[cctbxbb] The curious incident of the test at install time

Fri May 13 14:44:40 PDT 2016

Hi Markus,

Those changes were made by me and Oleg. I just tested a fresh installation 
of phenix-dev-2407-intel-linux-2.6-centos5 which is built with cctbx_project 
revision 24442. The test of 
cctbx_project/cctbx/regression/tst_grm_pickling.py passed without problems. 
I'm not aware of why this test is failing on dials after installation. Since 
the test is to do with the phenix restraints manager perhaps this test is 
not critical to dials. Perhaps the phenix restraints manager code together 
with this test should be moved into the phenix repository but that is not my 
call.

Rob

-----Original Message----- 
From: cctbxbb-request at phenix-online.org
Sent: Friday, May 13, 2016 20:00
To: cctbxbb at phenix-online.org
Subject: cctbxbb Digest, Vol 86, Issue 7

Message: 2
Date: Fri, 13 May 2016 09:47:18 +0000
From: <markus.gerstel at diamond.ac.uk>
To: <cctbxbb at phenix-online.org>
Subject: [cctbxbb] The curious incident of the test at install time
Message-ID:
<415F7F573406BB498256C68158D45674612998A2 at EXCHMBX01.fed.cclrc.ac.uk>
Content-Type: text/plain; charset=iso-8859-1

Hi everyone,

we have observed the test cctbx_project/cctbx/regression/tst_grm_pickling.py 
to be failing, however only on an installation installed from the installer. 
It appears to run successfully on our bootstrapped developer build.
I presume that the test requires some external data that we do not 
distribute?

The relevant change occurred between r24437 and r24441, and is almost 
certainly r24439, which enabled the failing bit of the test.

Stacktrace below.

-Markus

$ libtbx.python 
/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py
Time pickling/unpickling: 0.0187, 0.0097
Traceback (most recent call last):
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", 
line 198, in <module>
    exercise_all(sys.argv[1:])
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", 
line 195, in exercise_all
    test_nucleic_acid(mon_lib_srv, ener_lib)
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", 
line 177, in test_nucleic_acid
    log=null_out())
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 5455, in run
    log=log)
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 5005, in __init__
    restraints_loading_flags=restraints_loading_flags,
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 2956, in __init__
    log=log,
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 2343, in __init__
    m_j=mm)
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 1568, in get_lib_link
    return mon_lib_srv.link_link_id_dict["rna3p"]
KeyError: 'rna3p'

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Message: 3
Date: Fri, 13 May 2016 09:50:03 +0000
From: <Graeme.Winter at diamond.ac.uk>
To: <cctbxbb at phenix-online.org>
Subject: Re: [cctbxbb] The curious incident of the test at install
time
Message-ID:
<13999B6FC038EB44B067771E3CFBD091BC2E3E7A at EXCHMBX03.fed.cclrc.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Markus

I got this error this morning in the regular update / compile shuffle and 
it's on my to-nag list, also feel like I have seen this before...

Cheerio G

-----Original Message-----
From: cctbxbb-bounces at phenix-online.org 
[mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of 
markus.gerstel at diamond.ac.uk
Sent: 13 May 2016 10:47
To: cctbxbb at phenix-online.org
Subject: [cctbxbb] The curious incident of the test at install time

Hi everyone,

we have observed the test cctbx_project/cctbx/regression/tst_grm_pickling.py 
to be failing, however only on an installation installed from the installer. 
It appears to run successfully on our bootstrapped developer build.
I presume that the test requires some external data that we do not 
distribute?

The relevant change occurred between r24437 and r24441, and is almost 
certainly r24439, which enabled the failing bit of the test.

Stacktrace below.

-Markus

$ libtbx.python 
/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py
Time pickling/unpickling: 0.0187, 0.0097 Traceback (most recent call last):
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", 
line 198, in <module>
    exercise_all(sys.argv[1:])
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", 
line 195, in exercise_all
    test_nucleic_acid(mon_lib_srv, ener_lib)
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", 
line 177, in test_nucleic_acid
    log=null_out())
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 5455, in run
    log=log)
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 5005, in __init__
    restraints_loading_flags=restraints_loading_flags,
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 2956, in __init__
    log=log,
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 2343, in __init__
    m_j=mm)
  File 
"/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 1568, in get_lib_link
    return mon_lib_srv.link_link_id_dict["rna3p"]
KeyError: 'rna3p'

--
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If 
you are not the intended addressee or an authorised recipient of the 
addressee please notify us of receipt by returning the e-mail and do not 
use, copy, retain, distribute or disclose the information in or attached to 
the e-mail.
Any opinions expressed within this e-mail are those of the individual and 
not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
attachments are free from viruses and we cannot accept liability for any 
damage which you may sustain as a result of software viruses which may be 
transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England 
and Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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