htsworkflow/settings.py

   1 """
   2 Generate settings for the Django Application.
   3
   4 To make it easier to customize the application the settings can be
   5 defined in a configuration file read by ConfigParser.
   6
   7 The options understood by this module are (with their defaults):
   8
   9   [frontend]
  10   email_host=localhost
  11   email_port=25
  12   database_engine=sqlite3
  13   database_name=/path/to/db
  14
  15   [admins]
  16   #name1=email1
  17
  18   [allowed_hosts]
  19   #name1=ip
  20   localhost=127.0.0.1
  21
  22   [allowed_analysis_hosts]
  23   #name1=ip
  24   localhost=127.0.0.1
  25
  26 """
  27 import ConfigParser
  28 import os
  29 import shlex
  30 import htsworkflow
  31 import django
  32
  33 HTSWORKFLOW_ROOT = os.path.abspath(os.path.split(htsworkflow.__file__)[0])
  34
  35 # make epydoc happy
  36 __docformat__ = "restructuredtext en"
  37
  38 def options_to_list(options, dest, section_name, option_name):
  39   """
  40   Load a options from section_name and store in a dictionary
  41   """
  42   if options.has_option(section_name, option_name):
  43     opt = options.get(section_name, option_name)
  44     dest.extend( shlex.split(opt) )
  45
  46 def options_to_dict(dest, section_name):
  47   """
  48   Load a options from section_name and store in a dictionary
  49   """
  50   if options.has_section(section_name):
  51     for name in options.options(section_name):
  52       dest[name] = options.get(section_name, name)
  53
  54 # define your defaults here
  55 options = ConfigParser.SafeConfigParser(
  56            { 'email_host': 'localhost',
  57              'email_port': '25',
  58              'database_engine': 'sqlite3',
  59              'database_name':
  60                   os.path.join(HTSWORKFLOW_ROOT, '..', 'fctracker.db'),
  61              'time_zone': 'America/Los_Angeles',
  62              'default_pm': '5',
  63              'link_flowcell_storage_device_url': "http://localhost:8000/inventory/lts/link/",
  64              'printer1_host': '127.0.0.1',
  65              'printer1_port': '9100',
  66              'printer2_host': '127.0.0.1',
  67              'printer2_port': '9100',
  68            })
  69
  70 options.read([os.path.expanduser("~/.htsworkflow.ini"),
  71               '/etc/htsworkflow.ini',])
  72
  73 # OptionParser will use the dictionary passed into the config parser as
  74 # 'Default' values in any section. However it still needs an empty section
  75 # to exist in order to retrieve anything.
  76 if not options.has_section('frontend'):
  77     options.add_section('frontend')
  78 if not options.has_section('bcprinter'):
  79     options.add_section('bcprinter')
  80
  81
  82 # Django settings for elandifier project.
  83
  84 DEBUG = True
  85 TEMPLATE_DEBUG = DEBUG
  86
  87 ADMINS = []
  88 options_to_list(options, ADMINS, 'frontend', 'admins')
  89
  90 MANAGERS = []
  91 options_to_list(options, MANAGERS, 'frontend', 'managers')
  92
  93 DEFAULT_PM=int(options.get('frontend', 'default_pm'))
  94
  95 AUTHENTICATION_BACKENDS = (
  96   'htsworkflow.frontend.samples.auth_backend.HTSUserModelBackend', )
  97 CUSTOM_USER_MODEL = 'samples.HTSUser'
  98
  99 EMAIL_HOST = options.get('frontend', 'email_host')
 100 EMAIL_PORT = int(options.get('frontend', 'email_port'))
 101
 102 if options.has_option('frontend', 'notification_sender'):
 103     NOTIFICATION_SENDER = options.get('frontend', 'notification_sender')
 104 else:
 105     NOTIFICATION_SENDER = "noreply@example.com"
 106 NOTIFICATION_BCC = []
 107 options_to_list(options, NOTIFICATION_BCC, 'frontend', 'notification_bcc')
 108
 109 database_section = options.get('frontend', 'database', 'database')
 110
 111 if not options.has_section(database_section):
 112     raise ConfigParser.NoSectionError(
 113         "No database=<database_section_name> defined")
 114
 115 # 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.
 116 DATABASE_ENGINE = options.get(database_section, 'engine')
 117 DATABASE_NAME = options.get(database_section, 'name')
 118 if options.has_option(database_section, 'user'):
 119     DATABASE_USER = options.get(database_section, 'user')
 120 if options.has_option(database_section, 'host'):
 121     DATABASE_HOST = options.get(database_section, 'host')
 122 if options.has_option(database_section, 'port'):
 123     DATABASE_PORT = options.get(database_section, 'port')
 124
 125 if options.has_option(database_section, 'password_file'):
 126     password_file = options.get(database_section, 'password_file')
 127     DATABASE_PASSWORD = open(password_file,'r').readline()
 128 elif options.has_option(database_section, 'password'):
 129     DATABASE_PASSWORD = options.get(database_section, 'password')
 130
 131 # Local time zone for this installation. Choices can be found here:
 132 # http://www.postgresql.org/docs/8.1/static/datetime-keywords.html#DATETIME-TIMEZONE-SET-TABLE
 133 # although not all variations may be possible on all operating systems.
 134 # If running in a Windows environment this must be set to the same as your
 135 # system time zone.
