February 2013 - Release-team - mailman3.cels.anl.gov

Re: [Release-team] [KBase-testing] KBase release 20130219-prod
by Land, Miriam L. 21 Feb '13

21 Feb '13

Tom, I believe that any changes Keith might want to make to the testing scripts won't matter for the production deploy because no one else will be testing it. Also, only script tests are applicable to the dmg and there we just test that it can execute. Would we want the testing changes that Keith deems necessary to be reflected in the Ubuntu image? Miriam On 2/20/13 6:26 PM, "Keith Keller" <kkeller(a)lbl.gov> wrote: >I committed a change to the protein_info test script (perhaps a bad >fid in the test data?), and it now passes. Is there a process for >handling commits to just test code after the official deployment? (I >think I may wish to commit the translation test script changes as >well.) > >--keith > >On Wed, Feb 20, 2013 at 3:08 PM, Keith Keller <kkeller(a)lbl.gov> wrote: >> The translation service passes (modulo configuration changes), which >> also confirms that ERDB is behaving reasonably well. I'm looking at >> protein_info now. >> >> --keith >> >> On Wed, Feb 20, 2013 at 2:44 PM, Dan Olson <dolson(a)mcs.anl.gov> wrote: >>> Most of the services components are now live for this release. >>> >>> Please feel free to test. >>> ---- >>> Daniel Murphy-Olson >>> Systems Administrator >>> Mathematics & Computer Science Division >>> Argonne National Laboratory >>> 630-252-0055 >>> >>> _______________________________________________ >>> KBase-testing mailing list >>> KBase-testing(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/kbase-testing >> >> >> >> -- >> Keith Keller >> kkeller(a)lbl.gov >> Physical Biosciences Division, Lawrence Berkeley National Lab >> >> On Wed, Feb 20, 2013 at 2:44 PM, Dan Olson <dolson(a)mcs.anl.gov> wrote: >>> Most of the services components are now live for this release. >>> >>> Please feel free to test. >>> ---- >>> Daniel Murphy-Olson >>> Systems Administrator >>> Mathematics & Computer Science Division >>> Argonne National Laboratory >>> 630-252-0055 >>> >>> _______________________________________________ >>> KBase-testing mailing list >>> KBase-testing(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/kbase-testing >> >> >> >> -- >> Keith Keller >> kkeller(a)lbl.gov >> Physical Biosciences Division, Lawrence Berkeley National Lab > > > >-- >Keith Keller >kkeller(a)lbl.gov >Physical Biosciences Division, Lawrence Berkeley National Lab >_______________________________________________ >KBase-testing mailing list >KBase-testing(a)lists.kbase.us >https://lists.kbase.us/mailman/listinfo/kbase-testing

1 0

Re: [Release-team] KBase release 20130219-prod
by Land, Miriam L. 21 Feb '13

21 Feb '13

Dan, Could we get these marked in the KBase services spreadsheet in the column for 'pass production deploy'. That would clear up what you mean by "most" services. As the testing team proceeds through the modules, we can mark the column 'pass production test'. Miriam On 2/20/13 5:44 PM, "Dan Olson" <dolson(a)mcs.anl.gov> wrote: >Most of the services components are now live for this release. > >Please feel free to test. >---- >Daniel Murphy-Olson >Systems Administrator >Mathematics & Computer Science Division >Argonne National Laboratory >630-252-0055 > >_______________________________________________ >Release-team mailing list >Release-team(a)lists.kbase.us >https://lists.kbase.us/mailman/listinfo/release-team

1 0

Re: [Release-team] [KBase-testing] KBase release 20130219-prod
by Thomas Brettin 20 Feb '13

20 Feb '13

Thanks Keith. ALL: Please fill in the kbase services spread sheet, "Feb 2013 Major Release". pass production deploy pass production testing pass production doc qc On Feb 20, 2013, at 5:40 PM, Keith Keller <kkeller(a)lbl.gov> wrote: > kb_seed passes (no changes), erdb_service passes (config changes in > the test script). > > --keith > > On Wed, Feb 20, 2013 at 2:44 PM, Dan Olson <dolson(a)mcs.anl.gov> wrote: >> Most of the services components are now live for this release. >> >> Please feel free to test. >> ---- >> Daniel Murphy-Olson >> Systems Administrator >> Mathematics & Computer Science Division >> Argonne National Laboratory >> 630-252-0055 >> >> _______________________________________________ >> KBase-testing mailing list >> KBase-testing(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-testing > > > > -- > Keith Keller > kkeller(a)lbl.gov > Physical Biosciences Division, Lawrence Berkeley National Lab > _______________________________________________ > KBase-testing mailing list > KBase-testing(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-testing Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

