def setup_web_files(hars, output_dir):
from jinja2 import Environment, FileSystemLoader
env = Environment(loader = FileSystemLoader('.'))
template_input = env.get_template('index-template.html')
output_file = open(filejoin(output_dir, 'index.html'), 'w')
template_input.stream(hars = hars, genome_url_prefixes = GENOME_URL_PREFIXES).dump(output_file)
output_file.close()
shutil.copyfile('style.css', filejoin(output_dir, 'style.css'))
def setup_web_files(hars, output_dir):
from jinja2 import Environment, FileSystemLoader
env = Environment(loader=FileSystemLoader('.'))
template_input = env.get_template('index-template.html')
output_file = open(filejoin(output_dir, 'index.html'), 'w')
template_input.stream(
hars=hars, genome_url_prefixes=GENOME_URL_PREFIXES).dump(output_file)
output_file.close()
shutil.copyfile('style.css', filejoin(output_dir, 'style.css'))
def convert_imgs(hars, output_dir):
img_dir = filejoin(output_dir, 'imgs')
os.mkdir(img_dir)
for har in hars:
har_dir = filejoin(img_dir, str(har))
if not isdir(har_dir): os.mkdir(har_dir)
for species in hars[har]['species']:
species_dir = filejoin(har_dir, species)
if not isdir(species_dir): os.mkdir(species_dir)
for img_num, original_path in hars[har]['species'][species]['imgs'].iteritems():
target_path = filejoin(species_dir, str(img_num))
convert_img(original_path, target_path)
def convert_imgs(hars, output_dir):
img_dir = filejoin(output_dir, 'imgs')
os.mkdir(img_dir)
for har in hars:
har_dir = filejoin(img_dir, str(har))
if not isdir(har_dir): os.mkdir(har_dir)
for species in hars[har]['species']:
species_dir = filejoin(har_dir, species)
if not isdir(species_dir): os.mkdir(species_dir)
for img_num, original_path in hars[har]['species'][species][
'imgs'].iteritems():
target_path = filejoin(species_dir, str(img_num))
convert_img(original_path, target_path)
def find_imgs(hars, img_dir_path, skipped):
for dirname, _, filenames in os.walk(img_dir_path):
for filename in filenames:
filepath = filejoin(dirname, filename)
match = ALLOWED_IMG_RE.match(filename)
if not match:
continue
har = int(match.group('har'))
if not har in hars:
if skipped: print "Skipping -- unknown HAR '%d': %s" % (har, filepath)
continue
img_species = match.group('species')
species = IMG_SPECIES_TO_CSV.get(img_species)
if not species:
if skipped: print "Skipping -- unknown species '%s': %s" % (species, filepath)
continue
img_num = int(match.group('num'))
hars[har]['species'][species]['imgs'][img_num] = filepath
def find_imgs(hars, img_dir_path, skipped):
for dirname, _, filenames in os.walk(img_dir_path):
for filename in filenames:
filepath = filejoin(dirname, filename)
match = ALLOWED_IMG_RE.match(filename)
if not match:
continue
har = int(match.group('har'))
if not har in hars:
if skipped:
print "Skipping -- unknown HAR '%d': %s" % (har, filepath)
continue
img_species = match.group('species')
species = IMG_SPECIES_TO_CSV.get(img_species)
if not species:
if skipped:
print "Skipping -- unknown species '%s': %s" % (species,
filepath)
continue
img_num = int(match.group('num'))
hars[har]['species'][species]['imgs'][img_num] = filepath
# http://www.i18nguy.com/unicode/language-identifiers.html LANGUAGE_CODE = 'en-us' SITE_ID = 1 # If you set this to False, Django will make some optimizations so as not # to load the internationalization machinery. USE_I18N = False # If you set this to False, Django will not format dates, numbers and # calendars according to the current locale USE_L10N = False # Absolute filesystem path to the directory that will hold user-uploaded files. # Example: "/home/media/media.lawrence.com/media/" MEDIA_ROOT = filejoin(SITE_DIR, 'media') # URL that handles the media served from MEDIA_ROOT. Make sure to use a # trailing slash. # Examples: "http://media.lawrence.com/media/", "http://example.com/media/" MEDIA_URL = urljoin(SITE_URL, 'media/') # Absolute path to the directory static files should be collected to. # Don't put anything in this directory yourself; store your static files # in apps' "static/" subdirectories and in STATICFILES_DIRS. # Example: "/home/media/media.lawrence.com/static/" STATIC_ROOT = '' # URL prefix for static files. # Example: "http://media.lawrence.com/static/" STATIC_URL = urljoin(SITE_URL, 'static/')
# http://www.i18nguy.com/unicode/language-identifiers.html LANGUAGE_CODE = 'en-us' SITE_ID = 1 # If you set this to False, Django will make some optimizations so as not # to load the internationalization machinery. USE_I18N = False # If you set this to False, Django will not format dates, numbers and # calendars according to the current locale USE_L10N = False # Absolute filesystem path to the directory that will hold user-uploaded files. # Example: "/home/media/media.lawrence.com/media/" MEDIA_ROOT = filejoin(SITE_DIR, 'media') #MEDIA_ROOT = os.path.join(SITE_DIR, 'media') # URL that handles the media served from MEDIA_ROOT. Make sure to use a # trailing slash. # Examples: "http://media.lawrence.com/media/", "http://example.com/media/" MEDIA_URL = urljoin(SITE_URL, 'media/') #MEDIA_URL = '/media/' # Absolute path to the directory static files should be collected to. # Don't put anything in this directory yourself; store your static files # in apps' "static/" subdirectories and in STATICFILES_DIRS. # Example: "/home/media/media.lawrence.com/static/" #STATIC_ROOT = '' STATIC_ROOT = SITE_DIR + "/static/"
