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

Re: [Release-team] genome annotation release
by Olson, Robert D. 20 Mar '14

20 Mar '14

Thanks - if you want to look at a running system the instance on 140.221.85.61 is running the current version of the services ________________________________ From: Murphy-Olson, Daniel E. Sent: Thursday, March 20, 2014 5:25 PM To: Olson, Robert D.; release-team(a)kbase.us Subject: RE: [Release-team] genome annotation release The version that was deployed is git ref 59906b0fc95caa079d9f0092be465fd42331564e, tag 20140224-prod I'm looking into the data problem now. ---- Daniel Murphy-Olson Sr. Systems Administrator Computing, Environment and Life Sciences Argonne National Laboratory 630-252-0055<callto:630-252-0055> ________________________________ 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, March 20, 2014 1:00 PM To: release-team(a)kbase.us Subject: [Release-team] genome annotation release Hi - it looks like the new genome annotation release was deployed, but without the data perhaps? >/ rast2-annotate-proteins-kmer-v2 < g.anno > glv2 Return code from rast2-annotate-proteins-kmer-v2: 255JSONRPC error: Error running kmer_search: kmer_search -a -g 200 -m 5 -d /kbase/deployments/20140109-prod/services/genome_annotation/data JSONRPC error code: -32603 JSONRPC error data:Error running kmer_search: kmer_search -a -g 200 -m 5 -d /kbase/deployments/20140109-prod/services/genome_annotation/data It also looks like the frontend is not running the up to date version either: >/ rast2-annotate-proteins-kmer-v1 < g.anno > glv2 rast2-annotate-proteins-kmer-v1: invalid command What version was it that got deployed?

1 0

Re: [Release-team] genome annotation release
by Murphy-Olson, Daniel E. 20 Mar '14

20 Mar '14

The version that was deployed is git ref 59906b0fc95caa079d9f0092be465fd42331564e, tag 20140224-prod I'm looking into the data problem now. ---- Daniel Murphy-Olson Sr. Systems Administrator Computing, Environment and Life Sciences Argonne National Laboratory 630-252-0055<callto:630-252-0055> ________________________________ 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, March 20, 2014 1:00 PM To: release-team(a)kbase.us Subject: [Release-team] genome annotation release Hi - it looks like the new genome annotation release was deployed, but without the data perhaps? >/ rast2-annotate-proteins-kmer-v2 < g.anno > glv2 Return code from rast2-annotate-proteins-kmer-v2: 255JSONRPC error: Error running kmer_search: kmer_search -a -g 200 -m 5 -d /kbase/deployments/20140109-prod/services/genome_annotation/data JSONRPC error code: -32603 JSONRPC error data:Error running kmer_search: kmer_search -a -g 200 -m 5 -d /kbase/deployments/20140109-prod/services/genome_annotation/data It also looks like the frontend is not running the up to date version either: >/ rast2-annotate-proteins-kmer-v1 < g.anno > glv2 rast2-annotate-proteins-kmer-v1: invalid command What version was it that got deployed?

1 0

genome annotation release
by Robert Olson 20 Mar '14

20 Mar '14

Hi - it looks like the new genome annotation release was deployed, but without the data perhaps? >/ rast2-annotate-proteins-kmer-v2 < g.anno > glv2 Return code from rast2-annotate-proteins-kmer-v2: 255JSONRPC error: Error running kmer_search: kmer_search -a -g 200 -m 5 -d /kbase/deployments/20140109-prod/services/genome_annotation/data JSONRPC error code: -32603 JSONRPC error data:Error running kmer_search: kmer_search -a -g 200 -m 5 -d /kbase/deployments/20140109-prod/services/genome_annotation/data It also looks like the frontend is not running the up to date version either: >/ rast2-annotate-proteins-kmer-v1 < g.anno > glv2 rast2-annotate-proteins-kmer-v1: invalid command What version was it that got deployed?