 136 TIME_ZONE = options.get('frontend', 'time_zone')
 137
 138 # Language code for this installation. All choices can be found here:
 139 # http://www.w3.org/TR/REC-html40/struct/dirlang.html#langcodes
 140 # http://blogs.law.harvard.edu/tech/stories/storyReader$15
 141 LANGUAGE_CODE = 'en-us'
 142
 143 SITE_ID = 1
 144
 145 # If you set this to False, Django will make some optimizations so as not
 146 # to load the internationalization machinery.
 147 USE_I18N = True
 148
 149 # Absolute path to the directory that holds media.
 150 # Example: "/home/media/media.lawrence.com/"
 151 MEDIA_ROOT = os.path.join(HTSWORKFLOW_ROOT, 'frontend', 'static', '')
 152
 153 # URL that handles the media served from MEDIA_ROOT.
 154 # Example: "http://media.lawrence.com"
 155 MEDIA_URL = '/static/'
 156
 157 # URL prefix for admin media -- CSS, JavaScript and images. Make sure to use a
 158 # trailing slash.
 159 # Examples: "http://foo.com/media/", "/media/".
 160 ADMIN_MEDIA_PREFIX = '/media/'
 161
 162 # Make this unique, and don't share it with anybody.
 163 SECRET_KEY = '(ekv^=gf(j9f(x25@a7r+8)hqlz%&_1!tw^75l%^041#vi=@4n'
 164
 165 # some of our urls need an api key
 166 DEFAULT_API_KEY = 'n7HsXGHIi0vp9j5u4TIRJyqAlXYc4wrH'
 167
 168 # List of callables that know how to import templates from various sources.
 169 TEMPLATE_LOADERS = (
 170     'django.template.loaders.filesystem.load_template_source',
 171     'django.template.loaders.app_directories.load_template_source',
 172 #     'django.template.loaders.eggs.load_template_source',
 173 )
 174
 175 MIDDLEWARE_CLASSES = [
 176     'django.middleware.common.CommonMiddleware',
 177     'django.contrib.sessions.middleware.SessionMiddleware',
 178     'django.contrib.auth.middleware.AuthenticationMiddleware',
 179     'django.middleware.doc.XViewMiddleware',
 180 ]
 181 # be forgiving for django 1.1 which doesn't have csrf protection
 182 # TODO remove this when we upgrade to django 1.2
 183 if django.VERSION[0] == 1 and django.VERSION[1] > 1:
 184     MIDDLEWARE_CLASSES.insert(0, 'django.middleware.csrf.CsrfViewMiddleware')
 185
 186
 187 ROOT_URLCONF = 'htsworkflow.frontend.urls'
 188
 189 TEMPLATE_DIRS = (
 190     # Put strings here, like "/home/html/django_templates" or "C:/www/django/templates".
 191     # Always use forward slashes, even on Windows.
 192     # Don't forget to use absolute paths, not relative paths.
 193     '/usr/share/python-support/python-django/django/contrib/admin/templates',
 194     #'/usr/lib/pymodules/python2.6/django/contrib/admin/templates/',
 195     os.path.join(HTSWORKFLOW_ROOT, 'frontend','templates'),
 196 )
 197
 198 INSTALLED_APPS = (
 199     'django.contrib.admin',
 200     'django.contrib.auth',
 201     'django.contrib.contenttypes',
 202     'django.contrib.humanize',
 203     'django.contrib.sessions',
 204     'django.contrib.sites',
 205     'htsworkflow.frontend.eland_config',
 206     'htsworkflow.frontend.samples',
 207     # modules from htsworkflow branch
 208     'htsworkflow.frontend.experiments',
 209     'htsworkflow.frontend.analysis',
 210     'htsworkflow.frontend.reports',
 211     'htsworkflow.frontend.inventory',
 212     'htsworkflow.frontend.bcmagic',
 213     'htsworkflow.frontend.labels',
 214     'django.contrib.databrowse',
 215 )
 216
 217 # Project specific settings
 218
 219 ALLOWED_IPS={'127.0.0.1': '127.0.0.1'}
 220 options_to_dict(ALLOWED_IPS, 'allowed_hosts')
 221
 222 ALLOWED_ANALYS_IPS = {'127.0.0.1': '127.0.0.1'}
 223 options_to_dict(ALLOWED_ANALYS_IPS, 'allowed_analysis_hosts')
 224 #UPLOADTO_HOME = os.path.abspath('../../uploads')
 225 #UPLOADTO_CONFIG_FILE = os.path.join(UPLOADTO_HOME, 'eland_config')
 226 #UPLOADTO_ELAND_RESULT_PACKS = os.path.join(UPLOADTO_HOME, 'eland_results')
 227 #UPLOADTO_BED_PACKS = os.path.join(UPLOADTO_HOME, 'bed_packs')
 228 # Where "results_dir" means directory with all the flowcells
 229 if options.has_option('frontend', 'results_dir'):
 230     RESULT_HOME_DIR=os.path.expanduser(options.get('frontend', 'results_dir'))
 231 else:
 232     RESULT_HOME_DIR='/tmp'
 233
 234 LINK_FLOWCELL_STORAGE_DEVICE_URL = options.get('frontend', 'link_flowcell_storage_device_url')
 235 # PORT 9100 is default for Zebra tabletop/desktop printers
 236 # PORT 6101 is default for Zebra mobile printers
 237 BCPRINTER_PRINTER1_HOST = options.get('bcprinter', 'printer1_host')
 238 BCPRINTER_PRINTER1_PORT = int(options.get('bcprinter', 'printer1_port'))
 239 BCPRINTER_PRINTER2_HOST = options.get('bcprinter', 'printer2_host')
 240 BCPRINTER_PRINTER2_PORT = int(options.get('bcprinter', 'printer2_port'))
 241