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

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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Redeploy request for workspace
by Gavin A Price 15 Jul '14

15 Jul '14

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] request to put KB Protein Structure Service
by Sean McCorkle 12 Jul '14

12 Jul '14

Hey you're right - it works from my home. I wasn't able to connect previously (from BNL, same exercise on a different instance, also Havana - same symptoms, localhost:7088 worked fine, internal request to IP hung up, and external from BNL did as well. Its possible I mistyped the address then). Thanks! On Sat, Jul 12, 2014 at 4:48 PM, Murphy-Olson, Daniel E. <dolson(a)mcs.anl.gov> wrote: > The external address seems to work for me from an outside connection. > > ________________________________________ > From: Sean McCorkle [sean.r.mccorkle(a)gmail.com] > Sent: Saturday, July 12, 2014 3:30 PM > To: Brettin, Thomas S. > Cc: release-team(a)kbase.us; Murphy-Olson, Daniel E. > Subject: Re: [Release-team] request to put KB Protein Structure Service > > Okay, done. Its in the repo now. I tried a clean build on a fresh VM > instance (using Havana) and every test checks out,up to the client > -server network connection on port 7088. A connection to > http://localhost:7088 works fine, but not one to the assigned IP > address http://140.221.67.170:7088, and I can't get that to work > externally either. I suspect I'm doing something wrong with the > Havana security group rules or something. (I don't think the issue is > in the service code) > > Thanks again! > =sean > > On Sat, Jul 12, 2014 at 10:49 AM, Sean McCorkle > <sean.r.mccorkle(a)gmail.com> wrote: >> No problem at all to change the name - I'll make the deployment directory >> >> /kb/deployment/services/protein_structure_service >> >> to match the repo name, and I assume the "official" url will have the >> same name as well? >> >> http://kbase.us/services/protein_structure_service >> >> will make the changes, run my checks and then push to git and let you >> know right afterwards. >> >> Thanks! >> >> =sean >> >> >> >> >> >> >> On Sat, Jul 12, 2014 at 9:03 AM, Thomas Brettin <brettin(a)anl.gov> wrote: >>> Hi Sean >>> >>> Usually the deployment directory syntactically the same as the repo name. There are a few deviants from this, and its usually causes a bit of a hassle. Would you mind changing the deployment directory name to the name of the git repo? >>> >>> Tom >>> >>> >>> On Jul 10, 2014, at 9:32 AM, Sean McCorkle <sean.r.mccorkle(a)gmail.com> wrote: >>> >>>> Hello, >>>> >>>> After some vetting by Shinjae last week, and a discussion with Dan >>>> yesterday, I would like to submit the KBase Protein Structure service >>>> that I've been working on as a candidate for production. The repo is >>>> "protein_structure_service" on git.kbase.us, the deployment target >>>> directory is "kbaseproteinstructure". There are two methods and two >>>> associated client scripts which give a est match PDB id given a KBase >>>> protein MD5 or feature id. I've done about as much as I can by way >>>> of documentation and testing. I sincerely hope this won't be a big >>>> hassle for anybody. >>>> >>>> Looking forward to hearing from anybody on this, and thank you for >>>> the consideration! >>>> >>>> -- >>>> >>>> Sean R. McCorkle >>>> sean.r.mccorkle(a)gmail.com >>>> _______________________________________________ >>>> Release-team mailing list >>>> Release-team(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/release-team >>> >> >> >> >> -- >> >> Sean R. McCorkle >> sean.r.mccorkle(a)gmail.com > > > > -- > > Sean R. McCorkle > sean.r.mccorkle(a)gmail.com -- Sean R. McCorkle sean.r.mccorkle(a)gmail.com

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Re: [Release-team] request to put KB Protein Structure Service
by Murphy-Olson, Daniel E. 12 Jul '14

