[cctbxbb] Broken iotbx/pdb/cif test
Nigel Moriarty
nwmoriarty at lbl.gov
Wed Dec 19 08:58:09 PST 2018
I think the best clue was in the origin email you sent me.
expected_type, looped_id.split(":",1)[0], val))
ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius
1,7
It's failing to parse a CIF loop. It can't convert "1,7" to a float. Are
you pointing your environment to a different monomer library that Phenix?
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Wed, Dec 19, 2018 at 8:42 AM richard.gildea at diamond.ac.uk <
richard.gildea at diamond.ac.uk> wrote:
> Hi Nigel,
>
>
> As I mentioned in my email, this issue also affects my local builds on
> both mac and linux. I don't think I am doing any thing particularly odd in
> my local environments, and the fact that Jenkins also thinks the test is
> broken suggests that the issue is with the test and not my environment.
> Graeme also confirmed it was failing for him.
>
>
> Is there anything in the error message that would suggest the underlying
> issue?
>
>
> $ libtbx.python $(libtbx.find_in_repositories
> iotbx/regression/tst_pdb_as_cif.py)
>
> Converting tst_pdb_as_cif_1.pdb to mmCIF format.
> Traceback (most recent call last):
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py",
> line 106, in <module>
> exercise_01()
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py",
> line 37, in exercise_01
> logger=null_out(),
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/cli_parser.py",
> line 71, in run_program
> task.run()
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/programs/pdb_as_cif.py",
> line 37, in run
> txt = model.model_as_mmcif()
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py",
> line 879, in model_as_mmcif
> if self.get_restraints_manager() is not None:
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py",
> line 622, in get_restraints_manager
> self.setup_restraints_manager()
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py",
> line 1042, in setup_restraints_manager
> self._process_input_model()
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py",
> line 959, in _process_input_model
> use_neutron_distances =
> self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances)
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/utils/__init__.py",
> line 998, in __init__
> use_neutron_distances=use_neutron_distances,
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py",
> line 675, in __init__
> use_neutron_distances=use_neutron_distances,
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py",
> line 689, in convert_all
> use_neutron_distances=use_neutron_distances,
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py",
> line 700, in convert_lib_atom
> entry = cif_types.energy_lib_atom(**dict(row))
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/cif_types.py",
> line 49, in __init__
> raise_value_error("Floating-point")
> File
> "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/cif_types.py",
> line 39, in raise_value_error
> expected_type, looped_id.split(":",1)[0], val))
> ValueError: Floating-point value expected in CIF file:
> _lib_atom.ion_radius 1,7
>
> Cheers,
>
>
> Richard
>
>
> Dr Richard Gildea
> Data Analysis Scientist
> Tel: +441235 77 8078
>
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science & Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
> ________________________________
> From: cctbxbb-bounces at phenix-online.org <cctbxbb-bounces at phenix-online.org>
> on behalf of Nigel Moriarty <nwmoriarty at lbl.gov>
> Sent: 19 December 2018 16:29:10
> To: cctbx mailing list
> Subject: Re: [cctbxbb] Broken iotbx/pdb/cif test
>
> These tests worked when I committed and they work for me now. Also works
> in BuildBot. Not sure what is the difference between my normal up-to-date
> Phenix environment, BuildBot and Jenkins that is causing the problems for
> you.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
> Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov>
>
>
> On Wed, Dec 19, 2018 at 1:11 AM richard.gildea at diamond.ac.uk<mailto:
> richard.gildea at diamond.ac.uk> <richard.gildea at diamond.ac.uk<mailto:
> richard.gildea at diamond.ac.uk>> wrote:
> According to Jenkins these two tests have been broken for several days -
> does anyone know what the issue is and could a fix be applied? Both look
> like the same error.
>
>
> iotbx/regression/tst_pdb_as_cif.py
>
> iotbx/regression/tst_data_manager.py
>
>
> These have been failing since this commit:
>
>
>
> https://github.com/cctbx/cctbx_project/commit/2c119fcf012ca4cc60dfce231902c6133b99a228
>
>
> The tests also fail locally for me (not just on Jenkins).
>
> Cheers,
>
>
> Richard
>
>
> Traceback (most recent call last):
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py",
> line 106, in <module>
> exercise_01()
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py",
> line 37, in exercise_01
> logger=null_out(),
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/cli_parser.py",
> line 71, in run_program
> task.run()
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/programs/pdb_as_cif.py",
> line 37, in run
> txt = model.model_as_mmcif()
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py",
> line 879, in model_as_mmcif
> if self.get_restraints_manager() is not None:
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py",
> line 622, in get_restraints_manager
> self.setup_restraints_manager()
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py",
> line 1042, in setup_restraints_manager
> self._process_input_model()
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py",
> line 959, in _process_input_model
> use_neutron_distances =
> self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances)
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py",
> line 998, in __init__
> use_neutron_distances=use_neutron_distances,
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py",
> line 675, in __init__
> use_neutron_distances=use_neutron_distances,
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py",
> line 689, in convert_all
> use_neutron_distances=use_neutron_distances,
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py",
> line 700, in convert_lib_atom
> entry = cif_types.energy_lib_atom(**dict(row))
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py",
> line 49, in __init__
> raise_value_error("Floating-point")
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py",
> line 39, in raise_value_error
> expected_type, looped_id.split(":",1)[0], val))
> ValueError: Floating-point value expected in CIF file:
> _lib_atom.ion_radius 1,7
>
>
> Traceback (most recent call last):
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py",
> line 532, in <module>
> test_model_datatype()
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py",
> line 233, in test_model_datatype
> dm.get_model().model_as_mmcif(), overwrite=True)
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py",
> line 879, in model_as_mmcif
> if self.get_restraints_manager() is not None:
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py",
> line 622, in get_restraints_manager
> self.setup_restraints_manager()
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py",
> line 1042, in setup_restraints_manager
> self._process_input_model()
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py",
> line 959, in _process_input_model
> use_neutron_distances =
> self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances)
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py",
> line 998, in __init__
> use_neutron_distances=use_neutron_distances,
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py",
> line 675, in __init__
> use_neutron_distances=use_neutron_distances,
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py",
> line 689, in convert_all
> use_neutron_distances=use_neutron_distances,
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py",
> line 700, in convert_lib_atom
> entry = cif_types.energy_lib_atom(**dict(row))
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py",
> line 49, in __init__
> raise_value_error("Floating-point")
> File
> "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py",
> line 39, in raise_value_error
> expected_type, looped_id.split(":",1)[0], val))
> ValueError: Floating-point value expected in CIF file:
> _lib_atom.ion_radius 1,7
>
>
> Dr Richard Gildea
> Data Analysis Scientist
> Tel: +441235 77 8078
>
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science & Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
>
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