[cctbxbb] [Dials-support] DIALS source tarball

[Aaron Brewster]

Hi Markus, two points.

First, you are correct that the dials builds are not passing tests related
to the chem_data folder which includes monomer libraries.  This is because
chem_data is required by mmtbx but isn't included in the dials build.
Partly because we're unsure if pieces of it are proprietary.  In the
meantime, I've worked with Nigel to change the
cctbx_regression.test_nightly to look for the chem_data repository and skip
the mmtbx tests if it's not present.  mmtbx will still be tested nightly as
part of the standalone cctbx and phenix packages.  Because of this change,
perhaps you could revert your recent changes to
cctbx/regression/tst_geometry_restraints_2.py?
It isn't necessary to check for chem_data in every sub test as it is tested
for at the top level now.

Second, the log you provided is not the one on buildbot.  Your log
indicates you have a CCP4 installation that includes a monomer library that
is being picked up by the tests.  Is one of the MMTBX_CCP4_MONOMER_LIB, or
CLIBD_MON environment variables set on the system in question?

Thanks,
-Aaron



On Tue, Apr 7, 2015 at 6:41 AM, <markus.gerstel at diamond.ac.uk> wrote:

> Cc'ing cctbx folks
>
> David Waterman wrote:
> > So maybe once we have a source tarball up at dials.diamond.ac.uk (..)
>
> Speaking of which: our DIALS builds are currently failing at the installer
> testing stage. This is due to cctbx/regression/tst_geometry_restraints_2.py
> failing deep in mmtbx territory.
> So far I could not figure out how to get this running properly.
>
>
> Call:
>
> libtbx.python tst_geometry_restraints_2.py
>
> Standard Output
>
> Skipping exercise_with_zeolite(): input file not available
> Skipping exercise_with_pdb(): chem_data directory not available
>
> Standard Error
>
> Traceback (most recent call last):
>   File
> "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py",
> line 866, in <module>
>     exercise_all(sys.argv[1:])
>   File
> "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py",
> line 862, in exercise_all
>     exercise_na_restraints_output_to_geo(verbose=verbose)
>   File
> "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py",
> line 805, in exercise_na_restraints_output_to_geo
>     log=out1)
>   File
> "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py",
> line 5270, in run
>     log=log)
>   File
> "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py",
> line 4876, in __init__
>     restraints_loading_flags=restraints_loading_flags,
>   File
> "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py",
> line 2902, in __init__
>     log=log,
>   File
> "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py",
> line 2287, in __init__
>     m_j=mm)
>   File
> "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py",
> line 1513, in get_lib_link
>     return mon_lib_srv.link_link_id_dict["rna3p"]
> KeyError: 'rna3p'
>
>
> (On a side note: We really should call multiple tests within the same
> python file separately, instead of running them together within a signle
> run() method. This file contains 4 tests, but these will result in only a
> single return value for any upstream processing of the test results, such
> as Jenkins.)
>
> -Markus
>
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