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

Re: [Release-team] Do we have a plan for gettting things all together and deployed for the 15th.
by Brettin, Thomas S. 04 Jan '14

04 Jan '14

Here is a draft announcement for the schedule for the deployments. Of course, the hard deadline for deployment to production is Jan 15. Builds are scheduled to take place from Jan 7-13, 2014. Activities will cease on the end of Jan 15 and at that time we will take inventory of what made it into production. The build pattern is mostly unchanged, module owners communicate to the release team modules that are ready. The release team deploys the module to the test environment, executes the tests, and then deploys the module to production. Triage based on failures occurs along the way, and module owners have the opportunity to fix problems and resubmit the module as ready to the release team. The release team will take no new deployment requests after Jan 13, so that the Jan 15 production deployment schedule can be kept. On Jan 16, a report to Adam will be compiled by the release team and submitted. On Monday, Jan 6, or as soon as a the release team arrives, the KBase services spread sheet will be finalized, and the build punchlist will be reviewed. Feedback welcome. I will send tomorrow or later this evening if Adam you are ok with this schedule. Tom On Jan 3, 2014, at 1:19 PM, Adam Arkin <aparkin(a)lbl.gov<mailto:[email protected]>> wrote: That would be great. We need to get a hard end to deploy. Do we have a plan for a public vs. "private" instance? A On Fri, Jan 3, 2014 at 11:05 AM, Thomas Brettin <brettint(a)gmail.com<mailto:[email protected]>> wrote: I can do a formal timeline for prod deploys. Would formally start on the 13th. of Jan.; after the hackathon, but we can start earlier on those that are ready. Would work out the logistics of tracking with Miriam, Nomi, Dan, Shane next week On Jan 3, 2014, at 12:58 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]>> wrote: I can do a timeline for prod deploys. Would formally start Sent from my Verizon Wireless 4G LTE DROID Adam Arkin <aparkin(a)lbl.gov<mailto:[email protected]>> wrote: Hi All, I know already people are pushing the deadline... I am very worried about this. If we are going to push the deadline we should do so formally and set the process for final deployment and testing. We also were going to have a public site and a site with more advanced functionality for friends. Is this going to happen? Should we get people on a schedule? How should we manage this? A -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us <http://kbase.us/> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu<http://synbio.berkeley.edu/> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov<http://vimss.lbl.gov/> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org<http://energybiosciencesinstitute.org/> Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov<http://genomics.lbl.gov/> V: 510-495-2366<tel:510-495-2366> C: 510-206-1389<tel:510-206-1389> F: 510-486-6219<tel:510-486-6219> Assistant: Gwyneth A. Terry V: 510-495-2116<tel:510-495-2116> E: GATerry(a)lbl.gov<mailto:[email protected]> ------------------------------------- -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us <http://kbase.us/> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu<http://synbio.berkeley.edu/> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov<http://vimss.lbl.gov/> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org<http://energybiosciencesinstitute.org/> Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov<http://genomics.lbl.gov/> V: 510-495-2366 C: 510-206-1389 F: 510-486-6219 Assistant: Gwyneth A. Terry V: 510-495-2116 E: GATerry(a)lbl.gov<mailto:[email protected]> -------------------------------------

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Re: [Release-team] Janurary release - time to start gathering info
by Brettin, Thomas S. 03 Jan '14

03 Jan '14

A friendly reminder to start talking with Miriam so she can set up (cc: release-team(a)lists.kbase.us) Thanks Tom ________________________________________ From: Brettin, Thomas S. Sent: Monday, December 16, 2013 12:17 PM To: KBase Development Cc: Gordon, India S. Subject: Janurary release - time to start gathering info kbase devels, We will start a new release on Jan 6, the first day of the hack a thon at LBL. To start preparing, we need everyone to help by sending to Miriam when you think your module will be ready for a deployment. We have some deadlines to work towards, so lets start the relase process early. Miriam has agreed to take care of the overall tracking of the release process. She will be updating our lists and making sure communication works smoothly, so please give her your support if she reaches out to you. Also, consistent with previous builds, any modules that haven't been through at least one round of black box testing by the test team needs to be. Miriam will follow up on that front to. Thanks in advance, Tom

