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

Re: [Release-team] magellan
by Boisvert, Sebastien 04 Sep '14

04 Sep '14

You have to: - stop the instance cleanly in the old OpenStack ("halt" in the shell) - create a snapshot of the root volume of the stopped instance - any snapshop and image is synced automatically to the new OpenStack deployment - in the new OpenStack cloud, boot an instance from the snapshot - associate a IP address - update your DNA A record, if any. ________________________________________ From: release-team-bounces(a)lists.kbase.us [release-team-bounces(a)lists.kbase.us] on behalf of Robert Olson [olson(a)mcs.anl.gov] Sent: Thursday, September 04, 2014 3:13 PM To: release-team(a)lists.kbase.us Subject: [Release-team] magellan I understand that the essex instances are all getting killed tomorrow. Does anyone have experience in directly bringing across instances? I think the production genome annotation is still running there so we may lose it for a while. Who knows what else we may lose as well. _______________________________________________ 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] magellan
by Robert Olson 04 Sep '14

04 Sep '14

Chris. On Sep 4, 2014, at 3:15 PM, Thomas Brettin <brettin(a)anl.gov> wrote: > Where did you learn this from? > > > On Sep 4, 2014, at 4:13 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > >> I understand that the essex instances are all getting killed tomorrow. Does anyone have experience in directly bringing across instances? I think the production genome annotation is still running there so we may lose it for a while. >> >> Who knows what else we may lose as well. >> >> >> _______________________________________________ >> 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] magellan
by Thomas Brettin 04 Sep '14

04 Sep '14

Where did you learn this from? On Sep 4, 2014, at 4:13 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > I understand that the essex instances are all getting killed tomorrow. Does anyone have experience in directly bringing across instances? I think the production genome annotation is still running there so we may lose it for a while. > > Who knows what else we may lose as well. > > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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magellan
by Robert Olson 04 Sep '14

04 Sep '14

I understand that the essex instances are all getting killed tomorrow. Does anyone have experience in directly bringing across instances? I think the production genome annotation is still running there so we may lose it for a while. Who knows what else we may lose as well.

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Re: [Release-team] [JIRA] (KBASE-620) Help Downloading Metabolic Models
by Nomi Harris 30 Aug '14

30 Aug '14

Regarding the runtime images, I talked to the infrastructure group several times about creating new images, but they haven't had a chance (or it hasn't been a high enough priority). The last time runtime images were created for download was October 2013. I declared in May 2014 (see https://atlassian.kbase.us/browse/KBASE-760) that if there wasn't time/resources to create new images, then I would take down the downloads page, rather than offer out-of-date images that would only create confusion for users and hassle for us as users submitted bug reports. I took the downloads page down in July 2014. We can quickly put it back up whenever the release team has time to create new images. In the meantime, the suggestion to create a script and then upload it to IRIS seems like the best advice. Is there any way for us to create a script for downloading metabolic models (even if the users needed to edit it a bit to get exactly what they wanted? We could perhaps give them a skeleton of a script?). Nomi On Aug 29, 2014, at 7:26 AM, Michael Mundy (JIRA) <help(a)kbase.us> wrote: > > > > Michael Mundy commented on KBASE-620 > Help Downloading Metabolic Models > There is a way to script in IRIS but it is limited. You can save commands in a file and then run all of the commands from the file using "execute". Unfortunately there are no variables or control flow features in IRIS scripting. You could generate the file with your favorite scripting language on your computer and then upload the script to IRIS. Run "whatsnew" from the IRIS command line to get some details on the scripting support. > > Using the restful API or command line is difficult right now with no pre-built client image available. Building your own client image can be done but that is not in a very good state at the moment. The fba modeling service has dependencies on the typecomp, kb_seed, workspace_service, auth, idserver, kb_model_seed, probabilistic_annotation, and workspace_deluxe services. I'm pretty sure the workspace_service and auth repos are not moving to github so you can't build fba modeling unless you have a developer account. And you would still need to track down a runtime image and I don't think there is a current image that is publicly available. > > Do we know what language the user wants to use when accessing the restful API? With Python it might be possible to grab the Client.py file and get something to work. Also, what type of system is the user running on (Linux, Mac, etc.)? > > This message is automatically generated by JIRA. > If you think it was sent incorrectly, please contact your JIRA administrators > For more information on JIRA, see: http://www.atlassian.com/software/jira

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Re: [Release-team] Need to update service info
by Thomas Brettin 20 Aug '14

