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

1:00 - 1:30 pm CST Release-team Telecon
by brettin＠mcs.anl.gov 22 Jul '13

22 Jul '13

The following meeting has been modified: Subject: 1:00 - 1:30 pm CST Release-team Telecon Organizer: brettin(a)mcs.anl.gov Sent By: "India S. Gordon" <igordon(a)cels.anl.gov> Location: 888-850-4523, passcode: 416791, leader passcode (Tom only) 4167913 Time: Monday, July 22, 2013, 1:00:00 PM - 1:30:00 PM GMT -06:00 US/Canada Central Invitees: release-team(a)kbase.us; scanon(a)lbl.gov; dolson(a)mcs.anl.gov; landml(a)ornl.gov *~*~*~*~*~*~*~*~*~* Dan and Tom are running late. They should be on the call momentarily. Thank you, India

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20130722 release started
by Dan Olson 22 Jul '13

22 Jul '13

The following modules have been tagged and deployment started: Requested (and in scope for service deployment): expression plant_expression_service invocation cluster_service auth_service registry Dependencies: typecomp kb_seed kbapi_common exchange_format_support experiment idserver auth typecomp ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055

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1:00 - 1:30 pm CST Release-team Telecon
by brettin＠mcs.anl.gov 19 Jul '13

19 Jul '13

The following is a new meeting request: Subject: 1:00 - 1:30 pm CST Release-team Telecon Organizer: brettin(a)mcs.anl.gov Sent By: "India S. Gordon" <igordon(a)cels.anl.gov> Location: 888-850-4523, passcode: 416791, leader passcode (Tom only) 4167913 Time: Monday, July 22, 2013, 1:00:00 PM - 1:30:00 PM GMT -06:00 US/Canada Central Invitees: release-team(a)kbase.us; scanon(a)lbl.gov; dolson(a)mcs.anl.gov *~*~*~*~*~*~*~*~*~*

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Re: [Release-team] mini build next week
by Thomas Brettin 19 Jul '13

19 Jul '13

Thanks Shane, I'll put it on the list. t On Jul 19, 2013, at 9:46 AM, Shane Canon <scanon(a)lbl.gov> wrote: > > We would like to redeploy cluster services. Shreyas made some changes to make the configuration > more consistent with the other services. > > --Shane > > > On Jul 19, 2013, at 6:47 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> we had a request for the following modules: >> >> expression (Jason - owner) >> plant_expression_service (Shinjae - owner) >> >> And I'm requesting: >> >> auth (Steve C - owner) to complete the deployment of the bug fix >> invocation (Bob - owner) to get any new commands in plant_expression_service deployed. >> >> And we can do others as well, I'll send a general email out today. >> >> Thanks, >> Tom >> _______________________________________________ >> 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] mini build next week
by Shane Canon 19 Jul '13

19 Jul '13

We would like to redeploy cluster services. Shreyas made some changes to make the configuration more consistent with the other services. --Shane On Jul 19, 2013, at 6:47 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > we had a request for the following modules: > > expression (Jason - owner) > plant_expression_service (Shinjae - owner) > > And I'm requesting: > > auth (Steve C - owner) to complete the deployment of the bug fix > invocation (Bob - owner) to get any new commands in plant_expression_service deployed. > > And we can do others as well, I'll send a general email out today. > > Thanks, > Tom > _______________________________________________ > 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] mini build next weejk
by Thomas Brettin 19 Jul '13

19 Jul '13

Also, is there a plan for Monday morning? Dan will you be running the deployment or have you asked someone else to run the deployment? I will update the KBase Services spread sheet today creating a new tab for the mini build and put in enough information to get started. Thanks, Tom On Jul 18, 2013, at 7:54 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Would like to do one. Dan will need help though, as he is doing a switch over on the ANL accounts mgmt system in the morning. > > Thanks, > Tom

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mini build next week
by Thomas Brettin 19 Jul '13

19 Jul '13

we had a request for the following modules: expression (Jason - owner) plant_expression_service (Shinjae - owner) And I'm requesting: auth (Steve C - owner) to complete the deployment of the bug fix invocation (Bob - owner) to get any new commands in plant_expression_service deployed. And we can do others as well, I'll send a general email out today. Thanks, Tom

