TODO:

		- update errorcodes.txt
		- rewrite some webservice.py functions
		- File.py ods files are not read in correctly. Temp file deleted before it
			can be used

    
CHANGES:
		- mutalyzer.conf
				Added pidfile reference
				Added Output Headers for the Batch Jobs

		- Db.txt
				Updated the Db.txt file so that it reflects the database changes
					* BatchJob now contains an Arg1 attribute, which is used by the
						Conversion Batch to store the build version. This could be
						changed to use the Filter Field.
					* Dropped the Var table
					* BatchQueue -> AccNo, Gene, Variant are dropped and replaced by
						single column input. This fields contains a single full
						mutalyzer variant description.

		- Install.txt
				Added the python-daemon dependency

		- handler.py
				Added a downloads handler for the old and new batch files
				Other handlers are changed so the filter for extensions now matches the
				trailing characters

		- webservice.py
				Made the functions compatible with the new Mapper.Converter class
				*** This webservice.py can use a bit more structure ***

		- index.py
				Moved a lot of logic from the index file to the Mapper.py module
				Implemented the batch handler, which has multiple entry points
				positionConverter now uses the Mapper.Converter class

		- BatchChecker.py
				Fixed the multiprocessing bugs. Now uses python-daemon to spawn a
				process and uses the var/batch.pid as a lockfile for the process

		---- Modules

		- Ouput.py
				Added getSoapMessages, which returns Soap compatible Messages for over
				the wire
				Added getBatchMessages, which returns messages above %level and filters
				the ParseError to one line
		
		- LRGparser.py
				Included the usage of transcription.translate and transcribe for the
				main transcript

		- Config.py
				Added the Batch Headers to the configfile
				Added a Batch Config object for the PID file

		- Scheduler.py
				Added the SyntaxCheck Batch
				Added the Conversion Batch
				Have the BatchProcesser read the Argument from the Batch
				Changed outputfile format to csv

		- File.py
				Changed the csv sniffer to drop the ":" delimiter in batch entries
				Updated some Job logic to detect all lines with basic errors

		- Mapper.py
				Practically a complete refactor of the module
				Added the Converter class for chromosome to c and back conversions
				Added a SoapMessage class which instances can be send over the wire
				Updated the Mapper.Mapping class to use SoapMessage messages
				Basically create correct mappings between c 2 chrom 2 c [tested]
				Reduced the number of Database calls needed significantly

		- Db.py
				Implemented getAllFields to retrieve complete dataset of Fields of
				intereset, this reduced the number of database calls
				Updated the Db logic to encompass the new Batch Job logic:
						Input entries are 1 field
						Jobs have a type
						Jobs can have arguments (1 at the moment, use BITFLAGS)


		---- Templates

		REMOVED 
				- batchCheck.html				-> All Batch jobs are united in batch.html
				- batch_convert.html		->  								"
				- convert.html					-> Replaced by converter.html

		CHANGED
				- batch.html
						Included big file type help
						Made template compatible with the three different batchTypes

				- gbupload.html & menu.html
						Fixed an onload javascript bug which caused a stream of javascript
						errors on pages other than gbupload
		
				- interface.js
						Added the changeBatch and toggle_visibility functions

		ADDED
				- downloads
						Added example download files for old & new batchfiles


NOTES:
		- change permission on var/batch.pid to have apache read/write it
		- 



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg@67 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1