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.pl aborted due to compilation errors.


On Thu, Feb 6, 2014 at 2:51 PM, Murphy-Olson, Daniel E. <dolson@mcs.anl.gov> wrote:
Please try the tests again now.


----
Daniel Murphy-Olson      
Sr. Systems Administrator
Mathematics & Computer Science Division
Argonne National Laboratory
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.; release-team@kbase.us

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
From: Michael Sneddon [mwsneddon@lbl.gov]
Sent: Thursday, February 06, 2014 3:35 PM
To: Land, Miriam L.
Cc: Murphy-Olson, Daniel E.; Brettin, Thomas S.; release-team@kbase.us
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. <landml@ornl.gov> wrote:
Dan,

Thank you very much.

Mike,

You can retest now.  I'm running the make test now.

Miriam

From: <Murphy-Olson>, Dan Olson <dolson@mcs.anl.gov<mailto:dolson@mcs.anl.gov>>
Date: Thursday, February 6, 2014 4:01 PM
To: Miriam Land <landml@ornl.gov<mailto:landml@ornl.gov>>, "Brettin, Thomas S." <brettin@cels.anl.gov<mailto:brettin@cels.anl.gov>>
Cc: "release-team@kbase.us<mailto:release-team@kbase.us>" <release-team@kbase.us<mailto:release-team@kbase.us>>
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: release-team-bounces@lists.kbase.us<mailto:release-team-bounces@lists.kbase.us> [release-team-bounces@lists.kbase.us<mailto:release-team-bounces@lists.kbase.us>] on behalf of Land, Miriam L. [landml@ornl.gov<mailto:landml@ornl.gov>]
Sent: Thursday, February 06, 2014 2:20 PM
To: Brettin, Thomas S.
Cc: release-team@kbase.us<mailto:release-team@kbase.us>
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 <mwsneddon@lbl.gov<mailto:mwsneddon@lbl.gov>
Subject: [Release-team] Fwd: fba modeling service failed review for script standards
Date: February 6, 2014 2:11:36 PM EST
To: "release-team@kbase.us<mailto:release-team@kbase.us>" <release-team@kbase.us<mailto:release-team@kbase.us>>

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." <brettin@cels.anl.gov<mailto:brettin@cels.anl.gov><mailto:brettin@cels.anl.gov>>
Date: Thursday, February 6, 2014 2:04 PM
To: Miriam Land <landml@ornl.gov<mailto:landml@ornl.gov><mailto:landml@ornl.gov>>
Cc: "Brettin, Thomas S." <brettin@cels.anl.gov<mailto:brettin@cels.anl.gov><mailto:brettin@cels.anl.gov>>, Shane Canon <scanon@lbl.gov<mailto:scanon@lbl.gov><mailto:scanon@lbl.gov>>, Dan Olson <dolson@mcs.anl.gov<mailto:dolson@mcs.anl.gov><mailto:dolson@mcs.anl.gov>>, Nomi Harris <nlharris@lbl.gov<mailto:nlharris@lbl.gov><mailto:nlharris@lbl.gov>>, "Gordon, India S." <Igordon@anl.gov<mailto:Igordon@anl.gov><mailto:Igordon@anl.gov>>
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." <landml@ornl.gov<mailto:landml@ornl.gov><mailto:landml@ornl.gov>> 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 <chrisshenry@gmail.com<mailto:chrisshenry@gmail.com><mailto:chrisshenry@gmail.com><mailto:chrisshenry@gmail.com>>
Date: Thursday, February 6, 2014 1:57 PM
To: Michael Sneddon <mwsneddon@lbl.gov<mailto:mwsneddon@lbl.gov><mailto:mwsneddon@lbl.gov><mailto:mwsneddon@lbl.gov>>
Cc: Miriam Land <landml@ornl.gov<mailto:landml@ornl.gov><mailto:landml@ornl.gov><mailto:landml@ornl.gov>>, Nomi Harris <nlharris@lbl.gov<mailto:nlharris@lbl.gov><mailto:nlharris@lbl.gov><mailto:nlharris@lbl.gov>>
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 <mwsneddon@lbl.gov<mailto:mwsneddon@lbl.gov><mailto:mwsneddon@lbl.gov><mailto: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.


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