diff --git a/DEVELOPMENT.md b/DEVELOPMENT.md
index b62dbd47965dc144231af40b3e3224f9ec99a11b..09c43ca83f87780f75fcbfc4874de742dcaab79e 100644
--- a/DEVELOPMENT.md
+++ b/DEVELOPMENT.md
@@ -24,11 +24,11 @@ web service:
Now run the tests with:
- MUTALYZER_ENV=test nosetests -v
+ nosetests -v
Or, if you are in a hurry, skip the long-running tests with:
- MUTALYZER_ENV=test MUTALYZER_QUICK_TEST=1 nosetests -v
+ MUTALYZER_QUICK_TEST=1 nosetests -v
Working with feature branches
diff --git a/INSTALL.md b/INSTALL.md
index 7edef864fd4b996103edd6ad34e48b910fc07272..a4f7c2ce10940b26506b735f30b1fd6a4eb8f2ea 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -131,7 +131,7 @@ the batch daemon and the webserver (the SOAP part) running.
Now run the tests:
- MUTALYZER_ENV=test nosetests
+ nosetests
Upgrade Mutalyzer
diff --git a/fabfile.py b/fabfile.py
index fcbe006dec18eee7085a8722b0cca7d3959b5dc3..9f6f8542abffe9e9427c42b558ba622508fc2f25 100644
--- a/fabfile.py
+++ b/fabfile.py
@@ -70,7 +70,7 @@ def deploy(bootstrap='no'):
sudo('bash extras/post-upgrade.sh')
# Run unittests.
- #run('MUTALYZER_ENV=test nosetests -v')
+ #run('nosetests -v')
# Now that all is set up, delete the folder again.
# (I don't like to 'sudo rm -Rf'.)
diff --git a/mutalyzer/Scheduler.py b/mutalyzer/Scheduler.py
index d82ba140416ba83be5887ed840cb6e0b98b5f142..39494f5b416355307f5347492455fb7933f504a8 100644
--- a/mutalyzer/Scheduler.py
+++ b/mutalyzer/Scheduler.py
@@ -91,14 +91,8 @@ class Scheduler() :
@arg url: The url containing the results
@type url: string
"""
- if mutalyzer.is_test():
- return
-
- # Note: The above check with mutalyzer.is_test is bogus, since during
- # a normal unit test, the batch checker process is not started in the
- # environment of the unit tests.
- # As sort of a hack, we therefore check for the patented address
- # 'test@test.test', used in the unit tests.
+ # Mail is set to 'test@test.test" if the batch job was submitted from
+ # a unit test.
if mailTo == 'test@test.test':
return
diff --git a/mutalyzer/__init__.py b/mutalyzer/__init__.py
index d087516efbf7d2492a0d6669e419d2d32a5bf582..13b87384e1477a19038daeed26019e66516f8fcc 100644
--- a/mutalyzer/__init__.py
+++ b/mutalyzer/__init__.py
@@ -3,9 +3,6 @@ HGVS variant nomenclature checker.
"""
-import os
-
-
# On the event of a new release, we update the __version_info__ and __date__
# package globals and set RELEASE to True.
# Before a release, a development version is denoted by a __version_info__
@@ -38,27 +35,3 @@ NOMENCLATURE_VERSION = '.'.join(NOMENCLATURE_VERSION_INFO)
COPYRIGHT_YEARS = (2009, int(__date__[-4:]))
SOAP_NAMESPACE = 'http://mutalyzer.nl/2.0/services'
-
-
-def package_root():
- """
- Get the absolute path to the mutalyzer package. This is usefull for
- things like locating HTML templates (which are in a subdirectory of the
- package).
-
- @return: Absolute path to the mutalyzer package.
- @rtype: string
- """
- return os.path.realpath(os.path.split(__file__)[0])
-
-
-def is_test():
- """
- Check if we are in a test environment. This is determined by the
- MUTALYZER_ENV environment variable, which should then be set to 'test'.
-
- @return: True if we are in a test environment, False otherwise.
- @rtype: bool
- """
- return 'MUTALYZER_ENV' in os.environ \
- and os.environ['MUTALYZER_ENV'] == 'test'
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index ed87d273169c06658d42e31ad1e88117a57056af..bb1787fe2c9022a57fa29a66e15dd4475da8383d 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -5,7 +5,6 @@ General Mutalyzer website interface.
SERVICE_SOAP_LOCATION = '/services'
SERVICE_JSON_LOCATION = '/json'
-WSDL_VIEWER = 'templates/wsdl-viewer.xsl'
GENOME_BROWSER_URL = 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position={chromosome}:{start}-{stop}&hgt.customText={bed_file}'
@@ -27,6 +26,7 @@ import urllib
from collections import defaultdict
from lxml import etree
+import pkg_resources
from cStringIO import StringIO
from simpletal import simpleTALES
from simpletal import simpleTAL
@@ -176,7 +176,7 @@ class render_tal:
# TAL template render
-render = render_tal(os.path.join(mutalyzer.package_root(), 'templates'),
+render = render_tal(pkg_resources.resource_filename('mutalyzer', 'templates'),
globals = {
'version' : mutalyzer.__version__,
'nomenclatureVersion' : mutalyzer.NOMENCLATURE_VERSION,
@@ -231,7 +231,9 @@ class Download:
The url routing currently makes sure to only call this with filenames
of the form [a-zA-Z-]+\.(?:py|cs).
"""
- file_path = os.path.join(mutalyzer.package_root(), 'templates', file)
+ file_path = os.path.join(
+ pkg_resources.resource_filename('mutalyzer', 'templates'),
+ file)
if not os.path.isfile(file_path):
raise web.notfound()
@@ -263,8 +265,9 @@ class Downloads:
The url routing currently makes sure to only call this with filenames
of the form [a-zA-Z\._-]+.
"""
- file_path = os.path.join(mutalyzer.package_root(), 'templates',
- 'downloads', file)
+ file_path = os.path.join(
+ pkg_resources.resource_filename('mutalyzer', 'templates'),
+ 'downloads', file)
if not os.path.isfile(file_path):
raise web.notfound()
@@ -1541,8 +1544,9 @@ class SoapApi:
wsdl = Wsdl11(soap.application.interface)
wsdl.build_interface_document(url)
wsdl_handle = StringIO(wsdl.get_interface_document())
- xsl_handle = open(os.path.join(mutalyzer.package_root(), WSDL_VIEWER),
- 'r')
+ xsl_handle = open(os.path.join(
+ pkg_resources.resource_filename('mutalyzer', 'templates'),
+ 'wsdl-viewer.xsl'), 'r')
wsdl_doc = etree.parse(wsdl_handle)
xsl_doc = etree.parse(xsl_handle)
transform = etree.XSLT(xsl_doc)