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

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

06 Feb '14

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. <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:[email protected] > ><mailto:[email protected]>>, Shane Canon <scanon(a)lbl.gov<mailto: > scanon(a)lbl.gov><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: > Igordon(a)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(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:[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: > 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 >

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Re: [Release-team] fba modeling service failed review for script standards
by Land, Miriam L. 06 Feb '14

06 Feb '14

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]>> 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:[email protected]> [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:[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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Changes for deploy
by Shane Canon 06 Feb '14

06 Feb '14

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

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

06 Feb '14

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 [release-team-bounces(a)lists.kbase.us] on behalf of Land, Miriam L. [landml(a)ornl.gov] Sent: Thursday, February 06, 2014 2:20 PM To: Brettin, Thomas S. Cc: release-team(a)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(a)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(a)kbase.us" <release-team(a)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(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]>> Cc: "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]>>, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>>, "Gordon, India S." <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:[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]>> Date: Thursday, February 6, 2014 1:57 PM To: Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>> Cc: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<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]>> 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 https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] fba modeling service failed review for script standards
by Land, Miriam L. 06 Feb '14

06 Feb '14

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 >>> 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" <release-team(a)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(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]>> Cc: "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]>>, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>>, "Gordon, India S." <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:[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]>> Date: Thursday, February 6, 2014 1:57 PM To: Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>> Cc: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<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]>> 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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Re: [Release-team] Status of some services
by Nomi Harris 06 Feb '14

06 Feb '14

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> 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]>> > Date: Thursday, February 6, 2014 2:57 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 > > 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: > landml(a)ornl.gov>> 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: > nlharris(a)lbl.gov<mailto:[email protected]>>> > Date: Thursday, February 6, 2014 2:57 AM > To: "release-team(a)kbase.us<mailto:[email protected]><mailto: > release-team(a)kbase.us<mailto:[email protected]>>" < > release-team(a)kbase.us<mailto:[email protected]><mailto: > release-team(a)kbase.us<mailto:[email protected]>>> > Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<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] Status of some services
by Land, Miriam L. 06 Feb '14

06 Feb '14

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]>> Date: Thursday, February 6, 2014 2:57 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 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]>> 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]>>> Date: Thursday, February 6, 2014 2:57 AM 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]>>> Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<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] Status of some services
by Nomi Harris 06 Feb '14

06 Feb '14

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> 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]>> > Date: Thursday, February 6, 2014 2:57 AM > To: "release-team(a)kbase.us<mailto:[email protected]>" < > release-team(a)kbase.us<mailto:[email protected]>> > Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<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] Status of some services
by Land, Miriam L. 06 Feb '14

06 Feb '14

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]>> Date: Thursday, February 6, 2014 2:57 AM To: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<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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Fwd: fba modeling service failed review for script standards
by Michael Sneddon 06 Feb '14

06 Feb '14

FYI: a minor fix in FBA modeling, but in the client scripts only so I'm not sure if it needs a redeploy. ---------- Forwarded message ---------- From: Christopher Henry <chrisshenry(a)gmail.com> Date: Thu, Feb 6, 2014 at 10:57 AM Subject: Re: fba modeling service failed review for script standards To: Michael Sneddon <mwsneddon(a)lbl.gov> Cc: Miriam Land <landml(a)ornl.gov>, Nomi Harris <nlharris(a)lbl.gov> 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> 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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