February 2014 - Release-team - mailman3.cels.anl.gov

Re: [Release-team] Changes for deploy
by Shane Canon 07 Feb '14

07 Feb '14

I think this fell through the cracks with all the excitement. I've deployed in production. I'm worried there may be an issue. Can you check it out? --Shane On Feb 7, 2014, at 5:51 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > I know all the mongo problems got in the way, but any updates on deploying the FBA service to production? > thanks, > -michael > > > On Fri, Feb 7, 2014 at 9:19 AM, Shane Canon <scanon(a)lbl.gov> wrote: > > I'll quickly pull the update and then we can start promoting things to prod soon. Dan: Does this sound good? > > --Shane > > On Feb 7, 2014, at 9:08 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > > > I think this can up because we have FBAModeling in limbo. > > > > Chris fixed command-line help on "ga-annotate-ws-genome" and "fba-adjustmapcomplex" and checked them into master. > > > > WHAT is our next step? Are we going to > > > > 1. update the test VM with his latest changes or > > 2. promote the version in test to production? > > > > This is a critical module and we shouldn't postpone this decision any further. The burden in on the deploy team so I would like to hear their vote. > > > > Miriam > > > > > > From: Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> > > Date: Thursday, February 6, 2014 4:03 PM > > To: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> > > Subject: [Release-team] Changes for deploy > > > > > > FYI. For some modules, I've had to make some changes to get things to deploy. This makes pulling updates a bit of a pain. > > So I'm not trying to keep things in a branch, so that I can just do a merge to get any updates. I've been calling this branch > > deploy-20140206. I'm _not_ pushing it to git.kbase.us. It is just local to the t1 cluster. > > > > --Shane > > _______________________________________________ > > Release-team mailing list > > Release-team(a)lists.kbase.us<mailto:[email protected]> > > https://lists.kbase.us/mailman/listinfo/release-team > > > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team >

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Re: [Release-team] Changes for deploy
by Michael Sneddon 07 Feb '14

07 Feb '14

I know all the mongo problems got in the way, but any updates on deploying the FBA service to production? thanks, -michael On Fri, Feb 7, 2014 at 9:19 AM, Shane Canon <scanon(a)lbl.gov> wrote: > > I'll quickly pull the update and then we can start promoting things to > prod soon. Dan: Does this sound good? > > --Shane > > On Feb 7, 2014, at 9:08 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > > > I think this can up because we have FBAModeling in limbo. > > > > Chris fixed command-line help on "ga-annotate-ws-genome" and > "fba-adjustmapcomplex" and checked them into master. > > > > WHAT is our next step? Are we going to > > > > 1. update the test VM with his latest changes or > > 2. promote the version in test to production? > > > > This is a critical module and we shouldn't postpone this decision any > further. The burden in on the deploy team so I would like to hear their > vote. > > > > Miriam > > > > > > From: Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> > > Date: Thursday, February 6, 2014 4:03 PM > > To: "release-team(a)kbase.us<mailto:[email protected]>" < > release-team(a)kbase.us<mailto:[email protected]>> > > Subject: [Release-team] Changes for deploy > > > > > > FYI. For some modules, I've had to make some changes to get things to > deploy. This makes pulling updates a bit of a pain. > > So I'm not trying to keep things in a branch, so that I can just do a > merge to get any updates. I've been calling this branch > > deploy-20140206. I'm _not_ pushing it to git.kbase.us. It is just > local to the t1 cluster. > > > > --Shane > > _______________________________________________ > > Release-team mailing list > > Release-team(a)lists.kbase.us<mailto:[email protected]> > > https://lists.kbase.us/mailman/listinfo/release-team > > > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team >

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Re: [Release-team] Changes for deploy
by Shane Canon 07 Feb '14

07 Feb '14

I'll quickly pull the update and then we can start promoting things to prod soon. Dan: Does this sound good? --Shane On Feb 7, 2014, at 9:08 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > I think this can up because we have FBAModeling in limbo. > > Chris fixed command-line help on "ga-annotate-ws-genome" and "fba-adjustmapcomplex" and checked them into master. > > WHAT is our next step? Are we going to > > 1. update the test VM with his latest changes or > 2. promote the version in test to production? > > This is a critical module and we shouldn't postpone this decision any further. The burden in on the deploy team so I would like to hear their vote. > > Miriam > > > From: Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> > Date: Thursday, February 6, 2014 4:03 PM > To: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> > Subject: [Release-team] Changes for deploy > > > FYI. For some modules, I've had to make some changes to get things to deploy. This makes pulling updates a bit of a pain. > So I'm not trying to keep things in a branch, so that I can just do a merge to get any updates. I've been calling this branch > deploy-20140206. I'm _not_ pushing it to git.kbase.us. It is just local to the t1 cluster. > > --Shane > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us<mailto:[email protected]> > https://lists.kbase.us/mailman/listinfo/release-team >