1 0

Fwd: authorization in IRIS scripts
by Shane Canon 13 Mar '14

13 Mar '14

Another request. Gavin wants a redeploy of WS too. --Shane Begin forwarded message: > From: Alexey Kazakov <aekazakov(a)lbl.gov> > Subject: Re: authorization in IRIS scripts > Date: March 12, 2014 8:03:31 PM PDT > To: Shane Canon <scanon(a)lbl.gov> > Cc: Pavel Novichkov <PSNovichkov(a)lbl.gov> > > Hi Shane, > > I fixed scripts for cmonkey, inferelator and meme services. Could you please re-deploy them in IRIS? > > Thank you, > Alexey > > On 2/26/2014 10:16 PM, Shane Canon wrote: >> >> I'm not sure. Does it do this repeatedly? Dan is working through several issues with >> IRIS, but I don't know if any are related to this. The best thing may be to file a ticket in Jira so >> we can track it. >> >> --Shane >> >> On Feb 26, 2014, at 4:33 PM, Alexey Kazakov <aekazakov(a)lbl.gov> wrote: >> >>> Hi Shane, >>> >>> meme service scripts in IRIS return error "Failed to acquire token: >>> Failed to get auth token: Failed to query Globus Online: >>> 403 Forbidden at >>> /kbase/deployments/20140109-prod//lib/Bio/KBase/AuthToken.pm >>> line 574." >>> (for example: find_motifs_with_meme_from_ws >>> >>> --url=http://kbase.us/services/meme/ >>> --ws=AKtest --input="AKtest/mod_desulfovibrio" >>> --mod=oops --nmotifs=2 --minw=14 --maxw=28 >>> --user="aktest" --pw="1475rokegi") >>> The same command invoked from Linux command line works fine. How the error can be fixed? >>> >>> Thank you, >>> Alexey >> >

1 0

Re: [Release-team] Metagenomic Sequence QC service--is it working again?
by Land, Miriam L. 12 Mar '14

12 Mar '14

Feb. 24, in ticket KBASE-240, Andreas commented that "Scripts have been moved to pipeline repo. Reengineering service to target scalable workflow system." He also stated that it is still active and under development. I don't have an input file either. Miriam From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> Date: Wednesday, March 12, 2014 3:47 PM To: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: Re: [Release-team] Metagenomic Sequence QC service--is it working again? I heard no response to this. Time to follow up? Nomi On Mar 3, 2014, at 11:40 AM, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: Can someone update me on the status of the Metagenomic Sequence QC service? It is visible in IRIS, and I can run the commands with —help but I don’t have the right input files to test it more thoroughly. Miriam, could you do that? We had taken that service off the services page and taken down its tutorial (http://kbase.us/for-users/tutorials/analyzing-data/metagenome-analysis/sequ…) because the service wasn’t working. I need to know if those should be restored. Thanks, Nomi _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

1 0

Re: [Release-team] Metagenomic Sequence QC service--is it working again?
by Nomi Harris 12 Mar '14

12 Mar '14

I heard no response to this. Time to follow up? Nomi On Mar 3, 2014, at 11:40 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Can someone update me on the status of the Metagenomic Sequence QC service? It is visible in IRIS, and I can run the commands with —help but I don’t have the right input files to test it more thoroughly. Miriam, could you do that? > > We had taken that service off the services page and taken down its tutorial (http://kbase.us/for-users/tutorials/analyzing-data/metagenome-analysis/sequ…) because the service wasn’t working. I need to know if those should be restored. > > Thanks, > Nomi

