On Tue, Feb 11, 2014 at 3:41 PM, Dave Bouvier dave@bx.psu.edu wrote:
Peter,
Thanks for pointing this out, I've applied your changes in 12478:15fc8675064e on the default branch.
--Dave B.
Thanks Dave,
RE: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-February/018154.html https://bitbucket.org/galaxy/galaxy-central/commits/15fc8675064ea46b7e081d96...
I'm still digging into the underlying problem, by focussing on just one unit test from https://github.com/peterjc/pico_galaxy/blob/master/tools/mira4/mira4_de_novo...
Namely:
<test> <param name="job_type" value="genome" /> <param name="job_quality" value="accurate" /> <param name="type" value="none" /> <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" /> <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" /> </test>
After the test runs, we have five files, which is expected as I have one input and four outputs:
<outputs> <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" /> <data name="out_bam" format="bam" label="MIRA de novo assembly (BAM)" /> <data name="out_maf" format="mira" label="MIRA de novo assembly" /> <data name="out_log" format="txt" label="MIRA de novo log" /> </outputs>
$ ls /tmp/tmp09TawY/tmpFOX9hS/database/files/000/ dataset_1.dat dataset_2.dat dataset_3.dat dataset_4.dat dataset_5.dat
dataset_1.dat --> test-data/ecoli.fastq dataset_2.dat --> out_fasta dataset_3.dat --> out_bam dataset_4.dat --> out_maf dataset_5.dat --> out_log
Of these, the test should only attempt to compare dataset_2.dat (out_fasta) to my sample output file test-data/ecoli.mira4_de_novo.fasta which it matches:
$ diff test-data/ecoli.mira4_de_novo.fasta /tmp/tmp09TawY/tmpFOX9hS/database/files/000/dataset_2.dat
However, for reasons unknown, it is comparing dataset_5.dat (out_log) to the sample output file test-data/ecoli.mira4_de_novo.fasta instead.
A little more logging (e.g. [1]) shows the problem is when calling into the verify_dataset_correctness method (should use hid=2):
base.interactor: DEBUG: About to call verify_dataset_correctness('ecoli.mira4_de_novo.fasta', '5', ...) base.interactor: DEBUG: About to call verify_dataset_correctness(...) for output_data 'state': 'queued' base.interactor: DEBUG: About to call verify_dataset_correctness(...) for output_data 'hid': '5' base.interactor: DEBUG: About to call verify_dataset_correctness(...) for output_data 'id': '5' base.interactor: DEBUG: About to call verify_dataset_correctness(...) for output_data 'dbkey': 'hg17' base.interactor: DEBUG: About to call verify_dataset_correctness(...) for output_data 'name': 'MIRA de novo log' base.twilltestcase: DEBUG: Verifying dataset correctness for 'ecoli.mira4_de_novo.fasta' (hid='5')
Now what is strange is how can the call to get the hid for the current outfile can know if it should be 2, 3, 4, or 5? The bug appears to be in method _verify_outputs in test/functional/test_toolbox.py - which was last touched by John...
output_data = data_list[ len(data_list) - len(testdef.outputs) + output_index ]
In this example, we have data_list[5 - 1 + 0] = 4, meaning since data_list is essentially [dataset_1, ..., dataset_5] we get dataset_5
I believe the error is that rather than the number of defined test outputs (here 1), you should be subtracting the number of tool outputs (here 4). i.e. data_list[5 - 4 + 0] = data_list[1] = dataset_2
As a workaround, I could probably provide expected data for all four output files...
Regards,
Peter
[1] Patch which adds more logging to test/base/interactor.py (similar debugging added to other files to trace this.)
$ hg diff test/base/interactor.py diff -r f3dc213a5773 test/base/interactor.py --- a/test/base/interactor.py Mon Feb 10 22:13:35 2014 -0600 +++ b/test/base/interactor.py Tue Feb 11 16:19:51 2014 +0000 @@ -309,6 +309,9 @@
def verify_output( self, history, output_data, outfile, attributes, shed_tool_id, maxseconds ): hid = output_data.get( 'hid' ) + log.debug("About to call verify_dataset_correctness(%r, %r, ...)" % (outfile, hid)) + for key in output_data.keys(): + log.debug("About to call verify_dataset_correctness(...) for output_data %r: %r" % (key, output_data.get(key))) self.twill_test_case.verify_dataset_correctness( outfile, hid=hid, attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
def get_job_stream( self, history_id, output_data, stream ):