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

Re: [Release-team] communities_api failed script standard testing
by Michael Sneddon 06 Feb '14

06 Feb '14

Interesting- see below. These scripts were tested on the kbase test instance, and I'm not sure when bootstrap was last updated there... but this is probably low priority if everything else is working correctly. On Thu, Feb 6, 2014 at 10:59 AM, Travis Harrison <teharrison(a)anl.gov> wrote: > For the first error you mentioned, your VM is too old or was not installed > correctly. The error says that the python module scipy is missing, that > module was added to the bootstrap repo on 2013-01-13. > > For the second error, I fixed the bug and pushed the changes. > > - Travis > > > On Thu, Feb 6, 2014 at 12:44 PM, Michael Sneddon <mwsneddon(a)lbl.gov>wrote: > >> Hi Andreas, Tobi, and Travis, >> >> On testing for script standards, two scripts appear to be failing. It >> looks like communities_api is still set for production release, but you >> should probably be aware: >> >> >> root@t1:~/msneddon-work/2013doctests/testing/script-tests# grep fail >> tests/communities_api.report.txt >> ----------TEST communities_api mg-inbox-decompress with -h option fail >> ----------TEST communities_api mg-inbox-decompress with --help option >> fail >> ----------TEST communities_api mg-correlate-metadata with -h option fail >> ----------TEST communities_api mg-correlate-metadata with --help option >> fail >> >> root@t1:~/msneddon-work/2013doctests/testing/script-tests# >> mg-correlate-metadata -h >> Traceback (most recent call last): >> File >> "/kbase/deployments/20140109-prod//pybin/mg-correlate-metadata.py", line 9, >> in <module> >> from scipy import stats >> ImportError: No module named scipy >> >> root@t1:~/msneddon-work/2013doctests/testing/script-tests# >> mg-inbox-decompress -h >> Global symbol "$input" requires explicit package name at >> /kbase/deployments/20140109-prod//plbin/mg-inbox-decompress.pl line 61. >> Execution of /kbase/deployments/20140109-prod//plbin/ >> mg-inbox-decompress.pl aborted due to compilation errors. >> > >

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Re: [Release-team] broken java install in test environment
by Shane Canon 06 Feb '14

06 Feb '14

Dan, I think the boot strap is doing this… root@t1:/kbase/runtimes/bootstrap# grep ln kb_java_runtime/java_build.sh |grep bin ln -s $target/jdk1.7.0_45/bin/* $target/bin/ ln -s $target/ant/bin/ant $target/bin/ant Does this match what you were seeing? --Shane On Feb 6, 2014, at 10:50 AM, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: > what host? > > was this the runtime mount in test? > > > On Feb 6, 2014, at 10:00 AM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov> > wrote: > >> The same for ant. >> >> >> ---- >> Daniel Murphy-Olson >> Systems Administrator >> Mathematics & Computer Science Division >> Argonne National Laboratory >> 630-252-0055 >> >> ________________________________________ >> From: release-team-bounces(a)lists.kbase.us [release-team-bounces(a)lists.kbase.us] on behalf of Murphy-Olson, Daniel E. [dolson(a)mcs.anl.gov] >> Sent: Thursday, February 06, 2014 9:59 AM >> To: release-team(a)kbase.us >> Subject: [Release-team] broken java install in test environment >> >> Hi all, >> >> Somehow the runtime/java/bin directory was copied into the runtime/bin directory. >> >> Please don't do this, as it causes java to completely break. >> >> ---- >> 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 >> _______________________________________________ >> 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] broken java install in test environment
by Brettin, Thomas S. 06 Feb '14

06 Feb '14

what host? was this the runtime mount in test? On Feb 6, 2014, at 10:00 AM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov> wrote: > The same for ant. > > > ---- > Daniel Murphy-Olson > Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > > ________________________________________ > From: release-team-bounces(a)lists.kbase.us [release-team-bounces(a)lists.kbase.us] on behalf of Murphy-Olson, Daniel E. [dolson(a)mcs.anl.gov] > Sent: Thursday, February 06, 2014 9:59 AM > To: release-team(a)kbase.us > Subject: [Release-team] broken java install in test environment > > Hi all, > > Somehow the runtime/java/bin directory was copied into the runtime/bin directory. > > Please don't do this, as it causes java to completely break. > > ---- > 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 > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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FW: Testing of gene conservation
by Land, Miriam L. 06 Feb '14

