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 from django.conf import global_settings
  33
  34 HTSWORKFLOW_ROOT = os.path.abspath(os.path.split(htsworkflow.__file__)[0])
  35
  36 # make epydoc happy
  37 __docformat__ = "restructuredtext en"
  38
  39 def options_to_list(options, dest, section_name, option_name):
  40   """
  41   Load a options from section_name and store in a dictionary
  42   """
  43   if options.has_option(section_name, option_name):
  44     opt = options.get(section_name, option_name)
  45     dest.extend( shlex.split(opt) )
  46
  47 def options_to_dict(dest, section_name):
  48   """
  49   Load a options from section_name and store in a dictionary
  50   """
  51   if options.has_section(section_name):
  52     for name in options.options(section_name):
  53       dest[name] = options.get(section_name, name)
  54
  55 # define your defaults here
  56 options = ConfigParser.SafeConfigParser(
  57            { 'email_host': 'localhost',
  58              'email_port': '25',
  59              'database_engine': 'sqlite3',
  60              'database_name':
  61                   os.path.join(HTSWORKFLOW_ROOT, '..', 'fctracker.db'),
  62              'time_zone': 'America/Los_Angeles',
  63              'default_pm': '5',
  64              'link_flowcell_storage_device_url': "http://localhost:8000/inventory/lts/link/",
  65              'printer1_host': '127.0.0.1',
  66              'printer1_port': '9100',
  67              'printer2_host': '127.0.0.1',
  68              'printer2_port': '9100',
  69            })
  70
  71 options.read([os.path.expanduser("~/.htsworkflow.ini"),
  72               '/etc/htsworkflow.ini',])
  73
  74 # OptionParser will use the dictionary passed into the config parser as
  75 # 'Default' values in any section. However it still needs an empty section
  76 # to exist in order to retrieve anything.
  77 if not options.has_section('frontend'):
  78     options.add_section('frontend')
  79 if not options.has_section('bcprinter'):
  80     options.add_section('bcprinter')
  81
  82
  83 # Django settings for elandifier project.
  84
  85 DEBUG = True
  86 TEMPLATE_DEBUG = DEBUG
  87
  88 ADMINS = []
  89 options_to_list(options, ADMINS, 'frontend', 'admins')
  90
  91 MANAGERS = []
  92 options_to_list(options, MANAGERS, 'frontend', 'managers')
  93
  94 DEFAULT_PM=int(options.get('frontend', 'default_pm'))
  95
  96 AUTHENTICATION_BACKENDS = (
  97   'htsworkflow.frontend.samples.auth_backend.HTSUserModelBackend', )
  98 CUSTOM_USER_MODEL = 'samples.HTSUser'
  99
 100 EMAIL_HOST = options.get('frontend', 'email_host')
 101 EMAIL_PORT = int(options.get('frontend', 'email_port'))
 102
 103 if options.has_option('frontend', 'notification_sender'):
 104     NOTIFICATION_SENDER = options.get('frontend', 'notification_sender')
 105 else:
 106     NOTIFICATION_SENDER = "noreply@example.com"
 107 NOTIFICATION_BCC = []
 108 options_to_list(options, NOTIFICATION_BCC, 'frontend', 'notification_bcc')
 109
 110 database_section = options.get('frontend', 'database', 'database')
 111
 112 if not options.has_section(database_section):
 113     raise ConfigParser.NoSectionError(
 114         "No database=<database_section_name> defined")
 115
 116 # 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.
 117 DATABASE_ENGINE = options.get(database_section, 'engine')
 118 DATABASE_NAME = options.get(database_section, 'name')
 119 if options.has_option(database_section, 'user'):
 120     DATABASE_USER = options.get(database_section, 'user')
 121 if options.has_option(database_section, 'host'):
 122     DATABASE_HOST = options.get(database_section, 'host')
 123 if options.has_option(database_section, 'port'):
 124     DATABASE_PORT = options.get(database_section, 'port')
 125
 126 if options.has_option(database_section, 'password_file'):
 127     password_file = options.get(database_section, 'password_file')
 128     DATABASE_PASSWORD = open(password_file,'r').readline()
 129 elif options.has_option(database_section, 'password'):
 130     DATABASE_PASSWORD = options.get(database_section, 'password')
 131
 132 # Local time zone for this installation. Choices can be found here:
 133 # http://www.postgresql.org/docs/8.1/static/datetime-keywords.html#DATETIME-TIMEZONE-SET-TABLE
 134 # although not all variations may be possible on all operating systems.
 135 # If running in a Windows environment this must be set to the same as your
 136 # system time zone.
 137 TIME_ZONE = options.get('frontend', 'time_zone')
 138
 139 # Language code for this installation. All choices can be found here:
 140 # http://www.w3.org/TR/REC-html40/struct/dirlang.html#langcodes
 141 # http://blogs.law.harvard.edu/tech/stories/storyReader$15
 142 LANGUAGE_CODE = 'en-us'
 143
 144 SITE_ID = 1
 145
 146 # If you set this to False, Django will make some optimizations so as not
 147 # to load the internationalization machinery.