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mini build next weejk
by Thomas Brettin 18 Jul '13

18 Jul '13

Would like to do one. Dan will need help though, as he is doing a switch over on the ANL accounts mgmt system in the morning. Thanks, Tom

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mini build next weej
by Thomas Brettin 18 Jul '13

18 Jul '13

I'd like to have a mini build next week if there are a set of modules that people would like released. Please send to the release engineering team build targets. Tom

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Re: [Release-team] Expression Candidate for release
by Jason Baumohl 10 Jul '13

10 Jul '13

No I have not. Tom and I talked last week about this. The initial release (version 1) will be on expression on DB1. This will give people a chance to test things out. Hopefully in version2 we can move this into the CDM. Tom and I discussed Bruce doing the uploads at that point. Tom mentioned that there were some problems with Bruce doing uploads of other people's stuff in the past because there were errors in the uploads files. My stuff uses Gavin's exchange format stuff, which has the benefit of doing a lot of error checking to create the upload files. It does not guarantee there will never be a problem, but it should be smoother than the past experiences that Tom was referring to. -Jason On Wed, Jul 10, 2013 at 11:35 AM, Robert Olson <olson(a)mcs.anl.gov> wrote: > Have you been working with Bruce on the plan for doing an integration with > the production XML for the CDM ? > > On Jul 10, 2013, at 1:30 PM, Jason Baumohl wrote: > > Hi All, > > I am not opposed to creating some scripts for the command line. I have > not done this before, but I suspect it is essentially a wrapper to > functions in the service. > > As far as the autogenerated functions (get_entity_*.pl, > get_relationship_*.pl, and query_entity_*.pl) > I do have those for my db tables in > root@db1-expression:/kb/dev_container/modules/kb_seed/scripts# > > -Jason > > > > On Wed, Jul 10, 2013 at 9:50 AM, Robert Olson <olson(a)mcs.anl.gov> wrote: > >> If the expression stuff is actually integrated into the central store >> data model, it'll have the get_entity/get_rel/etc scripts created as a >> matter of course. >> >> If it's being maintained as a separate database, those will need to be >> separately generated (compile_dbd_to_typespec & friends). >> >> It seems we should have some command line scripts to do things like >> enumerate experiments that are relevant to a given genome ID; probes that >> match a given set of features, retrieval of normalized data for a given >> experiment, etc. >> >> --bob >> >> On Jul 9, 2013, at 5:45 PM, Thomas Brettin wrote: >> >> You should talk to Bob if you're wondering about automatically generated >> scripts. He, Ross and Terry also wrote many hand crafted scripts as well. >> >> The poster child I sent you (registry) was for the module Makefile, but >> it also includes commands. Additionally, it contains a template file that I >> used to auto generate the registry commands (see scripts/script.tt and >> scripts/tpage_command), but you should really* talk to Bob* about this >> as his auto generate skills are superior to mine. >> >> Tom >> >> >> >> On Jul 9, 2013, at 5:37 PM, Jason Baumohl <jkbaumohl(a)lbl.gov> wrote: >> >> Hi Tom, >> >> Tom you are welcome to play around with my make file. >> Yes, this would save me some time, but I have not made scripts and >> commands to work in IRIS before. >> That is why I was asking about a poster child example. So I really do >> not know what is involved. >> Currently there are over 30 (and growing) functions that I have made for >> expression. >> If it is only a wrapper then it should be ok. The automated relationship >> and entity functions do not go intp the scripts section. I believe these >> get made automatically when I run the CDMI stuff on mmy XML. >> The potential issue there