This way I can keep checking settings.py in.
Also since I implemented this be re-writing the settings file
I thought I'd clean out some of how we were storing some of our
previous default values. (Removed the hard coded - [defaults] section)
so they dont end up cluttering the users config file.
Since I removed the default for the linking hard disk tool
I changed the script to complain more helpfully if it can't find
the setting.
[frontend]
email_host=localhost
email_port=25
- database_engine=sqlite3
- database_name=/path/to/db
+ database=<section_name>
+
+ [database_name]
+ engine=sqlite3
+ name=/path/to/database
[admins]
#name1=email1
import django
from django.conf import global_settings
+from htsworkflow.util.api import make_django_secret_key
+
HTSWORKFLOW_ROOT = os.path.abspath(os.path.split(htsworkflow.__file__)[0])
# make epydoc happy
dest[name] = options.get(section_name, name)
# define your defaults here
-options = ConfigParser.SafeConfigParser(
- { 'email_host': 'localhost',
- 'email_port': '25',
- 'database_engine': 'sqlite3',
- 'database_name':
- os.path.join(HTSWORKFLOW_ROOT, '..', 'fctracker.db'),
- 'time_zone': 'America/Los_Angeles',
- 'default_pm': '5',
- 'link_flowcell_storage_device_url': "http://localhost:8000/inventory/lts/link/",
- 'printer1_host': '127.0.0.1',
- 'printer1_port': '9100',
- 'printer2_host': '127.0.0.1',
- 'printer2_port': '9100',
- })
-
-options.read([os.path.expanduser("~/.htsworkflow.ini"),
- '/etc/htsworkflow.ini',])
+options = ConfigParser.SafeConfigParser()
+
+def save_options(filename, options):
+ try:
+ ini_stream = open(filename, 'w')
+ options.write(ini_stream)
+ ini_stream.close()
+ except IOError, e:
+ LOGGER.debug("Error saving setting: %s" % (str(e)))
+
+INI_FILE = options.read([os.path.expanduser("~/.htsworkflow.ini"),
+ '/etc/htsworkflow.ini',])
# OptionParser will use the dictionary passed into the config parser as
# 'Default' values in any section. However it still needs an empty section
MANAGERS = []
options_to_list(options, MANAGERS, 'frontend', 'managers')
-DEFAULT_PM=int(options.get('frontend', 'default_pm'))
+if options.has_option('front', 'default_pm'):
+ DEFAULT_PM=int(options.get('frontend', 'default_pm'))
+else:
+ DEFAULT_PM=5
AUTHENTICATION_BACKENDS = (
'htsworkflow.frontend.samples.auth_backend.HTSUserModelBackend', )
CUSTOM_USER_MODEL = 'samples.HTSUser'
-EMAIL_HOST = options.get('frontend', 'email_host')
-EMAIL_PORT = int(options.get('frontend', 'email_port'))
+EMAIL_HOST = options.get('frontend', 'email_host', 'localhost')
+EMAIL_PORT = int(options.get('frontend', 'email_port', 25))
if options.has_option('frontend', 'notification_sender'):
NOTIFICATION_SENDER = options.get('frontend', 'notification_sender')
# although not all variations may be possible on all operating systems.
# If running in a Windows environment this must be set to the same as your
# system time zone.
-TIME_ZONE = options.get('frontend', 'time_zone')
+if options.has_option('frontend', 'time_zone'):
+ TIME_ZONE = options.get('frontend', 'time_zone')
+else:
+ TIME_ZONE = 'America/Los_Angeles'
# Language code for this installation. All choices can be found here:
# http://www.w3.org/TR/REC-html40/struct/dirlang.html#langcodes
ADMIN_MEDIA_PREFIX = '/media/'
