Opened 4 years ago

Closed 4 years ago

#4693 closed defect (fixed)

sqlite module broken

Reported by: johannes.elferich@… Owned by: Greg Couch
Priority: normal Milestone: 1.3
Component: Platform Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-67-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
I am developing an Plugin that should access a sqlite database, but the sqlite3 module in the python that is included with ChimeraX seems to be broken. (I've tested Linxu and Windows builds)

Is there anything I can do? 

Thank you,

Johannes

Log:
> devel install
> /groups/elferich/template_matching_chimerax/template_matching_command/

[toolshed install](help:user/commands/toolshed.html#install)  
/groups/elferich/template_matching_chimerax/template_matching_command/dist/ChimeraX_TemplateMatchingCommand-0.1-py3-none-  
any.whl reinstall true  
  
[toolshed install  
/groups/elferich/template_matching_chimerax/template_matching_command/dist/ChimeraX_TemplateMatchingCommand-0.1-py3-none-  
any.whl reinstall true](cxcmd:toolshed install  
/groups/elferich/template_matching_chimerax/template_matching_command/dist/ChimeraX_TemplateMatchingCommand-0.1-py3-none-  
any.whl reinstall true)  
  
Successfully installed ChimeraX-TemplateMatchingCommand-0.1  
Installed ChimeraX-TemplateMatchingCommand (0.1)  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> tm load_project
> /scratch_dublin/elferich/test/ER_Hox_compiled/ER_Hox_compiled.db 1 1

Traceback (most recent call last):  
File "/groups/cryoadmin/software/CHIMERAX/chimerax-1.1/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/groups/cryoadmin/software/CHIMERAX/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/groups/elferich/.local/share/ChimeraX/1.1/site-
packages/chimerax/template_matching_cmd/cmd.py", line 113, in loadtm_project  
import sqlite3  
File
"/groups/cryoadmin/software/CHIMERAX/chimerax-1.1/lib/python3.7/sqlite3/__init__.py",
line 23, in <module>  
from sqlite3.dbapi2 import *  
File
"/groups/cryoadmin/software/CHIMERAX/chimerax-1.1/lib/python3.7/sqlite3/dbapi2.py",
line 27, in <module>  
from _sqlite3 import *  
ModuleNotFoundError: No module named '_sqlite3'  
  
ModuleNotFoundError: No module named '_sqlite3'  
  
File
"/groups/cryoadmin/software/CHIMERAX/chimerax-1.1/lib/python3.7/sqlite3/dbapi2.py",
line 27, in  
from _sqlite3 import *  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3 (Core Profile) Mesa 20.0.8
OpenGL renderer: llvmpipe (LLVM 10.0.0, 256 bits)
OpenGL vendor: VMware, Inc.
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 96 Intel(R) Xeon(R) Platinum 8168 CPU @ 2.70GHz
Cache Size: 33792 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           503G         22G         36G        580M        444G        477G
	Swap:          2.0G        1.9G         95M

Graphics:
	0000:17:00.0 VGA compatible controller [0300]: NVIDIA Corporation GV100GL [Quadro GV100] [10de:1dba] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:121a]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
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    ChimeraX-Movie: 1.0
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    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
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    ChimeraX-STL: 1.0
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    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TemplateMatchingCommand: 0.1
    ChimeraX-Test: 1.0
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    ChimeraX-ViewDockX: 1.0
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    imagecodecs-lite: 2020.1.31
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    urllib3: 1.25.10
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    wheel: 0.34.2

Change History (6)

comment:1 by pett, 4 years ago

Cc: chimera-programmers added
Component: Unassigned → Platform
Milestone: → 1.3
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → sqlite module broken

Worked for me on Mac. Johannes reports it to be broken on Windows and Linux.

in reply to:  2 ; comment:2 by Johannes.Elferich@…, 4 years ago 

After double checking, it is just the Linux version ( I think I downloaded the generic Linux 64-bit executable).

Thanks,

Johannes

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Thursday, May 27, 2021 5:53 PM
Cc: chimera-programmers@cgl.ucsf.edu; gregc@cgl.ucsf.edu; Elferich, Johannes <Johannes.Elferich@umassmed.edu>
Subject: Re: [ChimeraX] #4693: sqlite module broken (was: ChimeraX bug report submission)

#4693: sqlite module broken
------------------------------------------+------------------------
          Reporter:  johannes.elferich@...  |      Owner:  Greg Couch
              Type:  defect               |     Status:  assigned
          Priority:  normal               |  Milestone:  1.3
         Component:  Platform             |    Version:
        Resolution:                       |   Keywords:
        Blocked By:                       |   Blocking:
Notify when closed:                       |   Platform:  all
           Project:  ChimeraX             |
------------------------------------------+------------------------
Changes (by Eric Pettersen):

 * status:  new => assigned
 * cc: chimera-programmers (added)
 * component:  Unassigned => Platform
 * project:   => ChimeraX
 * platform:   => all
 * milestone:   => 1.3
 * owner:  (none) => Greg Couch


Comment:

 Worked for me on Mac.  Johannes reports it to be broken on Windows and  Linux.

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comment:3 by Greg Couch, 4 years ago

Does the Ubuntu 18.04 deb package work for you?

in reply to:  4 ; comment:4 by Johannes.Elferich@…, 4 years ago 

No, it does not.

I noticed that the requirements for the linux build do not list "libsqlite3-dev", which would be required to compile python with the sqlite support.

Are the singularity build recipes already public somewhere?

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Friday, May 28, 2021 3:19 AM
Cc: chimera-programmers@cgl.ucsf.edu; gregc@cgl.ucsf.edu; Elferich, Johannes <Johannes.Elferich@umassmed.edu>
Subject: Re: [ChimeraX] #4693: sqlite module broken

#4693: sqlite module broken
------------------------------------------+------------------------
          Reporter:  johannes.elferich@...  |      Owner:  Greg Couch
              Type:  defect               |     Status:  assigned
          Priority:  normal               |  Milestone:  1.3
         Component:  Platform             |    Version:
        Resolution:                       |   Keywords:
        Blocked By:                       |   Blocking:
Notify when closed:                       |   Platform:  all
           Project:  ChimeraX             |
------------------------------------------+------------------------

Comment (by Greg Couch):

 Does the Ubuntu 18.04 deb package work for you?

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ChimeraX Issue Tracker

comment:5 by Greg Couch, 4 years ago

Status: assigned → accepted

So yes, sqlite it not available in ChimeraX's Python on Linux since ChimeraX compiles its own version of Python. ChimeraX uses the binary distributions from Python.org Windows and macOS, so sqlite is available on those platforms.

I'll look into adding the sqlite3 development environment to our singularity build images. And add any needed package dependencies to the .deb and .rpm files. The .deb and .rpm files will not depend on the developer package (eg., it will be libsqlite3 not libsqlite3-dev) unless the built _sqlite3.so needs it.

Version 0, edited 4 years ago by Greg Couch (next)

comment:6 by Greg Couch, 4 years ago

Resolution: → fixed
Status: accepted → closed

Added sqlite3 library and headers to all Linux singularity containers. Added sqlite3 library to .deb and .rpm package dependencies. It will show up in the next daily build (1.3 development builds), and, if we ever make a 1.2 bug fix release, it will show up in 1.2.6. So the ChimeraX-Core dependency for sqlite3 would be "~=1.2,>=1.2.6".

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