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

Re: [Release-team] Many services not ready for release because they lack release notes
by Thomas Brettin 07 Jun '13

07 Jun '13

I would just do a foreach repo, show me the git logs, or number of commits, or something. Many haven't really changed significantly. Based on a 15-30 minutes of detective work, i'd formulate a plan forward. analysis_book - not in the release - it's the ipython notebook that Folker did and its a MGRast product. aux_store, not in the release as far as I know because the public can't really touch it. registry - not in the release, it's an internal experimental module search - has api docs, just not in standard form. just ask guru where the url is On Jun 6, 2013, at 11:17 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > A few of the services have up-to-date release notes (and appropriately deployed API docs): > auth > jnomics > protein_info_service > translation > trees (? -- release notes updated 4/4) > > However, many do not have updated release notes and thus are not ready to be included in this release. (Some also don't have API docs in the expected location.) > analysis_book > assembly > auth_service > aux_store > cluster_service > communities_api > communities_qc > (erdb_service--internal only, right?) > experiment > feature_selection (also missing api docs) > (file_type_service) > genotype_phenotype_api > kb_seed > KBaseFBAModeling (also missing api docs) > matR > networks > ontology_service > phispy > plant_expression_service > (registry) > search (also missing api docs) > workspace_service > > What's the best way to get the missing release notes so we can finish up this release? Do Mike and I need to phone the relevant developers? > > Nomi > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Many services not ready for release because they lack release notes
by Nomi Harris 06 Jun '13

06 Jun '13

A few of the services have up-to-date release notes (and appropriately deployed API docs): auth jnomics protein_info_service translation trees (? -- release notes updated 4/4) However, many do not have updated release notes and thus are not ready to be included in this release. (Some also don't have API docs in the expected location.) analysis_book assembly auth_service aux_store cluster_service communities_api communities_qc (erdb_service--internal only, right?) experiment feature_selection (also missing api docs) (file_type_service) genotype_phenotype_api kb_seed KBaseFBAModeling (also missing api docs) matR networks ontology_service phispy plant_expression_service (registry) search (also missing api docs) workspace_service What's the best way to get the missing release notes so we can finish up this release? Do Mike and I need to phone the relevant developers? Nomi

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Re: [Release-team] Request iplant atmosphere accounts
by Dan Olson 06 Jun '13

06 Jun '13

According to the iplant folks, yes. I'll ask them to look in to this. ----- Original Message ----- > From: "Robert Olson" <olson(a)mcs.anl.gov> > To: "Dan Olson" <dolson(a)mcs.anl.gov> > Cc: release-team(a)kbase.us > Sent: Thursday, June 6, 2013 1:49:13 PM > Subject: Re: [Release-team] Request iplant atmosphere accounts > > should all iplant accounts work? Mine doesn't seem to > > On Jun 6, 2013, at 10:13 AM, Dan Olson wrote: > > > We have a running VM which you can logon to with your IPlant > > accounts -- > > > > ssh to 128.196.142.166 > > > > canon and landml have sudo access. > > > > ----- Original Message ----- > >> From: "Dan Olson" <dolson(a)mcs.anl.gov> > >> To: release-team(a)kbase.us > >> Sent: Wednesday, June 5, 2013 9:51:32 AM > >> Subject: [Release-team] Request iplant atmosphere accounts > >> > >> I need some help testing out a KBase image that we uploaded to > >> iplant > >> atmosphere. > >> > >> Can the test team go and create accounts at > >> http://user.iplantcollaborative.org/? > >> > >> Let me know when that is done, and I'll have the sysadmin there > >> add > >> you to our image's access list. > >> > >> ---- > >> 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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Re: [Release-team] Request iplant atmosphere accounts
by Shane Canon 06 Jun '13

06 Jun '13

Mine didn't either. I used the same password that I used to log into the web site. --Shane On Jun 6, 2013, at 11:49 AM, Robert Olson <olson(a)mcs.anl.gov> wrote: > should all iplant accounts work? Mine doesn't seem to > > On Jun 6, 2013, at 10:13 AM, Dan Olson wrote: > >> We have a running VM which you can logon to with your IPlant accounts -- >> >> ssh to 128.196.142.166 >> >> canon and landml have sudo access. >> >> ----- Original Message ----- >>> From: "Dan Olson" <dolson(a)mcs.anl.gov> >>> To: release-team(a)kbase.us >>> Sent: Wednesday, June 5, 2013 9:51:32 AM >>> Subject: [Release-team] Request iplant atmosphere accounts >>> >>> I need some help testing out a KBase image that we uploaded to iplant >>> atmosphere. >>> >>> Can the test team go and create accounts at >>> http://user.iplantcollaborative.org/? >>> >>> Let me know when that is done, and I'll have the sysadmin there add >>> you to our image's access list. >>> >>> ---- >>> 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] Request iplant atmosphere accounts
by Robert Olson 06 Jun '13

