Hi all,
Have looked through the list archives regarding this without much luck.
I have a repeat parameter which contains a boolean based conditional. I
wrote a simple test case for it but I think the test keeps failing at the
boolean parameter..
input section looks like:
<repeat name="inputs" title="Input read libraries">
<conditional name="is_separate">
<param name="separate" type="boolean" checked="false" truevalue="-separate"
falsevalue="" label="Are the reads paired and in two different files?" />
<when value="">
<param name="forwards_file" type="data" format="fasta,fastq,raw,sam,bam"
label="Read dataset"/>
</when>
<when value="-separate">
<param name="forwards_file" type="data" format="fasta,fastq,raw,sam,bam"
label="Read dataset for direction 1"/>
<param name="reverse_file" type="data" format="fasta,fastq,raw,sam,bam"
label="Read dataset for direction 2"/>
</when>
</conditional>
.......
</repeat>
test section looks like:
<tests>
<test>
<param name="start_kmer" value="21"/>
<param name="end_kmer" value="29"/>
<param name="inputs.is_separate.separate" value="false"/>
<param name="inputs.is_separate.forwards_file"
value="vopt_test_reads.dat" ftype="fasta"/>
<output name="contigs" file="vopt_test_contigs.dat"/>
</test>
</tests>
The output from run_functional tests is:
======================================================================
ERROR: test_tool_000000
(functional.test_toolbox.TestForTool_velvetoptimiser_vlsci)
Velvet Optimiser vlsci ( velvetoptimiser_vlsci ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/simon/Galaxy/galaxy-dist/test/functional/test_toolbox.py",
line 171, in test_tool
self.do_it( td, shed_tool_id=shed_tool_id )
File "/home/simon/Galaxy/galaxy-dist/test/functional/test_toolbox.py",
line 76, in do_it
page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[0],
all_inputs)
File "/home/simon/Galaxy/galaxy-dist/test/functional/test_toolbox.py",
line 131, in __expand_grouping
expanded_inputs.update( self.__expand_grouping( { new_prefix : r_value
}, declared_inputs, prefix = new_prefix ) )
File "/home/simon/Galaxy/galaxy-dist/test/functional/test_toolbox.py",
line 118, in __expand_grouping
if declared_inputs[ value.test_param.name ] == case.value:
KeyError: 'separate'
-------------------- >> begin captured stdout << ---------------------
kmer_step not declared in tool test, will not change default value.
filetype not declared in tool test, will not change default value.
--------------------- >> end captured stdout << ----------------------
-------------------- >> begin captured logging << --------------------
galaxy.web.framework: DEBUG: Error: this request returned None from
get_history(): http://localhost:8326/
galaxy.web.framework: DEBUG: Error: this request returned None from
get_history(): http://localhost:8326/
galaxy.web.framework: DEBUG: Error: this request returned None from
get_history(): http://localhost:8326/user/logout
galaxy.web.framework: DEBUG: Error: this request returned None from
get_history(): http://localhost:8326/
--------------------- >> end captured logging << ---------------------
----------------------------------------------------------------------
Ran 1 test in 0.675s
FAILED (errors=1)
My question: Can the testing framework handle the nesting of the boolean,
conditional and repeat parameters or have I made a mistake in the test xml?
Cheers,
Simon Gladman
VBC/VLSCI
Monash University
Australia.
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