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

Re: [Release-team] When will IRIS be updated?
by Dan Olson 25 Sep '13

25 Sep '13

This is the deploy.cfg service list from invocation: deploy-client = ontology_service, communities_api, communities_qc, trees, networks, genome_annotation, invocation, kb_seed, kbapi_common, sim_service, typecomp, idserver, genotype_phenotype_api, KBaseFBAModeling, workspace_service, phispy, plant_expression_service, translation, assembly deploy-service = invocation, genome_annotation, phispy deploy-master = auth The IRIS candidate column is not populated in the release spreadsheet, so I'm not sure what I should compare this list to. Maybe Tom or Nomi have an idea of all the services that should be present in Iris? ----- Original Message ----- > From: "Shane Canon" <scanon(a)lbl.gov> > To: "Dan Olson" <dolson(a)mcs.anl.gov> > Cc: release-team(a)kbase.us > Sent: Wednesday, September 25, 2013 10:28:33 AM > Subject: Re: [Release-team] When will IRIS be updated? > > > Are there any other new ones that we overlooked? > > --Shane > > On Sep 25, 2013, at 6:19 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > > > I think this didn't get deployed onto the production, or test iris > > instances because it > > didn't make it into the deploy.cfg file for either of them, it also > > didn't make it into > > the config file for the VM. > > > > It looks like we're still ironing out the details of adding modules > > to our process. > > > > I'll get this one into the config file, and I can attempt to deploy > > onto production. > > > > Jim, can you document what is needed to deploy an additional module > > onto a running IRIS > > deployment? For example, what command is needed to rebuild the > > whitelist, and if a new > > js client build is needed..etc. > > > > ----- Original Message ----- > >> From: "Miriam L. Land" <landml(a)ornl.gov> > >> To: "Thomas Brettin" <brettin(a)mcs.anl.gov> > >> Cc: "James Thomason" <thomason(a)cshl.edu>, release-team(a)kbase.us, > >> "Nomi Harris" <nlharris(a)lbl.gov> > >> Sent: Wednesday, September 25, 2013 6:45:03 AM > >> Subject: Re: [Release-team] When will IRIS be updated? > >> > >> Yes. > >> > >> On 9/25/13 7:43 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: > >> > >>> Did Functional Ortholog make it through the Aug Build? > >>> > >>> > >>> On Sep 25, 2013, at 6:42 AM, "Land, Miriam L." <landml(a)ornl.gov> > >>> wrote: > >>> > >>>> Invocation is one of the modules in the current mini build. > >>>> > >>>> Miriam > >>>> > >>>> On 9/25/13 12:38 AM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: > >>>> > >>>>> Dear Release Team, > >>>>> > >>>>> I just checked IRIS to see if the one (!?) script for > >>>>> Functional > >>>>> Ortholog > >>>>> Predictor was there, and it was not. I don't see any way to see > >>>>> when > >>>>> IRIS > >>>>> was last updated. (I filed a new JIRA ticket about this.) > >>>>> > >>>>> Does anyone know when IRIS will be updated? Is this something > >>>>> that has > >>>>> to > >>>>> be done manually? > >>>>> > >>>>> When IRIS is updated, will the FOP script, fop-rank-pgene.pl, > >>>>> then be > >>>>> accessible from IRIS? It should be, right? > >>>>> > >>>>> I am asking because the updated Services page (which includes > >>>>> the > >>>>> new > >>>>> service, Functional Ortholog Predictor) is basically ready to > >>>>> push to > >>>>> the > >>>>> public site but I don't want to push it out until the release > >>>>> is > >>>>> complete. > >>>>> > >>>>> 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 > >>> > >> > >> _______________________________________________ > >> 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 > >

