On Wed, 25 Mar 2009 12:03:05 -0700
Christopher Lee <l...@chem.ucla.edu> wrote:
> it would be helpful if you'd post the details of the traceback for
> the "int key" megatest error, and the location / procedure for
> running the megatests to reproduce the problem.
Sure! Note that since the portability patches still haven't been
committed to master, in my instruction I shall implicitly assume
running on leelab2 - doing it anywhere else now would be a hassle.
1. Download Pygr from Git, build it and set PYTHONPATH the usual way
2. cd tests/oldtests/
3. Non-portable megatests look for input files in the current
directory, so provide them there: 'ln -s /result/pygr_megatest/*.txt .'
4. Until the relevant change has been pushed to Git, in all *megatest.py
files except dm2_download_megatest.py, change all occurrences of
'pygr.Data.getResource.addResource' to 'pygr.Data.addResource'.
5. Again, until the relevant change has been propagated to Git: in
annotation_dm2_megatest.py and annotation_hg18_megatest.py, import
pygr.mapping and replace all occurrences of 'pygr.Data.Collection' with
'pygr.mapping.Collection'.
6. Run megatests the usual old-test way: 'python protest.py
filename(s)'
Presently, the following should happen:
- pairwise_hg18_megatest, nlmsa_hg18_megatest and nlmsa_dm2_megatest
complete successfully
- dm2_download_megatest fails with
------------------------------------------------------------
FAILED:dm2_download_megatest.NLMSADownload_Test.download_test()
------------------------------------------------------------
OUTPUT:
STDERR:
Traceback (most recent call last):
File "protest.py", line 123, in <module>
if do_test(sys.argv[2],sys.argv[3],sys.argv[4]):
File "protest.py", line 26, in do_test
obj.setup()
File "/result/aqq/pygr/tests/oldtests/dm2_download_megatest.py", line
32, in setup save_NLMSA_downloaders(self.url)
File
"/result/aqq/pygr/build/lib.linux-x86_64-2.5/pygr/apps/catalog_downloads.py",
line 57, in save_NLMSA_downloaders
pygr.Data.getResource.addResourceDict(d,layer) AttributeError:
'MetabaseList' object has no attribute 'addResourceDict'
- annotation_hg18_megatest fails with
------------------------------------------------------------
FAILED:annotation_hg18_megatest.Build_Test.collectionannot_test()
------------------------------------------------------------
OUTPUT:
STDERR:
[...]
Traceback (most recent call last):
File "protest.py", line 123, in <module>
if do_test(sys.argv[2],sys.argv[3],sys.argv[4]):
File "protest.py", line 33, in do_test
m()
File "/result/aqq/pygr/tests/oldtests/annotation_hg18_megatest.py", line 278,
in collectionannot_test
exlist1 = [(ix.exon_id, ix) for ix in ex1.keys()]
File "cnestedlist.pyx", line 617, in pygr.cnestedlist.NLMSASlice.keys
File "cnestedlist.pyx", line 929, in
pygr.cnestedlist.NLMSASlice.groupBySequences
File "cnestedlist.pyx", line 590, in
pygr.cnestedlist.NLMSASlice.get_seq_interval
File "/result/aqq/pygr/build/lib.linux-x86_64-2.5/pygr/nlmsa_utils.py", line
15, in getSeq
return self.nlmsaSeqDict.nlmsa.seqDict[seqID]
File "/result/aqq/pygr/build/lib.linux-x86_64-2.5/pygr/seqdb.py", line 562,
in __getitem__
return self.get_subitem(self.prefixDict[prefix], seqID)
File "/result/aqq/pygr/build/lib.linux-x86_64-2.5/pygr/seqdb.py", line 555,
in get_subitem
return d[seqID]
File "/result/aqq/pygr/build/lib.linux-x86_64-2.5/pygr/annotation.py", line
153, in __getitem__
return self.sliceAnnotation(k,self.sliceDB[k])
File "/result/aqq/pygr/build/lib.linux-x86_64-2.5/pygr/mapping.py", line 389,
in __getitem__
return self.d[self.saveKey(k)]
File "/usr/local/lib/python2.5/shelve.py", line 112, in __getitem__
f = StringIO(self.dict[key])
TypeError: 'int' object is unsubscriptable
- annotation_dm2_megatest fails with
------------------------------------------------------------
FAILED:annotation_dm2_megatest.Build_Test.collectionannot_test()
------------------------------------------------------------
OUTPUT:
STDERR:
[...]
Traceback (most recent call last):
File "protest.py", line 123, in <module>
if do_test(sys.argv[2],sys.argv[3],sys.argv[4]):
File "protest.py", line 33, in do_test
m()
File "/result/aqq/pygr/tests/oldtests/annotation_dm2_megatest.py", line 202,
in collectionannot_test
exlist1 = [(ix.exon_id, ix) for ix in ex1.keys()]
File "cnestedlist.pyx", line 617, in pygr.cnestedlist.NLMSASlice.keys
File "cnestedlist.pyx", line 929, in
pygr.cnestedlist.NLMSASlice.groupBySequences
File "cnestedlist.pyx", line 590, in
pygr.cnestedlist.NLMSASlice.get_seq_interval
File "/result/aqq/pygr/build/lib.linux-x86_64-2.5/pygr/nlmsa_utils.py", line
15, in getSeq
return self.nlmsaSeqDict.nlmsa.seqDict[seqID]
File "/result/aqq/pygr/build/lib.linux-x86_64-2.5/pygr/seqdb.py", line 562,
in __getitem__
return self.get_subitem(self.prefixDict[prefix], seqID)
File "/result/aqq/pygr/build/lib.linux-x86_64-2.5/pygr/seqdb.py", line 555,
in get_subitem
return d[seqID]
File "/result/aqq/pygr/build/lib.linux-x86_64-2.5/pygr/annotation.py", line
153, in __getitem__
return self.sliceAnnotation(k,self.sliceDB[k])
File "/result/aqq/pygr/build/lib.linux-x86_64-2.5/pygr/mapping.py", line 389,
in __getitem__
return self.d[self.saveKey(k)]
File "/usr/local/lib/python2.5/shelve.py", line 112, in __getitem__
f = StringIO(self.dict[key])
TypeError: 'int' object is unsubscriptable
Hope that helps!
--
MS
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