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SciLifeLab / facs

Fast and Accurate Classification of Sequences using Bloom filters
http://facs.scilifelab.se/
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python: returning a JSON document is gone #89

Closed brainstorm closed 11 years ago

brainstorm commented 11 years ago

Somewhere in between those two builds:

https://travis-ci.org/SciLifeLab/facs/builds/13155812#L629 https://travis-ci.org/SciLifeLab/facs/builds/13128914#L629

The python JSON output for facs.query got lost:

$ python
Python 2.7.1 (r271:86832, Feb 14 2011, 14:03:18) 
[GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import facs
>>> facs.query('../tests/data/synthetic_fastq/simngs_phiX_100.fastq', '../tests/data/bloom/eschColi_K12.bloom')

''
>>>

@tzcoolman Could you please help me fix this one? It seems that it originated from pull request #75 while introducing changes for MPI someone slipped under my radar :-/

It is probably related to the new handling of the report() function in that PR (https://github.com/SciLifeLab/facs/pull/75/files#diff-f011c1f4c85573e7323c6a9d9dc721e8L226), but I am not sure...

This direcly affects the benchmarks since the JSON results are not being reported, so we need this fixed asap.

Thanks Enze!

tzcoolman commented 11 years ago

I ll take over from here. no worries @brainstorm I ll let you know when the new PR is good to merge

tzcoolman commented 11 years ago

good to merge i guess... the results on travis look correct

brainstorm commented 11 years ago

Enze, can you try running cd tests && nosetests -v -s test_basic.py? I'm still not getting output after merging your PR locally:

$ nosetests -v -s test_basic.py
Build bloom filters out of the reference genomes directory. ... ('dev/facs/tests/data/reference/dm3/seq/dm3.fa', 'dev/facs/tests/data/bloom/dm3.bloom')
('dev/facs/tests/data/reference/eschColi_K12/seq/eschColi_K12.fa', 'dev/facs/tests/data/bloom/eschColi_K12.bloom')
('dev/facs/tests/data/reference/phiX/seq/phiX.fa', 'dev/facs/tests/data/bloom/phiX.bloom')
ok
Query against the uncompressed FastQ files files manually deposited ... ok

----------------------------------------------------------------------
Ran 2 tests in 0.005s

OK
brainstorm commented 11 years ago

Actually, the output for test_basic.py does not show up in travis either:

https://travis-ci.org/SciLifeLab/facs/builds/14794075#L632

It is not only about the output, self.results in test_basic.py should contain JSON documents...

brainstorm commented 11 years ago

Got it! My fault indeed https://github.com/SciLifeLab/facs/commit/35e2a0ad18bbf7eadc74d921cca36c1f0006cc1b