1 0

Re: [Release-team] release process stuck on cbd
by Dan Olson 25 Sep '13

25 Sep '13

I would recommend that Shane work on this. The reason cdmi can contact production is because it is talking to the database directly, not the api which the kbase.us name resolves to. I'm of the opinion that the test environment should be self contained, and developers should identify the necessary datasets that need to be in the test environment for their code to pass testing there. To move forward on the cbd service we should identify the necessary datasets, and load them into the test shock instance. Not the local cbd instance, but the shock VM in the test environment. ----- Original Message ----- > From: "Thomas Brettin" <brettin(a)mcs.anl.gov> > To: "Dan Olson" <dolson(a)mcs.anl.gov>, sysadmins(a)kbase.us > Cc: release-team(a)kbase.us > Sent: Wednesday, September 25, 2013 10:12:34 AM > Subject: Re: [Release-team] release process stuck on cbd > > The curl on the test head node doesn't work. > > I can't get to the bcd test host cause it's not in the etc/hosts > file. > > Dan, please assign a sysadmin assigned to this module so we can get > it done today and let me know who that is. > > > > We should not take the position that the cbd module can not contact > the production shock service for read only access. > > brettin@t13:/$ source /kb/deployment/user-env.sh > brettin@t13:/$ all_entities_Genome | wc > 6321 6321 63505 > > > > t1:~> curl http://140.221.43.50/services/shock-api > > <html> > <head><title>502 Bad Gateway</title></head> > <body bgcolor="white"> > <center><h1>502 Bad Gateway</h1></center> > <hr><center>nginx/1.0.5</center> > </body> > </html> > > > > > On Sep 25, 2013, at 10:04 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > > > I'm not sure, you could try entering the ip address for production > > 140.221.43.50 into the > > deployment configuration. > > > > ----- Original Message ----- > >> From: "Thomas Brettin" <brettin(a)mcs.anl.gov> > >> To: "Dan Olson" <dolson(a)mcs.anl.gov> > >> Cc: release-team(a)kbase.us > >> Sent: Wednesday, September 25, 2013 10:01:56 AM > >> Subject: Re: [Release-team] release process stuck on cbd > >> > >> can we give them an IP address? > >> > >> > >> On Sep 25, 2013, at 10:01 AM, Dan Olson <dolson(a)mcs.anl.gov> > >> wrote: > >> > >>> kbase.us doesn't make it out of the test environment. It is > >>> redirected based on the host name. > >>> There is no easy way around this. > >>> > >>> If they have data that is necessary to build in the production > >>> shock - they will > >>> need to load this data into the test shock. > >>> > >>> ----- Original Message ----- > >>>> From: "Thomas Brettin" <brettin(a)mcs.anl.gov> > >>>> To: release-team(a)kbase.us > >>>> Sent: Wednesday, September 25, 2013 9:55:16 AM > >>>> Subject: [Release-team] release process stuck on cbd > >>>> > >>>> This is in the deploy team hands. It appears that a connection > >>>> to > >>>> kbase.us/services/shock-api/node is failing because. > >>>> > >>>> Network controls needs to be investigated. > >>>> > >>>> Can we get this one unstuck? > >>>> > >>>> Thanks, > >>>> Tom > >>>> _______________________________________________ > >>>> Release-team mailing list > >>>> Release-team(a)lists.kbase.us > >>>> https://lists.kbase.us/mailman/listinfo/release-team > >>>> > >> > >> > >

1 0

Re: [Release-team] When will IRIS be updated?
by Shane Canon 25 Sep '13

25 Sep '13

Are there any other new ones that we overlooked? --Shane On Sep 25, 2013, at 6:19 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > I think this didn't get deployed onto the production, or test iris instances because it > didn't make it into the deploy.cfg file for either of them, it also didn't make it into > the config file for the VM. > > It looks like we're still ironing out the details of adding modules to our process. > > I'll get this one into the config file, and I can attempt to deploy onto production. > > Jim, can you document what is needed to deploy an additional module onto a running IRIS > deployment? For example, what command is needed to rebuild the whitelist, and if a new > js client build is needed..etc. > > ----- Original Message ----- >> From: "Miriam L. Land" <landml(a)ornl.gov> >> To: "Thomas Brettin" <brettin(a)mcs.anl.gov> >> Cc: "James Thomason" <thomason(a)cshl.edu>, release-team(a)kbase.us, "Nomi Harris" <nlharris(a)lbl.gov> >> Sent: Wednesday, September 25, 2013 6:45:03 AM >> Subject: Re: [Release-team] When will IRIS be updated? >> >> Yes. >> >> On 9/25/13 7:43 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >> >>> Did Functional Ortholog make it through the Aug Build? >>> >>> >>> On Sep 25, 2013, at 6:42 AM, "Land, Miriam L." <landml(a)ornl.gov> >>> wrote: >>> >>>> Invocation is one of the modules in the current mini build. >>>> >>>> Miriam >>>> >>>> On 9/25/13 12:38 AM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: >>>> >>>>> Dear Release Team, >>>>> >>>>> I just checked IRIS to see if the one (!?) script for Functional >>>>> Ortholog >>>>> Predictor was there, and it was not. I don't see any way to see >>>>> when >>>>> IRIS >>>>> was last updated. (I filed a new JIRA ticket about this.) >>>>> >>>>> Does anyone know when IRIS will be updated? Is this something >>>>> that has >>>>> to >>>>> be done manually? >>>>> >>>>> When IRIS is updated, will the FOP script, fop-rank-pgene.pl, >>>>> then be >>>>> accessible from IRIS? It should be, right? >>>>> >>>>> I am asking because the updated Services page (which includes the >>>>> new >>>>> service, Functional Ortholog Predictor) is basically ready to >>>>> push to >>>>> the >>>>> public site but I don't want to push it out until the release is >>>>> complete. >>>>> >>>>> 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 >>> >> >> _______________________________________________ >> 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