1 0

Re: [Release-team] [KBase-testing] KBase release 20130219-prod
by Keith Keller 20 Feb '13

20 Feb '13

The translation service passes (modulo configuration changes), which also confirms that ERDB is behaving reasonably well. I'm looking at protein_info now. --keith On Wed, Feb 20, 2013 at 2:44 PM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > Most of the services components are now live for this release. > > Please feel free to test. > ---- > Daniel Murphy-Olson > Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > > _______________________________________________ > KBase-testing mailing list > KBase-testing(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-testing -- Keith Keller kkeller(a)lbl.gov Physical Biosciences Division, Lawrence Berkeley National Lab On Wed, Feb 20, 2013 at 2:44 PM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > Most of the services components are now live for this release. > > Please feel free to test. > ---- > Daniel Murphy-Olson > Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > > _______________________________________________ > KBase-testing mailing list > KBase-testing(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-testing -- Keith Keller kkeller(a)lbl.gov Physical Biosciences Division, Lawrence Berkeley National Lab

1 0

KBase release 20130219-prod
by Dan Olson 20 Feb '13

20 Feb '13

Most of the services components are now live for this release. Please feel free to test. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

1 0

Re: [Release-team] Release
by Dan Olson 19 Feb '13

19 Feb '13

Things are a little disorganized still, but are coming together. Our test toolset has diverged significantly from the production, so I'm spending time moving things up to production, and making sure they work as intended before I pull the trigger. ----- Original Message ----- > From: "Nomi Harris" <nlharris(a)lbl.gov> > To: release-team(a)lists.kbase.us > Sent: Tuesday, February 19, 2013 12:43:19 PM > Subject: [Release-team] Release > > How's the release going? Someone here asked me what was happening > with the production deploy, and I wasn't sure, though I assume Dan > et al. are working on it. > Do we need to have another phone call to sync up? > Nomi > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team >

1 0

Release
by Nomi Harris 19 Feb '13

19 Feb '13

How's the release going? Someone here asked me what was happening with the production deploy, and I wasn't sure, though I assume Dan et al. are working on it. Do we need to have another phone call to sync up? Nomi

1 0

Re: [Release-team] plant ontolog, . expression, and co-expression networks in IRIS
by Thomas Brettin 15 Feb '13

15 Feb '13

On Feb 15, 2013, at 3:08 PM, "Yoo, Shinjae" <sjyoo(a)bnl.gov> wrote: > Thanks Tom, > > Plant expression service is ready to go and passed `make test`… > > Shane, please do `rm -rf /kb/deployment` first… > If not, it can not create `/kb/deployment/rsbin' directory. The make clean target does a rm -rf on ($TARGET) We need to fix this properly, though. The rest of the directories can be left in place, why not this? > > Thanks, > -SJ > > On Feb 15, 2013, at 3:57 PM, Thomas Brettin wrote: > >> Also, for the plant_expression service, you will need to pull changes to the dev_container out of the kbase.us git repo before doing the make. >> >> >> >> On Feb 15, 2013, at 2:56 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> >>> Hey Guys, I've been working with Shinjae. Here is where we stand (sorry if you already know this): >>> >>> 1) redeploy ontology_service immediately >>> 2) redeploy networks immediately >>> 3) redeploy plant_expression on Shinjae's command >>> >>> Shinjae needs to verify a few more things on plant_expression service. >>> >>> Tom >>> >>> >>> >>> >>> On Feb 15, 2013, at 10:43 AM, Sergei Maslov <maslov(a)bnl.gov> wrote: >>> >>>> Tom, >>>> >>>> I just wanted to confirm that these services will be available in IRIS. >>>> My understanding is that if it will pass all the tests it will start being deployed next Tuesday. >>>> >>>> I may be showing a video demo walking through these steps >>>> https://docs.google.com/document/d/1kIBk19jjWsegApoG4QNAKEZ48eBNae8jXQW8EFq… >>>> at the Bethesda meeting and I would like to record it using the IRIS interface. >>>> Shinjae promised to help with recording. >>>> >>>> Sergei >>>> >>>> -- >>>> Dr. Sergei Maslov, >>>> Department of Biology, >>>> Brookhaven National Laboratory, >>>> Upton, New York, 11973 >>>> Tel: (631) 344-3742; >>>> FAX: (631) 344-3407 >>>> E@mail: maslov(a)bnl.gov >>>> WWW: http://www.cmth.bnl.gov/~maslov >>>> >>> >>> Thomas Brettin >>> 865-603-7760 (cell) >>> brettin(a)mcs.anl.gov >>> >>> >>> >> >> Thomas Brettin >> 865-603-7760 (cell) >> brettin(a)mcs.anl.gov >> >> >> > Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

