[chimera-dev] chimerax - registering an external tool problem

[Wolfgang Lugmayr]

dear chimerax developers,

i think i have tracked down the problem (centos7):
when i removed the ~/.cache/ChimeraX directory everything runs fine now.

first i tried to remove only the lock
.cache/ChimeraX/0.1/toolshed/bundle_info.cache.lock
but this file stays even when chimerax is closed.
and is overwritten with a new timestamp when a new instance is started.

i tested to start in parallel a global chimerax and my development 
instance and the "ts list" for both instances is correct.
so i am not sure what messed up my chimerax cache.

cheers,
wolfgang


On 01/05/2017 05:13 PM, Wolfgang Lugmayr wrote:
> dear chimera developers,
>
> i'm currently porting one of our chimera 1.x plugins called starmap to 
> chimerax.
>
> basic questions:
> 1. should the package be e.g. chimerax-starmap or just starmap?
> 2. is there a recommended way when i should upload to the toolshed 
> repository?
>
> my current problem:
> i use chimerax's python3.5 pip to install and remove my tests.
> my test package is called chimerax.starmapx (+.__init.py__)
>
> i had a look at your toolshed and added test categories like follows 
> to the metadata (installed version):
> Classifier: ChimeraX :: Bundle :: Volume data :: 1,1 :: 
> chimerax.starmap :: chimerax.starmap ::
> Classifier: ChimeraX :: Tool :: StarMapX :: Volume data :: Run Rosetta 
> refinements
> Classifier: ChimeraX :: Command :: apix :: Volume data :: Run Rosetta 
> apix
> Requires-Dist: ChimeraX-Core (>=0.1)
> Requires-Dist: pyparsing
>
> i also used "General" instead of "Volume data" for debugging.
>
> i have overriden the BundleAPI get_class, start_tools, 
> register_command similar to blastprotein.
>
> unfortunatly my test plugin never shows up in chimerax (e.g. ts list) 
> and the command "stm apix" is not registered.
>
> i debugged the toolshed (standalone - not in chimerax) and if i print 
> the contents of line 720 - end of_load_bundle_infos()
> i get
> ...using SteamVR]], ChimeraX-StarMap (installed) [version: 0.1.2] [api 
> package: chimerax.starmap] [category: Volume data] [tool: StarMap 
> [categories: Volume data] [synopsis: Run Rosetta refinements]] 
> [command: apix [categories: Volume data] [synopsis: Run Rosetta 
> refinements]], ChimeraX-Stringdb (installed) [version: 0.1]...
> and a little bit before
> ('checking', <InstalledDistribution 'ChimeraX-StarMap' 0.1.2 at 
> '/projects/marlovits/lugmayr/workspace/ChimeraX/lib/python3.5/site-packages/ChimeraX_StarMap-0.1.2.dist-info'>) 
>
>
> do i miss something during the registration process?
>
> cheers,
> wolfgang
>
> ---
> Universitätsklinikum Hamburg-Eppendorf (UKE)
> @ Centre for Structral Systems Biology (CSSB)
> @ Institute of Molecular Biotechnology (IMBA)
> Dr. Bohr-Gasse 3-7 (Room 6.14)
> 1030 Vienna, Austria
> Tel.: +43 (1) 790 44-4649
> Email: w.lugmayr at uke.de
> http://www.cssb-hamburg.de/
>
> -- 
>
> _____________________________________________________________________
>
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen 
> Rechts; Gerichtsstand: Hamburg | www.uke.de
> Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. 
> Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
> _____________________________________________________________________
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-- 
Universitätsklinikum Hamburg-Eppendorf (UKE)
@ Centre for Structral Systems Biology (CSSB)
@ Institute of Molecular Biotechnology (IMBA)
Dr. Bohr-Gasse 3-7 (Room 6.14)
1030 Vienna, Austria
Tel.: +43 (1) 790 44-4649
Email: w.lugmayr at uke.de
http://www.cssb-hamburg.de/

--

_____________________________________________________________________

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de
Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
_____________________________________________________________________

SAVE PAPER - THINK BEFORE PRINTING