06 Feb '14

Tom, Here is a test of our resolve. The gene_conservation service will not have unit tests because they carried over the tests from a previous module (interlog_projection). We could attempt black-box testing and see if we get it done in time. Miriam From: <Yoo>, Shinjae Yoo <sjyoo(a)bnl.gov<mailto:[email protected]>> Date: Thursday, February 6, 2014 1:07 PM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>> Cc: Gang Fang <fang.fg(a)gmail.com<mailto:[email protected]>> Subject: Re: Testing of gene conservation Oh Miriam, The test scripts are not for gene_conservation service… I don’t think I committed my test script… but it failed… and thus I haen’t committed them yet… I got more works for narrative today and tomorrow… So, I guess I don’t have enough time to work on this… Sorry :-( Thanks, -SJ On Feb 6, 2014, at 11:41 AM, Land, Miriam L. <landml(a)ornl.gov<mailto:[email protected]>> wrote: Gang, I'm testing the gene_conservation module and it starts out fine and then runs into this problem: ------------------------ ./test_start_service starting test gene_conservation service. gene_conservation service is listening on port 9999. perl t/client-tests/basic_tests.t 1..16 ok 1 - Did an object get defined OBJECT: Bio::KBase::interlog_projection::Client=HASH(0x254d290) ok 2 - 'Is it in the right class' isa 'Bio::KBase::interlog_projection::Client' ok 3 - Bio::KBase::interlog_projection::Client->can(...) Error invoking method project_network_with_custom_methods HTTP status: 500 Internal Server Error Function invoked: project_network_with_custom_methods Trace begun at lib/Bio/KBase/interlog_projection/Client.pm line 144 Bio::KBase::interlog_projection::Client::project_network_with_custom_methods('Bio::KBase::interlog_projection::Client=HASH(0x254d290)', 'HASH(0x25d27c8)', 'kb|g.3907', 'any', 0.001) called at t/client-tests/basic_tests.t line 43 eval {...} at t/client-tests/basic_tests.t line 42 not ok 4 - project_network_with_custom_methods # Failed test 'project_network_with_custom_methods' # at t/client-tests/basic_tests.t line 46. ---------------------------- Does something need to be started or configured? It looks like it is trying to invoke the interlog_projection module. Miriam

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Re: [Release-team] Status of some services
by Land, Miriam L. 06 Feb '14

