Failure: ValueError (No such test TestForTool_sartools_edger) ... ERROR

8 Jun 2015

      errors and questions with run_tests.sh and
    install_and_test_tool_shed_repositories.sh
...
在 2015年6月8日，17:00，galaxy-dev-request@lists.galaxyproject.org 写道：
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Today's Topics:

Re: Multi-level datatype conversions (Keith Suderman)
Re: Bismark doesn't end and blocks the server (Björn Grüning)
Re: errors and questions with run_tests.sh and
install_and_test_tool_shed_repositories.sh (Loraine Guéguen)

Message: 1
Date: Sun, 7 Jun 2015 16:37:08 -0400
From: Keith Suderman suderman@cs.vassar.edu
To: David Kelly davidkelly@uchicago.edu
Cc: "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Multi-level datatype conversions
Message-ID: 12AB4920-B9A0-4993-B320-B225394C237E@cs.vassar.edu
Content-Type: text/plain; charset="utf-8"
Hi David,
...
On Jun 5, 2015, at 2:10 PM, David Kelly davidkelly@uchicago.edu wrote:
Hi Keith,
I am able to manually convert from a->b and then separately b->c, but not directly from a->c. I'm still thinking about how to approach this as well, but I'll share my thoughts so far.
Does Galaxy automatically do the conversions for you in the workflow editor?  For example, if you have a tool A that produces format 'a' and another tool B that consumes format 'b' you should be able to drag the "noodle" from A to B and Galaxy will do an implicit format conversion.  If this is working for you then someone from the Galaxy team will have to jump in.  If Galaxy is not doing implicit format conversions then it likely means your datatype(s) are not fully defined.  I didn't get the implicit format conversion working properly until I implemented the format sniffers.
...
In our use case, we have a collection of climate tools we'd like to use. The tools are written by different groups, so most use their own file formats. Ideally we would like users to be able to upload their data in any of these file formats and use all tools without having to explicitly convert their data.
Let's say there are 10 climate datatypes. My understanding is that in order to achieve this kind of interoperability, I'd have to write 90 converters.
If Galaxy could chain converters together, I could write 1 converter per datatype and chain them together like this:
a -> b -> c -> d -> e -> f -> g -> h -> i -> j -> a
Another scenario I've been thinking about is picking one data type to be the 'standard'. Let's say it's 'a' in this example. You could write 18 converters:
a->b, a->c, a->d,...
b->a, c->a, d->a,...
This is what we do. We have a standard "pivot format" then converters from the other formats to/from the pivot format.
Cheers,
Keith
...
Then suppose you wanted to plug a 'd' file into a 'c' tool. You could first manually convert d->a, then use the automatic conversion for a->c. Not fully automatic, but not too bad.
On Thu, Jun 4, 2015 at 5:20 PM, Keith Suderman suderman@anc.org wrote:
Hi David,
We just got it working for the single conversions, that is, getting Galaxy to automatically convert from a -> b when needed.  Are you able to do the conversion, i.e a -> b and b -> c individually?
We are just coming to a similar use case and I'm definitely interested in how you make out, even if I can't be much help.
Cheers,
Keith
...
On Jun 3, 2015, at 4:15 PM, David Kelly davidkelly@uchicago.edu wrote:
Hello,
Suppose I have three custom datatypes defined: a, b, and c
I have a datatype converter that converts from a -> b
I have a datatype converter that converts from b -> c
Can I then send 'a' files as input into tools that accept type 'c'?
This doesn't seem to work in my test case, but I thought it might be worth asking to see if anyone has tried this before. Thanks!
Regards,
David
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Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY

Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY
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Message: 2
Date: Mon, 08 Jun 2015 11:22:44 +0200
From: Björn Grüning bjoern.gruening@gmail.com
To: "C. Ch." tuto345@hotmail.com,
  "galaxy-dev@lists.galaxyproject.org"
  galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Bismark doesn't end and blocks the server
Message-ID: 55755EE4.1080902@gmail.com
Content-Type: text/plain; charset=utf-8
Hi,
I think this is a general problem you encountered here with unsorted BAM
files. We can reproduce it locally. Will let you know if I find a
workaround.
Cheers,
Bjoer
...
Am 05.06.2015 um 14:23 schrieb C. Ch.:
Hi all, I have a clean local install of galaxy from git (commit:
40b69cb948eed2cece82a32dfc5c6116414ab97c).I've installed bismark and
I get an error message (see below) if I do not choose the 'sort'
option.I have the impression that this might be related more to
galaxy than to bismark itself. The result is that the server gets
blocked and the only solution is to restart galaxy. Any help is
appreciated!Cristian The error message:galaxy.datatypes.metadata
DEBUG 2015-06-05 11:14:12,514 setting metadata externally failed for
HistoryDatasetAssociation 1305: External set_meta() not
called[bam_index_core] the alignment is not sorted
(HWI-ST278R:398:C1WUTACXX:3:1101:9378:2574): 2-th chr > 1-th
chr[bam_index_build2] fail to index the BAM file.
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Message: 3
Date: Mon, 08 Jun 2015 12:30:29 +0200
From: Loraine Guéguen  loraine.gueguen@sb-roscoff.fr
To: John Chilton jmchilton@gmail.com
Cc: Galaxy Dev List galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] errors and questions with run_tests.sh and
  install_and_test_tool_shed_repositories.sh
Message-ID: 55756EC5.70303@sb-roscoff.fr
Content-Type: text/plain; charset=utf-8; format=flowed
Thanks for your answers !
I will try "./run_tests.sh -installed" and see if it can solve the 2 
first points. By the way, I didn't know this option (not displayed with 
run_tests.sh --help) or documented on the wiki if I'm not mistaken.
For point 3, I'll try the new "planemo shed_test" subcommand. The 
subcommand "planemo test" uses the run_tests.sh script, isn't it ? Does 
the "planemo shed_test" subcommand use all or any part of the Tool Shed 
Install and Test Framework 
(https://wiki.galaxyproject.org/AutomatedToolTests) or is it completely 
different ?
Is there any way to launch the tool tests against an external server 
(point 4) with Planemo ?
Loraine
Le 02/06/2015 15:16, John Chilton a écrit :
...
On Tue, Jun 2, 2015 at 4:14 AM, Loraine Guéguen
loraine.gueguen@sb-roscoff.fr wrote:
...
Hi,
I have investigated the testing possibilities within a Galaxy local instance
and within a toolshed. I met some difficulties and I have 4 questions listed
below.
1- Tests on tools installed in a local Galaxy instance (with run_tests.sh) :
It seems that it is only possible to test the tools that have been manually
installed (run_test.sh -id ...), not the tools that have been installed
through a toolshed. Is that true ? When I try to launch the tests of a
toolshed installed tool, I have the following error message :
#########
Failure: ValueError (No such test TestForTool_sartools_edger) ... ERROR
ERROR: Failure: ValueError (No such test TestForTool_sartools_edger)
Traceback (most recent call last):
 File
"/projet/htdocs/galaxy-dev/galaxy-dist/eggs/nose-0.11.1-py2.7.egg/nose/failure.py",
line 39, in runTest
   raise self.exc_class(self.exc_val)
ValueError: No such test TestForTool_sartools_edger

