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