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

[Patrick G. <pg...@ma...>]

Thank you for clearing that up.  Run as administrator, the test 
completes successfully.

On 04/25/2018 12:09 PM, Gregory Sharov wrote:
> 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 <tel:+44%201223%20267542>
> e-mail: gs...@mr... <mailto:gs...@mr...>
> 
> On Wed, Apr 25, 2018 at 5:37 PM, Patrick Goetz <pg...@ma... 
> <mailto: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/hemoglobin_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?
> 
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