication.doi_label, r.text))
# Then create the associated Deposit object (saving the metadata to a file)
- content = ContentFile(json.dumps(publication.metadata_DOAJ))
deposit = DOAJDeposit(publication=publication, timestamp=timestamp,
metadata_DOAJ=publication.metadata_DOAJ, deposition_date=timezone.now())
- deposit.metadata_DOAJ_file.save(path, content)
deposit.response_text = r.text
- deposit.save()
- # Save a copy to the filename without timestamp
- path1 = (settings.MEDIA_ROOT + publication.in_issue.path + '/'
- + publication.get_paper_nr() + '/' + publication.doi_label.replace('.', '_')
- + '_DOAJ.json')
- f = open(path1, 'w')
+ # Save a copy to the filename with and without timestamp
+ path_with_timestamp = '{issue}/{paper}/{doi}_DOAJ_{timestamp}.json'.format(
+ issue=publication.in_issue.path,
+ paper=publication.get_paper_nr(),
+ doi=publication.doi_label.replace('.', '_'),
+ timestamp=timestamp)
+ f = open(settings.MEDIA_ROOT + path_with_timestamp, 'w')
f.write(json.dumps(publication.metadata_DOAJ))
f.close()
+ # Copy file
+ path_without_timestamp = '{issue}/{paper}/{doi}_DOAJ.json'.format(
+ issue=publication.in_issue.path,
+ paper=publication.get_paper_nr(),
+ doi=publication.doi_label.replace('.', '_'))
+ shutil.copyfile(settings.MEDIA_ROOT + path_with_timestamp,
+ settings.MEDIA_ROOT + path_without_timestamp)
+
+ # Save the database entry
+ deposit.metadata_DOAJ_file = path_with_timestamp
+ deposit.save()
+
messages.success(request, '<h3>%s</h3>Successfull deposit of metadata DOAJ.'
% publication.doi_label)
return redirect(reverse('journals:manage_metadata',
@@ -863,7 +892,7 @@ def mark_doaj_deposit_success(request, deposit_id, success):
deposit.deposit_successful = False
deposit.save()
return redirect(reverse('journals:manage_metadata',
- kwargs={'doi_label': deposit.publication.doi_label}))
+ kwargs={'doi_label': deposit.publication.doi_label}))
@permission_required('scipost.can_publish_accepted_submission', return_403=True)
diff --git a/scipost/services.py b/scipost/services.py
index 3df2ce70fb903edf7ea290f81830ce69094d566c..1e7a9c06881035b2a03440c817a499693649ef95 100644
--- a/scipost/services.py
+++ b/scipost/services.py
@@ -3,11 +3,17 @@ import feedparser
import requests
import datetime
import dateutil.parser
+import logging
+
+arxiv_logger = logging.getLogger('scipost.services.arxiv')
+doi_logger = logging.getLogger('scipost.services.doi')
class DOICaller:
def __init__(self, doi_string):
self.doi_string = doi_string
+ doi_logger.info('New DOI call for %s' % doi_string)
+
self._call_crosslink()
if self.is_valid:
self._format_data()
@@ -15,12 +21,24 @@ class DOICaller:
def _call_crosslink(self):
url = 'http://api.crossref.org/works/%s' % self.doi_string
request = requests.get(url)
+
+ doi_logger.info('GET [{doi}] [request] | {url}'.format(
+ doi=self.doi_string,
+ url=url,
+ ))
+
if request.ok:
self.is_valid = True
self._crossref_data = request.json()['message']
else:
self.is_valid = False
+ doi_logger.info('GET [{doi}] [response {valid}] | {response}'.format(
+ doi=self.doi_string,
+ valid='VALID' if self.is_valid else 'INVALID',
+ response=request.text,
+ ))
+
def _format_data(self):
data = self._crossref_data
title = data['title'][0]
@@ -41,6 +59,11 @@ class DOICaller:
'pub_date': pub_date,
}
+ doi_logger.info('GET [{doi}] [formatted data] | {data}'.format(
+ doi=self.doi_string,
+ data=self.data,
+ ))
+
def _get_pages(self, data):
# For Physical Review
pages = data.get('article-number', '')
@@ -68,6 +91,7 @@ class ArxivCaller:
def __init__(self, identifier):
self.identifier = identifier
+ arxiv_logger.info('New ArXiv call for identifier %s' % identifier)
self._call_arxiv()
if self.is_valid:
self._format_data()
@@ -76,14 +100,25 @@ class ArxivCaller:
url = self.query_base_url % self.identifier
request = requests.get(url)
response_content = feedparser.parse(request.content)
- arxiv_data = response_content['entries'][0]
- if self._search_result_present(arxiv_data):
+ arxiv_logger.info('GET [{arxiv}] [request] | {url}'.format(
+ arxiv=self.identifier,
+ url=url,
+ ))
+
+ if self._search_result_present(response_content):
+ arxiv_data = response_content['entries'][0]
self.is_valid = True
self._arxiv_data = arxiv_data
self.metadata = response_content
else:
self.is_valid = False
+ arxiv_logger.info('GET [{arxiv}] [response {valid}] | {response}'.format(
+ arxiv=self.identifier,
+ valid='VALID' if self.is_valid else 'INVALID',
+ response=response_content,
+ ))
+
def _format_data(self):
data = self._arxiv_data
title = data['title']
