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=<section_name>
  13
  14   [database_name]
  15   engine=sqlite3
  16   name=/path/to/database
  17
  18   [admins]
  19   #name1=email1
  20
  21   [allowed_hosts]
  22   #name1=ip
  23   localhost=127.0.0.1
  24
  25   [allowed_analysis_hosts]
  26   #name1=ip
  27   localhost=127.0.0.1
  28
  29 """
  30 import ConfigParser
  31 import logging
  32 import os
  33 import shlex
  34 import htsworkflow
  35 import django
  36 from django.conf import global_settings
  37
  38 from htsworkflow.util.api import make_django_secret_key
  39
  40 HTSWORKFLOW_ROOT = os.path.abspath(os.path.split(htsworkflow.__file__)[0])
  41 LOGGER = logging.getLogger(__name__)
  42
  43 # make epydoc happy
  44 __docformat__ = "restructuredtext en"
  45
  46 def options_to_list(options, dest, section_name, option_name):
  47   """
  48   Load a options from section_name and store in a dictionary
  49   """
  50   if options.has_option(section_name, option_name):
  51     opt = options.get(section_name, option_name)
  52     dest.extend( shlex.split(opt) )
  53
  54 def options_to_dict(dest, section_name):
  55   """
  56   Load a options from section_name and store in a dictionary
  57   """
  58   if options.has_section(section_name):
  59     for name in options.options(section_name):
  60       dest[name] = options.get(section_name, name)
  61
  62 # define your defaults here
  63 options = ConfigParser.SafeConfigParser()
  64
  65 def save_options(filename, options):
  66     try:
  67         ini_stream = open(filename, 'w')
  68         options.write(ini_stream)
  69         ini_stream.close()
  70     except IOError, e:
  71         LOGGER.debug("Error saving setting: %s" % (str(e)))
  72
  73 INI_FILE = options.read([os.path.expanduser("~/.htsworkflow.ini"),
  74                          '/etc/htsworkflow.ini',])
  75
  76 # OptionParser will use the dictionary passed into the config parser as
  77 # 'Default' values in any section. However it still needs an empty section
  78 # to exist in order to retrieve anything.
  79 if not options.has_section('frontend'):
  80     options.add_section('frontend')
  81 if not options.has_section('bcprinter'):
  82     options.add_section('bcprinter')
  83
  84
  85 # Django settings for elandifier project.
  86
  87 DEBUG = True
  88 TEMPLATE_DEBUG = DEBUG
  89
  90 ADMINS = []
  91 options_to_list(options, ADMINS, 'frontend', 'admins')
  92
  93 MANAGERS = []
  94 options_to_list(options, MANAGERS, 'frontend', 'managers')
  95
  96 if options.has_option('front', 'default_pm'):
  97     DEFAULT_PM=int(options.get('frontend', 'default_pm'))
  98 else:
  99     DEFAULT_PM=5
 100
 101 AUTHENTICATION_BACKENDS = (
 102   'htsworkflow.frontend.samples.auth_backend.HTSUserModelBackend', )
 103 CUSTOM_USER_MODEL = 'samples.HTSUser'
 104
 105 EMAIL_HOST = options.get('frontend', 'email_host', 'localhost')
 106 EMAIL_PORT = int(options.get('frontend', 'email_port', 25))
 107
 108 if options.has_option('frontend', 'notification_sender'):
 109     NOTIFICATION_SENDER = options.get('frontend', 'notification_sender')
 110 else:
 111     NOTIFICATION_SENDER = "noreply@example.com"
 112 NOTIFICATION_BCC = []
 113 options_to_list(options, NOTIFICATION_BCC, 'frontend', 'notification_bcc')
 114
 115 database_section = options.get('frontend', 'database', 'database')
 116
 117 if not options.has_section(database_section):
 118     raise ConfigParser.NoSectionError(
 119         "No database=<database_section_name> defined")
 120
 121 # 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.
 122 DATABASE_ENGINE = options.get(database_section, 'engine')
 123 DATABASE_NAME = options.get(database_section, 'name')
 124 if options.has_option(database_section, 'user'):
 125     DATABASE_USER = options.get(database_section, 'user')
 126 if options.has_option(database_section, 'host'):
 127     DATABASE_HOST = options.get(database_section, 'host')
 128 if options.has_option(database_section, 'port'):
 129     DATABASE_PORT = options.get(database_section, 'port')
 130
 131 if options.has_option(database_section, 'password_file'):
 132     password_file = options.get(database_section, 'password_file')
 133     DATABASE_PASSWORD = open(password_file,'r').readline()
 134 elif options.has_option(database_section, 'password'):
 135     DATABASE_PASSWORD = options.get(database_section, 'password')
 136
 137 # Local time zone for this installation. Choices can be found here:
 138 # http://www.postgresql.org/docs/8.1/static/datetime-keywords.html#DATETIME-TIMEZONE-SET-TABLE
 139 # although not all variations may be possible on all operating systems.
 140 # If running in a Windows environment this must be set to the same as your
 141 # system time zone.
 142 if options.has_option('frontend', 'time_zone'):
 143   TIME_ZONE = options.get('frontend', 'time_zone')
 144 else:
 145   TIME_ZONE = 'America/Los_Angeles'
 146
 147 # Language code for this installation. All choices can be found here:
 148 # http://www.w3.org/TR/REC-html40/struct/dirlang.html#langcodes
 149 # http://blogs.law.harvard.edu/tech/stories/storyReader$15
 150 LANGUAGE_CODE = 'en-us'
 151
 152 SITE_ID = 1
 153
 154 # If you set this to False, Django will make some optimizations so as not
 155 # to load the internationalization machinery.