12 Jul '14

The external address seems to work for me from an outside connection. ________________________________________ From: Sean McCorkle [sean.r.mccorkle(a)gmail.com] Sent: Saturday, July 12, 2014 3:30 PM To: Brettin, Thomas S. Cc: release-team(a)kbase.us; Murphy-Olson, Daniel E. Subject: Re: [Release-team] request to put KB Protein Structure Service Okay, done. Its in the repo now. I tried a clean build on a fresh VM instance (using Havana) and every test checks out,up to the client -server network connection on port 7088. A connection to http://localhost:7088 works fine, but not one to the assigned IP address http://140.221.67.170:7088, and I can't get that to work externally either. I suspect I'm doing something wrong with the Havana security group rules or something. (I don't think the issue is in the service code) Thanks again! =sean On Sat, Jul 12, 2014 at 10:49 AM, Sean McCorkle <sean.r.mccorkle(a)gmail.com> wrote: > No problem at all to change the name - I'll make the deployment directory > > /kb/deployment/services/protein_structure_service > > to match the repo name, and I assume the "official" url will have the > same name as well? > > http://kbase.us/services/protein_structure_service > > will make the changes, run my checks and then push to git and let you > know right afterwards. > > Thanks! > > =sean > > > > > > > On Sat, Jul 12, 2014 at 9:03 AM, Thomas Brettin <brettin(a)anl.gov> wrote: >> Hi Sean >> >> Usually the deployment directory syntactically the same as the repo name. There are a few deviants from this, and its usually causes a bit of a hassle. Would you mind changing the deployment directory name to the name of the git repo? >> >> Tom >> >> >> On Jul 10, 2014, at 9:32 AM, Sean McCorkle <sean.r.mccorkle(a)gmail.com> wrote: >> >>> Hello, >>> >>> After some vetting by Shinjae last week, and a discussion with Dan >>> yesterday, I would like to submit the KBase Protein Structure service >>> that I've been working on as a candidate for production. The repo is >>> "protein_structure_service" on git.kbase.us, the deployment target >>> directory is "kbaseproteinstructure". There are two methods and two >>> associated client scripts which give a est match PDB id given a KBase >>> protein MD5 or feature id. I've done about as much as I can by way >>> of documentation and testing. I sincerely hope this won't be a big >>> hassle for anybody. >>> >>> Looking forward to hearing from anybody on this, and thank you for >>> the consideration! >>> >>> -- >>> >>> Sean R. McCorkle >>> sean.r.mccorkle(a)gmail.com >>> _______________________________________________ >>> Release-team mailing list >>> Release-team(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/release-team >> > > > > -- > > Sean R. McCorkle > sean.r.mccorkle(a)gmail.com -- Sean R. McCorkle sean.r.mccorkle(a)gmail.com

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Re: [Release-team] request to put KB Protein Structure Service
by Sean McCorkle 12 Jul '14

12 Jul '14

Okay, done. Its in the repo now. I tried a clean build on a fresh VM instance (using Havana) and every test checks out,up to the client -server network connection on port 7088. A connection to http://localhost:7088 works fine, but not one to the assigned IP address http://140.221.67.170:7088, and I can't get that to work externally either. I suspect I'm doing something wrong with the Havana security group rules or something. (I don't think the issue is in the service code) Thanks again! =sean On Sat, Jul 12, 2014 at 10:49 AM, Sean McCorkle <sean.r.mccorkle(a)gmail.com> wrote: > No problem at all to change the name - I'll make the deployment directory > > /kb/deployment/services/protein_structure_service > > to match the repo name, and I assume the "official" url will have the > same name as well? > > http://kbase.us/services/protein_structure_service > > will make the changes, run my checks and then push to git and let you > know right afterwards. > > Thanks! > > =sean > > > > > > > On Sat, Jul 12, 2014 at 9:03 AM, Thomas Brettin <brettin(a)anl.gov> wrote: >> Hi Sean >> >> Usually the deployment directory syntactically the same as the repo name. There are a few deviants from this, and its usually causes a bit of a hassle. Would you mind changing the deployment directory name to the name of the git repo? >> >> Tom >> >> >> On Jul 10, 2014, at 9:32 AM, Sean McCorkle <sean.r.mccorkle(a)gmail.com> wrote: >> >>> Hello, >>> >>> After some vetting by Shinjae last week, and a discussion with Dan >>> yesterday, I would like to submit the KBase Protein Structure service >>> that I've been working on as a candidate for production. The repo is >>> "protein_structure_service" on git.kbase.us, the deployment target >>> directory is "kbaseproteinstructure". There are two methods and two >>> associated client scripts which give a est match PDB id given a KBase >>> protein MD5 or feature id. I've done about as much as I can by way >>> of documentation and testing. I sincerely hope this won't be a big >>> hassle for anybody. >>> >>> Looking forward to hearing from anybody on this, and thank you for >>> the consideration! >>> >>> -- >>> >>> Sean R. McCorkle >>> sean.r.mccorkle(a)gmail.com >>> _______________________________________________ >>> Release-team mailing list >>> Release-team(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/release-team >> > > > > -- > > Sean R. McCorkle > sean.r.mccorkle(a)gmail.com -- Sean R. McCorkle sean.r.mccorkle(a)gmail.com

