From 038d7febb7224b9088ef628bee16b3c54ebf98ed Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Wed, 6 Apr 2011 13:49:26 -0700
Subject: [PATCH] django-nose didn't work with django 1.1, so I went back to
 the nose plugin NoseDjango I needed to move the settings file around a bit so
 the default build of nosedjango will find it (instead of my previously hacked
 copy).

I got tired of modifying the location of the settings files and
discovered that django has a standardized way of grabbign the config
file. with "from django.conf import settings", though that will
only show uppercased config entries.
---
 extra/fix_ob3.py                                | 2 +-
 htsworkflow/frontend/analysis/main.py           | 9 ++++++---
 htsworkflow/frontend/analysis/models.py         | 2 +-
 htsworkflow/frontend/auth.py                    | 3 +--
 htsworkflow/frontend/bcmagic/utils.py           | 4 ++--
 htsworkflow/frontend/eland_config/views.py      | 2 +-
 htsworkflow/frontend/experiments/experiments.py | 2 +-
 htsworkflow/frontend/experiments/models.py      | 5 +++--
 htsworkflow/frontend/experiments/tests.py       | 2 ++
 htsworkflow/frontend/inventory/views.py         | 5 ++---
 htsworkflow/frontend/reports/libinfopar.py      | 2 +-
 htsworkflow/frontend/samples/models.py          | 1 -
 htsworkflow/frontend/samples/results.py         | 2 +-
 htsworkflow/frontend/samples/views.py           | 2 +-
 htsworkflow/frontend/urls.py                    | 2 +-
 scripts/htsw-record-runfolder                   | 7 ++++---
 htsworkflow/settings.py => settings.py          | 6 +++---
 17 files changed, 31 insertions(+), 27 deletions(-)
 rename htsworkflow/settings.py => settings.py (97%)

diff --git a/extra/fix_ob3.py b/extra/fix_ob3.py
index 1278901..9955f69 100644
--- a/extra/fix_ob3.py
+++ b/extra/fix_ob3.py
@@ -7,7 +7,7 @@ import re
 import sys
 
 from django.core.management import setup_environ
-from htsworkflow.frontend import settings
+from django.conf import settings
 setup_environ(settings)
 
 import htsworkflow.frontend.samples.models as samples
diff --git a/htsworkflow/frontend/analysis/main.py b/htsworkflow/frontend/analysis/main.py
index b57ad20..ba2a739 100644
--- a/htsworkflow/frontend/analysis/main.py
+++ b/htsworkflow/frontend/analysis/main.py
@@ -1,11 +1,14 @@
 # some core functions of analysis manager module
-from django.http import HttpResponse
+
 from datetime import datetime
 from string import *
 import re
-from htsworkflow.frontend import settings
-from htsworkflow.frontend.analysis.models import Task, Project
+
+from django.conf import settings
 from django.core.exceptions import ObjectDoesNotExist
+from django.http import HttpResponse
+
+from htsworkflow.frontend.analysis.models import Task, Project
 
 def updStatus(request):
     ClIP = request.META['REMOTE_ADDR']
diff --git a/htsworkflow/frontend/analysis/models.py b/htsworkflow/frontend/analysis/models.py
index 41ecf42..5a580e0 100644
--- a/htsworkflow/frontend/analysis/models.py
+++ b/htsworkflow/frontend/analysis/models.py
@@ -1,6 +1,6 @@
 from django.db import models
+from django.conf import settings
 from datetime import datetime
-from htsworkflow.frontend import settings
 from htsworkflow.frontend.samples.models import Library 
 from string import *
 
diff --git a/htsworkflow/frontend/auth.py b/htsworkflow/frontend/auth.py
index 4df771b..31650a6 100644
--- a/htsworkflow/frontend/auth.py
+++ b/htsworkflow/frontend/auth.py
@@ -2,8 +2,7 @@
 Define some alternate authentication methods
 """
 from django.core.exceptions import PermissionDenied
-
-from htsworkflow.frontend import settings
+from django.conf import settings
 
 apidata = {'apiid': u'0', 'apikey': settings.DEFAULT_API_KEY}
 
diff --git a/htsworkflow/frontend/bcmagic/utils.py b/htsworkflow/frontend/bcmagic/utils.py
index e7d89d3..78919b0 100644
--- a/htsworkflow/frontend/bcmagic/utils.py
+++ b/htsworkflow/frontend/bcmagic/utils.py
@@ -1,4 +1,4 @@
-from htsworkflow.frontend import settings
+from django.conf import settings
 
