bbcf/track — comment on commit ad8b7e318d333f5df4ab8b74b9c016713ef59e7f
File:  line 0
By xapple:

I'm sorry to bother you with this again, but seeing that this commit leaves the library in a non-working state, could I suggest once more running the test suite before committing ? If you did so, you would immediatly see that the job was not finished on line 1116.

No programmer gets his code right in the first shot, that's normal. One always needs to run the code to see if it works...

[user@computer track]$ nosetests
...........EEEEEEE.EE............
----------------------------------------------------------------------
Ran 33 tests in 2.967s

FAILED (errors=9)

======================================================================
ERROR: runTest (track.test.format_bed.TestConversion)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/My Folders/BBCF/Repos/track/track/test/format_bed.py", line 32, in runTest
track.convert(orig_bed_path, test_sql_path, assembly='sacCer2')
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 280, in convert
return parser(serializer)
File "/My Folders/BBCF/Repos/track/track/parse/__init__.py", line 61, in __call__
with handler as self.handler: self.parse()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 29, in __exit__
if self.current_track: self.closeCurrentTrack()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 74, in closeCurrentTrack
if hasattr(self, 'current_assembly'): self.current_track.assembly = self.current_assembly
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 1116, in assembly
if not assembly_name: return
NameError: global name 'assembly_name' is not defined

======================================================================
ERROR: runTest (track.test.format_bed.TestRoundtrip)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/My Folders/BBCF/Repos/track/track/test/format_bed.py", line 46, in runTest
track.convert(orig_bed_path, test_sql_path, assembly='sacCer2')
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 280, in convert
return parser(serializer)
File "/My Folders/BBCF/Repos/track/track/parse/__init__.py", line 61, in __call__
with handler as self.handler: self.parse()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 29, in __exit__
if self.current_track: self.closeCurrentTrack()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 74, in closeCurrentTrack
if hasattr(self, 'current_assembly'): self.current_track.assembly = self.current_assembly
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 1116, in assembly
if not assembly_name: return
NameError: global name 'assembly_name' is not defined

======================================================================
ERROR: runTest (track.test.format_bedgraph.TestRoundtrip)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/My Folders/BBCF/Repos/track/track/test/format_bedgraph.py", line 32, in runTest
track.convert(orig_bedgraph_path, test_sql_path, assembly='sacCer2')
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 280, in convert
return parser(serializer)
File "/My Folders/BBCF/Repos/track/track/parse/__init__.py", line 61, in __call__
with handler as self.handler: self.parse()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 29, in __exit__
if self.current_track: self.closeCurrentTrack()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 74, in closeCurrentTrack
if hasattr(self, 'current_assembly'): self.current_track.assembly = self.current_assembly
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 1116, in assembly
if not assembly_name: return
NameError: global name 'assembly_name' is not defined

======================================================================
ERROR: runTest (track.test.format_bigwig.TestRoundtrip)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/My Folders/BBCF/Repos/track/track/test/format_bigwig.py", line 32, in runTest
track.convert(orig_bigwig_path, test_sql_path, assembly='sacCer2')
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 280, in convert
return parser(serializer)
File "/My Folders/BBCF/Repos/track/track/parse/__init__.py", line 61, in __call__
with handler as self.handler: self.parse()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 29, in __exit__
if self.current_track: self.closeCurrentTrack()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 74, in closeCurrentTrack
if hasattr(self, 'current_assembly'): self.current_track.assembly = self.current_assembly
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 1116, in assembly
if not assembly_name: return
NameError: global name 'assembly_name' is not defined

======================================================================
ERROR: runTest (track.test.format_gff.TestRoundtrip)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/My Folders/BBCF/Repos/track/track/test/format_gff.py", line 33, in runTest
track.convert(orig_gff_path, test_sql_path, assembly='sacCer2')
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 280, in convert
return parser(serializer)
File "/My Folders/BBCF/Repos/track/track/parse/__init__.py", line 61, in __call__
with handler as self.handler: self.parse()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 29, in __exit__
if self.current_track: self.closeCurrentTrack()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 74, in closeCurrentTrack
if hasattr(self, 'current_assembly'): self.current_track.assembly = self.current_assembly
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 1116, in assembly
if not assembly_name: return
NameError: global name 'assembly_name' is not defined

======================================================================
ERROR: runTest (track.test.format_gtf.TestConversion)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/My Folders/BBCF/Repos/track/track/test/format_gtf.py", line 34, in runTest
track.convert(orig_gtf_path, test_sql_path, assembly=12)
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 280, in convert
return parser(serializer)
File "/My Folders/BBCF/Repos/track/track/parse/__init__.py", line 61, in __call__
with handler as self.handler: self.parse()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 29, in __exit__
if self.current_track: self.closeCurrentTrack()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 74, in closeCurrentTrack
if hasattr(self, 'current_assembly'): self.current_track.assembly = self.current_assembly
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 1116, in assembly
if not assembly_name: return
NameError: global name 'assembly_name' is not defined

======================================================================
ERROR: runTest (track.test.format_gzip.TestConversion)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/My Folders/BBCF/Repos/track/track/test/format_gzip.py", line 30, in runTest
track.convert(orig_gzip_path, test_sql_path, assembly='sacCer2')
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 280, in convert
return parser(serializer)
File "/My Folders/BBCF/Repos/track/track/parse/__init__.py", line 61, in __call__
with handler as self.handler: self.parse()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 29, in __exit__
if self.current_track: self.closeCurrentTrack()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 74, in closeCurrentTrack
if hasattr(self, 'current_assembly'): self.current_track.assembly = self.current_assembly
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 1116, in assembly
if not assembly_name: return
NameError: global name 'assembly_name' is not defined

======================================================================
ERROR: runTest (track.test.format_wig.TestConversion)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/My Folders/BBCF/Repos/track/track/test/format_wig.py", line 32, in runTest
track.convert(orig_wig_path, test_sql_path, assembly='sacCer2')
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 280, in convert
return parser(serializer)
File "/My Folders/BBCF/Repos/track/track/parse/__init__.py", line 61, in __call__
with handler as self.handler: self.parse()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 29, in __exit__
if self.current_track: self.closeCurrentTrack()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 74, in closeCurrentTrack
if hasattr(self, 'current_assembly'): self.current_track.assembly = self.current_assembly
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 1116, in assembly
if not assembly_name: return
NameError: global name 'assembly_name' is not defined

======================================================================
ERROR: runTest (track.test.format_wig.TestRoundtrip)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/My Folders/BBCF/Repos/track/track/test/format_wig.py", line 48, in runTest
track.convert(orig_wig_path, test_sql_path, assembly='sacCer2')
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 280, in convert
return parser(serializer)
File "/My Folders/BBCF/Repos/track/track/parse/__init__.py", line 61, in __call__
with handler as self.handler: self.parse()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 29, in __exit__
if self.current_track: self.closeCurrentTrack()
File "/My Folders/BBCF/Repos/track/track/serialize/sql.py", line 74, in closeCurrentTrack
if hasattr(self, 'current_assembly'): self.current_track.assembly = self.current_assembly
File "/My Folders/BBCF/Repos/track/track/__init__.py", line 1116, in assembly
if not assembly_name: return
NameError: global name 'assembly_name' is not defined