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  • Gerben Stouten's avatar
    TODO: · 7e91c366
    Gerben Stouten authored
    		- 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
    7e91c366