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='localhost'
 106 if options.has_option('frontend', 'email_host'):
 107   EMAIL_HOST = options.get('frontend', 'email_host')
 108
 109 EMAIL_PORT = 25
 110 if options.has_option('frontend', 'email_port'):
 111   EMAIL_PORT = int(options.get('frontend', 'email_port'))
 112
 113 if options.has_option('frontend', 'notification_sender'):
 114     NOTIFICATION_SENDER = options.get('frontend', 'notification_sender')
 115 else:
 116     NOTIFICATION_SENDER = "noreply@example.com"
 117 NOTIFICATION_BCC = []
 118 options_to_list(options, NOTIFICATION_BCC, 'frontend', 'notification_bcc')
 119
 120 if not options.has_option('frontend', 'database'):
 121   raise ConfigParser.NoSectionError(
 122     "Please define [frontend] database=<Section>")
 123
 124 database_section = options.get('frontend', 'database')
 125
 126 if not options.has_section(database_section):
 127     raise ConfigParser.NoSectionError(
 128         "No database=<database_section_name> defined")
 129
 130 # 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.
 131 DATABASE_ENGINE = options.get(database_section, 'engine')
 132 DATABASE_NAME = options.get(database_section, 'name')
 133 if options.has_option(database_section, 'user'):
 134     DATABASE_USER = options.get(database_section, 'user')
 135 if options.has_option(database_section, 'host'):
 136     DATABASE_HOST = options.get(database_section, 'host')
 137 if options.has_option(database_section, 'port'):
 138     DATABASE_PORT = options.get(database_section, 'port')
 139
 140 if options.has_option(database_section, 'password_file'):
 141     password_file = options.get(database_section, 'password_file')
 142     DATABASE_PASSWORD = open(password_file,'r').readline()
 143 elif options.has_option(database_section, 'password'):
 144     DATABASE_PASSWORD = options.get(database_section, 'password')
 145
 146 # Local time zone for this installation. Choices can be found here:
 147 # http://www.postgresql.org/docs/8.1/static/datetime-keywords.html#DATETIME-TIMEZONE-SET-TABLE
 148 # although not all variations may be possible on all operating systems.
 149 # If running in a Windows environment this must be set to the same as your
 150 # system time zone.
 151 if options.has_option('frontend', 'time_zone'):
 152   TIME_ZONE = options.get('frontend', 'time_zone')
 153 else:
 154   TIME_ZONE = 'America/Los_Angeles'
 155
 156 # Language code for this installation. All choices can be found here:
 157 # http://www.w3.org/TR/REC-html40/struct/dirlang.html#langcodes
 158 # http://blogs.law.harvard.edu/tech/stories/storyReader$15
 159 LANGUAGE_CODE = 'en-us'
 160
 161 SITE_ID = 1
 162
 163 # If you set this to False, Django will make some optimizations so as not
 164 # to load the internationalization machinery.
 165 USE_I18N = True
 166
 167 # Absolute path to the directory that holds media.
 168 # Example: "/home/media/media.lawrence.com/"
 169 MEDIA_ROOT = os.path.join(HTSWORKFLOW_ROOT, 'frontend', 'static', '')
 170
 171 # URL that handles the media served from MEDIA_ROOT.
 172 # Example: "http://media.lawrence.com"
 173 MEDIA_URL = '/static/'
 174
 175 # URL prefix for admin media -- CSS, JavaScript and images. Make sure to use a
 176 # trailing slash.
 177 # Examples: "http://foo.com/media/", "/media/".
 178 ADMIN_MEDIA_PREFIX = '/media/'
 179
 180 # Make this unique, and don't share it with anybody.
 181 if not options.has_option('frontend', 'secret'):
 182     options.set('frontend', 'secret_key', make_django_secret_key(458))
 183     save_options(INI_FILE[0], options)
 184 SECRET_KEY = options.get('frontend', 'secret_key')
 185
 186 # some of our urls need an api key
 187 DEFAULT_API_KEY = 'n7HsXGHIi0vp9j5u4TIRJyqAlXYc4wrH'
 188
 189 # List of callables that know how to import templates from various sources.