# URL prefix for admin static files -- CSS, JavaScript and images.
# Make sure to use a trailing slash.
# Examples: "http://foo.com/static/admin/", "/static/admin/".
# (This setting is deprecated since Django 1.4--Samad)
# ADMIN_MEDIA_PREFIX = urljoin(SITE_URL, 'static/admin/')
ALLOWED_HOSTS = ['*']
if DJANGO_STATIC_AND_MEDIA:
# Additional locations of static files
STATICFILES_DIRS = (
# Put strings here, like "/home/html/static" or "C:/www/django/static".
# Always use forward slashes, even on Windows.
# Don't forget to use absolute paths, not relative paths.
filejoin(SITE_DIR, 'static'),
)
# List of finder classes that know how to find static files in
# various locations.
STATICFILES_FINDERS = (
'django.contrib.staticfiles.finders.FileSystemFinder',
'django.contrib.staticfiles.finders.AppDirectoriesFinder',
# 'django.contrib.staticfiles.finders.DefaultStorageFinder',
)
# List of callables that know how to import templates from various sources.
TEMPLATE_LOADERS = (
'django.template.loaders.filesystem.Loader',
'django.template.loaders.app_directories.Loader',
# 'django.template.loaders.eggs.Loader',
# settings for xapian indexing
from os.path import join as filejoin
try:
from conf.paths import SITE_DIR
except ImportError:
from conf.mock import SITE_DIR
XAPIAN_INDICES_DIR = filejoin(SITE_DIR, 'xapian_indices')
# settings for GeoIP from os.path import join as filejoin, abspath from paths import SITE_DIR # the download/geolite directory has a Makefile that automatically downloads # the latest GeoLite data files GEOIP_PATH = abspath(filejoin(SITE_DIR, 'download', 'geolite')) # the absolute path to the GeoIP library file; ends in *.dylib on Mac, or *.a on Linux GEOIP_LIBRARY_PATH = ''
"""
WSGI config for Cytoscape AppStore project.
It exposes the WSGI callable as a module-level variable named ``application``.
For more information on this file, see
https://docs.djangoproject.com/en/1.8/howto/deployment/wsgi/
"""
import os
import sys
from os.path import join as filejoin
from django.core.wsgi import get_wsgi_application
SITE_PARENT_DIR = '/var/www'
SITE_DIR = filejoin(SITE_PARENT_DIR, 'appstore')
sys.path.append(SITE_PARENT_DIR)
sys.path.append(SITE_DIR)
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "appstore.settings.local")
application = get_wsgi_application()
# URL prefix for admin static files -- CSS, JavaScript and images.
# Make sure to use a trailing slash.
# Examples: "http://foo.com/static/admin/", "/static/admin/".
# (This setting is deprecated since Django 1.4--Samad)
# ADMIN_MEDIA_PREFIX = urljoin(SITE_URL, 'static/admin/')
ALLOWED_HOSTS = ['*']
if DJANGO_STATIC_AND_MEDIA:
# Additional locations of static files
STATICFILES_DIRS = (
# Put strings here, like "/home/html/static" or "C:/www/django/static".
# Always use forward slashes, even on Windows.
# Don't forget to use absolute paths, not relative paths.
filejoin(SITE_DIR, 'static'), )
# List of finder classes that know how to find static files in
# various locations.
STATICFILES_FINDERS = (
'django.contrib.staticfiles.finders.FileSystemFinder',
'django.contrib.staticfiles.finders.AppDirectoriesFinder',
# 'django.contrib.staticfiles.finders.DefaultStorageFinder',
)
# List of callables that know how to import templates from various sources.
TEMPLATE_LOADERS = (
'django.template.loaders.filesystem.Loader',
'django.template.loaders.app_directories.Loader',
# 'django.template.loaders.eggs.Loader',
)
# http://www.i18nguy.com/unicode/language-identifiers.html LANGUAGE_CODE = 'en-us' SITE_ID = 1 # If you set this to False, Django will make some optimizations so as not # to load the internationalization machinery. USE_I18N = False # If you set this to False, Django will not format dates, numbers and # calendars according to the current locale USE_L10N = False # Absolute filesystem path to the directory that will hold user-uploaded files. # Example: "/home/media/media.lawrence.com/media/" MEDIA_ROOT = filejoin(SITE_DIR, 'media') # URL that handles the media served from MEDIA_ROOT. Make sure to use a # trailing slash. # Examples: "http://media.lawrence.com/media/", "http://example.com/media/" MEDIA_URL = urljoin(SITE_URL, 'media/') # Absolute path to the directory static files should be collected to. # Don't put anything in this directory yourself; store your static files # in apps' "static/" subdirectories and in STATICFILES_DIRS. # Example: "/home/media/media.lawrence.com/static/" STATIC_ROOT = '' # URL prefix for static files. # Example: "http://media.lawrence.com/static/" STATIC_URL = urljoin(SITE_URL, 'static/')