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

release notes
by Land, Miriam L. 22 Apr '13

22 Apr '13

All, Do we have anything like release notes for this build? For testing purposes, it would be nice to have a list of things to specifically test for. Miriam

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Re: [Release-team] genome_annotation module
by Dan Olson 22 Apr '13

22 Apr '13

There is a good cert for kbase.us now. ----- Original Message ----- > From: "Robert Olson" <olson(a)mcs.anl.gov> > To: "Thomas Brettin" <brettin(a)mcs.anl.gov> > Cc: "Dan Olson" <dolson(a)mcs.anl.gov>, release-team(a)lists.kbase.us > Sent: Monday, April 22, 2013 11:28:46 AM > Subject: Re: genome_annotation module > > excellent, thanks tom > > have we tested out all the services against the https target? I'm > wondering if the perl client stuff is doing the right thing in the > face of SSL endpoints that do not have known host certs (or do we > have a good cert on there now?) > > > On Apr 22, 2013, at 11:27 AM, Thomas Brettin wrote: > > > I just pushed the changes to git.kbase.us master. > > > > In short, changed references to bio-data to kbase.us > > > > Changed the protocol from http to https. > > > > In a couple scripts, the url of the id server changed to point at > > https://kbase.us/.… > > > > > > t > >

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of special interest to test
by Thomas Brettin 22 Apr '13

22 Apr '13

Hi Miriam, Here is the list of files that I modified in the genome_annotation module this morning. They should be tested more rigorously than just ensuring that the script returns 0. Chris, I'm including you because these are related to your bootcamps. The change could be in production by the end of this week. Tom # modified: recompile_typespec # modified: scripts/annotate_genome.pl # modified: scripts/assign_functions_to_CDSs.pl # modified: scripts/call_CDSs.pl # modified: scripts/call_CDSs_by_glimmer.pl # modified: scripts/call_CDSs_by_projection.pl # modified: scripts/call_RNAs.pl # modified: scripts/call_pyrrolysoproteins.pl # modified: scripts/call_selenoproteins.pl # modified: scripts/cs_to_genome.pl # modified: scripts/fasta_to_genome.pl # modified: scripts/genomeTO_strep_pneumo_repeats.pl # modified: scripts/genomeTO_strep_suis_repeats.pl # modified: scripts/genomeTO_to_coding_regions.pl # modified: scripts/genomeTO_to_feature_data.pl # modified: scripts/genomeTO_to_reconstructionTO.pl # modified: scripts/merge_features.pl # modified: scripts/reconstructionTO_to_roles.pl # modified: scripts/reconstructionTO_to_subsystems.pl

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Re: [Release-team] genome_annotation module
by Thomas Brettin 22 Apr '13

22 Apr '13

good question for Dan. I'm just going a statement from Dan that we are ready to cut over to https. Guess we'll find out soon :-) (Miriam) t On Apr 22, 2013, at 11:28 AM, Robert Olson <olson(a)mcs.anl.gov> wrote: > excellent, thanks tom > > have we tested out all the services against the https target? I'm wondering if the perl client stuff is doing the right thing in the face of SSL endpoints that do not have known host certs (or do we have a good cert on there now?) > > > On Apr 22, 2013, at 11:27 AM, Thomas Brettin wrote: > >> I just pushed the changes to git.kbase.us master. >> >> In short, changed references to bio-data to kbase.us >> >> Changed the protocol from http to https. >> >> In a couple scripts, the url of the id server changed to point at https://kbase.us/.… >> >> >> t >

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Re: [Release-team] genome_annotation module
by Robert Olson 22 Apr '13

22 Apr '13

excellent, thanks tom have we tested out all the services against the https target? I'm wondering if the perl client stuff is doing the right thing in the face of SSL endpoints that do not have known host certs (or do we have a good cert on there now?) On Apr 22, 2013, at 11:27 AM, Thomas Brettin wrote: > I just pushed the changes to git.kbase.us master. > > In short, changed references to bio-data to kbase.us > > Changed the protocol from http to https. > > In a couple scripts, the url of the id server changed to point at https://kbase.us/.… > > > t

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genome_annotation module
by Thomas Brettin 22 Apr '13

22 Apr '13

I just pushed the changes to git.kbase.us master. In short, changed references to bio-data to kbase.us Changed the protocol from http to https. In a couple scripts, the url of the id server changed to point at https://kbase.us/.… t

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Re: [Release-team] [Kbase-devel] starting a new minor release
by Robert Olson 22 Apr '13