1 0

Re: [Release-team] release process stuck on cbd
by Thomas Brettin 25 Sep '13

25 Sep '13

The curl on the test head node doesn't work. I can't get to the bcd test host cause it's not in the etc/hosts file. Dan, please assign a sysadmin assigned to this module so we can get it done today and let me know who that is. We should not take the position that the cbd module can not contact the production shock service for read only access. brettin@t13:/$ source /kb/deployment/user-env.sh brettin@t13:/$ all_entities_Genome | wc 6321 6321 63505 t1:~> curl http://140.221.43.50/services/shock-api <html> <head><title>502 Bad Gateway</title></head> <body bgcolor="white"> <center><h1>502 Bad Gateway</h1></center> <hr><center>nginx/1.0.5</center> </body> </html> On Sep 25, 2013, at 10:04 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > I'm not sure, you could try entering the ip address for production 140.221.43.50 into the > deployment configuration. > > ----- Original Message ----- >> From: "Thomas Brettin" <brettin(a)mcs.anl.gov> >> To: "Dan Olson" <dolson(a)mcs.anl.gov> >> Cc: release-team(a)kbase.us >> Sent: Wednesday, September 25, 2013 10:01:56 AM >> Subject: Re: [Release-team] release process stuck on cbd >> >> can we give them an IP address? >> >> >> On Sep 25, 2013, at 10:01 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: >> >>> kbase.us doesn't make it out of the test environment. It is >>> redirected based on the host name. >>> There is no easy way around this. >>> >>> If they have data that is necessary to build in the production >>> shock - they will >>> need to load this data into the test shock. >>> >>> ----- Original Message ----- >>>> From: "Thomas Brettin" <brettin(a)mcs.anl.gov> >>>> To: release-team(a)kbase.us >>>> Sent: Wednesday, September 25, 2013 9:55:16 AM >>>> Subject: [Release-team] release process stuck on cbd >>>> >>>> This is in the deploy team hands. It appears that a connection to >>>> kbase.us/services/shock-api/node is failing because. >>>> >>>> Network controls needs to be investigated. >>>> >>>> Can we get this one unstuck? >>>> >>>> Thanks, >>>> Tom >>>> _______________________________________________ >>>> Release-team mailing list >>>> Release-team(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/release-team >>>> >> >>

1 0

Re: [Release-team] release process stuck on cbd
by Dan Olson 25 Sep '13

25 Sep '13

I'm not sure, you could try entering the ip address for production 140.221.43.50 into the deployment configuration. ----- Original Message ----- > From: "Thomas Brettin" <brettin(a)mcs.anl.gov> > To: "Dan Olson" <dolson(a)mcs.anl.gov> > Cc: release-team(a)kbase.us > Sent: Wednesday, September 25, 2013 10:01:56 AM > Subject: Re: [Release-team] release process stuck on cbd > > can we give them an IP address? > > > On Sep 25, 2013, at 10:01 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > > > kbase.us doesn't make it out of the test environment. It is > > redirected based on the host name. > > There is no easy way around this. > > > > If they have data that is necessary to build in the production > > shock - they will > > need to load this data into the test shock. > > > > ----- Original Message ----- > >> From: "Thomas Brettin" <brettin(a)mcs.anl.gov> > >> To: release-team(a)kbase.us > >> Sent: Wednesday, September 25, 2013 9:55:16 AM > >> Subject: [Release-team] release process stuck on cbd > >> > >> This is in the deploy team hands. It appears that a connection to > >> kbase.us/services/shock-api/node is failing because. > >> > >> Network controls needs to be investigated. > >> > >> Can we get this one unstuck? > >> > >> Thanks, > >> Tom > >> _______________________________________________ > >> Release-team mailing list > >> Release-team(a)lists.kbase.us > >> https://lists.kbase.us/mailman/listinfo/release-team > >> > >

1 0

Re: [Release-team] release process stuck on cbd
by Thomas Brettin 25 Sep '13

25 Sep '13

can we give them an IP address? On Sep 25, 2013, at 10:01 AM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > kbase.us doesn't make it out of the test environment. It is redirected based on the host name. > There is no easy way around this. > > If they have data that is necessary to build in the production shock - they will > need to load this data into the test shock. > > ----- Original Message ----- >> From: "Thomas Brettin" <brettin(a)mcs.anl.gov> >> To: release-team(a)kbase.us >> Sent: Wednesday, September 25, 2013 9:55:16 AM >> Subject: [Release-team] release process stuck on cbd >> >> This is in the deploy team hands. It appears that a connection to >> kbase.us/services/shock-api/node is failing because. >> >> Network controls needs to be investigated. >> >> Can we get this one unstuck? >> >> Thanks, >> Tom >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team >>

