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Any new services to add to http://kbase.us/developer-zone/services/?
by Nomi Harris 20 Apr '14

20 Apr '14

I am putting together a service catalog for the grant renewal. It will be based on http://kbase.us/developer-zone/services/. Have we added any new services (or restored broken services to working) since Feb? (For example, MAK isn’t on there—was it successfully deployed to production? Bambi? Communities QC?) Thanks, Nomi

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Re: [Release-team] new prod deploy requested for IdMap
by Thomas Brettin 03 Apr '14

03 Apr '14

Thomass-MacBook-Pro-2:wire brettin$ curl -s -d '{"params":[],"method":"IdMap.version","version":"1.1"}' http://kbase.us/services/id_map returns {"version":"1.1","result":["0.1.0”]} On Apr 3, 2014, at 12:45 AM, Shane Canon <scanon(a)lbl.gov> wrote: > > Done. > > Tom, > > Can you provide me with a curl-style test I can use to monitor id_map and handle_service? > > --Shane > > > On Apr 2, 2014, at 7:34 AM, Thomas Brettin <brettin(a)anl.gov> wrote: > >> Fixes that were required as a result of a schema change in the CS are completed. >> >> Unit tests pass in dev environment. >> >> Please redeploy into production. >> >> Include Jason in any correspondence. >> >> Thanks, >> Tomn >> _______________________________________________ >> 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] new prod deploy requested for IdMap
by Shane Canon 02 Apr '14

02 Apr '14

Done. Tom, Can you provide me with a curl-style test I can use to monitor id_map and handle_service? --Shane On Apr 2, 2014, at 7:34 AM, Thomas Brettin <brettin(a)anl.gov> wrote: > Fixes that were required as a result of a schema change in the CS are completed. > > Unit tests pass in dev environment. > > Please redeploy into production. > > Include Jason in any correspondence. > > Thanks, > Tomn > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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new prod deploy requested for IdMap
by Thomas Brettin 02 Apr '14

02 Apr '14

Fixes that were required as a result of a schema change in the CS are completed. Unit tests pass in dev environment. Please redeploy into production. Include Jason in any correspondence. Thanks, Tomn

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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?

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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?

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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?

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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 >> >

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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

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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

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