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

@@ -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
 -----------------

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:

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.

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

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',