1 0

Re: [Release-team] Defunct services
by Nomi Harris 12 Mar '14

12 Mar '14

Latest list of services that are presumed defunct: feature_selection (fizzy) file_type_service genotype_phenotype experiment prom_service regulation (regprecise) Any changes before we send the list to the devel team? Nomi On Feb 26, 2014, at 6:34 AM, Land, Miriam L. <landml(a)ornl.gov> wrote: > Nomi, > > Andreas has been working on JIRA tickets this week for communities_qc and feature_selection. He may not consider them defunct. > > Miriam > > From: Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> > Date: Tuesday, February 25, 2014 4:07 PM > To: Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> > Cc: "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> > Subject: Re: [Release-team] Defunct services > > Ok, thanks for checking. Sounds like ERDB is still needed. So the revised list of services that can go is: > feature_selection (fizzy) > file_type_service > genotype_phenotype > experiment > prom_service > communities_qc > regulation (regprecise) > > On Feb 25, 2014, at 12:54 PM, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> wrote: > > > So ERDB may still be needed by translation and trees. > > --Shane > > root@t1:/kbase/deployments/20140214-prod/dev_container/modules# grep -i erdb */DEP* > experiment/DEPENDENCIES:erdb_service > prom_service/DEPENDENCIES:erdb_service > translation/DEPENDENCIES:erdb_service > trees/DEPENDENCIES:erdb_service > > On Feb 25, 2014, at 12:09 PM, "Brettin, Thomas S." <brettin(a)anl.gov<mailto:[email protected]>> wrote: > > I think the list is accurate. The only exception might be ERDB service. A recursive grep might be needed for that one. > > Sent from my Verizon Wireless 4G LTE DROID > > > Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: > > Sure. We can follow up on it during tomorrow's devel call if needed. > > > On Tue, Feb 25, 2014 at 11:57 AM, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> wrote: > > This is very helpful. Should we notify the devel list as well? > > --Shane > > > On Feb 25, 2014, at 11:38 AM, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: > >> I believe the following services are not currently supported and can be shut down (if they haven’t been already): >> >> feature_selection (fizzy) >> file_type_services >> genotype_phenotype >> experiment >> prom_service >> communities_qc >> regulation (regprecise) >> erdb_service >> >> Ccing the release team in case they have any adjustments to that list. >> >> Nomi >> >> On Feb 24, 2014, at 5:54 PM, Shane Canon <scanon(a)lbl.gov<mailto:[email protected]>> wrote: >> >>> >>> So we can retire this service? Are there other services we can shutdown? >>> >>> Shane >>> >>> Sent from my iPhone >>> >>>> On Feb 24, 2014, at 11:56 AM, Nomi Harris <nlharris(a)lbl.gov<mailto:[email protected]>> wrote: >>>> >>>> I forgot to forward this to you. Ranjan says to leave the genotype/phenotype service out of this release. >>>> Nomi >>>> >>>> Begin forwarded message: >>>> >>>>> From: "Ranjan, Priya" <pranjan(a)utk.edu<mailto:[email protected]>> >>>>> Subject: Re: Genotype/Phenotype service repo? >>>>> Date: February 18, 2014 at 2:59:58 PM PST >>>>> To: Nomi Harris <nlharris(a)gmail.com<mailto:[email protected]>> >>>>> >>>>> Yes. Thanks. >>>>> Ranjan >>>>> >>>>> >>>>>> On Feb 18, 2014, at 5:40 PM, "Nomi Harris" <nlharris(a)gmail.com<mailto:[email protected]>> wrote: >>>>>> >>>>>> Ok—so the release of IRIS we’re doing this week should not include Genotype/Phenotype commands, and I should remove it from the Services web page? >>>>>> Nomi >>>>>> >>>>>>> On Feb 18, 2014, at 12:03 PM, Ranjan, Priya <pranjan(a)utk.edu<mailto:[email protected]>> wrote: >>>>>>> >>>>>>> Hi Nomi, >>>>>>> Both these services are obsolete and their functionality are being incorporated into gwas service. >>>>>>> I will request them to be deleted in few weeks. >>>>>>> Thanks >>>>>>> Ranjan >>>>>>> >>>>>>> >>>>>>> ________________________________________ >>>>>>> From: Nomi Harris [nlharris(a)gmail.com<mailto:[email protected]>] >>>>>>> Sent: Tuesday, February 18, 2014 3:00 PM >>>>>>> To: pranjan77(a)gmail.com<mailto:[email protected]>; Ranjan, Priya >>>>>>> Cc: release-team(a)kbase.us<mailto:[email protected]> >>>>>>> Subject: Genotype/Phenotype service repo? >>>>>>> >>>>>>> Hi Ranjan, >>>>>>> What is the correct repo for the Genotype/Phenotype service? >>>>>>> There’s a repo called genotype_phenotype, which hasn’t been updated since Sept. >>>>>>> There’s one called genotype_phenotype_api, which I think is the current repo. >>>>>>> The Master tab of the Services repo (https://docs.google.com/spreadsheet/ccc?key=0AriSbOyynCz1dDdJRHJBcGszaldlUE…) claims that the repo is called geno_pheno_service, which I guess is just wrong. >>>>>>> If genotype_phenotype_api is the live repo, then I would suggest deleting genotype_phenotype to avoid confusion. >>>>>>> Thanks, >>>>>>> Nomi >> > > > >