22 Apr '13

Do you have a complete list of modules that will be included? I'd like to do a dmg refresh. --bob On Apr 22, 2013, at 9:38 AM, Dan Olson wrote: > The final list is: > > Requested: > invocation > auth > auth_service > protein_info_service > trees > > Required deps: > typecomp > kb_seed > erdb_service > kbapi_common > > > ----- Original Message ----- >> From: "Dan Olson" <dolson(a)mcs.anl.gov> >> To: "Thomas Brettin" <brettin(a)mcs.anl.gov> >> Cc: "kbase-devel(a)lists.kbase.us devel" <kbase-devel(a)lists.kbase.us>, release-team(a)lists.kbase.us >> Sent: Monday, April 22, 2013 9:32:39 AM >> Subject: Re: [Release-team] starting a new minor release >> >> I'm starting this deploy in our test environment right now. >> >> ----- Original Message ----- >>> From: "Thomas Brettin" <brettin(a)mcs.anl.gov> >>> To: "Thomas Brettin" <brettin(a)mcs.anl.gov> >>> Cc: "kbase-devel(a)lists.kbase.us devel" >>> <kbase-devel(a)lists.kbase.us>, release-team(a)lists.kbase.us >>> Sent: Monday, April 22, 2013 4:50:18 AM >>> Subject: Re: [Release-team] starting a new minor release >>> >>> These are the services that were requested for release this week >>> >>> Git Repository Requestor >>> >>> invocation Tom >>> auth Steve >>> auth_service Steve >>> protein_info Keith >>> trees Mike >>> >>> >>> Tom >>> >>> On Apr 18, 2013, at 11:10 AM, Thomas Brettin <brettin(a)mcs.anl.gov> >>> wrote: >>> >>>> We're going to start a minor release on Monday. Right now, we >>>> have >>>> the Invocation Service scheduled. >>>> >>>> Any module that would benefit from having a redeployment to >>>> production with updated service URLS, this is a good chance to >>>> get >>>> that done. >>>> >>>> Let me know if you want your module on the schedule. >>>> >>>> Thanks, >>>> Tom >>> >>> _______________________________________________ >>> 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 >> > _______________________________________________ > 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] starting a new minor release
by Dan Olson 22 Apr '13

22 Apr '13

So, having multiple g* accounts is somewhat of a nightmare.. It looks like google is getting better about linking support for multiple accounts, but still not perfect. My dan(a)olsonsolutions.net account has access to the "KBase Project" folder. Are these docs not in that folder? If not, why? It seems like I run across this a lot - it would be nice if folks would uniformly use the "KBase Project" folder. ----- Original Message ----- > From: "Nomi Harris" <nlharris(a)lbl.gov> > To: "Thomas Brettin" <brettin(a)mcs.anl.gov> > Cc: "Dan Olson" <dolson(a)mcs.anl.gov>, release-team(a)lists.kbase.us > Sent: Monday, April 22, 2013 10:57:44 AM > Subject: Re: [Release-team] [Kbase-devel] starting a new minor release > > Dan, I gave you access to these docs with your personal email > address. (You already had access with your anl address.) > > On Apr 22, 2013, at 8:42 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > > > For today's release meeting, do we want to look at / revise these? > > Minor Release Punch List: > > https://docs.google.com/a/lbl.gov/document/d/12e_r8w7ean5hTp-WYiKbWdxET7Emt… > > (last edited Feb 1) > Sorry, wrong URL, should be > https://docs.google.com/document/d/1QxZtbKUtAp_7Dj6ArEEaQvUcyl92xn80PzIVm_K… > > > Minor Release Standard Emails: > > https://docs.google.com/a/lbl.gov/document/d/12e_r8w7ean5hTp-WYiKbWdxET7Emt… > > (last edited Feb 19) > > Nomi > > > >

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Re: [Release-team] [Kbase-devel] starting a new minor release
by Land, Miriam L. 22 Apr '13

22 Apr '13

Ditto on the Standard Emails. Miriam On 4/22/13 11:57 AM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: >Dan, I gave you access to these docs with your personal email address. >(You already had access with your anl address.) > >On Apr 22, 2013, at 8:42 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> For today's release meeting, do we want to look at / revise these? >> Minor Release Punch List: >>https://docs.google.com/a/lbl.gov/document/d/12e_r8w7ean5hTp-WYiKbWdxET7E >>mtohOH0TPuy3qUqs/edit (last edited Feb 1) >Sorry, wrong URL, should be >https://docs.google.com/document/d/1QxZtbKUtAp_7Dj6ArEEaQvUcyl92xn80PzIVm_ >KtKLo/edit > >> Minor Release Standard Emails: >>https://docs.google.com/a/lbl.gov/document/d/12e_r8w7ean5hTp-WYiKbWdxET7E >>mtohOH0TPuy3qUqs/edit (last edited Feb 19) >> Nomi >> > >_______________________________________________ >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] starting a new minor release
by Nomi Harris 22 Apr '13

22 Apr '13

Dan, I gave you access to these docs with your personal email address. (You already had access with your anl address.) On Apr 22, 2013, at 8:42 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > For today's release meeting, do we want to look at / revise these? > Minor Release Punch List: https://docs.google.com/a/lbl.gov/document/d/12e_r8w7ean5hTp-WYiKbWdxET7Emt… (last edited Feb 1) Sorry, wrong URL, should be https://docs.google.com/document/d/1QxZtbKUtAp_7Dj6ArEEaQvUcyl92xn80PzIVm_K… > Minor Release Standard Emails: https://docs.google.com/a/lbl.gov/document/d/12e_r8w7ean5hTp-WYiKbWdxET7Emt… (last edited Feb 19) > Nomi >

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