1 0

Re: [Release-team] release process stuck on cbd
by Dan Olson 25 Sep '13

25 Sep '13

kbase.us doesn't make it out of the test environment. It is redirected based on the host name. There is no easy way around this. If they have data that is necessary to build in the production shock - they will need to load this data into the test shock. ----- Original Message ----- > From: "Thomas Brettin" <brettin(a)mcs.anl.gov> > To: release-team(a)kbase.us > Sent: Wednesday, September 25, 2013 9:55:16 AM > Subject: [Release-team] release process stuck on cbd > > This is in the deploy team hands. It appears that a connection to > kbase.us/services/shock-api/node is failing because. > > Network controls needs to be investigated. > > Can we get this one unstuck? > > Thanks, > Tom > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team >

1 0

release process stuck on cbd
by Thomas Brettin 25 Sep '13

25 Sep '13

This is in the deploy team hands. It appears that a connection to kbase.us/services/shock-api/node is failing because. Network controls needs to be investigated. Can we get this one unstuck? Thanks, Tom

1 0

Re: [Release-team] When will IRIS be updated?
by Dan Olson 25 Sep '13

25 Sep '13

I think this didn't get deployed onto the production, or test iris instances because it didn't make it into the deploy.cfg file for either of them, it also didn't make it into the config file for the VM. It looks like we're still ironing out the details of adding modules to our process. I'll get this one into the config file, and I can attempt to deploy onto production. Jim, can you document what is needed to deploy an additional module onto a running IRIS deployment? For example, what command is needed to rebuild the whitelist, and if a new js client build is needed..etc. ----- Original Message ----- > From: "Miriam L. Land" <landml(a)ornl.gov> > To: "Thomas Brettin" <brettin(a)mcs.anl.gov> > Cc: "James Thomason" <thomason(a)cshl.edu>, release-team(a)kbase.us, "Nomi Harris" <nlharris(a)lbl.gov> > Sent: Wednesday, September 25, 2013 6:45:03 AM > Subject: Re: [Release-team] When will IRIS be updated? > > Yes. > > On 9/25/13 7:43 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: > > >Did Functional Ortholog make it through the Aug Build? > > > > > >On Sep 25, 2013, at 6:42 AM, "Land, Miriam L." <landml(a)ornl.gov> > >wrote: > > > >> Invocation is one of the modules in the current mini build. > >> > >> Miriam > >> > >> On 9/25/13 12:38 AM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: > >> > >>> Dear Release Team, > >>> > >>> I just checked IRIS to see if the one (!?) script for Functional > >>>Ortholog > >>> Predictor was there, and it was not. I don't see any way to see > >>> when > >>>IRIS > >>> was last updated. (I filed a new JIRA ticket about this.) > >>> > >>> Does anyone know when IRIS will be updated? Is this something > >>> that has > >>>to > >>> be done manually? > >>> > >>> When IRIS is updated, will the FOP script, fop-rank-pgene.pl, > >>> then be > >>> accessible from IRIS? It should be, right? > >>> > >>> I am asking because the updated Services page (which includes the > >>> new > >>> service, Functional Ortholog Predictor) is basically ready to > >>> push to > >>>the > >>> public site but I don't want to push it out until the release is > >>>complete. > >>> > >>> 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 > > > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team >

1 0

Re: [Release-team] When will IRIS be updated?
by Land, Miriam L. 25 Sep '13

25 Sep '13

Yes. On 9/25/13 7:43 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >Did Functional Ortholog make it through the Aug Build? > > >On Sep 25, 2013, at 6:42 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > >> Invocation is one of the modules in the current mini build. >> >> Miriam >> >> On 9/25/13 12:38 AM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: >> >>> Dear Release Team, >>> >>> I just checked IRIS to see if the one (!?) script for Functional >>>Ortholog >>> Predictor was there, and it was not. I don't see any way to see when >>>IRIS >>> was last updated. (I filed a new JIRA ticket about this.) >>> >>> Does anyone know when IRIS will be updated? Is this something that has >>>to >>> be done manually? >>> >>> When IRIS is updated, will the FOP script, fop-rank-pgene.pl, then be >>> accessible from IRIS? It should be, right? >>> >>> I am asking because the updated Services page (which includes the new >>> service, Functional Ortholog Predictor) is basically ready to push to >>>the >>> public site but I don't want to push it out until the release is >>>complete. >>> >>> 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 >

1 0