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A Django app for adding sets of scientific publications with PubMed metadata to a Django site with django CMS-specific features

Project description

djangocms-lab-publications is a Django app for adding sets of scientific publications with PubMed metadata to a Django site with django CMS-specific features. It uses pubmed-lookup to query PubMed using PubMed IDs or PubMed URLs.

Source code is available on GitHub at mfcovington/djangocms-lab-publications. Information about and source code for pubmed-lookup is available on GitHub at mfcovington/pubmed-lookup.

Installation

PyPI

pip install djangocms-lab-publications

GitHub

pip install https://github.com/mfcovington/djangocms-lab-publications/releases/download/0.1.4/djangocms-lab-publications-0.1.4.tar.gz

Configuration

Do the following in settings.py:

  • Add cms_lab_publications and its dependencies to INSTALLED_APPS:
INSTALLED_APPS = (
    ...
    'taggit',
    'taggit_helpers',
    'cms_lab_publications',
    'easy_thumbnails',
    'filer',
    'mptt',
)
  • Specify your media settings, if necessary:
MEDIA_URL = '/media/'
MEDIA_ROOT = os.path.join(BASE_DIR, 'media')
  • Add filer and easy_thumbnail settings:
# For filer's Django 1.7 compatibility
MIGRATION_MODULES = {
    ...
    'filer': 'filer.migrations_django',
}

# For easy_thumbnails to support retina displays (recent MacBooks, iOS)
THUMBNAIL_HIGH_RESOLUTION = True
THUMBNAIL_QUALITY = 95
THUMBNAIL_PROCESSORS = (
    'easy_thumbnails.processors.colorspace',
    'easy_thumbnails.processors.autocrop',
    'filer.thumbnail_processors.scale_and_crop_with_subject_location',
    'easy_thumbnails.processors.filters',
)
THUMBNAIL_PRESERVE_EXTENSIONS = ('png', 'gif')
THUMBNAIL_SUBDIR = 'versions'

If cms_lab_publications is used in a project served by Apache, a config directory must be created within the Apache user’s home directory. This config directory is used by code within biopython’s Bio.Entrez.Parser.DataHandler which is used by pubmed_lookup, a dependency of cms_lab_publications.

# In this snippet, the Apache user is 'www-data' and
# the Apache user's home directory is '/var/www/'
sudo su - root
cd /var/www/
chown :www-data
chmod g+s
mkdir -p /var/www/.config/biopython/Bio/Entrez/DTDs

Migrations

Create and perform cms_lab_publications migrations:

python manage.py makemigrations cms_lab_publications
python manage.py migrate

Usage

  • Start the development server:
python manage.py runserver
  • Visit: http://127.0.0.1:8000/
  • Create a CMS page.
  • Insert the Publication Set Plugin into a placeholder field.

Version 0.1.4

Revision History

0.1.4 2015-06-24

  • Allow manual entry of Publications that don’t have a PubMed ID
  • Use django-taggit-helpers in admin
  • Rename deprecated queryset method
  • Configure bumpversion & wheel for easier distribution
  • Convert README and changelog to reStructuredText for distribution via PyPI
  • Minor changes to admin interface
    • Change pagination description to ‘pubs per page’
    • Add/update help text for ‘tags’ and ‘pagination’

0.1.3 2015-06-03

  • Allow bulk PubMed queries for a Publication Set
  • Allow a Publication Set to be created without publications
  • Default to no pagination (hides page ‘1’ button for short publication sets)
  • Set default Publication Set label to ‘Publications’
  • Admin improvements
    • Publication Admin
      • Reorder Publication Admin’s inlines
      • Add year and PubMed ID to Publication Admin search field
      • Display (and sort by) # of Publication Sets in Publication Admin
    • Publication Set Admin
      • In Publication Set Admin, move publications from a tabular inline to a vertical filter
      • Reorder Publication Set Admin’s list display items
      • Filter Publication Set records by whether its Bulk PubMed Query failed
      • Display whether a Publication Set’s Bulk PubMed Query status is OK
    • Other
      • Update and improve layout of help text
      • Add short descriptions for custom list display items
      • Add docstring for MissingAttachmentListFilter

0.1.2 2015-05-27

  • Expand documentation for installation and configuration
  • Add mini_citation field to Publication
    • Helps identify publication when in edit mode (without expanding PubMed Metadata fieldset)
    • Helps naming associated files (PDF, Supplemental, and Image) by providing a base name
    • Bumps pubmed-lookup dependency to version 0.1.1
  • Many improvements to Publication and Publication Set Admins
    • Rearrange Publication Admin fieldsets
    • Add PublicationSetInline to PublicationAdmin
    • Add save button across tops of Publication and Publication Set Admins
    • Now Powered by Blackina
    • Display whether a record has PDF/Supp/Image attachments in Publication Admin
    • Filter PublicationAdmin by missing/existing attachments
    • Filter Publication and Publication Set Admins by tags for the current model only
    • Show (and sort by) ‘number of publications’ for records in Publication Set Admin

0.1.1 2015-05-23

  • Allow multiple Publication Set plugins per page
  • Use Publication Set’s name, not label, for __str__ and ordering

0.1.0 2015-05-22

  • A Django app for adding sets of scientific publications with PubMed metadata to a Django site with django CMS-specific features

Project details


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