From 4a941a654bfc796240cd23b8e907eccc60cf45f9 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Fri, 19 Aug 2011 11:02:32 +0000
Subject: [PATCH] Add website debugging flag to config file.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@335 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
INSTALL | 4 ++++
README | 8 ++++----
extras/config.example | 3 +++
mutalyzer/config.py | 3 ++-
mutalyzer/website.py | 7 ++++---
5 files changed, 17 insertions(+), 8 deletions(-)
diff --git a/INSTALL b/INSTALL
index 72856076..3b799b4a 100644
--- a/INSTALL
+++ b/INSTALL
@@ -132,6 +132,10 @@ Now run the tests:
MUTALYZER_ENV=test nosetests
+Note: Currently it is not advised to run the tests on a production server
+since they need write access to the main Mutalyzer cache and log. A separate
+cache and log for local users and tests is planned functionality.
+
Upgrade Mutalyzer
-----------------
diff --git a/README b/README
index 0774f980..dc7d6ad1 100644
--- a/README
+++ b/README
@@ -32,6 +32,10 @@ Or, if you are in a hurry, skip the long-running tests with:
MUTALYZER_ENV=test MUTALYZER_QUICK_TEST=1 nosetests -v
+Note: Currently it is not advised to run the tests on a production server
+since they need write access to the main Mutalyzer cache and log. A separate
+cache and log for local users and tests is planned functionality.
+
Development notes
-----------------
@@ -45,8 +49,6 @@ Todo list:
- Test all uses of mkstemp().
- Use naming conventions for modules Crossmap, Db, File, GenRecord, Mapper,
Retriever, Scheduler.
-- Integrate fuzzy offsets from this branch:
- https://www.mutalyzer.nl/projects/mutalyzer2/changeset?old_path=%2Ftrunk&old=228&new_path=%2Fbranches%2Fexon-deletions-branch&new=228#file5
- Use standard logging module, with rotating functionality. Race conditions
on the log file are probably a problem in the current setup.
Instead of that rotating, we could also use logrotate:
@@ -71,8 +73,6 @@ Todo list:
- In deployment, remove old versions of Mutalyzer package?
- Use https protocol.
- Check for os.path.join vulnerabilities.
-- Use web.config.debug=False on production server and perhaps put this in
- the configuration file.
- Solution for database schema migration on version updates.
Code style guide:
diff --git a/extras/config.example b/extras/config.example
index dfc8a135..05e01241 100644
--- a/extras/config.example
+++ b/extras/config.example
@@ -78,6 +78,9 @@ loglevel = 3
# Level of output messages.
outputlevel = 1
+# Show debug info in the web interface.
+debug = yes
+
#
# These settings are used by the Mutator module.
diff --git a/mutalyzer/config.py b/mutalyzer/config.py
index 2d8837af..4f222c97 100644
--- a/mutalyzer/config.py
+++ b/mutalyzer/config.py
@@ -61,6 +61,7 @@ class Config():
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)
@@ -105,6 +106,7 @@ class Config():
self.Output.datestring = config["datestring"]
self.Output.loglevel = int(config["loglevel"])
self.Output.outputlevel = int(config["outputlevel"])
+ self.Output.debug = config.as_bool('debug')
# Set the variables needed by the Mutator module.
self.Mutator.flanksize = int(config["flanksize"])
@@ -133,7 +135,6 @@ 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
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index be9c833b..faa35853 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -42,13 +42,14 @@ from mutalyzer import Retriever
from mutalyzer import File
-web.config.debug = True
-
-
# Load configuration from configuration file
config = Config()
+# Show web.py debugging information.
+web.config.debug = config.Output.debug
+
+
# URL dispatch table
urls = (
'', 'RedirectHome',
--
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