1 0

Re: [Release-team] plant ontolog, . expression, and co-expression networks in IRIS
by Shane Canon 15 Feb '13

15 Feb '13

ontology and networks should be ready. --Shane On Feb 15, 2013, at 12:56 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Hey Guys, I've been working with Shinjae. Here is where we stand (sorry if you already know this): > > 1) redeploy ontology_service immediately > 2) redeploy networks immediately > 3) redeploy plant_expression on Shinjae's command > > Shinjae needs to verify a few more things on plant_expression service. > > Tom > > > > > On Feb 15, 2013, at 10:43 AM, Sergei Maslov <maslov(a)bnl.gov> wrote: > >> Tom, >> >> I just wanted to confirm that these services will be available in IRIS. >> My understanding is that if it will pass all the tests it will start being deployed next Tuesday. >> >> I may be showing a video demo walking through these steps >> https://docs.google.com/document/d/1kIBk19jjWsegApoG4QNAKEZ48eBNae8jXQW8EFq… >> at the Bethesda meeting and I would like to record it using the IRIS interface. >> Shinjae promised to help with recording. >> >> Sergei >> >> -- >> Dr. Sergei Maslov, >> Department of Biology, >> Brookhaven National Laboratory, >> Upton, New York, 11973 >> Tel: (631) 344-3742; >> FAX: (631) 344-3407 >> E@mail: maslov(a)bnl.gov >> WWW: http://www.cmth.bnl.gov/~maslov >> > > Thomas Brettin > 865-603-7760 (cell) > brettin(a)mcs.anl.gov > > > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

1 0

Re: [Release-team] plant ontolog, . expression, and co-expression networks in IRIS
by Yoo, Shinjae 15 Feb '13

15 Feb '13

Thanks Tom, Plant expression service is ready to go and passed `make test`… Shane, please do `rm -rf /kb/deployment` first… If not, it can not create `/kb/deployment/rsbin' directory. Thanks, -SJ On Feb 15, 2013, at 3:57 PM, Thomas Brettin wrote: > Also, for the plant_expression service, you will need to pull changes to the dev_container out of the kbase.us git repo before doing the make. > > > > On Feb 15, 2013, at 2:56 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> Hey Guys, I've been working with Shinjae. Here is where we stand (sorry if you already know this): >> >> 1) redeploy ontology_service immediately >> 2) redeploy networks immediately >> 3) redeploy plant_expression on Shinjae's command >> >> Shinjae needs to verify a few more things on plant_expression service. >> >> Tom >> >> >> >> >> On Feb 15, 2013, at 10:43 AM, Sergei Maslov <maslov(a)bnl.gov> wrote: >> >>> Tom, >>> >>> I just wanted to confirm that these services will be available in IRIS. >>> My understanding is that if it will pass all the tests it will start being deployed next Tuesday. >>> >>> I may be showing a video demo walking through these steps >>> https://docs.google.com/document/d/1kIBk19jjWsegApoG4QNAKEZ48eBNae8jXQW8EFq… >>> at the Bethesda meeting and I would like to record it using the IRIS interface. >>> Shinjae promised to help with recording. >>> >>> Sergei >>> >>> -- >>> Dr. Sergei Maslov, >>> Department of Biology, >>> Brookhaven National Laboratory, >>> Upton, New York, 11973 >>> Tel: (631) 344-3742; >>> FAX: (631) 344-3407 >>> E@mail: maslov(a)bnl.gov >>> WWW: http://www.cmth.bnl.gov/~maslov >>> >> >> Thomas Brettin >> 865-603-7760 (cell) >> brettin(a)mcs.anl.gov >> >> >> > > Thomas Brettin > 865-603-7760 (cell) > brettin(a)mcs.anl.gov > > >

1 0