 import ftplib
 import socket
@@ -53,4 +53,4 @@ def autofill(field, value):
     Return a bcm dictionary with a command to automatically fill the
     corresponding "field" with "value"
     """
-    return {'mode': 'autofill', 'field': field, 'value': value}
\ No newline at end of file
+    return {'mode': 'autofill', 'field': field, 'value': value}
diff --git a/htsworkflow/frontend/eland_config/views.py b/htsworkflow/frontend/eland_config/views.py
index 6169f8a..d21f86b 100644
--- a/htsworkflow/frontend/eland_config/views.py
+++ b/htsworkflow/frontend/eland_config/views.py
@@ -1,9 +1,9 @@
+from django.conf import settings
 from django.http import HttpResponse
 from django.shortcuts import render_to_response
 from django.core.exceptions import ObjectDoesNotExist
 
 from htsworkflow.frontend.eland_config import forms
-from htsworkflow.frontend import settings
 from htsworkflow.frontend.experiments import models
 
 import os
diff --git a/htsworkflow/frontend/experiments/experiments.py b/htsworkflow/frontend/experiments/experiments.py
index 882ea89..5dec8cf 100755
--- a/htsworkflow/frontend/experiments/experiments.py
+++ b/htsworkflow/frontend/experiments/experiments.py
@@ -12,9 +12,9 @@ from django.contrib.auth.decorators import login_required
 from django.core.exceptions import ObjectDoesNotExist
 from django.core.mail import send_mail, mail_admins
 from django.http import HttpResponse, Http404
+from django.conf import settings
 
 from htsworkflow.frontend.auth import require_api_key
-from htsworkflow.frontend import settings
 from htsworkflow.frontend.experiments.models import \
     FlowCell, \
     DataRun, \
diff --git a/htsworkflow/frontend/experiments/models.py b/htsworkflow/frontend/experiments/models.py
index 10599e2..8a71e25 100755
--- a/htsworkflow/frontend/experiments/models.py
+++ b/htsworkflow/frontend/experiments/models.py
@@ -5,7 +5,8 @@ from django.core import urlresolvers
 from django.db import models
 
 from htsworkflow.frontend.samples.models import *
-from htsworkflow.frontend.settings import options
+#from htsworkflow.frontend.settings import options
+from django.conf import settings
 
 class ClusterStation(models.Model):
   name = models.CharField(max_length=50, unique=True)
@@ -21,7 +22,7 @@ class Sequencer(models.Model):
 
 default_pM = 5
 try:
-  default_pM = int(options.get('frontend', 'default_pm'))
+  default_pM = int(settings.DEFAULT_PM)
 except ValueError,e:
   logging.error("invalid value for frontend.default_pm")
 
diff --git a/htsworkflow/frontend/experiments/tests.py b/htsworkflow/frontend/experiments/tests.py
index 9088b46..7bfebfe 100644
--- a/htsworkflow/frontend/experiments/tests.py
+++ b/htsworkflow/frontend/experiments/tests.py
@@ -4,6 +4,7 @@ try:
     import json
 except ImportError, e:
     import simplejson as json
+import os
 import sys
 
 from django.core import mail
@@ -206,3 +207,4 @@ class TestEmailNotify(TestCase):
         # require that navigation back to the admin page exists
         self.failUnless(re.search('<a href="/admin/experiments/flowcell/153/">[^<]+</a>', response.content))
         
+
diff --git a/htsworkflow/frontend/inventory/views.py b/htsworkflow/frontend/inventory/views.py
index dfb92a9..69848cc 100644
--- a/htsworkflow/frontend/inventory/views.py
+++ b/htsworkflow/frontend/inventory/views.py
@@ -5,15 +5,14 @@ from htsworkflow.frontend.bcmagic.plugin import register_search_plugin
 from htsworkflow.frontend.experiments.models import FlowCell
 from htsworkflow.frontend.bcmagic.forms import BarcodeMagicForm
 from htsworkflow.frontend.bcmagic.utils import print_zpl_socket
-from htsworkflow.frontend import settings
-#from htsworkflow.util.jsonutil import encode_json
 
+from django.conf import settings
+from django.contrib.auth.decorators import login_required
 from django.core.exceptions import ObjectDoesNotExist
 from django.http import HttpResponse, HttpResponseRedirect
 from django.shortcuts import render_to_response
 from django.template import RequestContext, Template
 from django.template.loader import get_template
-from django.contrib.auth.decorators import login_required
 
 register_search_plugin('Inventory Item', item_search)
 
diff --git a/htsworkflow/frontend/reports/libinfopar.py b/htsworkflow/frontend/reports/libinfopar.py
index 954fce6..73072af 100644
--- a/htsworkflow/frontend/reports/libinfopar.py
+++ b/htsworkflow/frontend/reports/libinfopar.py
@@ -1,4 +1,4 @@
-from htsworkflow.frontend import settings
+from django.conf import settings
 from django.http import HttpResponse
 from datetime import datetime
 from string import *
diff --git a/htsworkflow/frontend/samples/models.py b/htsworkflow/frontend/samples/models.py
index a8201c9..aac0ff6 100644
--- a/htsworkflow/frontend/samples/models.py
+++ b/htsworkflow/frontend/samples/models.py
@@ -4,7 +4,6 @@ from django.db import models
 from django.contrib.auth.models import User, UserManager
 from django.db.models.signals import pre_save, post_save
 from django.db import connection
-from htsworkflow.frontend import settings
 from htsworkflow.frontend.reports.libinfopar import *
 
