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  • Laros's avatar
    Added: · 5371f394
    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
    5371f394