On Tue, Nov 2, 2010 at 1:57 PM, Nate Coraor nate@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

Peter,

It looks like you have two dashes in your -sid option, whereas the parser expects just one.

--Dave B.

On 2/11/13 06:56:03.000, Peter wrote:

On Wed, Nov 3, 2010 at 11:48 AM, Peter peter@maubp.freeserve.co.uk wrote:

...

On Tue, Nov 2, 2010 at 1:57 PM, Nate Coraor nate@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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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