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Re: [Release-team] request to put KB Protein Structure Service
by Sean McCorkle 12 Jul '14

12 Jul '14

No problem at all to change the name - I'll make the deployment directory /kb/deployment/services/protein_structure_service to match the repo name, and I assume the "official" url will have the same name as well? http://kbase.us/services/protein_structure_service will make the changes, run my checks and then push to git and let you know right afterwards. Thanks! =sean On Sat, Jul 12, 2014 at 9:03 AM, Thomas Brettin <brettin(a)anl.gov> wrote: > Hi Sean > > Usually the deployment directory syntactically the same as the repo name. There are a few deviants from this, and its usually causes a bit of a hassle. Would you mind changing the deployment directory name to the name of the git repo? > > Tom > > > On Jul 10, 2014, at 9:32 AM, Sean McCorkle <sean.r.mccorkle(a)gmail.com> wrote: > >> Hello, >> >> After some vetting by Shinjae last week, and a discussion with Dan >> yesterday, I would like to submit the KBase Protein Structure service >> that I've been working on as a candidate for production. The repo is >> "protein_structure_service" on git.kbase.us, the deployment target >> directory is "kbaseproteinstructure". There are two methods and two >> associated client scripts which give a est match PDB id given a KBase >> protein MD5 or feature id. I've done about as much as I can by way >> of documentation and testing. I sincerely hope this won't be a big >> hassle for anybody. >> >> Looking forward to hearing from anybody on this, and thank you for >> the consideration! >> >> -- >> >> Sean R. McCorkle >> sean.r.mccorkle(a)gmail.com >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team > -- Sean R. McCorkle sean.r.mccorkle(a)gmail.com

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Re: [Release-team] request to put KB Protein Structure Service
by Thomas Brettin 12 Jul '14

12 Jul '14

Hi Sean Usually the deployment directory syntactically the same as the repo name. There are a few deviants from this, and its usually causes a bit of a hassle. Would you mind changing the deployment directory name to the name of the git repo? Tom On Jul 10, 2014, at 9:32 AM, Sean McCorkle <sean.r.mccorkle(a)gmail.com> wrote: > Hello, > > After some vetting by Shinjae last week, and a discussion with Dan > yesterday, I would like to submit the KBase Protein Structure service > that I've been working on as a candidate for production. The repo is > "protein_structure_service" on git.kbase.us, the deployment target > directory is "kbaseproteinstructure". There are two methods and two > associated client scripts which give a est match PDB id given a KBase > protein MD5 or feature id. I've done about as much as I can by way > of documentation and testing. I sincerely hope this won't be a big > hassle for anybody. > > Looking forward to hearing from anybody on this, and thank you for > the consideration! > > -- > > Sean R. McCorkle > sean.r.mccorkle(a)gmail.com > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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request to put KB Protein Structure Service
by Sean McCorkle 09 Jul '14

09 Jul '14

Hello, After some vetting by Shinjae last week, and a discussion with Dan yesterday, I would like to submit the KBase Protein Structure service that I've been working on as a candidate for production. The repo is "protein_structure_service" on git.kbase.us, the deployment target directory is "kbaseproteinstructure". There are two methods and two associated client scripts which give a est match PDB id given a KBase protein MD5 or feature id. I've done about as much as I can by way of documentation and testing. I sincerely hope this won't be a big hassle for anybody. Looking forward to hearing from anybody on this, and thank you for the consideration! -- Sean R. McCorkle sean.r.mccorkle(a)gmail.com

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