20 Aug '14

i’m ok with just sending it out. On Aug 20, 2014, at 2:14 PM, Nomi Harris <nlharris(a)gmail.com> wrote: > Dear Release Team, > Erik and I are starting a review of all the service documentation (including API docs, release notes, and tutorials). In order to make sure our list of services is current and complete, we need to update the master Services spreadsheet (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) Erik had the good suggestion that we should add a column where the service owner can indicate that they have updated or verified the information for their service—I have added column H for this purpose. > > Should I go ahead and send a note to kbase-devel to ask people to update that spreadsheet (adding any missing services, striking out obsolete ones, changing info as needed), or do you guys want a chance to work on it before I send that out? > > Thanks, > Nomi > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Need to update service info
by Nomi Harris 20 Aug '14

20 Aug '14

Dear Release Team, Erik and I are starting a review of all the service documentation (including API docs, release notes, and tutorials). In order to make sure our list of services is current and complete, we need to update the master Services spreadsheet (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) Erik had the good suggestion that we should add a column where the service owner can indicate that they have updated or verified the information for their service—I have added column H for this purpose. Should I go ahead and send a note to kbase-devel to ask people to update that spreadsheet (adding any missing services, striking out obsolete ones, changing info as needed), or do you guys want a chance to work on it before I send that out? Thanks, Nomi

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Re: [Release-team] tree service redeployed pointing to production WS
by Michael Sneddon 18 Jul '14

18 Jul '14

You should email him, and probably you should copy the email to ' release-team(a)kbase.us' as well. We used to have a more official process, but I don't think it is being followed currently. On Fri, Jul 18, 2014 at 10:24 AM, Roman Sutormin <rsutormin(a)lbl.gov> wrote: > Thanks. > Mike, if you need to ask Shane to put service into production what would > you do? You send email to him or you rather create jira-task for that? > > > On Fri, Jul 18, 2014 at 10:20 AM, Michael Sneddon <mwsneddon(a)lbl.gov> > wrote: > >> This service is pointing to production: >> http://dev19.berkeley.kbase.us:7047 >> >> This is still pointing to dev: >> http://140.221.67.152:7047 >> > >

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Re: [Release-team] Redeploy request for workspace
by Gavin Price 17 Jul '14

17 Jul '14

They'd need refreshing if you wanted to use the new functionality but not otherwise. Sent from my Cray XC30 On Jul 17, 2014 6:20 AM, "Shane Canon" <scanon(a)lbl.gov> wrote: > > Gavin > > Would WS client libraries need to be refreshed or are the changes just in > the server side? > > Shane > > Sent from my iPhone > > > On Jul 15, 2014, at 10:02 AM, Gavin A Price <gavinaprice(a)gmail.com> > wrote: > > > > Hi, the workspace team would like a redeploy for the production > workspace service. This will move the workspace service from v 0.1.6 to > 0.2.1. There are several important bugfixes, as well as much less memory > use and about a 50% speed increase (in admittedly somewhat limited tests). > > > > v0.2.0 has been available on the dev workspace for a couple months now > with only one reported problem. This problem should be fixed in 0.2.1. > Also, a couple scripts have been fixed to work properly in IRIS with the > new IRIS config mechanism. > > > > There's a document with notes about how to upgrade from 0.1.6 to 0.2.0. > Upgrading to 0.2.1 requires no special actions: > > > > > https://docs.google.com/a/lbl.gov/document/d/1zRU7jvXuL01Ru6gUpcGAFYngDGBtG… > > > > We would prefer the redeploy to happen this week, prior to the tests > next week. > > > > Thanks, Gavin, official spokesperson of KBase Workspaces Ltd. >

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Re: [Release-team] Redeploy request for workspace
by Shane Canon 17 Jul '14

17 Jul '14

Gavin Would WS client libraries need to be refreshed or are the changes just in the server side? Shane Sent from my iPhone > On Jul 15, 2014, at 10:02 AM, Gavin A Price <gavinaprice(a)gmail.com> wrote: > > Hi, the workspace team would like a redeploy for the production workspace service. This will move the workspace service from v 0.1.6 to 0.2.1. There are several important bugfixes, as well as much less memory use and about a 50% speed increase (in admittedly somewhat limited tests). > > v0.2.0 has been available on the dev workspace for a couple months now with only one reported problem. This problem should be fixed in 0.2.1. Also, a couple scripts have been fixed to work properly in IRIS with the new IRIS config mechanism. > > There's a document with notes about how to upgrade from 0.1.6 to 0.2.0. Upgrading to 0.2.1 requires no special actions: > > https://docs.google.com/a/lbl.gov/document/d/1zRU7jvXuL01Ru6gUpcGAFYngDGBtG… > > We would prefer the redeploy to happen this week, prior to the tests next week. > > Thanks, Gavin, official spokesperson of KBase Workspaces Ltd.

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