From cdf893aca0b45f8a3c9b6e79f9c537b21edf3e04 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 22 Aug 2011 14:20:11 +0000
Subject: [PATCH] Support merging user configuration and system configuration.
mutalyzer/config.py:
- Try to load system configuration and user configuration, in that order, and
merge them if we find both.
tests/test_website.py:
- Use running webserver to retrieve batch results.
extras/config.user.example:
- Example user configuration, overwriting some values from system
configuration.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@336 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
README | 4 --
extras/config.example | 3 +-
extras/config.user.example | 11 ++++
mutalyzer/config.py | 114 +++++++++++++++---------------------
mutalyzer/variantchecker.py | 1 -
tests/test_website.py | 28 ++++++---
6 files changed, 79 insertions(+), 82 deletions(-)
create mode 100644 extras/config.user.example
diff --git a/README b/README
index dc7d6ad1..5120e879 100644
--- a/README
+++ b/README
@@ -42,10 +42,6 @@ Development notes
Todo list:
- Improve the web interface design :)
-- Running Mutalyzer as a local user (either bin/mutalyzer-website.wsgi on port
- 8080, or bin/mutalyzer for example) should be able with a partly different
- configuration. Expecially cache and log file locations, because they are
- owned by www-data.
- Test all uses of mkstemp().
- Use naming conventions for modules Crossmap, Db, File, GenRecord, Mapper,
Retriever, Scheduler.
diff --git a/extras/config.example b/extras/config.example
index 05e01241..bce2c1e4 100644
--- a/extras/config.example
+++ b/extras/config.example
@@ -1,8 +1,7 @@
#
# Mutalyzer config file.
#
-# Copy this file to /etc/mutalyzer/config or ~/.config/mutalyzer/config and
-# modify to suit your preferences.
+# Copy this file to /etc/mutalyzer/config and modify to suit your preferences.
#
# These settings are used by the Retriever module.
diff --git a/extras/config.user.example b/extras/config.user.example
new file mode 100644
index 00000000..8abc160f
--- /dev/null
+++ b/extras/config.user.example
@@ -0,0 +1,11 @@
+#
+# Mutalyzer config file.
+#
+# Copy this file to ~/.config/mutalyzer/config to overwrite definitions from
+# /etc/mutalyzer.config.
+
+# The cache directory.
+cache = "/home/user/.cache/mutalyzer"
+
+# Name and location of the log file.
+log = "/tmp/mutalyzer.log"
diff --git a/mutalyzer/config.py b/mutalyzer/config.py
index 4f222c97..1f5b36cd 100644
--- a/mutalyzer/config.py
+++ b/mutalyzer/config.py
@@ -6,10 +6,14 @@ module.
import os
-import tempfile
from configobj import ConfigObj
-import mutalyzer
+
+SYSTEM_CONFIGURATION = '/etc/mutalyzer/config'
+USER_CONFIGURATION = os.path.join(
+ os.environ.get('XDG_CONFIG_HOME', None) or \
+ os.path.join(os.path.expanduser('~'), '.config'),
+ 'mutalyzer', 'config')
class ConfigurationError(Exception):
@@ -36,10 +40,16 @@ class Config():
hard coded constant is used (the name and path to the configuration
file).
- The configuration file location is automatically detected, in the
- following order:
- 1) $XDG_CONFIG_HOME/mutalyzer/config
- 2) /etc/mutalyzer/config
+ Configuration values are read from two locations, in this order:
+ 1) /etc/mutalyzer/config
+ 2) $XDG_CONFIG_HOME/mutalyzer/config
+
+ If both files exist, values defined in the second overwrite values
+ defined in the first.
+
+ An exception to this system is when the optional {filename} argument
+ is set. In that case, the locations listed above are ignored and the
+ configuration is read from {filename}.
By the DRY-principle, we don't enumerate the configuration variables
for each class in documentation. Instead, what variables are used by
@@ -55,32 +65,23 @@ class Config():
- Supplied argument {filename} could not be opened.
- Configuration file could not be parsed.
- Not all variables are present in configuration file.
-
- @todo: Be able to have /etc/mutalyzer/config as 'base' configuration
- and some additional configuration in ~/.mutalyzer/config to
- overwrite the base configuration.
- For example, a normal user could use a different cache directory
- (writable by the user) than the system wide Mutalyzer config.
- We could use the 'merge' method from configobj.
