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Laros authored
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
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