Hello,

don't worry John, I understand that there are plenty of things before this
and also there is the Galaxy conference, so I can wait, no problem.
I will go through the things that you suggest.

Best regards

On 22 May 2015 at 16:11, John Chilton <jmchil...@gmail.com> wrote:

> Roberto -
>
> Sorry for consistently taking so long to respond to these parallelism
> inquires - you are doing awesome work but I am just constantly swamped
> - I'll try to do more testing today.
>
> I can confirm both of those tests fail - it has nothing to do with your
> setup.
>
> compare_bam_as_sam was added here:
>
>
> https://github.com/galaxyproject/galaxy/commit/a38bae5cca98177eacaa3cdbeb74d3722263f377
>
> It looks like I added a failing test to demonstrate metadata
> generation was broken - and I was going to follow up on it and never
> did.
>
> parallelism_bam_filter_reads only ever existed in my fork on github
> right? I am not sure why it failed - but you had some clues and I was
> going to try to follow up. Once it is working I will open a pull
> request for it.
>
> If you are working on tests that is great - but I would focus on the
> tests that work as examples. Some relevant ones may be:
>
> test/functional/tools/parallelism_optional.xml
> test/functional/tools/parallelism.xml
> test/functional/tools/metadata_bam.xml
> test/functional/tools/metadata_bcf.xml
>
> These can be executed one at a time with:
>
> ./run_tests.sh -framework -id <tool_id>
>
> ... where tool id is the id in the tool XML file (which for these
> tools usually match the basename of the file without the .xml
> extension).
>
> Will try to get to the pull requests today.
>
> Thanks a bunch for your patience.
> -John
>
> On Mon, May 11, 2015 at 6:51 AM, Roberto Alonso CIPF <ralo...@cipf.es>
> wrote:
> > Hello,
> >
> > I am designing some test and I have a problem, it works under the Galaxy
> web
> > environment, but it doesn't work when I try to use it as a test case.
> Indeed
> > I am trying other tests and they fail as well.
> >
> > My test  ./run_tests.sh -framework -id parallelism_bam_filter_reads says
> the
> > next:
> >
> > ======================================================================
> > ERROR: filter reads ( parallelism_bam_filter_reads ) > Test-1
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 268,
> in
> > test_tool
> >     self.do_it( td )
> >   File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 55,
> in
> > do_it
> >     raise e
> > RunToolException: Error creating a job for these tool inputs - {u'type':
> > u'error', u'data': {u'input': u'History does not include a dataset of the
> > required format / build'}}
> >
> >
> >
> >
> > And the other test  ./run_tests.sh -framework -id compare_bam_as_sam
> >
> > ======================================================================
> > ERROR: compare_bam_as_sam ( compare_bam_as_sam ) > Test-1
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 268,
> in
> > test_tool
> >     self.do_it( td )
> >   File "/home/ralonso/galaxy/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 "/home/ralonso/galaxy/test/base/interactor.py", line 38, in
> > stage_data_in_history
> >     upload_wait()
> >   File "/home/ralonso/galaxy/test/base/interactor.py", line 279, in wait
> >     while not self.__history_ready( history_id ):
> >   File "/home/ralonso/galaxy/test/base/interactor.py", line 297, in
> > __history_ready
> >     return self._state_ready( state, error_msg="History in error state."
> )
> >   File "/home/ralonso/galaxy/test/base/interactor.py", line 356, in
> > _state_ready
> >     raise Exception( error_msg )
> > Exception: History in error state.
> > -------------------- >> begin captured logging << --------------------
> >
> > Besides than it tries to migrate the database each time I try a test case
> > and it takes too long. I have seen that you can use --db postgres but it
> > doesn't work, I think this option should be user with --dockerize (that
> is
> > not my case).
> >
> > would you have any idea of what is going on?
> >
> > Best regards
> >
> > --
> > Roberto Alonso
> > Functional Genomics Unit
> > Bioinformatics and Genomics Department
> > Prince Felipe Research Center (CIPF)
> > C./Eduardo Primo Yúfera (Científic), nº 3
> > (junto Oceanografico)
> > 46012 Valencia, Spain
> > Tel: +34 963289680 Ext. 1021
> > Fax: +34 963289574
> > E-Mail: ralo...@cipf.es
> >
> > ___________________________________________________________
> > 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:
> >   https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
>



-- 
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: ralo...@cipf.es
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