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

Re: [Release-team] Please test VM candidate
by Dan Olson 17 Sep '13

17 Sep '13

This link should work better -- http://bioseed.mcs.anl.gov/~dolson/KBase_20130904.vmdk.gz ----- Original Message ----- > From: "Dan Olson" <dolson(a)mcs.anl.gov> > To: release-team(a)kbase.us > Sent: Tuesday, September 17, 2013 9:04:06 AM > Subject: Please test VM candidate > > Hi all, > > Please have a look at the latest ubuntu VM release candidate. > > http://bioseed.mcs.anl.gov/~dolson/kbase-20130904.vmdk.gz > > ---- > Daniel Murphy-Olson > Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > >

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Please test VM candidate
by Dan Olson 17 Sep '13

17 Sep '13

Hi all, Please have a look at the latest ubuntu VM release candidate. http://bioseed.mcs.anl.gov/~dolson/kbase-20130904.vmdk.gz ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

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Re: [Release-team] updating release notes on kbase.us
by Thomas Brown 17 Sep '13

17 Sep '13

Thanks Neal ----- Original Message ----- From: "Neal Conrad" <nconrad(a)mcs.anl.gov> To: release-team(a)kbase.us, sysadmins(a)kbase.us Cc: "Thomas Brown" <tomasbrown(a)gmail.com>, "Nomi Harris" <nlharris(a)lbl.gov>, "Michael Sneddon" <mwsneddon(a)lbl.gov> Sent: Monday, September 16, 2013 4:51:44 PM Subject: updating release notes on kbase.us I just learned that there is a release-team email list as well, so I'm including that list too. if we're pulling release notes to post on the kbase site, just a reminder that we need to make sure we are pulling them from the git versions that are tagged for release, not just the latest on master. For instance, in 'trees' I've already started some notes since the last release that shouldn't be posted until we complete the next future release. This should also help us to ensure that we are not posting release notes for services that aren't being released. Yes, this was our concern too. Can git.kbase.us:<service_name>/RELEASE_NOTES.txt be pushed to http://www.kbase.us/services/docs/ <service_name>/ on deployment, so that api and release note documentation updates on kbase.us aren't done two different ways? Thanks, Neal

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error on deploy of the regprecise module
by Dan Olson 16 Sep '13

16 Sep '13

Hi Pavel, The regprecise module is getting an error on redeployment -- /kb/runtime//glassfish3/bin/asadmin stop-domain CLI306 Warning - The server located at /kb/runtime/glassfish3/glassfish/domains/domain1 is not running. Command stop-domain executed successfully. remote failure: java.lang.NullPointerException remote failure: http-listener-1 protocol doesn't exist remote failure: Http Listener named http-listener-1 already exists. /kb/runtime//glassfish3/bin/asadmin deploy --force=true ./dist/KBaseRegPreciseRPC.war;\ remote failure: Error occurred during deployment: Exception while loading the app : java.lang.Exception: WEB0113: Virtual server [server] already has a web module [KBaseRegPreciseRPC] loaded at [/KBaseRegPreciseRPC]; therefore web module [KBaseRegPreciseRPC] cannot be loaded at this context path on this virtual server. . Please see server.log for more details. Command deploy failed. make[1]: *** [deploy_war] Error 1 make[1]: Leaving directory `/kb/dev_container/modules/regprecise' make: *** [deploy] Error 1 Can you please advise what needs to be done? ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

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updating release notes on kbase.us
by Neal Conrad 16 Sep '13

16 Sep '13

I just learned that there is a release-team email list as well, so I'm including that list too. > if we're pulling release notes to post on the kbase site, just a reminder that we need to make sure we are pulling them from the git versions that are tagged for release, not just the latest on master. For instance, in 'trees' I've already started some notes since the last release that shouldn't be posted until we complete the next future release. This should also help us to ensure that we are not posting release notes for services that aren't being released. Yes, this was our concern too. Can git.kbase.us:<service_name>/RELEASE_NOTES.txt be pushed to http://www.kbase.us/services/docs/<service_name>/ on deployment, so that api and release note documentation updates on kbase.us aren't done two different ways? Thanks, Neal

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Re: [Release-team] Communities API through IRIS
by Nomi Harris 16 Sep '13