1 0

Re: [Release-team] Question about testing environment
by Brettin, Thomas S. 10 Mar '14

10 Mar '14

Hi Roman. There are a couple things in your email. a) the why don't we -- we are working on this right now. I just came out of a design session that will make standing up development enviornments easier. Until now, our services were not that complex. As things on the project are maturing, we now see developers requiring more complex dev environments. b) on continous integration, we are well aware of jenkins and other tools for doing this. We had CI running before christmas as a prototype, and then took it off line. We are working on bringing this back on line and have a target timeline to have this in place for the next major build. Tom On Mar 10, 2014, at 4:11 PM, Roman Sutormin <rsutormin(a)lbl.gov<mailto:[email protected]>> wrote: Hello everybody, I have little bit strange question. Why don't we make testing environment for tests in our projects? My problem is that now I need to install local workspace service (and shock server + mongo that are used in WS) and job status service in order to be able to run tests for my service (genome comparison). But I'm sure that everybody who is developing services would be glad to have testing services and dbs that are necessary for running tests without installing all necessary parts on some random magellan instances or even locally. Another useful outcome of testing env will be ability to install automation testing software like https://wiki.jenkins-ci.org/display/JENKINS/Unit+Test . Thanks for your ideas and suggestions. -Roman. _______________________________________________ Release-team mailing list Release-team(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/release-team

1 0

Fwd: Question about testing environment
by Nomi Harris 10 Mar '14

10 Mar '14

Forwarding this question to the release-team mailing list because Roman isn’t a member of that list (and I’m not an admin of it, so I can’t approve his post). Nomi Begin forwarded message: > From: Roman Sutormin <rsutormin(a)lbl.gov> > Date: Mon, Mar 10, 2014 at 2:11 PM > Subject: Question about testing environment > To: Release-team(a)lists.kbase.us > Cc: Adam Arkin <aparkin(a)lbl.gov> > > > Hello everybody, > > I have little bit strange question. Why don't we make testing environment for tests in our projects? > > My problem is that now I need to install local workspace service (and shock server + mongo that are used in WS) and job status service in order to be able to run tests for my service (genome comparison). But I'm sure that everybody who is developing services would be glad to have testing services and dbs that are necessary for running tests without installing all necessary parts on some random magellan instances or even locally. > > Another useful outcome of testing env will be ability to install automation testing software like https://wiki.jenkins-ci.org/display/JENKINS/Unit+Test . > > Thanks for your ideas and suggestions. > > -Roman.

1 0

Question about testing environment
by Roman Sutormin 10 Mar '14

10 Mar '14

Hello everybody, I have little bit strange question. Why don't we make testing environment for tests in our projects? My problem is that now I need to install local workspace service (and shock server + mongo that are used in WS) and job status service in order to be able to run tests for my service (genome comparison). But I'm sure that everybody who is developing services would be glad to have testing services and dbs that are necessary for running tests without installing all necessary parts on some random magellan instances or even locally. Another useful outcome of testing env will be ability to install automation testing software like https://wiki.jenkins-ci.org/display/JENKINS/Unit+Test. Thanks for your ideas and suggestions. -Roman.

1 0