 190 TEMPLATE_LOADERS = (
 191     'django.template.loaders.filesystem.load_template_source',
 192     'django.template.loaders.app_directories.load_template_source',
 193 #     'django.template.loaders.eggs.load_template_source',
 194 )
 195
 196 MIDDLEWARE_CLASSES = (
 197     'django.contrib.csrf.middleware.CsrfMiddleware',
 198     'django.middleware.common.CommonMiddleware',
 199     'django.contrib.sessions.middleware.SessionMiddleware',
 200     'django.contrib.auth.middleware.AuthenticationMiddleware',
 201     'django.middleware.doc.XViewMiddleware',
 202 )
 203
 204 TEMPLATE_CONTEXT_PROCESSORS = global_settings.TEMPLATE_CONTEXT_PROCESSORS + (
 205     'htsworkflow.frontend.thispage.thispage',
 206 )
 207 ROOT_URLCONF = 'htsworkflow.frontend.urls'
 208
 209 TEMPLATE_DIRS = (
 210     # Put strings here, like "/home/html/django_templates" or "C:/www/django/templates".
 211     # Always use forward slashes, even on Windows.
 212     # Don't forget to use absolute paths, not relative paths.
 213     '/usr/share/python-support/python-django/django/contrib/admin/templates',
 214     #'/usr/lib/pymodules/python2.6/django/contrib/admin/templates/',
 215     os.path.join(HTSWORKFLOW_ROOT, 'frontend', 'templates'),
 216     os.path.join(HTSWORKFLOW_ROOT, 'templates'),
 217 )
 218
 219 INSTALLED_APPS = (
 220     'django.contrib.admin',
 221     'django.contrib.auth',
 222     'django.contrib.contenttypes',
 223     'django.contrib.humanize',
 224     'django.contrib.sessions',
 225     'django.contrib.sites',
 226     'htsworkflow.frontend.eland_config',
 227     'htsworkflow.frontend.samples',
 228     # modules from htsworkflow branch
 229     'htsworkflow.frontend.experiments',
 230     'htsworkflow.frontend.analysis',
 231     'htsworkflow.frontend.reports',
 232     'htsworkflow.frontend.inventory',
 233     'htsworkflow.frontend.bcmagic',
 234     'htsworkflow.frontend.labels',
 235     'django.contrib.databrowse',
 236 )
 237
 238 # Project specific settings
 239
 240 ALLOWED_IPS={'127.0.0.1': '127.0.0.1'}
 241 options_to_dict(ALLOWED_IPS, 'allowed_hosts')
 242
 243 ALLOWED_ANALYS_IPS = {'127.0.0.1': '127.0.0.1'}
 244 options_to_dict(ALLOWED_ANALYS_IPS, 'allowed_analysis_hosts')
 245 #UPLOADTO_HOME = os.path.abspath('../../uploads')
 246 #UPLOADTO_CONFIG_FILE = os.path.join(UPLOADTO_HOME, 'eland_config')
 247 #UPLOADTO_ELAND_RESULT_PACKS = os.path.join(UPLOADTO_HOME, 'eland_results')
 248 #UPLOADTO_BED_PACKS = os.path.join(UPLOADTO_HOME, 'bed_packs')
 249 # Where "results_dir" means directory with all the flowcells
 250 if options.has_option('frontend', 'results_dir'):
 251     RESULT_HOME_DIR=os.path.expanduser(options.get('frontend', 'results_dir'))
 252 else:
 253     RESULT_HOME_DIR='/tmp'
 254
 255 if options.has_option('frontend', 'link_flowcell_storage_device_url'):
 256     LINK_FLOWCELL_STORAGE_DEVICE_URL = options.get('frontend',
 257                                                    'link_flowcell_storage_device_url')
 258 else:
 259     LINK_FLOWCELL_STORAGE_DEVICE_URL = None
 260 # PORT 9100 is default for Zebra tabletop/desktop printers
 261 # PORT 6101 is default for Zebra mobile printers
 262 BCPRINTER_PRINTER1_HOST = None
 263 if options.has_option('bcprinter', 'printer1_host'):
 264     BCPRINTER_PRINTER1_HOST = options.get('bcprinter', 'printer1_host')
 265 BCPRINTER_PRINTER1_PORT=9100
 266 if options.has_option('bcprinter', 'printer1_port'):
 267     BCPRINTER_PRINTER1_PORT = int(options.get('bcprinter', 'printer1_port'))
 268 BCPRINTER_PRINTER2_HOST = None
 269 if options.has_option('bcprinter', 'printer2_host'):
 270     BCPRINTER_PRINTER1_HOST = options.get('bcprinter', 'printer2_host')
 271 BCPRINTER_PRINTER2_PORT=9100
 272 if options.has_option('bcprinter', 'printer2_port'):
 273     BCPRINTER_PRINTER2_PORT = int(options.get('bcprinter', 'printer2_port'))
 274