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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
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