From fd469a1029d0a44ff03743c535a5fdaaf6e3033a Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Thu, 21 Jul 2011 08:46:24 +0000
Subject: [PATCH] Fixes for failing unit tests (disabled temporary config
values).
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@306 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/config.py | 39 +++++++++++++++++++++++++++++++--------
tests/test_website.py | 4 ++++
2 files changed, 35 insertions(+), 8 deletions(-)
diff --git a/mutalyzer/config.py b/mutalyzer/config.py
index baa40b4f..339ec46e 100644
--- a/mutalyzer/config.py
+++ b/mutalyzer/config.py
@@ -138,14 +138,37 @@ class Config():
# We don't remove these after the tests, since they might be
# useful for debugging.
if mutalyzer.is_test():
- handle, filename = tempfile.mkstemp(suffix='.log',
- prefix='mutalyzer-tests-')
- os.close(handle)
- self.Output.log = filename
- dirname = tempfile.mkdtemp(suffix='.cache',
- prefix='mutalyzer-tests-')
- self.Retriever.cache = dirname
- self.Scheduler.resultsDir = dirname
+ # Todo:
+ #
+ # This needs some refactoring. The problem with the temporary
+ # file and dir names is that they will not be used by the
+ # (running) batch daemon, which will thus save its results to
+ # to 'normal' directory.
+ # Furthermore, subsequent web requests from a unit test will
+ # use different configuration instantiations, so might not
+ # see results from previous requests.
+ #
+ # We need a more robust solution for different configurations,
+ # depending of the running user/setting (e.g. unit tests).
+ #
+ # Idea: Don't create a local instance of the website in the
+ # unit tests, but only use running instances of all servers
+ # (website, webservice, batch daemon). They will use their
+ # own 'normal' configuration.
+ # All other parts of the unit tests will use temporary test
+ # configuration values. We might even decorate the tests
+ # needing server access as such and provide the option of
+ # skipping these.
+
+ #handle, filename = tempfile.mkstemp(suffix='.log',
+ # prefix='mutalyzer-tests-')
+ #os.close(handle)
+ #self.Output.log = filename
+ #dirname = tempfile.mkdtemp(suffix='.cache',
+ # prefix='mutalyzer-tests-')
+ #self.Retriever.cache = dirname
+ #self.Scheduler.resultsDir = dirname
+ pass
except KeyError as e:
raise ConfigurationError('Missing configuration value: %s' % e)
diff --git a/tests/test_website.py b/tests/test_website.py
index ae3512be..e740edd4 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -15,6 +15,7 @@ I just installed webtest by 'easy_install webtest'.
import os
import re
import time
+import web
from nose.tools import *
from webtest import TestApp
@@ -32,6 +33,7 @@ class TestWSGI():
"""
Initialize test application.
"""
+ web.config.debug = False
application = website.app.wsgifunc()
self.app = TestApp(application)
@@ -448,6 +450,8 @@ facilisi."""
def test_batch_multicolumn(self):
"""
Submit the batch syntax checker with a multiple-colums input file.
+
+ This by the way also tests for the correct order of batch results.
"""
variants = [('AB026906.1(SDHD):g.7872G>T', 'NM_003002.1:c.3_4insG'),
('NM_003002.1:c.3_4insG', 'AB026906.1(SDHD):g.7872G>T'),
--
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