06 Jun '13

should all iplant accounts work? Mine doesn't seem to On Jun 6, 2013, at 10:13 AM, Dan Olson wrote: > We have a running VM which you can logon to with your IPlant accounts -- > > ssh to 128.196.142.166 > > canon and landml have sudo access. > > ----- Original Message ----- >> From: "Dan Olson" <dolson(a)mcs.anl.gov> >> To: release-team(a)kbase.us >> Sent: Wednesday, June 5, 2013 9:51:32 AM >> Subject: [Release-team] Request iplant atmosphere accounts >> >> I need some help testing out a KBase image that we uploaded to iplant >> atmosphere. >> >> Can the test team go and create accounts at >> http://user.iplantcollaborative.org/? >> >> Let me know when that is done, and I'll have the sysadmin there add >> you to our image's access list. >> >> ---- >> 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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Re: [Release-team] [Kbase-devel] VM for testing
by Paramvir Dehal 06 Jun '13

06 Jun '13

It's packed twice. You have to uncompress it twice, then it will expand to a 13gig file. On Thu, Jun 6, 2013 at 9:07 AM, Travis Harrison <teharrison(a)anl.gov> wrote: > I tried to open the VM in VirtualBox (latest version 4.2.12) and got the > following error: > > Could not get the storage format of the medium >> '/Users/travis/VirtualBoxVMs/kbase_20130604.vmdk' >> (VERR_NOT_SUPPORTED). >> >> Result Code: >> VBOX_E_IPRT_ERROR (0x80BB0005) >> Component: >> Medium >> Interface: >> IMedium {29989373-b111-4654-8493-2e1176cba890} >> Callee: >> IVirtualBox {3b2f08eb-b810-4715-bee0-bb06b9880ad2} >> Callee RC: >> VBOX_E_OBJECT_NOT_FOUND (0x80BB0001) >> > > Anyone have any ideas? > > - Travis Harrison > > > On Wed, Jun 5, 2013 at 7:18 PM, Thomas Brettin <brettin(a)mcs.anl.gov>wrote: > >> ok, here it is. please test away! >> >> >> On Jun 5, 2013, at 3:44 PM, Dan Olson <dolson(a)mcs.anl.gov> wrote: >> >> > Please test the VM image here-> >> > http://bioseed.mcs.anl.gov/~dolson/kbase_20130604.vmdk.gz >> > >> > This vmdk format should work with virtualbox or vmware. >> > >> > ---- >> > 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 >> >> _______________________________________________ >> Kbase-devel mailing list >> Kbase-devel(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/kbase-devel >> > > > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel > >

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Re: [Release-team] [Kbase-devel] VM for testing
by Travis Harrison 06 Jun '13

06 Jun '13

I tried to open the VM in VirtualBox (latest version 4.2.12) and got the following error: Could not get the storage format of the medium > '/Users/travis/VirtualBoxVMs/kbase_20130604.vmdk' > (VERR_NOT_SUPPORTED). > > Result Code: > VBOX_E_IPRT_ERROR (0x80BB0005) > Component: > Medium > Interface: > IMedium {29989373-b111-4654-8493-2e1176cba890} > Callee: > IVirtualBox {3b2f08eb-b810-4715-bee0-bb06b9880ad2} > Callee RC: > VBOX_E_OBJECT_NOT_FOUND (0x80BB0001) > Anyone have any ideas? - Travis Harrison On Wed, Jun 5, 2013 at 7:18 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > ok, here it is. please test away! > > > On Jun 5, 2013, at 3:44 PM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > > > Please test the VM image here-> > > http://bioseed.mcs.anl.gov/~dolson/kbase_20130604.vmdk.gz > > > > This vmdk format should work with virtualbox or vmware. > > > > ---- > > 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 > > _______________________________________________ > Kbase-devel mailing list > Kbase-devel(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel >

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Re: [Release-team] Request iplant atmosphere accounts
by Dan Olson 06 Jun '13

06 Jun '13

We have a running VM which you can logon to with your IPlant accounts -- ssh to 128.196.142.166 canon and landml have sudo access. ----- Original Message ----- > From: "Dan Olson" <dolson(a)mcs.anl.gov> > To: release-team(a)kbase.us > Sent: Wednesday, June 5, 2013 9:51:32 AM > Subject: [Release-team] Request iplant atmosphere accounts > > I need some help testing out a KBase image that we uploaded to iplant > atmosphere. > > Can the test team go and create accounts at > http://user.iplantcollaborative.org/? > > Let me know when that is done, and I'll have the sysadmin there add > you to our image's access list. > > ---- > 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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Re: [Release-team] VM for testing
by Thomas Brettin 05 Jun '13

05 Jun '13

ok, here it is. please test away! On Jun 5, 2013, at 3:44 PM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > Please test the VM image here-> > http://bioseed.mcs.anl.gov/~dolson/kbase_20130604.vmdk.gz > > This vmdk format should work with virtualbox or vmware. > > ---- > 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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VM for testing
by Dan Olson 05 Jun '13

05 Jun '13

Please test the VM image here-> http://bioseed.mcs.anl.gov/~dolson/kbase_20130604.vmdk.gz This vmdk format should work with virtualbox or vmware. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

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