 
diff --git a/htsworkflow/frontend/samples/results.py b/htsworkflow/frontend/samples/results.py
index 39797b1..3c6543a 100644
--- a/htsworkflow/frontend/samples/results.py
+++ b/htsworkflow/frontend/samples/results.py
@@ -1,4 +1,4 @@
-from htsworkflow.frontend import settings
+from django.conf import settings
 
 import glob
 import os
diff --git a/htsworkflow/frontend/samples/views.py b/htsworkflow/frontend/samples/views.py
index c96b718..2bbcc89 100644
--- a/htsworkflow/frontend/samples/views.py
+++ b/htsworkflow/frontend/samples/views.py
@@ -18,7 +18,6 @@ from htsworkflow.frontend.bcmagic.forms import BarcodeMagicForm
 from htsworkflow.pipelines.runfolder import load_pipeline_run_xml
 from htsworkflow.pipelines import runfolder
 from htsworkflow.pipelines.eland import ResultLane
-from htsworkflow.frontend import settings
 from htsworkflow.util.conversion import unicode_or_none
 from htsworkflow.util import makebed
 from htsworkflow.util import opener
@@ -30,6 +29,7 @@ from django.shortcuts import render_to_response, get_object_or_404
 from django.template import RequestContext
 from django.template.loader import get_template
 from django.contrib.auth.decorators import login_required
+from django.conf import settings
 
 LANE_LIST = [1,2,3,4,5,6,7,8]
 SAMPLES_CONTEXT_DEFAULTS = {
diff --git a/htsworkflow/frontend/urls.py b/htsworkflow/frontend/urls.py
index c9ce79b..8cdb82c 100644
--- a/htsworkflow/frontend/urls.py
+++ b/htsworkflow/frontend/urls.py
@@ -9,7 +9,7 @@ admin.autodiscover()
 #databrowse.site.register(Library)
 #databrowse.site.register(FlowCell)
 
-from htsworkflow.frontend import settings
+from django.conf import settings
 
 
 urlpatterns = patterns('',
diff --git a/scripts/htsw-record-runfolder b/scripts/htsw-record-runfolder
index 288ec1a..42bb614 100755
--- a/scripts/htsw-record-runfolder
+++ b/scripts/htsw-record-runfolder
@@ -1,8 +1,5 @@
 #!/usr/bin/env python
 
-from htsworkflow.util.hdquery import get_hd_serial_num
-from htsworkflow.frontend import settings
-
 from optparse import OptionParser
 import os
 import re
@@ -10,6 +7,10 @@ import sys
 import urllib2
 import urlparse
 
+from django.conf import settings
+
+from htsworkflow.util.hdquery import get_hd_serial_num
+
 runfolder_pattern = re.compile(r'[0-9]{6}_[-A-Za-z\d]+_\d+_(?P<flowcell>[A-Z\d]+)\.tgz')
 
 def extract_flowcell(runfolder_name):
diff --git a/htsworkflow/settings.py b/settings.py
similarity index 97%
rename from htsworkflow/settings.py
rename to settings.py
index 9569d3e..0f2d4da 100644
--- a/htsworkflow/settings.py
+++ b/settings.py
@@ -169,7 +169,8 @@ TEMPLATE_DIRS = (
     # Don't forget to use absolute paths, not relative paths.
     '/usr/share/python-support/python-django/django/contrib/admin/templates',
     #'/usr/lib/pymodules/python2.6/django/contrib/admin/templates/',
-    os.path.join(os.path.split(__file__)[0], 'frontend','templates'),
+    os.path.join(os.path.split(__file__)[0],
+                 'htsworkflow', 'frontend','templates'),
 )
 
 INSTALLED_APPS = (
@@ -179,7 +180,6 @@ INSTALLED_APPS = (
     'django.contrib.humanize',
     'django.contrib.sessions',
     'django.contrib.sites',
-    'django_nose',
     'htsworkflow.frontend.eland_config',
     'htsworkflow.frontend.samples',
     # modules from htsworkflow branch
@@ -216,4 +216,4 @@ BCPRINTER_PRINTER1_PORT = int(options.get('bcprinter', 'printer1_port'))
 BCPRINTER_PRINTER2_HOST = options.get('bcprinter', 'printer2_host')
 BCPRINTER_PRINTER2_PORT = int(options.get('bcprinter', 'printer2_port'))
 
-TEST_RUNNER='django_nose.NoseTestSuiteRunner'
+DEFAULT_PM=int(options.get('frontend', 'default_pm'))
-- 
2.30.2