 156 USE_I18N = True
 157
 158 # Absolute path to the directory that holds media.
 159 # Example: "/home/media/media.lawrence.com/"
 160 MEDIA_ROOT = os.path.join(HTSWORKFLOW_ROOT, 'frontend', 'static', '')
 161
 162 # URL that handles the media served from MEDIA_ROOT.
 163 # Example: "http://media.lawrence.com"
 164 MEDIA_URL = '/static/'
 165
 166 # URL prefix for admin media -- CSS, JavaScript and images. Make sure to use a
 167 # trailing slash.
 168 # Examples: "http://foo.com/media/", "/media/".
 169 ADMIN_MEDIA_PREFIX = '/media/'
 170
 171 # Make this unique, and don't share it with anybody.
 172 if not options.has_option('frontend', 'secret'):
 173     options.set('frontend', 'secret_key', make_django_secret_key(458))
 174     save_options(INI_FILE[0], options)
 175 SECRET_KEY = options.get('frontend', 'secret_key')
 176
 177 # some of our urls need an api key
 178 DEFAULT_API_KEY = 'n7HsXGHIi0vp9j5u4TIRJyqAlXYc4wrH'
 179
 180 # List of callables that know how to import templates from various sources.
 181 TEMPLATE_LOADERS = (
 182     'django.template.loaders.filesystem.load_template_source',
 183     'django.template.loaders.app_directories.load_template_source',
 184 #     'django.template.loaders.eggs.load_template_source',
 185 )
 186
 187 MIDDLEWARE_CLASSES = (
 188     'django.contrib.csrf.middleware.CsrfMiddleware',
 189     'django.middleware.common.CommonMiddleware',
 190     'django.contrib.sessions.middleware.SessionMiddleware',
 191     'django.contrib.auth.middleware.AuthenticationMiddleware',
 192     'django.middleware.doc.XViewMiddleware',
 193 )
 194
 195 TEMPLATE_CONTEXT_PROCESSORS = global_settings.TEMPLATE_CONTEXT_PROCESSORS + (
 196     'htsworkflow.frontend.thispage.thispage',
 197 )
 198 ROOT_URLCONF = 'htsworkflow.frontend.urls'
 199
 200 TEMPLATE_DIRS = (
 201     # Put strings here, like "/home/html/django_templates" or "C:/www/django/templates".
 202     # Always use forward slashes, even on Windows.
 203     # Don't forget to use absolute paths, not relative paths.
 204     '/usr/share/python-support/python-django/django/contrib/admin/templates',
 205     #'/usr/lib/pymodules/python2.6/django/contrib/admin/templates/',
 206     os.path.join(HTSWORKFLOW_ROOT, 'frontend', 'templates'),
 207     os.path.join(HTSWORKFLOW_ROOT, 'templates'),
 208 )
 209
 210 INSTALLED_APPS = (
 211     'django.contrib.admin',
 212     'django.contrib.auth',
 213     'django.contrib.contenttypes',
 214     'django.contrib.humanize',
 215     'django.contrib.sessions',
 216     'django.contrib.sites',
 217     'htsworkflow.frontend.eland_config',
 218     'htsworkflow.frontend.samples',
 219     # modules from htsworkflow branch
 220     'htsworkflow.frontend.experiments',
 221     'htsworkflow.frontend.analysis',
 222     'htsworkflow.frontend.reports',
 223     'htsworkflow.frontend.inventory',
 224     'htsworkflow.frontend.bcmagic',
 225     'htsworkflow.frontend.labels',
 226     'django.contrib.databrowse',
 227 )
 228
 229 # Project specific settings
 230
 231 ALLOWED_IPS={'127.0.0.1': '127.0.0.1'}
 232 options_to_dict(ALLOWED_IPS, 'allowed_hosts')
 233
 234 ALLOWED_ANALYS_IPS = {'127.0.0.1': '127.0.0.1'}
 235 options_to_dict(ALLOWED_ANALYS_IPS, 'allowed_analysis_hosts')
 236 #UPLOADTO_HOME = os.path.abspath('../../uploads')
 237 #UPLOADTO_CONFIG_FILE = os.path.join(UPLOADTO_HOME, 'eland_config')
 238 #UPLOADTO_ELAND_RESULT_PACKS = os.path.join(UPLOADTO_HOME, 'eland_results')
 239 #UPLOADTO_BED_PACKS = os.path.join(UPLOADTO_HOME, 'bed_packs')
 240 # Where "results_dir" means directory with all the flowcells
 241 if options.has_option('frontend', 'results_dir'):
 242     RESULT_HOME_DIR=os.path.expanduser(options.get('frontend', 'results_dir'))
 243 else:
 244     RESULT_HOME_DIR='/tmp'
 245
 246 if options.has_option('frontend', 'link_flowcell_storage_device_url'):
 247     LINK_FLOWCELL_STORAGE_DEVICE_URL = options.get('frontend',
 248                                                    'link_flowcell_storage_device_url')
 249 else:
 250     LINK_FLOWCELL_STORAGE_DEVICE_URL = None
 251 # PORT 9100 is default for Zebra tabletop/desktop printers
 252 # PORT 6101 is default for Zebra mobile printers
 253 BCPRINTER_PRINTER1_HOST = options.get('bcprinter', 'printer1_host')
 254 BCPRINTER_PRINTER1_PORT = int(options.get('bcprinter', 'printer1_port'))
 255 BCPRINTER_PRINTER2_HOST = options.get('bcprinter', 'printer2_host')
 256 BCPRINTER_PRINTER2_PORT = int(options.get('bcprinter', 'printer2_port'))
 257