Re: [scipion-users] Spider MDA Workflow not working again

[Gregory S. <sha...@gm...>]

Hi Patrick,

in your case all test data by default is located in /opt/scipion/data/tests
folder. ScipionUserData is used only for user projects. Test data is
supposed to be downloaded by admin/the person who installed scipion.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267542 <+44%201223%20267542>
e-mail: gs...@mr...

On Wed, Apr 25, 2018 at 5:37 PM, Patrick Goetz <pg...@ma...>
wrote:

> Hi -
>
> Sorry for continuously spamming the list, but the Spider MDA Workflow test
> isn't working again, I just want to make sure I haven't introduced
> structural installation problems.
>
> First, I re-installed Scipion in /opt so that the users can access it, and
> made sure to install the spider package.  Now running scipion as an
> ordinary user:
>
>    /opt/scipion/scipion tests em.workflows.test_workflow_spiderMDA
>
> I get error messages and "2 Tests failed" again.  Snooping around in the
> locally created ScipionUserData folder, I found this note in
>
> ~/ScipionUserData/projects/TestSpiderWorkflow/Runs/000002_
> ProtImportParticles/logs/run.stdout:
>
> -------
> Traceback (most recent call last):
>   File "/opt/scipion/pyworkflow/protocol/protocol.py", line 186, in run
>     self._run()
>   File "/opt/scipion/pyworkflow/protocol/protocol.py", line 1104, in _run
>     'Protocol.run: Validation errors:\n' + '\n'.join(errors))
> Exception: Protocol.run: Validation errors:
> There are no files matching the pattern /opt/scipion/data/tests/hemogl
> obin_mda/particles/*.spi
> -------
>
>
> So apparently the test is trying to install data to /opt/scipion/data
> rather than ~/ScipionUserData ?
>
> Am I missing a configuration step that would instruct the system to
> process all data in the user's ScipionUserData folder?
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>