"""
- if filename is None:
- base = os.environ.get('XDG_CONFIG_HOME', None)
- if base is None:
- base = os.path.join(os.path.expanduser('~'), '.config')
- filename = os.path.join(base, 'mutalyzer', 'config')
-
- if not os.path.isfile(filename):
- filename = '/etc/mutalyzer/config'
- if not os.path.isfile(filename):
- raise ConfigurationError('Could not locate configuration.')
-
- try:
- config = ConfigObj(filename)
- except IOError:
- raise ConfigurationError('Could not open configuration file: %s' \
- % filename)
- except SyntaxError:
- raise ConfigurationError('Could not parse configuration file.')
+ config = None
+
+ if filename:
+ config = self._load_config(filename)
+ else:
+ if os.path.isfile(SYSTEM_CONFIGURATION):
+ config = self._load_config(SYSTEM_CONFIGURATION)
+ if os.path.isfile(USER_CONFIGURATION):
+ user_config = self._load_config(USER_CONFIGURATION)
+ if config:
+ config.merge(user_config)
+ else:
+ config = user_config
+
+ if not config:
+ raise ConfigurationError('Could not locate configuration.')
try:
@@ -135,44 +136,21 @@ class Config():
self.GenRecord.spliceAlarm = int(config["spliceAlarm"])
self.GenRecord.spliceWarn = int(config["spliceWarn"])
- # If we are in a testing environment, use a temporary file for
- # logging and a temporary directory for the cache.
- # We don't remove these after the tests, since they might be
- # useful for debugging.
- if mutalyzer.is_test():
- # 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)
#__init__
+
+ def _load_config(self, filename):
+ """
+ Create a ConfigObj from the configuration in {filename}.
+ """
+ try:
+ return ConfigObj(filename)
+ except IOError:
+ raise ConfigurationError('Could not open configuration file: %s' \
+ % filename)
+ except SyntaxError:
+ raise ConfigurationError('Could not parse configuration file: %s' \
+ % filename)
+ #_load_config
#Config
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index 12c4be66..5f4cb61e 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -20,7 +20,6 @@ from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from mutalyzer import util
-from mutalyzer.config import Config
from mutalyzer.grammar import Grammar
from mutalyzer.mutator import Mutator
from mutalyzer import Retriever
diff --git a/tests/test_website.py b/tests/test_website.py
index 7d01e93d..7b3b0f01 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -14,6 +14,7 @@ I just installed webtest by 'easy_install webtest'.
#import logging; logging.basicConfig()
import os
import re
+import urllib2
import time
import web
from nose.tools import *
@@ -24,6 +25,9 @@ from mutalyzer import website
from mutalyzer.util import slow
+BATCH_RESULT_URL = 'http://localhost/mutalyzer/Results_{id}.txt'
+
+
class TestWSGI():
"""
Test the Mutalyzer WSGI interface.
@@ -255,6 +259,14 @@ class TestWSGI():
@return: The batch result document.
@rtype: string
+
+ @note: Since the batch files are processed by a running batch daemon
+ process, the result gets written to the directory defined by the
+ system-wide configuration (e.g. /var/mutalyzer/cache), thus
+ inaccessible for the TestApp instance under our current user.
+ The 'solution' for this is to download the results via a running
+ webserver that should be using the same configuration as the batch
+ daemon. Yes, this is a hack.
"""
r = self.app.get('/batch')
form = r.forms[0]
@@ -275,17 +287,19 @@ class TestWSGI():
assert re.match('[0-9]+', r.body)
time.sleep(2)
assert_equal(r.body, 'OK')
- r = self.app.get('/Results_' + id + '.txt')
- assert_equal(r.content_type, 'text/plain')
- r.mustcontain(header)
+ # This is a hack to get to the batch results (see @note above).
+ response = urllib2.urlopen(BATCH_RESULT_URL.format(id=id))
+ assert_equal(response.info().getheader('Content-Type'), 'text/plain')
+ result = response.read()
+ assert header in result
if not lines:
lines = size
- if len(r.body.strip().split('\n')) -1 != lines:
+ if len(result.strip().split('\n')) -1 != lines:
# Heisenbug, whenever it occurs we want to see some info.
print 'File: /Results_' + id + '.txt'
- print r.body
- assert_equal(len(r.body.strip().split('\n')) - 1, lines)
- return r.body
+ print result
+ assert_equal(len(result.strip().split('\n')) - 1, lines)
+ return result
def test_batch_namechecker(self):
"""
--
GitLab