FYI: a minor fix in FBA modeling, but in the client scripts only so I'm not sure if it needs a redeploy.

---------- Forwarded message ----------
From: Christopher Henry <chrisshenry@gmail.com>
Date: Thu, Feb 6, 2014 at 10:57 AM
Subject: Re: fba modeling service failed review for script standards
To: Michael Sneddon <mwsneddon@lbl.gov>
Cc: Miriam Land <landml@ornl.gov>, Nomi Harris <nlharris@lbl.gov>


1.) The "kbfba" commands and their "fba" equivalents point to the same perl script, so those errors are equivalent
2.) "jobdone" is a meaningless command only for internal use, and the users should never use it. I removed it from the COMMANDS file.
3.) The "ga-annotate-ws-genome" and "fba-adjustmapcomplex" errors are genuine

I just checked in a fix for ALL of this on master. Can we do a git pull and proceed?

On Feb 6, 2014, at 12:30 PM, Michael Sneddon <mwsneddon@lbl.gov> wrote:

> Hi Chris,
>
> On script standard review, a few scripts are failing (see below).
>
> Miriam - I hate to request this, but if possible we should still deploy FBA modeling to production, as the scripts do not affect the actual fba server code, and the faster the FBA service is in production, the faster we can test and push out the narrative... but of course this is not my call.
>
>
> The problems seem to be
> 1) You are still using several methods in a WS library that we did not port over from the old WS ScriptHelpers (auth and getObjectInfo, which were obsolete/not needed by the new WS scripts).  I can either try to add them to the new WS (we do not need a need a WS production redeploy because these are client libs only), or we can try to fix the FBA scripts (I might be able to help with that).
>
> 2) fba-jobdone is not being deployed properly or does not exist, but it is picked up by the COMMANDS file.
>
>
>
>
> ----------TEST KBaseFBAModeling ga-annotate-ws-genome with -h option  fail
> ----------TEST KBaseFBAModeling ga-annotate-ws-genome with --help option      fail
> ----------TEST KBaseFBAModeling kbfba-adjustmapcomplex with -h option fail
> ----------TEST KBaseFBAModeling kbfba-adjustmapcomplex with --help option     fail
> ----------TEST KBaseFBAModeling kbfba-jobdone with -h option  fail
> ----------TEST KBaseFBAModeling kbfba-jobdone with --help option      fail
> ----------TEST KBaseFBAModeling fba-jobdone with -h option    fail
> ----------TEST KBaseFBAModeling fba-jobdone with --help option        fail
> ----------TEST KBaseFBAModeling fba-adjustmapcomplex with -h option   fail
> ----------TEST KBaseFBAModeling fba-adjustmapcomplex with --help option       fail
>
> root@t1:~/msneddon-work/2013doctests/testing/script-tests/tests# ga-annotate-ws-genome -h
> "auth" is not exported by the Bio::KBase::workspace::ScriptHelpers module
> Can't continue after import errors at /kbase/deployments/20140109-prod/dev_container/..//plbin/ga-annotate-ws-genome.pl line 9.
> BEGIN failed--compilation aborted at /kbase/deployments/20140109-prod/dev_container/..//plbin/ga-annotate-ws-genome.pl line 9.
>
> root@t1:~/msneddon-work/2013doctests/testing/script-tests/tests# kbfba-adjustmapcomplex --help
> "getObjectInfo" is not exported by the Bio::KBase::workspace::ScriptHelpers module
> Can't continue after import errors at /kbase/deployments/20140109-prod/dev_container/..//plbin/fba-adjustmapcomplex.pl line 9.
> BEGIN failed--compilation aborted at /kbase/deployments/20140109-prod/dev_container/..//plbin/fba-adjustmapcomplex.pl line 9.
>
> root@t1:~/msneddon-work/2013doctests/testing/script-tests/tests# kbfba-jobdone --help
> Can't open perl script "/kbase/deployments/20140109-prod/dev_container/..//plbin/fba-jobdone.pl": No such file or directory
>
> root@t1:~/msneddon-work/2013doctests/testing/script-tests/tests# fba-jobdone --help
> fba-jobdone: command not found
>
> root@t1:~/msneddon-work/2013doctests/testing/script-tests/tests# fba-adjustmapcomplex --help
> "getObjectInfo" is not exported by the Bio::KBase::workspace::ScriptHelpers module
> Can't continue after import errors at /kbase/deployments/20140109-prod/dev_container/..//plbin/fba-adjustmapcomplex.pl line 9.
> BEGIN failed--compilation aborted at /kbase/deployments/20140109-prod/dev_container/..//plbin/fba-adjustmapcomplex.pl line 9.