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Re: [Release-team] handle service
by Nomi Harris 27 Nov '13

27 Nov '13

Is this new service for internal use only, or will it be exposed to users (via Iris)? Are we doing an actual release this month, or just (re)deploying some services? Will there be a new dmg? When should the new services (e.g., m5nr) be added to our services page (https://kbase.us/developer-zone/services/)? Can someone provide a list of new user-facing (i.e., not just for internal use) services that should be added to that page? Thanks, Nomi On Nov 27, 2013, at 10:56 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Please include this in the next deployment. It requires a relational database as a one time setup. Should be on db1/db2. > > Tests are working. > > Documentation at API level is there. > > I'm wrapping up a tutorial of sorts to augment the design documentation. > > Tom > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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handle service
by Thomas Brettin 27 Nov '13

27 Nov '13

Please include this in the next deployment. It requires a relational database as a one time setup. Should be on db1/db2. Tests are working. Documentation at API level is there. I'm wrapping up a tutorial of sorts to augment the design documentation. Tom

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Re: [Release-team] What to tell a user who wants to download KBase data
by Nomi Harris 23 Nov '13

23 Nov '13

On Nov 23, 2013, at 8:03 AM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: > We do have the cs database dumps on the FTP server, if they are just looking for raw data. Would that be ftp://dtn.chicago.kbase.us/assets/kbase-20131010.vdi.gz ? Or something in ftp://dtn.chicago.kbase.us/assets/build/ ? What format are the dumps in? We have no information on kbase.us that explains what the various files are in the ftp site, where to find the data dumps, and what format they're in. (I realize that we probably don't want to advertise the data dumps prominently, since they are for experts only, and will probably result in our getting a barrage of questions about the data format and how to use it.) Can one of you CLI experts advise on the best way to download all the genome sequences and annotations of metabolic networks? Is there somewhere where this is documented? If they generated a file in Iris containing all the genome sequences, would it be too big to download? Would they need to do it chunks? What would be the best way to do that? These seem like questions we might well get asked again, so it would be great to put the answers somewhere where users can find them. If someone can send me the answers, I'll work with Outreach and the documentation team to find an appropriate place to put the information. Thanks, Nomi > > --Dan > >> On Nov 22, 2013, at 11:21 PM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >> >> You can tell them what commands to use from the CLI. >> >> That's what I would probably do. >> >> t >>> On Nov 22, 2013, at 12:51 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>> A user asked (in https://atlassian.kbase.us/browse/KBASE-474) >>>> I noticed that KBase has a lot of genome sequences and annotations of >>>> metabolic networks. Is there anyway I can get a hold of these data? If not >>>> on KBase, do you have any suggestions for where to get, e.g. SEED >>>> annotations? Thanks! >>> >>> This seems like a pretty basic question, but I wasn’t sure what to tell them. Search is not functional right now, but I’m not sure that would be the right way to bulk-download data anyway. There are probably Iris commands that could do this, but what are they? We have no plan to offer bulk data dumps for people to download, right? (I’m not saying we should.) >>> >>> Any advice? >>> >>> Thanks, >>> Nomi

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Re: [Release-team] What to tell a user who wants to download KBase data
by Thomas Brettin 23 Nov '13

