6 Feb
2014
6 Feb
'14
3:35 p.m.
I am assuming it was a redeploy of communities_api and not of the fba
services yet?
RE: communities_api, I still get the same script errors as before. Was it
redeployed on the same test host (t1)?
root@t1:~# source /kbase/deployments/20140109-prod/user-env.sh
root@t1:~# mg-inbox-decompress -h
Global symbol "$input" requires explicit package name at
/kbase/deployments/20140109-prod//plbin/mg-inbox-decompress.pl line 61.
Execution of /kbase/deployments/20140109-prod//plbin/mg-inbox-decompress.plaborted
due to compilation errors.
root@t1:~# mg-correlate-metadata -h
Traceback (most recent call last):
File "/kbase/deployments/20140109-prod//pybin/mg-correlate-metadata.py",
line 9, in <module>
from scipy import stats
ImportError: No module named scipy
On Thu, Feb 6, 2014 at 1:09 PM, Land, Miriam L. <[email protected]> wrote:
> Dan,
>
> Thank you very much.
>
> Mike,
>
> You can retest now. I'm running the make test now.
>
> Miriam
>
> From: <Murphy-Olson>, Dan Olson <[email protected]<mailto:
> [email protected]>>
> Date: Thursday, February 6, 2014 4:01 PM
> To: Miriam Land <[email protected]<mailto:[email protected]>>, "Brettin,
> Thomas S." <[email protected]<mailto:[email protected]>>
> Cc: "[email protected]<mailto:[email protected]>" <
> [email protected]<mailto:[email protected]>>
> Subject: RE: [Release-team] fba modeling service failed review for script
> standards
>
> communities_api has been redeployed to test.
>
> Miriam, do you have bandwidth to test it out?
>
>
> ----
> Daniel Murphy-Olson
> Systems Administrator
> Mathematics & Computer Science Division
> Argonne National Laboratory
> 630-252-0055
>
> ________________________________________
> From: [email protected]<mailto:
> [email protected]> [[email protected]
> <mailto:[email protected]>] on behalf of Land, Miriam
> L. [[email protected]<mailto:[email protected]>]
> Sent: Thursday, February 06, 2014 2:20 PM
> To: Brettin, Thomas S.
> Cc: [email protected]<mailto:[email protected]>
> Subject: Re: [Release-team] fba modeling service failed review for script
> standards
>
> Mike Sneddon made this comment in a different thread that I received. It
> is my understanding that updates to the test VM aren't as simple as a new
> git pull because there are other things involved (such as tagging).
>
> Miriam
>
> From: Michael Sneddon <[email protected]<mailto:[email protected]>
> Subject: [Release-team] Fwd: fba modeling service failed review for script
> standards
> Date: February 6, 2014 2:11:36 PM EST
> To: "[email protected]<mailto:[email protected]>" <
> [email protected]<mailto:[email protected]>>
>
> FYI: a minor fix in FBA modeling, but in the client scripts only so I'm
> not sure if it needs a redeploy.
>
> From: <Brettin>, "Thomas S." <[email protected]<mailto:
> [email protected]><mailto:[email protected]>>
> Date: Thursday, February 6, 2014 2:04 PM
> To: Miriam Land <[email protected]<mailto:[email protected]><mailto:
> [email protected]>>
> Cc: "Brettin, Thomas S." <[email protected]<mailto:[email protected]
> ><mailto:[email protected]>>, Shane Canon <[email protected]<mailto:
> [email protected]><mailto:[email protected]>>, Dan Olson <[email protected]
> <mailto:[email protected]><mailto:[email protected]>>, Nomi Harris <
> [email protected]<mailto:[email protected]><mailto:[email protected]>>,
> "Gordon, India S." <[email protected]<mailto:[email protected]><mailto:
> [email protected]>>
> Subject: Re: fba modeling service failed review for script standards
>
> I'd like to hear what Dan has to say on this one.
>
> Tom
>
>
> On Feb 6, 2014, at 1:01 PM, "Land, Miriam L." <[email protected]<mailto:
> [email protected]><mailto:[email protected]>> wrote:
>
> Tom,
> Chris has pushed a couple of corrections to FBAModeling to fix
> command-line problems. Given its complexity and the nature of the "fix",
> do we proceed to production or repeat the deploy/test cycle?
> Miriam
> From: Chris Henry <[email protected]<mailto:[email protected]
> ><mailto:[email protected]><mailto:[email protected]>>
> Date: Thursday, February 6, 2014 1:57 PM
> To: Michael Sneddon <[email protected]<mailto:[email protected]><mailto:
> [email protected]><mailto:[email protected]>>
> Cc: Miriam Land <[email protected]<mailto:[email protected]><mailto:
> [email protected]><mailto:[email protected]>>, Nomi Harris <[email protected]
> <mailto:[email protected]><mailto:[email protected]><mailto:[email protected]
> >>
> Subject: Re: fba modeling service failed review for script standards
> 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 <[email protected]<mailto:
> [email protected]><mailto:[email protected]><mailto:[email protected]>>
> 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.
>
>
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