On Wed, Apr 3, 2013 at 2:48 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Wed, Apr 3, 2013 at 2:37 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
>> For the outputs, rgClean.xml provides an example of comparing a
>> composite output dataset with the expected test data.
>
> Here there is a tag <extra_files> used within the <output> tag.
>
> Many thanks Dave - those should be enough to get me started, and
> maybe I can update the wiki once I'm happy with how this works...
I'm trying this for makeblastdb which produces a single output,
a composite datatype which is a BLAST database.
The examples I found all seemed to be composite datatypes with
a central file (e.g. HTML plus images), i.e.
composite_type='auto_primary_file'
In the case of the BLAST databases, this is a composite datatype
without a primary file, aka composite_type='basic'. Leaving the
<param> without a file gives:
Exception: Test output does not have a 'file'
Using a empty value doesn't work,
Traceback (most recent call last):
File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py",
line 171, in test_tool
self.do_it( td, shed_tool_id=shed_tool_id )
File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py",
line 102, in do_it
self.verify_dataset_correctness( outfile, hid=elem_hid,
maxseconds=testdef.maxseconds, attributes=attributes,
shed_tool_id=shed_tool_id )
File "/mnt/galaxy/galaxy-central/test/base/twilltestcase.py", line
828, in verify_dataset_correctness
self.files_diff( local_name, temp_name, attributes=attributes )
File "/mnt/galaxy/galaxy-central/test/base/twilltestcase.py", line
66, in files_diff
local_file = open( file1, 'U' ).readlines()
IOError: [Errno 21] Is a directory: '/mnt/galaxy/galaxy-central/test-data'
Using /dev/null gets a bit further but something is confusing the
comparisons.
My current experimental test looks like this:
<tests>
<test>
<param name="dbtype" value="prot"/>
<param name="file" value="four_human_proteins.fasta"/>
<param name="title" value="Just 4 human proteins"/>
<param name="parse_seqids" value=""/>
<param name="hash_index" value="-hash_index"/>
<output name="out_file" file="/dev/null" ftype="blastdbp">
<extra_files type="file"
value="four_human_proteins.fasta.phd" name="blastdb.pdb"/>
<extra_files type="file"
value="four_human_proteins.fasta.phi" name="blastdb.phi"/>
<extra_files type="file"
value="four_human_proteins.fasta.phr" name="blastdb.phr"/>
<extra_files type="file"
value="four_human_proteins.fasta.pin" name="blastdb.pin"/>
<extra_files type="file"
value="four_human_proteins.fasta.pog" name="blastdb.pog"/>
<extra_files type="file"
value="four_human_proteins.fasta.psd" name="blastdb.psd"/>
<extra_files type="file"
value="four_human_proteins.fasta.psi" name="blastdb.psi"/>
<extra_files type="file"
value="four_human_proteins.fasta.psq" name="blastdb.psq"/>
</output>
</test>
</tests>
Any advice?
Thanks,
Peter
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