Thanks Dan.

"mg-correlate-metadata" is fixed.  We still have an error in
"mg-inbox-decompress", but this looks like a developer bug, not a
dependency error.

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.


On Thu, Feb 6, 2014 at 2:51 PM, Murphy-Olson, Daniel E.
<[email protected]>wrote:

>  Please try the tests again now.
>
>
>  ----
> Daniel Murphy-Olson
> Sr. Systems Administrator
> Mathematics & Computer Science Division
> Argonne National Laboratory
> 630-252-0055 <callto:630-252-0055>
>   ------------------------------
> *From:* Murphy-Olson, Daniel E.
> *Sent:* Thursday, February 06, 2014 4:04 PM
> *To:* Michael Sneddon; Land, Miriam L.
> *Cc:* Brettin, Thomas S.; [email protected]
>
> *Subject:* RE: [Release-team] fba modeling service failed review for
> script standards
>
>   scipy isn't installed properly.  Working on this now.
>
>  ----
> Daniel Murphy-Olson
> Sr. Systems Administrator
> Mathematics & Computer Science Division
> Argonne National Laboratory
> 630-252-0055 <callto:630-252-0055>
>   ------------------------------
> *From:* Michael Sneddon [[email protected]]
> *Sent:* Thursday, February 06, 2014 3:35 PM
> *To:* Land, Miriam L.
> *Cc:* Murphy-Olson, Daniel E.; Brettin, Thomas S.; [email protected]
> *Subject:* Re: [Release-team] fba modeling service failed review for
> script standards
>
>   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.pl aborted 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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>>  [email protected]<mailto:[email protected]>
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>>
>> _______________________________________________
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>>
>
>