06 Feb '14

Excellent! I'll get started. Miriam From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]>> Date: Thursday, February 6, 2014 11:07 AM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: RE: [Release-team] Status of some services I was able to deploy everything that was outstanding in the spreadsheet to test. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]>] Sent: Thursday, February 06, 2014 9:58 AM To: Murphy-Olson, Daniel E.; Nomi Harris; release-team(a)kbase.us<mailto:[email protected]> Subject: Re: [Release-team] Status of some services I think the change to the deployment process also made it difficult for you to rope in more help as we watched the list of last-minute modules grow last week. Let me know if there is anything I can do to help. Miriam From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected]>> Date: Thursday, February 6, 2014 10:47 AM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>> Subject: RE: [Release-team] Status of some services With only Shane and I working on deployments, we're very resource constrained. I'm going to pause my work on production, and circle back to test. I've already marked 2 out of 6 ready. In the future, we will definitely need more resources for these major pushes, particularly as we've expanded the number of services, and the changes to backend data stores. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]>] Sent: Thursday, February 06, 2014 9:26 AM To: Murphy-Olson, Daniel E.; Nomi Harris; release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]> Subject: Re: [Release-team] Status of some services We had a deadline of Monday 8am for people of get their final code checked in and a deadline of Tues. 8am for the stragglers. Who is deploying the new code to the test VM so I can get it tested? Miriam From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Date: Thursday, February 6, 2014 10:05 AM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Subject: RE: [Release-team] Status of some services I've been primarily working on production. Here is the updated status from Miriam's update. Modules ready for production deployment I'm still working on these * CBD - (Mike Mundy)- will need black box testing at some point * Handle Service (on t6) - internal service - will need black box testing at some point * Interlog projection - will need black box testing at some point * m5nr - (Andreas and Travis) - also will need black box testing at some point These are clients only, and will be deployed into iris (hopefully this morning!) * Communities API – passed tests except for two that need to be withdrawn (Andreas and Travis) * Genotyping Service These are deployed * Authentication and Authorization Client * Workspace_deluxe – * Awe Service – internal service * Shock Service – internal service I have been working with FBA Modeling in test. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]> [release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>] on behalf of Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>] Sent: Thursday, February 06, 2014 8:55 AM To: Nomi Harris; release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]> Subject: Re: [Release-team] Status of some services All, Did anything get deployed to test yesterday? I don't see any changes in the spreadsheet. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Date: Thursday, February 6, 2014 2:57 AM To: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Subject: [Release-team] Status of some services Someone was going to ask Andreas whether the Communities QC service has been fixed. Did anyone ask? I'm still unsure about whether the following new services should be added to the Services web page: Bambi (did it get deployed?) cMonkey Expression Inferelator MEME I found out that MAK is internal (for now, anyway)--it was used to create some datasets but is not publicly accessible, so it doesn't need to be added to the Services page. That might also be true of cMonkey and possibly some of the other services I listed. Thanks, Nomi _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] Status of some services
by Shane Canon 06 Feb '14

06 Feb '14

Thanks Dan. I'm BARTing in now and can help out shortly. Perhaps you and I could have a quick sync up call. Shane Sent from my iPhone > On Feb 6, 2014, at 8:07 AM, "Murphy-Olson, Daniel E." <dolson(a)mcs.anl.gov> wrote: > > I was able to deploy everything that was outstanding in the spreadsheet to test. > > > ---- > Daniel Murphy-Olson > Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > > ________________________________________ > From: Land, Miriam L. [landml(a)ornl.gov] > Sent: Thursday, February 06, 2014 9:58 AM > To: Murphy-Olson, Daniel E.; Nomi Harris; release-team(a)kbase.us > Subject: Re: [Release-team] Status of some services > > I think the change to the deployment process also made it difficult for you to rope in more help as we watched the list of last-minute modules grow last week. Let me know if there is anything I can do to help. > > Miriam > > From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]>> > Date: Thursday, February 6, 2014 10:47 AM > To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> > Subject: RE: [Release-team] Status of some services > > With only Shane and I working on deployments, we're very resource constrained. > > I'm going to pause my work on production, and circle back to test. I've already marked 2 out of 6 ready. > > In the future, we will definitely need more resources for these major pushes, particularly as we've expanded the number of services, and the changes to backend data stores. > > ---- > Daniel Murphy-Olson > Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > > ________________________________________ > From: Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]>] > Sent: Thursday, February 06, 2014 9:26 AM > To: Murphy-Olson, Daniel E.; Nomi Harris; release-team(a)kbase.us<mailto:[email protected]> > Subject: Re: [Release-team] Status of some services > > We had a deadline of Monday 8am for people of get their final code checked in and a deadline of Tues. 8am for the stragglers. Who is deploying the new code to the test VM so I can get it tested? > > Miriam > > From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected]>> > Date: Thursday, February 6, 2014 10:05 AM > To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>> > Subject: RE: [Release-team] Status of some services > > I've been primarily working on production. > > Here is the updated status from Miriam's update. > > Modules ready for production deployment > I'm still working on these > * CBD - (Mike Mundy)- will need black box testing at some point > * Handle Service (on t6) - internal service - will need black box testing at some point > * Interlog projection - will need black box testing at some point > * m5nr - (Andreas and Travis) - also will need black box testing at some point > > These are clients only, and will be deployed into iris (hopefully this morning!) > * Communities API – passed tests except for two that need to be withdrawn (Andreas and Travis) > * Genotyping Service > > These are deployed > * Authentication and Authorization Client > * Workspace_deluxe – > * Awe Service – internal service > * Shock Service – internal service > > I have been working with FBA Modeling in test. > > ---- > Daniel Murphy-Olson > Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > > ________________________________________ > From: release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]> [release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]>] on behalf of Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]>] > Sent: Thursday, February 06, 2014 8:55 AM > To: Nomi Harris; release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]> > Subject: Re: [Release-team] Status of some services > > All, > > Did anything get deployed to test yesterday? I don't see any changes in the spreadsheet. > > Miriam > > From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> > Date: Thursday, February 6, 2014 2:57 AM > To: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> > Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> > Subject: [Release-team] Status of some services > > Someone was going to ask Andreas whether the Communities QC service has been fixed. Did anyone ask? > > I'm still unsure about whether the following new services should be added to the Services web page: > Bambi (did it get deployed?) > cMonkey > Expression > Inferelator > MEME > > I found out that MAK is internal (for now, anyway)--it was used to create some datasets but is not publicly accessible, so it doesn't need to be added to the Services page. That might also be true of cMonkey and possibly some of the other services I listed. > > Thanks, > Nomi > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]> > 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] Status of some services
by Murphy-Olson, Daniel E. 06 Feb '14