 148 USE_I18N = True
 149
 150 # Absolute path to the directory that holds media.
 151 # Example: "/home/media/media.lawrence.com/"
 152 MEDIA_ROOT = os.path.join(HTSWORKFLOW_ROOT, 'frontend', 'static', '')
 153
 154 # URL that handles the media served from MEDIA_ROOT.
 155 # Example: "http://media.lawrence.com"
 156 MEDIA_URL = '/static/'
 157
 158 # URL prefix for admin media -- CSS, JavaScript and images. Make sure to use a
 159 # trailing slash.
 160 # Examples: "http://foo.com/media/", "/media/".
 161 ADMIN_MEDIA_PREFIX = '/media/'
 162
 163 # Make this unique, and don't share it with anybody.
 164 SECRET_KEY = '(ekv^=gf(j9f(x25@a7r+8)hqlz%&_1!tw^75l%^041#vi=@4n'
 165
 166 # some of our urls need an api key
 167 DEFAULT_API_KEY = 'n7HsXGHIi0vp9j5u4TIRJyqAlXYc4wrH'
 168
 169 # List of callables that know how to import templates from various sources.
 170 TEMPLATE_LOADERS = (
 171     'django.template.loaders.filesystem.load_template_source',
 172     'django.template.loaders.app_directories.load_template_source',
 173 #     'django.template.loaders.eggs.load_template_source',
 174 )
 175
 176 MIDDLEWARE_CLASSES = (
 177     'django.contrib.csrf.middleware.CsrfMiddleware',
 178     'django.middleware.common.CommonMiddleware',
 179     'django.contrib.sessions.middleware.SessionMiddleware',
 180     'django.contrib.auth.middleware.AuthenticationMiddleware',
 181     'django.middleware.doc.XViewMiddleware',
 182 )
 183
 184 TEMPLATE_CONTEXT_PROCESSORS = global_settings.TEMPLATE_CONTEXT_PROCESSORS + (
 185     'htsworkflow.frontend.thispage.thispage',
 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     os.path.join(HTSWORKFLOW_ROOT, 'templates'),
 197 )
 198
 199 INSTALLED_APPS = (
 200     'django.contrib.admin',
 201     'django.contrib.auth',
 202     'django.contrib.contenttypes',
 203     'django.contrib.humanize',
 204     'django.contrib.sessions',
 205     'django.contrib.sites',
 206     'htsworkflow.frontend.eland_config',
 207     'htsworkflow.frontend.samples',
 208     # modules from htsworkflow branch
 209     'htsworkflow.frontend.experiments',
 210     'htsworkflow.frontend.analysis',
 211     'htsworkflow.frontend.reports',
 212     'htsworkflow.frontend.inventory',
 213     'htsworkflow.frontend.bcmagic',
 214     'htsworkflow.frontend.labels',
 215     'django.contrib.databrowse',
 216 )
 217
 218 # Project specific settings
 219
 220 ALLOWED_IPS={'127.0.0.1': '127.0.0.1'}
 221 options_to_dict(ALLOWED_IPS, 'allowed_hosts')
 222
 223 ALLOWED_ANALYS_IPS = {'127.0.0.1': '127.0.0.1'}
 224 options_to_dict(ALLOWED_ANALYS_IPS, 'allowed_analysis_hosts')
 225 #UPLOADTO_HOME = os.path.abspath('../../uploads')
 226 #UPLOADTO_CONFIG_FILE = os.path.join(UPLOADTO_HOME, 'eland_config')
 227 #UPLOADTO_ELAND_RESULT_PACKS = os.path.join(UPLOADTO_HOME, 'eland_results')
 228 #UPLOADTO_BED_PACKS = os.path.join(UPLOADTO_HOME, 'bed_packs')
 229 # Where "results_dir" means directory with all the flowcells
 230 if options.has_option('frontend', 'results_dir'):
 231     RESULT_HOME_DIR=os.path.expanduser(options.get('frontend', 'results_dir'))
 232 else:
 233     RESULT_HOME_DIR='/tmp'
 234
 235 LINK_FLOWCELL_STORAGE_DEVICE_URL = options.get('frontend', 'link_flowcell_storage_device_url')
 236 # PORT 9100 is default for Zebra tabletop/desktop printers
 237 # PORT 6101 is default for Zebra mobile printers
 238 BCPRINTER_PRINTER1_HOST = options.get('bcprinter', 'printer1_host')
 239 BCPRINTER_PRINTER1_PORT = int(options.get('bcprinter', 'printer1_port'))
 240 BCPRINTER_PRINTER2_HOST = options.get('bcprinter', 'printer2_host')
 241 BCPRINTER_PRINTER2_PORT = int(options.get('bcprinter', 'printer2_port'))
 242