23 Nov '13

That's a good option too. On Nov 23, 2013, at 10:03 AM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov> wrote: > We do have the cs database dumps on the FTP server, if they are just looking for raw data. > > --Dan > >> On Nov 22, 2013, at 11:21 PM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >> >> You can tell them what commands to use from the CLI. >> >> That's what I would probably do. >> >> t >>> On Nov 22, 2013, at 12:51 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>> A user asked (in https://atlassian.kbase.us/browse/KBASE-474) >>>> I noticed that KBase has a lot of genome sequences and annotations of >>>> metabolic networks. Is there anyway I can get a hold of these data? If not >>>> on KBase, do you have any suggestions for where to get, e.g. SEED >>>> annotations? Thanks! >>> >>> This seems like a pretty basic question, but I wasn’t sure what to tell them. Search is not functional right now, but I’m not sure that would be the right way to bulk-download data anyway. There are probably Iris commands that could do this, but what are they? We have no plan to offer bulk data dumps for people to download, right? (I’m not saying we should.) >>> >>> Any advice? >>> >>> Thanks, >>> Nomi >>> _______________________________________________ >>> Release-team mailing list >>> Release-team(a)lists.kbase.us >>> 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] What to tell a user who wants to download KBase data
by Murphy-Olson, Daniel E. 23 Nov '13

23 Nov '13

We do have the cs database dumps on the FTP server, if they are just looking for raw data. --Dan > On Nov 22, 2013, at 11:21 PM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: > > You can tell them what commands to use from the CLI. > > That's what I would probably do. > > t >> On Nov 22, 2013, at 12:51 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >> A user asked (in https://atlassian.kbase.us/browse/KBASE-474) >>> I noticed that KBase has a lot of genome sequences and annotations of >>> metabolic networks. Is there anyway I can get a hold of these data? If not >>> on KBase, do you have any suggestions for where to get, e.g. SEED >>> annotations? Thanks! >> >> This seems like a pretty basic question, but I wasn’t sure what to tell them. Search is not functional right now, but I’m not sure that would be the right way to bulk-download data anyway. There are probably Iris commands that could do this, but what are they? We have no plan to offer bulk data dumps for people to download, right? (I’m not saying we should.) >> >> Any advice? >> >> Thanks, >> Nomi >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> 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] What to tell a user who wants to download KBase data
by Thomas Brettin 22 Nov '13

22 Nov '13

You can tell them what commands to use from the CLI. That's what I would probably do. t On Nov 22, 2013, at 12:51 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > A user asked (in https://atlassian.kbase.us/browse/KBASE-474) >> I noticed that KBase has a lot of genome sequences and annotations of >> metabolic networks. Is there anyway I can get a hold of these data? If not >> on KBase, do you have any suggestions for where to get, e.g. SEED >> annotations? Thanks! > > This seems like a pretty basic question, but I wasn’t sure what to tell them. Search is not functional right now, but I’m not sure that would be the right way to bulk-download data anyway. There are probably Iris commands that could do this, but what are they? We have no plan to offer bulk data dumps for people to download, right? (I’m not saying we should.) > > Any advice? > > Thanks, > Nomi > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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What to tell a user who wants to download KBase data
by Nomi Harris 22 Nov '13

22 Nov '13

A user asked (in https://atlassian.kbase.us/browse/KBASE-474) > I noticed that KBase has a lot of genome sequences and annotations of > metabolic networks. Is there anyway I can get a hold of these data? If not > on KBase, do you have any suggestions for where to get, e.g. SEED > annotations? Thanks! This seems like a pretty basic question, but I wasn’t sure what to tell them. Search is not functional right now, but I’m not sure that would be the right way to bulk-download data anyway. There are probably Iris commands that could do this, but what are they? We have no plan to offer bulk data dumps for people to download, right? (I’m not saying we should.) Any advice? Thanks, Nomi

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List of new or deleted services in this release?
by Nomi Harris 22 Nov '13

22 Nov '13

Maybe there’s not a complete list yet for this release, but I need a list of new services that need to be added to our Services web page (e.g., m5nr), and any that need to be removed or commented out (e.g., PROM). There have been various emails from people saying “please add my new service to the release” but I’m not clear on what has made the final cut. What would be the best way to get a list of newly released services (those that are publicly accessible, not just for internal use)? Thanks, Nomi

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