06 Feb '14

I was able to deploy everything that was outstanding in the spreadsheet to test. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: Land, Miriam L. [landml(a)ornl.gov] Sent: Thursday, February 06, 2014 9:58 AM To: Murphy-Olson, Daniel E.; Nomi Harris; release-team(a)kbase.us Subject: Re: [Release-team] Status of some services I think the change to the deployment process also made it difficult for you to rope in more help as we watched the list of last-minute modules grow last week. Let me know if there is anything I can do to help. Miriam From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]>> Date: Thursday, February 6, 2014 10:47 AM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: RE: [Release-team] Status of some services With only Shane and I working on deployments, we're very resource constrained. I'm going to pause my work on production, and circle back to test. I've already marked 2 out of 6 ready. In the future, we will definitely need more resources for these major pushes, particularly as we've expanded the number of services, and the changes to backend data stores. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]>] Sent: Thursday, February 06, 2014 9:26 AM To: Murphy-Olson, Daniel E.; Nomi Harris; release-team(a)kbase.us<mailto:[email protected]> Subject: Re: [Release-team] Status of some services We had a deadline of Monday 8am for people of get their final code checked in and a deadline of Tues. 8am for the stragglers. Who is deploying the new code to the test VM so I can get it tested? Miriam From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected]>> Date: Thursday, February 6, 2014 10:05 AM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>> Subject: RE: [Release-team] Status of some services I've been primarily working on production. Here is the updated status from Miriam's update. Modules ready for production deployment I'm still working on these * CBD - (Mike Mundy)- will need black box testing at some point * Handle Service (on t6) - internal service - will need black box testing at some point * Interlog projection - will need black box testing at some point * m5nr - (Andreas and Travis) - also will need black box testing at some point These are clients only, and will be deployed into iris (hopefully this morning!) * Communities API – passed tests except for two that need to be withdrawn (Andreas and Travis) * Genotyping Service These are deployed * Authentication and Authorization Client * Workspace_deluxe – * Awe Service – internal service * Shock Service – internal service I have been working with FBA Modeling in test. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]> [release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]>] on behalf of Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]>] Sent: Thursday, February 06, 2014 8:55 AM To: Nomi Harris; release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]> Subject: Re: [Release-team] Status of some services All, Did anything get deployed to test yesterday? I don't see any changes in the spreadsheet. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Date: Thursday, February 6, 2014 2:57 AM To: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Subject: [Release-team] Status of some services Someone was going to ask Andreas whether the Communities QC service has been fixed. Did anyone ask? I'm still unsure about whether the following new services should be added to the Services web page: Bambi (did it get deployed?) cMonkey Expression Inferelator MEME I found out that MAK is internal (for now, anyway)--it was used to create some datasets but is not publicly accessible, so it doesn't need to be added to the Services page. That might also be true of cMonkey and possibly some of the other services I listed. Thanks, Nomi _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

