Altered the Output module in such a way that all messages are stored in a

list with priorities, and all output is stored in a dictionary. This dictionary
can be read at a later time.
The Retriever module is changed to accommodate for uploaded GenBank files and
slices of a chromosome.
A Scheduler was added for batch checking.

mutalyzer.conf:
- Added variables for the Retriever module:
  - maxDldSize, minDldSize ; Maximum and minimum sizes for slices and uploaded 
    GenBank files.
- Added variables for the Output module:
  - loglevel, outputlevel ; Specify default verbosity levels for logging and 
    output.
- Added variables for the Scheduler module:
  - processName ; Name of the running scheduler.

Db.txt:
- Added information on how to create the newly used tables GbInfo, BatchQueue
  and BatchJob.

errorcodes.txt:
- Short description of the error codes used in the Output module.

webservice.py:
- Added a Complex class to test more complicated return types (see the web_dev
  branch).
- Modified the code to work with the new Output module.

index.py:
- Made a first upload page.

Mutalyzer.py:
- Modified the code to work with the new Output module.

UCSC_update.py:
- Modified the code to work with the new Output module.

Variant_info.py:
- Modified the code to work with the new Output module.

GenRecord.py:
- Added documentation.

Mutator.py:
- Modified the code to work with the new Output module.

Misc.py:
- New file, used for generating unique IDs.

Parser.py:
- Made a change to the definition of an UD accession number.
- Modified the code to work with the new Output module.

Scheduler.py:
- Made a batch checker scheduler.
  - isDaemonRunning() ; See if we need to be started.
  - process() ; Start the batch checker.
  - addJob() ; Add jobs to a queue in the database.

Output.py:
- Added a Message class to store all debug, info, warning, error and fatal
  messages.
  - If a message is given that exceeds the configured log level, it will be
    logged immediately.
- A function is added to the Output class to read all messages that exceed a 
  certain verbosity level.
- A function is added to create a named list as an output node.
- With the getOutput function the content of this list can be retrieved.

Config.py:
- Several sub-classes were added for each configurable module.

Db.py:
- Added documentation.
- Added functionality that is used by the Retriever module.
- Added functionality that is used by the Scheduler module.

Retriever.py:
- Added functionality to be able to use custom GenBank files and chromosome
  slices.
  - Information on these created files are stored in a database to be able to
    re-create them when the cache is cleaned.
  - The hash of each file is stored for error detection.

BatchChecker.py:
- A wrapper that is called either from the addJob() function from the Scheduler
  module, or from cron. It dispatches a background process that processes the
  batch jobs.

gbupload.html:
- Test template for uploading files (copied from Mutalyzer 1.0.4).

sp.py:
- Some test with a complex return type.

download.html:
- Did some first tests with a METAL template.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@26 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1