16 Sep '13

The build should be completed this week and all deployed commands should be accessible in IRIS. If the communities API service had problems, you should be able to determine that by looking at the Services sheet (https://docs.google.com/spreadsheet/ccc?key=0Ana5oznWypH2dFppaEJzOUdfMV8zN0…) and/or checking with Miriam. Not sure why you would think Adam and Rick would have any info about that. Note that there's an open ticket https://atlassian.kbase.us/browse/KBASE-146 about communities_api Not sure if that got fixed. > I can see two reasons the scripts not being found in IRIS: > All scripts are prefixed and have to follow a naming convention now. So get_metagenome.pl will be mg-get-metagenome. Did you try with the prefix? All commands will still work with their old command names for a while (months, at least). Nomi On Sep 16, 2013, at 9:54 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > Hi Andreas, > > frankly I'm using the REST interface directly, not the Perl API nor IRIS. I was asking because I did go to IRIS just to check some of the Tree stuff and noticed that the Communities API methods are not in the list of modules nor do they show up when you run "commands". Perhaps they just haven't been deployed to the public site yet? What's the ETA on that? > > Thanks, > - Dylan > > > > On Mon, Sep 16, 2013 at 6:56 AM, Andreas Wilke <wilke(a)mcs.anl.gov> wrote: > Hi Dylan, > > On Sep 13, 2013, at 9:44 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > >> I'm not seeing the Communities API methods on the live IRIS. Where did it go? > > The API is accessible via http or language specific libraries. The best way to use the libraries is starting your own VM with KBase runtime and do the following steps: > ssh ubuntu(a)your.ip > sudo -u root -H bash > # check out dev_container and setup dev environment > # deployment is always from a dev_container > cd /kb > git clone [email protected]:dev_container.git > cd dev_container > ./bootstrap /kb/runtime > source user-env.sh > cd modules > # check out all required modules > git clone [email protected]:communities_api.git > git clone [email protected]:idserver.git > git clone [email protected]:typecomp.git > git clone [email protected]:auth > cd .. > ./bootstrap /kb/runtime > source user-env.sh > # check the make output it will tell you if required modules/dependencies are missing > make > # deploy > make deploy > # now source the deployment environment and start using the scripts or APIs > cd /kb/deployment > source user-env.sh > # execute scripts > mg-get-metagenome-list --help > # use libraries: > use CommunitiesAPIClient; > use Bio::KBase::Exceptions; > my $client = new CommunitiesAPIClient($host); > > The communities command line scripts will be accessible through IRIS after successful deployment and test. I don't know when IRIS gets updated with new scripts after a successful deployment. Despite this I can see two reasons the scripts not being found in IRIS: > All scripts are prefixed and have to follow a naming convention now. So get_metagenome.pl will be mg-get-metagenome. Did you try with the prefix? > As you know everything in KBase has to follow the deployment procedure and pass "make deploy" and "make test" automatically. If something went wrong there scripts won't be deployed either. In addition there is the COMMANDS file, only scripts matching the pattern in the COMMANDS file will be deployed in IRIS. > I have to touch base with the deployment and testing team to get a report but I expect them to show up in IRIS this week. > > Keep in mind that IRIS is a front-end and not suited for search/indexing tasks and that all KBase services/products have to have a Makefile following the deployment rules. It did cost me some time in the beginning to adapt and be compliant. > > Andreas > >> >> Thanks, >> - Dylan >> > > Andreas Wilke > Argonne National Laboratory > Mathematics and Computer Science Division > Bldg. 240 , 4F8 > 9700 South Cass Avenue > Argonne, IL 60439 > (630) 252-3190 (phone) > (630) 252-5986.(fax) > >

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Re: [Release-team] [Kbase-devel] service build this week.
by Thomas Brettin 16 Sep '13

16 Sep '13

OMG, well, to be honest I'm having a hard time thinking that far ahead. As it stands right now, we're a go on the 18-22. Most developers won't be traveling to the SAC, so that's ok there. We can talk about it later this week. On Sep 16, 2013, at 11:40 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Build still planned for Nov 18-22?

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Re: [Release-team] [Kbase-devel] service build this week.
by Nomi Harris 16 Sep '13

16 Sep '13

On Sep 16, 2013, at 9:37 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Dan is working on finishing the Aug build. The DMG. Ok, great--please keep me updated on progress with that. I'd like to push out the changes to the website when the release is done. Neal is working on that with Tom Brown and they keep asking me what the deadline is. > I'm planning the next one. Build still planned for Nov 18-22? Nomi > > > On Sep 16, 2013, at 11:36 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> Wait, so we're doing a mini-build instead of finishing the August full build? >> >> On Sep 16, 2013, at 6:57 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> >>> Are there service modules that are ready for deployment this week? I'd like to see if there is enough to organize a mini build. >>> >>> Tom >> >

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Re: [Release-team] [Kbase-devel] service build this week.
by Thomas Brettin 16 Sep '13

16 Sep '13

Dan is working on finishing the Aug build. The DMG. I'm planning the next one. On Sep 16, 2013, at 11:36 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Wait, so we're doing a mini-build instead of finishing the August full build? > > On Sep 16, 2013, at 6:57 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> Are there service modules that are ready for deployment this week? I'd like to see if there is enough to organize a mini build. >> >> Tom >

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Re: [Release-team] [Kbase-devel] service build this week.
by Nomi Harris 16 Sep '13

16 Sep '13

Wait, so we're doing a mini-build instead of finishing the August full build? On Sep 16, 2013, at 6:57 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Are there service modules that are ready for deployment this week? I'd like to see if there is enough to organize a mini build. > > Tom

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