[Biopython-dev] [Bug 2893] New: Jython test_prosite fix+patch

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2893

           Summary: Jython test_prosite fix+patch
           Product: Biopython
           Version: 1.51b
          Platform: Other
        OS/Version: Other
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Unit Tests
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: kellrott at ucsd.edu
 BugsThisDependsOn: 2890,2891,2892


Jython is limited to JVM method sizes, overly large methods cause JVM
exceptions (java.lang.ClassFormatError: Invalid method Code length ...).  The
test_prosite unit test contains a few methods that are larger then the
JVM limit.  

This can be fixed by breaking separate methods into smaller methods. 

This patch combined with other bug fixes brings Biopython to the point where
"jython setup.py test" can complete without throwing exceptions:

Ran 122 tests in 39.295 seconds

FAILED (failures = 74)

Patch tested with Jython2.5.0


3742c3742
<     def test_read1(self):
---
>     def test_read1a(self):
4096a4097,4103
> 
> 
>     def test_read1b(self):
>         "Parsing Prosite record ps00107.txt"
>         filename = os.path.join('Prosite', 'ps00107.txt')
>         handle = open(filename)
>         record = Prosite.read(handle)
4499a4507,4515
> 
> 
> 
> 
>     def test_read1c(self):
>         "Parsing Prosite record ps00107.txt"
>         filename = os.path.join('Prosite', 'ps00107.txt')
>         handle = open(filename)
>         record = Prosite.read(handle)
4934a4951,4956
> 
>     def test_read1d(self):
>         "Parsing Prosite record ps00107.txt"
>         filename = os.path.join('Prosite', 'ps00107.txt')
>         handle = open(filename)
>         record = Prosite.read(handle)
5190a5213,5218
> 
>     def test_read1e(self):
>         "Parsing Prosite record ps00107.txt"
>         filename = os.path.join('Prosite', 'ps00107.txt')
>         handle = open(filename)
>         record = Prosite.read(handle)
5611a5640,5645
> 
>     def test_read1f(self):
>         "Parsing Prosite record ps00107.txt"
>         filename = os.path.join('Prosite', 'ps00107.txt')
>         handle = open(filename)
>         record = Prosite.read(handle)
5892a5927,5932
> 
>     def test_read1g(self):
>         "Parsing Prosite record ps00107.txt"
>         filename = os.path.join('Prosite', 'ps00107.txt')
>         handle = open(filename)
>         record = Prosite.read(handle)
6417c6457
<     def test_read4(self):
---
>     def test_read4a(self):
6617a6658,6663
> 
>    def test_read4b(self):
>         "Parsing Prosite record ps00432.txt"
>         filename = os.path.join('Prosite', 'ps00432.txt')
>         handle = open(filename)
>         record = Prosite.read(handle)


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