#58 ExeConfig breaks reading in custom exe_t_coffee.dat

v1.0 (example)
closed-fixed
5
2014-04-25
2012-05-30
No

As reported by Roberto:

togawa@proteinmodelling-server:/temp/test$ /usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py

Error: Error while building alingnments.
<type 'exceptions.TypeError'> in /usr/lib/python2.7/dist-packages/Biskit/scripts/Mod/align.py line 123:
("cannot create 'NoneType' instances",).
TraceBack:
align: 123 (<module>) a.align_for_modeller_inp()
Aligner: 273 (align_for_modeller_inp) fasta_sequences, fasta_target )
Aligner: 227 (__default_input_files) cwd = TCoffee( '' ).cwd or os.getcwd()
Aligner: 56 (__init__) node=host, **kw )
Executor: 315 (__init__) self.exe = ExeConfigCache.get( name, strict=strict )
ExeConfigCache: 68 (get) ExeConfigCache.CACHE[ name ] = ExeConfig( name, **kw )
ExeConfig: 157 (__init__) self.update()
ExeConfig: 194 (update) self.__dict__[ key ] = t( value )

Discussion

  • Raik Gruenberg

    Raik Gruenberg - 2012-05-30

    pickled state of local variables in affected method before breaking

     
  • Raik Gruenberg

    Raik Gruenberg - 2014-04-25

    Sorry about the delay ;)
    I don't know exactly what went wrong with this config file but what eventually goes wrong is a type casting attempt in ExeConfig line 194. ExeConfig tries to guess the type of a parameter from its default value. In this case this gave the type NoneType which should never be used. I am now eliminating NoneType from the list. Should work but not tested with this particular file.

     
  • Raik Gruenberg

    Raik Gruenberg - 2014-04-25
    • status: open --> closed-fixed
    • Group: --> v1.0 (example)
     

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