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Re: [Release-team] Changes for deploy
by Land, Miriam L. 07 Feb '14

07 Feb '14

I think this can up because we have FBAModeling in limbo. Chris fixed command-line help on "ga-annotate-ws-genome" and "fba-adjustmapcomplex" and checked them into master. WHAT is our next step? Are we going to 1. update the test VM with his latest changes or 2. promote the version in test to production? This is a critical module and we shouldn't postpone this decision any further. The burden in on the deploy team so I would like to hear their vote. Miriam From: Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> Date: Thursday, February 6, 2014 4:03 PM To: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: [Release-team] Changes for deploy FYI. For some modules, I've had to make some changes to get things to deploy. This makes pulling updates a bit of a pain. So I'm not trying to keep things in a branch, so that I can just do a merge to get any updates. I've been calling this branch deploy-20140206. I'm _not_ pushing it to git.kbase.us. It is just local to the t1 cluster. --Shane _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

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KBase module status as of Feb. 7, 2014
by Land, Miriam L. 07 Feb '14

07 Feb '14

Release Team, Here are the outstanding items that I know about this morning: * FBA Modeling has a small number of command-line script errors that the developer has fixed but are not in the test VM. Need a decision on whether to proceed with what is in test or update test first. * Gene conservation – has no unit tests and I'll try to get some black-box testing for it today. Don't know if this is demo-critical. * communities_api was redeployed yesterday and now two command-line scripts are failing but don't know if they are demo-critical. * Search – it is listed as having on failed test. Don't know if this got resolved. * kb_seed – has a small number of command-line scripts that don't support —help and/or –help. Need a decision on whether to proceed with what we have or wait for a developer correction. * Bambi and MAK did not meet our cutoffs and have not been deployed. I welcome correction, comments, and/or decisions. Miriam

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Re: [Release-team] fba modeling service failed review for script standards
by Land, Miriam L. 07 Feb '14

07 Feb '14

TOM, Everyone has been pretty quiet on this subject. I'm told that FBAModeling is critical to other modules. Can we take the test version and move it to production even if it doesn't have the corrections the the —help commands? My concern is that doing a workaround to update t1 might have unexpected consequences when we push to production. Miriam From: <Land>, Miriam Land <landml(a)ornl.gov<mailto:[email protected]>> Date: Thursday, February 6, 2014 3:20 PM To: "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]>> Cc: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<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 <mwsneddon(a)lbl.gov<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: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<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." <brettin(a)cels.anl.gov<mailto:[email protected]><mailto:[email protected]>> Date: Thursday, February 6, 2014 2:04 PM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]>> Cc: "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]><mailto:[email protected]>>, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>>, "Gordon, India S." <Igordon(a)anl.gov<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." <landml(a)ornl.gov<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 <chrisshenry(a)gmail.com<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Date: Thursday, February 6, 2014 1:57 PM To: Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Cc: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<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 <mwsneddon(a)lbl.gov<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. _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] Status of some services
by Land, Miriam L. 07 Feb '14

07 Feb '14

I don't see anyone expressing any strong opinions. I'm okay with putting it in if that is what your gut is telling you. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> Date: Thursday, February 6, 2014 3:09 PM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>> Cc: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: Re: [Release-team] Status of some services Yeah, but several other services on that page (e.g., Protein Info, ID Service) also have no command-line commands and are only available via the API. I think if ID Mapping has been deployed to production and can be called via the API, we should include it. On Thu, Feb 6, 2014 at 12:00 PM, Land, Miriam L. <landml(a)ornl.gov<mailto:[email protected]>> wrote: It doesn't have any command-line commands yet. I would vote 'No' this time around. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Date: Thursday, February 6, 2014 2:57 PM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Cc: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Subject: Re: [Release-team] Status of some services Thanks for the update. Marcin said that MAK was used to produce some datasets but is not (yet) exposed to the public. Did we determine that ID Mapping should be added to the Services page? Nomi On Thu, Feb 6, 2014 at 11:54 AM, Land, Miriam L. <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> wrote: Nomi, Bambi and MAK did not make the cutoff and will not be deployed. All the others are moving alone nicely. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>> Date: Thursday, February 6, 2014 2:57 AM To: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>> Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>> Subject: [Release-team] Status of some services Someone was going to ask Andreas whether the Communities QC service has been fixed. Did anyone ask? I'm still unsure about whether the following new services should be added to the Services web page: Bambi (did it get deployed?) cMonkey Expression Inferelator MEME I found out that MAK is internal (for now, anyway)--it was used to create some datasets but is not publicly accessible, so it doesn't need to be added to the Services page. That might also be true of cMonkey and possibly some of the other services I listed. Thanks, Nomi