@@ -102,6 +137,12 @@ class ArxivCaller:
'abstract': abstract, # Duplicate for Commentary/Submission cross-compatibility
'pub_date': pub_date,
}
+ arxiv_logger.info('GET [{arxiv}] [formatted data] | {data}'.format(
+ arxiv=self.identifier,
+ data=self.data,
+ ))
def _search_result_present(self, data):
- return 'title' in data
+ if len(data.get('entries', [])) > 0:
+ return 'title' in data['entries'][0]
+ return False
diff --git a/scipost/static/scipost/assets/css/_navbar.scss b/scipost/static/scipost/assets/css/_navbar.scss
index c74f30a0f50d61d9ff505251fbcd1dfa3548353d..8b32a2115a3afdcae2c6d4f521dbdf295a5c026e 100644
--- a/scipost/static/scipost/assets/css/_navbar.scss
+++ b/scipost/static/scipost/assets/css/_navbar.scss
@@ -15,10 +15,10 @@
.navbar-nav {
flex-direction: row;
- overflow: scroll;
- -ms-overflow-style: none;
+ overflow: auto;
+ // -ms-overflow-style: none;
-webkit-overflow-scrolling: touch;
- overflow: -moz-scrollbars-none;
+ // overflow: -moz-scrollbars-none;
.nav-link {
padding-left: .5rem;
@@ -29,17 +29,17 @@
}
// Hide scrollbars... trying to
-::-webkit-scrollbar,
-::-webkit-scrollbar-button,
-::-webkit-scrollbar-track,
-::-webkit-scrollbar-track-piece,
-::-webkit-scrollbar-thumb,
-::-webkit-scrollbar-corner,
-::-webkit-resizer {
- display: none;
- background: rgba(0,0,0,0);
- background-color: rgba(0,0,0,0);
-}
+// ::-webkit-scrollbar,
+// ::-webkit-scrollbar-button,
+// ::-webkit-scrollbar-track,
+// ::-webkit-scrollbar-track-piece,
+// ::-webkit-scrollbar-thumb,
+// ::-webkit-scrollbar-corner,
+// ::-webkit-resizer {
+// // display: none;
+// background: rgba(0,0,0,0);
+// background-color: rgba(0,0,0,0);
+// }
.container-outside {
&.main-nav {
diff --git a/submissions/constants.py b/submissions/constants.py
index 5252e752e27ddad562a456d07f9893ef681cef8f..b360f7f6f3c74e164d86266b63dc11c7e165ce91 100644
--- a/submissions/constants.py
+++ b/submissions/constants.py
@@ -164,7 +164,7 @@ RANKING_CHOICES = (
REPORT_REC = (
(None, '-'),
- (1, 'Publish as Tier I (top 10% of papers in this journal, qualifies as Select) NOTE: SELECT NOT YET OPEN, STARTS EARLY 2017'),
+ (1, 'Publish as Tier I (top 10% of papers in this journal, qualifies as Select)'),
(2, 'Publish as Tier II (top 50% of papers in this journal)'),
(3, 'Publish as Tier III (meets the criteria of this journal)'),
(-1, 'Ask for minor revision'),
diff --git a/submissions/forms.py b/submissions/forms.py
index ee1365c2b8033b8aca7292f66a0cee41ed5facb5..c13adbe6e338f45fe1a42840c05e0d26ca5ec337 100644
--- a/submissions/forms.py
+++ b/submissions/forms.py
@@ -187,7 +187,7 @@ class SubmissionChecks:
class SubmissionIdentifierForm(SubmissionChecks, forms.Form):
- IDENTIFIER_PATTERN_NEW = r'^[0-9]{4,}.[0-9]{4,5}v[0-9]{1,2}$'
+ IDENTIFIER_PATTERN_NEW = r'^[0-9]{4,}\.[0-9]{4,5}v[0-9]{1,2}$'
IDENTIFIER_PLACEHOLDER = 'new style (with version nr) ####.####(#)v#(#)'
identifier = forms.RegexField(regex=IDENTIFIER_PATTERN_NEW, strip=True,
@@ -818,7 +818,7 @@ class iThenticateReportForm(forms.ModelForm):
client = self.client
response = client.documents.get(self.document_id)
if response['status'] == 200:
- return response.get('data')[0].get('documents')
+ 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:
diff --git a/submissions/migrations/0002_auto_20180118_1033.py b/submissions/migrations/0002_auto_20180118_1033.py
new file mode 100644
index 0000000000000000000000000000000000000000..d4e1758aebb750e181a711cbf7cebe74e6a0875f
--- /dev/null
+++ b/submissions/migrations/0002_auto_20180118_1033.py
@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.4 on 2018-01-18 09:33
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('submissions', '0001_initial'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='eicrecommendation',
+ name='recommendation',
+ field=models.SmallIntegerField(choices=[(None, '-'), (1, 'Publish as Tier I (top 10% of papers in this journal, qualifies as Select)'), (2, 'Publish as Tier II (top 50% of papers in this journal)'), (3, 'Publish as Tier III (meets the criteria of this journal)'), (-1, 'Ask for minor revision'), (-2, 'Ask for major revision'), (-3, 'Reject')]),
+ ),
+ migrations.AlterField(
+ model_name='report',
+ name='recommendation',
+ field=models.SmallIntegerField(choices=[(None, '-'), (1, 'Publish as Tier I (top 10% of papers in this journal, qualifies as Select)'), (2, 'Publish as Tier II (top 50% of papers in this journal)'), (3, 'Publish as Tier III (meets the criteria of this journal)'), (-1, 'Ask for minor revision'), (-2, 'Ask for major revision'), (-3, 'Reject')]),
+ ),
+ ]