[Biopython-dev] [Bug 2891] New: Jython test_NCBITextParser fix+patch
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Fri Jul 31 20:06:32 UTC 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2891
Summary: Jython test_NCBITextParser 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
Jython is limited to JVM method sizes, overly large methods cause JVM
exceptions (java.lang.ClassFormatError: Invalid method Code length ...). The
test_NCBITextParser unit test contains a few methods that are larger then the
JVM limit. This can be fixed by breaking some of the methods into multi
segment tests. So test_bt007 becomes test_bt007a and test_bt007b.
A sample fix patch, tested with Jython2.5.0:
713c713
< def test_bt007(self):
---
> def test_bt007a(self):
1242a1243,1250
>
> def test_bt007b(self):
> "Test parsing PHI-BLAST, BLASTP 2.0.10 output, three rounds (bt007)"
>
> path = os.path.join('Blast', 'bt007')
> handle = open(path)
> record = self.pb_parser.parse(handle)
>
1891c1899
< def test_bt009(self):
---
> def test_bt009a(self):
2525a2534,2541
>
>
> def test_bt009b(self):
> "Test parsing PHI-BLAST, BLASTP 2.0.10 output, two rounds (bt009)"
>
> path = os.path.join('Blast', 'bt009')
> handle = open(path)
> record = self.pb_parser.parse(handle)
5635c5651
< def test_bt047(self):
---
> def test_bt047a(self):
6251a6268,6275
>
> def test_bt047b(self):
> "Test parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (bt047)"
>
> path = os.path.join('Blast', 'bt047')
> handle = open(path)
> record = self.pb_parser.parse(handle)
>
9959c9983
< def test_bt060(self):
---
> def test_bt060a(self):
10330a10355,10362
>
> def test_bt060b(self):
> "Test parsing BLASTP 2.0.12 output (bt060)"
>
> path = os.path.join('Blast', 'bt060')
> handle = open(path)
> record = self.pb_parser.parse(handle)
>
11000a11033,11041
>
>
> def test_bt060c(self):
> "Test parsing BLASTP 2.0.12 output (bt060)"
>
> path = os.path.join('Blast', 'bt060')
> handle = open(path)
> record = self.pb_parser.parse(handle)
>
11504a11546,11552
>
> def test_bt060d(self):
> "Test parsing BLASTP 2.0.12 output (bt060)"
>
> path = os.path.join('Blast', 'bt060')
> handle = open(path)
> record = self.pb_parser.parse(handle)
11812a11861,11866
>
> def test_bt060e(self):
> "Test parsing BLASTP 2.0.12 output (bt060)"
>
> path = os.path.join('Blast', 'bt060')
> handle = open(path)
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