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Laros authored
- Todo.txt. - handler.py: A general handler for mod_python. This handler dispatches SOAP services and a normal HTML publisher. Furthermore, it is able to handle raw requests to dump HTML or XML files. This handler is TAL enabled. - webservice.py: A publisher for webservices. When a new webservice is added, this is the entrypoint for the server side (just like index.py, add a function). - getTranscripts.py: A webservice that reports all transcripts that overlap with a certain genomic position (chomosome, position). - getGeneName.py: A webservice that finds the gene name of a given transcript. - service.wsdl: This is the definition of the interface for webservices. A client must download this file and parse it to obtain a programming interface, then the client can use this interface just like any local function. - Obsoleted.txt: A list of things that will be deleted in the future (but are still functional for backwards compatibility). - client/sp.py: A test client for the two webservices. Renamed Main.py to Mutalyzer.py. Modified: - mutalyzer.conf: Added a configurable date prefix for logging. - Install.txt: - To reflect the difference in configuration of apache to work with the new handler (requires less configuration). - Added TAL as a new dependency. - html/check.html: Made it a full TAL template. Title, version and output are now separated from the HTML design. - Mutator.py: Made the shiftpos() function public, this is needed for insertion checking. - Parser.py: Updated the comments. - Variant_info: Made all internal functions private. - Output.py: Updated the comments. - Config.py: Modified to reflect the changes in mutalyzer.conf. - Db.py: - We now keep the handle to the database open until the object is deleted. - Added a destructor that closes the handle to the database. - Added getTranscripts(): Get a list of transcripts, given a chromosome and a position on that chromosome. - Added get_GeneName(): Get the gene name of a given transcript. - Retriever.py: Updated the comments. - Crossmap.py: - Made a patch that handles a CDS start on the first position of the transcript. - Added more unit tests. - index.py: - Added a switch for older versions of LOVD, to generate the expected output in Variant_info. - Made this publisher compatible with TAL. - Mutalyzer.py: Made all internal functions private. git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@13 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
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