[Biopython-dev] [Bug 2893] New: Jython test_prosite fix+patch
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Fri Jul 31 21:28:25 UTC 2009
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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