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Re: [Release-team] broken java install in test environment
by Murphy-Olson, Daniel E. 06 Feb '14

06 Feb '14

The same for ant. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: release-team-bounces(a)lists.kbase.us [release-team-bounces(a)lists.kbase.us] on behalf of Murphy-Olson, Daniel E. [dolson(a)mcs.anl.gov] Sent: Thursday, February 06, 2014 9:59 AM To: release-team(a)kbase.us Subject: [Release-team] broken java install in test environment Hi all, Somehow the runtime/java/bin directory was copied into the runtime/bin directory. Please don't do this, as it causes java to completely break. ---- 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

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broken java install in test environment
by Murphy-Olson, Daniel E. 06 Feb '14

06 Feb '14

Hi all, Somehow the runtime/java/bin directory was copied into the runtime/bin directory. Please don't do this, as it causes java to completely break. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

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Re: [Release-team] Status of some services
by Land, Miriam L. 06 Feb '14

06 Feb '14

I think the change to the deployment process also made it difficult for you to rope in more help as we watched the list of last-minute modules grow last week. Let me know if there is anything I can do to help. Miriam From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]>> Date: Thursday, February 6, 2014 10:47 AM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: RE: [Release-team] Status of some services With only Shane and I working on deployments, we're very resource constrained. I'm going to pause my work on production, and circle back to test. I've already marked 2 out of 6 ready. In the future, we will definitely need more resources for these major pushes, particularly as we've expanded the number of services, and the changes to backend data stores. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]>] Sent: Thursday, February 06, 2014 9:26 AM To: Murphy-Olson, Daniel E.; Nomi Harris; release-team(a)kbase.us<mailto:[email protected]> Subject: Re: [Release-team] Status of some services We had a deadline of Monday 8am for people of get their final code checked in and a deadline of Tues. 8am for the stragglers. Who is deploying the new code to the test VM so I can get it tested? Miriam From: <Murphy-Olson>, Dan Olson <dolson(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected]>> Date: Thursday, February 6, 2014 10:05 AM To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]>>, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]>> Subject: RE: [Release-team] Status of some services I've been primarily working on production. Here is the updated status from Miriam's update. Modules ready for production deployment I'm still working on these * CBD - (Mike Mundy)- will need black box testing at some point * Handle Service (on t6) - internal service - will need black box testing at some point * Interlog projection - will need black box testing at some point * m5nr - (Andreas and Travis) - also will need black box testing at some point These are clients only, and will be deployed into iris (hopefully this morning!) * Communities API – passed tests except for two that need to be withdrawn (Andreas and Travis) * Genotyping Service These are deployed * Authentication and Authorization Client * Workspace_deluxe – * Awe Service – internal service * Shock Service – internal service I have been working with FBA Modeling in test. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ________________________________________ From: release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]> [release-team-bounces(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]>] on behalf of Land, Miriam L. [landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]>] Sent: Thursday, February 06, 2014 8:55 AM To: Nomi Harris; release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]> Subject: Re: [Release-team] Status of some services All, Did anything get deployed to test yesterday? I don't see any changes in the spreadsheet. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Date: Thursday, February 6, 2014 2:57 AM To: "release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Subject: [Release-team] Status of some services Someone was going to ask Andreas whether the Communities QC service has been fixed. Did anyone ask? I'm still unsure about whether the following new services should be added to the Services web page: Bambi (did it get deployed?) cMonkey Expression Inferelator MEME I found out that MAK is internal (for now, anyway)--it was used to create some datasets but is not publicly accessible, so it doesn't need to be added to the Services page. That might also be true of cMonkey and possibly some of the other services I listed. Thanks, Nomi _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]><mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

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