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Re: [Release-team] fba modeling service failed review for script standards
by Michael Sneddon 06 Feb '14

06 Feb '14

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 "$input" requires explicit package name at /kbase/deployments/20140109-prod//plbin/mg-inbox-decompress.pl line 61. Execution of /kbase/deployments/20140109-prod//plbin/mg-inbox-decompress.plaborted due to compilation errors. On Thu, Feb 6, 2014 at 2:51 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov>wrote: > Please try the tests again now. > > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 <callto:630-252-0055> > ------------------------------ > *From:* Murphy-Olson, Daniel E. > *Sent:* Thursday, February 06, 2014 4:04 PM > *To:* Michael Sneddon; Land, Miriam L. > *Cc:* Brettin, Thomas S.; release-team(a)kbase.us > > *Subject:* RE: [Release-team] fba modeling service failed review for > script standards > > scipy isn't installed properly. Working on this now. > > ---- > Daniel Murphy-Olson > Sr. Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 <callto:630-252-0055> > ------------------------------ > *From:* Michael Sneddon [mwsneddon(a)lbl.gov] > *Sent:* Thursday, February 06, 2014 3:35 PM > *To:* Land, Miriam L. > *Cc:* Murphy-Olson, Daniel E.; Brettin, Thomas S.; release-team(a)kbase.us > *Subject:* Re: [Release-team] fba modeling service failed review for > script standards > > I am assuming it was a redeploy of communities_api and not of the fba > services yet? > > RE: communities_api, I still get the same script errors as before. Was > it redeployed on the same test host (t1)? > > root@t1:~# source /kbase/deployments/20140109-prod/user-env.sh > root@t1:~# mg-inbox-decompress -h > Global symbol "$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(a)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(a)mcs.anl.gov<mailto: >> dolson(a)mcs.anl.gov>> >> Date: Thursday, February 6, 2014 4:01 PM >> To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>>, "Brettin, >> Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]>> >> Cc: "release-team(a)kbase.us<mailto:[email protected]>" < >> release-team(a)kbase.us<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: release-team-bounces(a)lists.kbase.us<mailto: >> release-team-bounces(a)lists.kbase.us> [release-team-bounces(a)lists.kbase.us >> <mailto:[email protected]>] on behalf of Land, Miriam >> L. [landml(a)ornl.gov<mailto:[email protected]>] >> Sent: Thursday, February 06, 2014 2:20 PM >> To: Brettin, Thomas S. >> Cc: release-team(a)kbase.us<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 <mwsneddon(a)lbl.gov<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: "release-team(a)kbase.us<mailto:[email protected]>" < >> release-team(a)kbase.us<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." <brettin(a)cels.anl.gov<mailto: >> brettin(a)cels.anl.gov><mailto:[email protected]>> >> Date: Thursday, February 6, 2014 2:04 PM >> To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto: >> landml(a)ornl.gov>> >> Cc: "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto: >> brettin(a)cels.anl.gov><mailto:[email protected]>>, Shane Canon < >> scanon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>>, Dan Olson >> <dolson(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected]>>, >> Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto: >> nlharris(a)lbl.gov>>, "Gordon, India S." <Igordon(a)anl.gov<mailto: >> Igordon(a)anl.gov><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." <landml(a)ornl.gov<mailto: >> landml(a)ornl.gov><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 <chrisshenry(a)gmail.com<mailto:[email protected] >> ><mailto:[email protected]><mailto:[email protected]>> >> Date: Thursday, February 6, 2014 1:57 PM >> To: Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]><mailto: >> mwsneddon(a)lbl.gov><mailto:[email protected]>> >> Cc: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto: >> landml(a)ornl.gov><mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov >> <mailto:[email protected]><mailto:[email protected]><mailto: >> nlharris(a)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(a)lbl.gov<mailto: >> mwsneddon(a)lbl.gov><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. >> >> >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us<mailto:[email protected]> >> https://lists.kbase.us/mailman/listinfo/release-team >> >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team >> > >

