On Wed, Nov 3, 2010 at 11:48 AM, Peter <pe...@maubp.freeserve.co.uk> wrote:
> On Tue, Nov 2, 2010 at 1:57 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>>
>> Peter wrote:
>>> Hi,
>>>
>>> I'm trying to use run_functional_tests.sh to run all the tests
>>> for a section (group of tools). I've read the output from:
>>>
>>> ./run_functional_tests.sh help
>>>
>>> For example, from the tools_conf.xml.sample we have
>>>
>>>   <section name="ENCODE Tools" id="EncodeTools">
>>>     <tool file="encode/gencode_partition.xml" />
>>>     <tool file="encode/random_intervals.xml" />
>>>   </section>
>>>
>>> And looking at these tools' XML files,
>>>
>>> <tool id="gencode_partition1" name="Gencode Partition">
>>>
>>> and:
>>>
>>> <tool id="random_intervals1" name="Random Intervals">
>>>
>>> I'd like to run the functional tests for the ENCODE tools,
>>> Using the switch for an individual tool id (-id) works,
>>>
>>> ./run_functional_tests.sh -id gencode_partition1
>>> ...
>>> Ran 1 test in 22.302s
>>> ...
>>>
>>> and so does this (well, it say the tool doesn't have any
>>> tests which is true in this example):
>>>
>>> ./run_functional_tests.sh -id random_intervals1
>>> ...
>>> Ran 1 test in 0.027s
>>> ...
>>>
>>> However, I also tried using the section id switch (-sid),
>>>
>>> ./run_functional_tests.sh -sid EncodeTools
>>> ...
>>> Ran 0 tests in 0.000s
>>> ...
>>>
>>> I also tried using the section name,
>>>
>>> /run_functional_tests.sh -sid  "ENCODE Tools"
>>>
>>> Is this (-sid not working) a known issue, or am I using it wrong?
>>
>> As presently written it expects the name concatenated with the id, with
>> spaces converted to dashes.  You can see the list of valid sections by
>> running 'python tool_list.py'.  Everything after "section::" is what
>> would follow the '-sid' flag.
>>
>> --nate
>
> Ah - that worked. I don't really understand that design choice when you have a
> section id, but how about a clarification along these lines since the current
> text doesn't make sense to me:
>
> diff -r ae6c56ad5a49 run_functional_tests.sh
> --- a/run_functional_tests.sh   Wed Nov 03 11:42:24 2010 +0000
> +++ b/run_functional_tests.sh   Wed Nov 03 11:46:02 2010 +0000
> @@ -10,7 +10,8 @@
>         echo "'run_functional_tests.sh'                       for testing
> all the tools in functional directory"
>         echo "'run_functional_tests.sh aaa'                   for testing
> one test case of 'aaa' ('aaa' is the file name with path)"
>         echo "'run_functional_tests.sh -id bbb'               for testing
> one tool with id 'bbb' ('bbb' is the tool id)"
> -       echo "'run_functional_tests.sh -sid ccc'              for testing
> one section with sid 'ccc' ('ccc' is the string after 'section::')"
> +       echo "'run_functional_tests.sh -sid ccc'              for testing
> one section with sid 'ccc' ('ccc' is the string after"
> +       echo "                                                'section::' in
> the --list output, not just the id from tool_conf XML)"
>         echo "'run_functional_tests.sh -list'                 for listing
> all the tool ids"
>  elif [ $1 = '-id' ]; then
>         python ./scripts/functional_tests.py -v
> functional.test_toolbox:TestForTool_$2 --with-nosehtml
> --html-report-file run_functional_tests.html
>
>
> Thanks,
>
> Peter

Hi all,

I'm running into a little trouble with the --sid option, something
seems to have broken:

$ ./run_functional_tests.sh --sid NCBI_BLAST+-ncbi_blast_plus_tools
...
Usage: functional_tests.py [options]

functional_tests.py: error: no such option: --sid
functional_tests.py ERROR 2013-02-11 11:34:42,959 Failure running tests
Traceback (most recent call last):
  File "./scripts/functional_tests.py", line 430, in main
    test_config.configure( sys.argv )
  File "/mnt/galaxy/galaxy-central/eggs/nose-0.11.1-py2.6.egg/nose/config.py",
line 249, in configure
    options, args = self._parseArgs(argv, cfg_files)
  File "/mnt/galaxy/galaxy-central/eggs/nose-0.11.1-py2.6.egg/nose/config.py",
line 237, in _parseArgs
    return parser.parseArgsAndConfigFiles(argv[1:], cfg_files)
  File "/mnt/galaxy/galaxy-central/eggs/nose-0.11.1-py2.6.egg/nose/config.py",
line 133, in parseArgsAndConfigFiles
    return self._parser.parse_args(args, values)
  File "/usr/lib64/python2.6/optparse.py", line 1396, in parse_args
    self.error(str(err))
  File "/usr/lib64/python2.6/optparse.py", line 1578, in error
    self.exit(2, "%s: error: %s\n" % (self.get_prog_name(), msg))
  File "/usr/lib64/python2.6/optparse.py", line 1568, in exit
    sys.exit(status)
SystemExit: 2
...

Reading run_functional_tests.sh it handles the --sid argument via tool_list.py,
it calls this command which seems to work:

$ python tool_list.py NCBI_BLAST+-ncbi_blast_plus_tools
 functional.test_toolbox:TestForTool_ncbi_blastn_wrapper
functional.test_toolbox:TestForTool_ncbi_blastp_wrapper
functional.test_toolbox:TestForTool_ncbi_blastx_wrapper
functional.test_toolbox:TestForTool_ncbi_tblastn_wrapper
functional.test_toolbox:TestForTool_ncbi_tblastx_wrapper
functional.test_toolbox:TestForTool_blastxml_to_tabular

Before digging much further, does the --sid argument still work for others,
or might it be just something on my setup which has gone awry?

Thanks,

Peter
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