# Make this unique, and don't share it with anybody.
-SECRET_KEY = '(ekv^=gf(j9f(x25@a7r+8)hqlz%&_1!tw^75l%^041#vi=@4n'
+if not options.has_option('frontend', 'secret'):
+ options.set('frontend', 'secret_key', make_django_secret_key(458))
+ save_options(INI_FILE[0], options)
+SECRET_KEY = options.get('frontend', 'secret_key')
# some of our urls need an api key
DEFAULT_API_KEY = 'n7HsXGHIi0vp9j5u4TIRJyqAlXYc4wrH'
else:
RESULT_HOME_DIR='/tmp'
-LINK_FLOWCELL_STORAGE_DEVICE_URL = options.get('frontend', 'link_flowcell_storage_device_url')
+if options.has_option('frontend', 'link_flowcell_storage_device_url'):
+ LINK_FLOWCELL_STORAGE_DEVICE_URL = options.get('frontend',
+ 'link_flowcell_storage_device_url')
+else:
+ LINK_FLOWCELL_STORAGE_DEVICE_URL = None
# PORT 9100 is default for Zebra tabletop/desktop printers
# PORT 6101 is default for Zebra mobile printers
BCPRINTER_PRINTER1_HOST = options.get('bcprinter', 'printer1_host')
"""Common functions for accessing the HTS Workflow REST API
"""
+import base64
from ConfigParser import SafeConfigParser
+import random
import logging
# try to deal with python <2.6
return json.loads(contents)
class HtswApi(object):
- def __init__(self, root_url, authdata):
- self.root_url = root_url
- self.authdata = authdata
+ def __init__(self, root_url, authdata):
+ self.root_url = root_url
+ self.authdata = authdata
- def get_flowcell(self, flowcellId):
- url = flowcell_url(self.root_url, flowcellId)
- return retrieve_info(url, self.authdata)
+ def get_flowcell(self, flowcellId):
+ url = flowcell_url(self.root_url, flowcellId)
+ return retrieve_info(url, self.authdata)
- def get_library(self, libraryId):
- url = library_url(self.root_url, libraryId)
- return retrieve_info(url, self.authdata)
+ def get_library(self, libraryId):
+ url = library_url(self.root_url, libraryId)
+ return retrieve_info(url, self.authdata)
- def get_lanes_for_user(self, user):
- url = lanes_for_user(self.root_url, user)
- return retrieve_info(url, self.authdata)
+ def get_lanes_for_user(self, user):
+ url = lanes_for_user(self.root_url, user)
+ return retrieve_info(url, self.authdata)
- def get_url(self, url):
- return retrieve_info(url, self.authdata)
+ def get_url(self, url):
+ return retrieve_info(url, self.authdata)
+
+def make_django_secret_key(size=216):
+ """return key suitable for use as secret key"""
+ try:
+ source = random.SystemRandom()
+ except AttributeError, e:
+ source = random.random()
+ bits = source.getrandbits(size)
+ chars = []
+ while bits > 0:
+ byte = bits & 0xff
+ chars.append(chr(byte))
+ bits >>= 8
+ return base64.encodestring("".join(chars)).strip()
if __name__ == "__main__":
from optparse import OptionParser
--- /dev/null
+import copy
+import os
+import unittest
+
+from htsworkflow.util import api
+
+class testApi(unittest.TestCase):
+ def test_make_key(self):
+ k1 = api.make_django_secret_key()
+ k2 = api.make_django_secret_key()
+
+ self.failUnless(len(k1), 85)
+ self.failUnless(len(k2), 85)
+ self.failUnless(k1 != k2)
+
+def suite():
+ return unittest.makeSuite(testApi, 'test')
+
+if __name__ == "__main__":
+ unittest.main(defaultTest='suite')
return match.group('flowcell')
else:
return None
-
+
def construct_parser():
"""
"""
help="device flowcell is being archived to")
parser.add_option("-s", "--serial", type="string", help="serial num. of archive device")
parser.add_option("-v", "--verbose", action="store_true", default=False)
-
+
return parser
"""
for fc in flowcells:
url = urlparse.urljoin(root_url, '%s/%s/' % (fc, serial))
-
+
req = urllib2.Request(url)
try:
response = urllib2.urlopen(req)
if debug:
print e.read()
sys.exit(e.code)
-
+
print "DB Update of %s & %s succeeded" % (fc, serial)
print response.read()
-
+
def process_args(parser):
"""
returns flowcell and serial#
"""
options, args = parser.parse_args()
-
+
msg = []
-
+
# Only provide device or serial
if options.device is not None and options.serial is not None:
parser.error("Please provide only --device or --serial.\n"\
else:
root_url = settings.LINK_FLOWCELL_STORAGE_DEVICE_URL
+ if root_url is None:
+ parser.error("Please set path to flowcell storage url")
+
# if device and serial missing:
if options.device is None and options.serial is None:
parser.error('One of --device or --serial is required')
flowcells = []
-
- # sanitize args
+
+ # sanitize args
for runfolder in args:
flowcell_id = extract_flowcell(runfolder)
if flowcell_id is None:
'(got %s)' % (runfolder,))
else:
flowcells.append(flowcell_id)
-
+
if options.flowcell is not None:
flowcells.append(options.flowcell)
-
+
if len(flowcells) == 0:
parser.error('please specify a --flowcell or list of runfolder archives\n'\
'for archival. I need something to do.')
else:
msg ="FATAL should not happen error occured; i.e. the best kind!"
raise ValueError, msg
-
-
+
+
def main():
"""
"""
parser = construct_parser()
process_args(parser)
-
+
#print "Database Updated."
sys.exit(0)
projects / htsworkflow.git / commitdiff