1 0

Re: [Release-team] fba modeling service failed review for script standards
by Murphy-Olson, Daniel E. 06 Feb '14

06 Feb '14

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.; release-team(a)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<callto:630-252-0055> ________________________________ From: Michael Sneddon [mwsneddon(a)lbl.gov] Sent: Thursday, February 06, 2014 3:35 PM To: Land, Miriam L. Cc: Murphy-Olson, Daniel E.; Brettin, Thomas S.; release-team(a)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<http://mg-inbox-decompress.pl> line 61. Execution of /kbase/deployments/20140109-prod//plbin/mg-inbox-decompress.pl<http://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(a)ornl.gov<mailto:[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 <dolson(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Date: Thursday, February 6, 2014 4:01 PM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>, "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Cc: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[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<tel:630-252-0055> ________________________________________ From: release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> [release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>] on behalf of Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>] Sent: Thursday, February 06, 2014 2:20 PM To: Brettin, Thomas S. Cc: release-team(a)kbase.us<mailto:[email protected]><mailto:[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 <mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[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: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[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." <brettin(a)cels.anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>> Date: Thursday, February 6, 2014 2:04 PM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>> Cc: "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>>, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>>, "Gordon, India S." <Igordon(a)anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[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." <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[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 <chrisshenry(a)gmail.com<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>> Date: Thursday, February 6, 2014 1:57 PM To: Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>> Cc: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[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 <mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[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<http://ga-annotate-ws-genome.pl> line 9. BEGIN failed--compilation aborted at /kbase/deployments/20140109-prod/dev_container/..//plbin/ga-annotate-ws-genome.pl<http://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<http://fba-adjustmapcomplex.pl> line 9. BEGIN failed--compilation aborted at /kbase/deployments/20140109-prod/dev_container/..//plbin/fba-adjustmapcomplex.pl<http://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<http://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<http://fba-adjustmapcomplex.pl> line 9. BEGIN failed--compilation aborted at /kbase/deployments/20140109-prod/dev_container/..//plbin/fba-adjustmapcomplex.pl<http://fba-adjustmapcomplex.pl> line 9. _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> https://lists.kbase.us/mailman/listinfo/release-team _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

1 0

Re: [Release-team] fba modeling service failed review for script standards
by Murphy-Olson, Daniel E. 06 Feb '14

06 Feb '14

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 [mwsneddon(a)lbl.gov] Sent: Thursday, February 06, 2014 3:35 PM To: Land, Miriam L. Cc: Murphy-Olson, Daniel E.; Brettin, Thomas S.; release-team(a)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<http://mg-inbox-decompress.pl> line 61. Execution of /kbase/deployments/20140109-prod//plbin/mg-inbox-decompress.pl<http://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(a)ornl.gov<mailto:[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 <dolson(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Date: Thursday, February 6, 2014 4:01 PM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>, "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> Cc: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[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<tel:630-252-0055> ________________________________________ From: release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> [release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>] on behalf of Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>] Sent: Thursday, February 06, 2014 2:20 PM To: Brettin, Thomas S. Cc: release-team(a)kbase.us<mailto:[email protected]><mailto:[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 <mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[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: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[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." <brettin(a)cels.anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>> Date: Thursday, February 6, 2014 2:04 PM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>> Cc: "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>>, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>>, "Gordon, India S." <Igordon(a)anl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[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." <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[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 <chrisshenry(a)gmail.com<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>> Date: Thursday, February 6, 2014 1:57 PM To: Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>> Cc: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]>>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[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 <mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[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<http://ga-annotate-ws-genome.pl> line 9. BEGIN failed--compilation aborted at /kbase/deployments/20140109-prod/dev_container/..//plbin/ga-annotate-ws-genome.pl<http://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<http://fba-adjustmapcomplex.pl> line 9. BEGIN failed--compilation aborted at /kbase/deployments/20140109-prod/dev_container/..//plbin/fba-adjustmapcomplex.pl<http://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<http://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<http://fba-adjustmapcomplex.pl> line 9. BEGIN failed--compilation aborted at /kbase/deployments/20140109-prod/dev_container/..//plbin/fba-adjustmapcomplex.pl<http://fba-adjustmapcomplex.pl> line 9. _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> https://lists.kbase.us/mailman/listinfo/release-team _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

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