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

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From: Michael Sneddon <[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]" <[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]>> Date: Thursday, February 6, 2014 2:04 PM To: Miriam Land <[email protected]<mailto:[email protected]>> Cc: "Brettin, Thomas S." <[email protected]<mailto:[email protected]>>, Shane Canon <[email protected]<mailto:[email protected]>>, Dan Olson <[email protected]<mailto:[email protected]>>, Nomi Harris <[email protected]<mailto:[email protected]>>, "Gordon, India S." <[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]>> 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]>> Date: Thursday, February 6, 2014 1:57 PM To: Michael Sneddon <[email protected]<mailto:[email protected]><mailto:[email protected]>> Cc: Miriam Land <[email protected]<mailto:[email protected]><mailto:[email protected]>>, Nomi Harris <[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]>> 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.