Ran 1 test in 0.002s
FAILED (errors=1)
./run_tests.sh -installed runs the tests of all installed tool shed
tools. It might be possible to combine that with -id - for a specific
tool but I am not sure. It may be possible to construct that test even
if -id doesn't work - but it is probably pretty hacky. Let me know if
-installed works for you but not when combined with -id and we can
work out the details.
...
#########
2- Tests on tools installed in a local Galaxy instance (with run_tests.sh) :
Is it possible to test tools which have repository or tool dependencies ? I
have a tool (manually installed in galaxy-dist/tools/) with a dependence to
a datatype installed from a toolshed. The datatype (no_unzip.zip) is defined
in the <param> input tag (in <test>) with attribute "ftype". When running
run_tests.sh, it seems that the dataype is not known :
#########
======================================================================
ERROR: test_tool_000001 (functional.test_toolbox.TestForTool_sartools_edger)
SARTools edgeR ( sartools_edger ) > Test-2

Traceback (most recent call last):
 File
"/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py", line
268, in test_tool
   self.do_it( td )
 File
"/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py", line
37, in do_it
   stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
 File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py", line
36, in stage_data_in_history
   upload_waits.append( galaxy_interactor.stage_data_async( test_data,
history, shed_tool_id ) )
 File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py", line
182, in stage_data_async
   raise Exception(submit_response)
Exception: {u'message': {u'type': u'error', u'data': {u'file_type': u"An
invalid option was selected for file_type, u'no_unzip.zip', please verify.",
u'files_metadata': [u"An invalid option was selected for file_type,
u'no_unzip.zip', please verify."]}}}
#########
It is possible it is the case that tool shed datatypes are not loaded
unless running with the -installed flag.  I would either setup the
tests to run locally (manually add datatypes and tools) or run
installed tools with -installed.
...
3- Toolshed Install and Test framework (
install_and_test_tool_shed_repositories.sh) : For my tool, the test fails if
I don't explicitely defined the dbkey attribute to "unknown" (dbkey="?") in
the <param> input tag (in <test>). The default dbkey value seems to be
"hg17" (whereas hg17 is not defined on the server running my toolshed). So I
have the following error message if I don't add dbkey="?" in <test> :
#########
======================================================================
ERROR: test_tool_000001
(functional.test_toolbox.TestForTool_galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209)
SARTools edgeR (
galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209 )
...
Test-2

Traceback (most recent call last):
 File
"/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py", line
268, in test_tool
   self.do_it( td )
 File
"/w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py", line
37, in do_it
   stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
 File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py", line
36, in stage_data_in_history
   upload_waits.append( galaxy_interactor.stage_data_async( test_data,
history, shed_tool_id ) )
 File "/w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py", line
182, in stage_data_async
   raise Exception(submit_response)
Exception: {u'message': {u'type': u'error', u'data': {u'dbkey': u"An invalid
option was selected for dbkey, u'hg17', please verify."}}}
#########
Well that is frustrating. I am not aware of the internals of that
script or why that is happening - but my personal recommendation would
be not to use the install and test framework at this point - it seems
rather un-maintained. I recently added a subcommnd to planemo called
shed_test (http://planemo.readthedocs.org/en/master/commands.html#shed-test-command)

that will install and test a tool shed repository. It probably

requires modifying your tool shed development process to use planemo
(http://planemo.readthedocs.org/en/latest/publishing.html#shed).
...
4- Is it possible to launch the tests against an external server ? That
would be very useful to be able run the tests on a production Galaxy
instance in order to test the tools in real condition, within the whole
environment.
This would be great - but as I understand it - it is not possible at
this time. The test framework needs local access to some aspects of
the Galaxy app. Last year I outlined a Trello card to add this option
back to Galaxy (https://trello.com/c/8K86l4Qk) - it was available
years ago.
...
Thanks in advance for your answers.
Loraine
--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/

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-- 
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
29680 Roscoff
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http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/

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End of galaxy-dev Digest, Vol 108, Issue 8

Re: [galaxy-dev] galaxy-dev Digest, Vol 108, Issue 8

Failure: ValueError (No such test TestForTool_sartools_edger) ... ERROR

ERROR: Failure: ValueError (No such test TestForTool_sartools_edger)