is that expression is in a different database. >> >> -Jason >> >> >> >> >> On Tue, Jul 9, 2013 at 2:26 PM, Thomas Brettin <brettin(a)mcs.anl.gov>wrote: >> >>> I haven't enforced a policy on the script requirement yet, although it >>> seems having scripts for standard services, particularly those in the CDMI >>> space could be required. >>> >>> I do enforce a policy that all modules must have a COMMANDS file, but it >>> is not unheard of that someone will just create an empty file in their >>> module. >>> >>> Jason, if I were to take on cleaning up the make file for the release >>> would you then have time to get some commands in place before we release. >>> Also, is it possible to automate the generation of the Entity and Relations >>> type of commands? I'm sure Bob didn't hand write all those. >>> >>> Tom >>> >>> >>> On Jul 9, 2013, at 3:17 PM, Rick Stevens <stevens(a)anl.gov> wrote: >>> >>> For the initial release we should have command line and iris I would >>> think in addition to whatever we have in the API? >>> >>> We have several others working on pipelines for RNAseq analysis and I >>> think we need to harmonize these before too long. >>> >>> On Jul 9, 2013, at 2:47 PM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >>> >>> Rick asked for the commands. >>> >>> >>> On Jul 9, 2013, at 1:51 PM, Jason Baumohl <jkbaumohl(a)lbl.gov> wrote: >>> >>> I do not have scripts for iris. This is something that we can >>> potentially add later, but not for the initial release. >>> >>> -Jason >>> >>> >>> On Tue, Jul 9, 2013 at 11:42 AM, Jason Baumohl <jkbaumohl(a)lbl.gov>wrote: >>> >>>> Hi Tom, >>>> >>>> I do not pretend to be a make expert. This project is the first time >>>> that I have used it. Do you have an example of what you like me to change >>>> it to? >>>> >>>> Thanks, >>>> Jason >>>> >>>> >>>> On Tue, Jul 9, 2013 at 6:34 AM, Thomas Brettin <brettint(a)gmail.com>wrote: >>>> >>>>> Hi Jason, >>>>> >>>>> I was reviewing your module makefile, and I'd like to help you make >>>>> some changes that will rely more on templates. Since your code is all perl, >>>>> this should be pretty straight forward. >>>>> >>>>> As an example, you have in your make file: >>>>> >>>>> deploy-service-scripts: >>>>> # First create the start script (should be a better way to do >>>>> this…) >>>>> … >>>>> >>>>> Usually, we use tpage as a templating tool and use start_service.ttand >>>>> stop_service.tt templates that get filled in at make time. >>>>> >>>>> Also, I don't see a scripts directory. Do you have scripts that will >>>>> be executable from IRIS? >>>>> >>>>> Thanks, >>>>> Tom >>>>> >>>>> >>>>> >>>>> On Jul 8, 2013, at 7:49 PM, Jason Baumohl <jkbaumohl(a)lbl.gov> wrote: >>>>> >>>>> Works for me. >>>>> >>>>> -Jason >>>>> >>>>> >>>>> On Mon, Jul 8, 2013 at 5:40 PM, Thomas Brettin <brettint(a)gmail.com>wrote: >>>>> >>>>>> I'd like to schedule this for a minor release and not wait until the >>>>>> Aug build. We'll do at least one minor release this month. >>>>>> >>>>>> >>>>>> On Jul 1, 2013, at 5:06 PM, Jason Baumohl <jkbaumohl(a)lbl.gov> wrote: >>>>>> >>>>>> > Hi Tom and Paramvir, >>>>>> > >>>>>> > I think I have an official candidate for release for expression. >>>>>> > >>>>>> > I have a bunch of stuff but includes the following: >>>>>> > spec file >>>>>> > impl code with 30 complete functions that have been tested (note 2 >>>>>> are currently incomplete functions - related to GEO parsing). >>>>>> > automated testing for all completed functions >>>>>> > readme >>>>>> > releasenotes >>>>>> > exchangeformat specs >>>>>> > uploader >>>>>> > preprocessors >>>>>> > initial data loaded into expression on DB1 >>>>>> > automated doc for Impl code >>>>>> > documentation for exchange format (file format for uploads). >>>>>> > >>>>>> > I think I have everything except scripts and commands to be run >>>>>> from the command line and iris. >>>>>> > >>>>>> > All of the code is committed to git. >>>>>> > >>>>>> > -Jason >>>>>> >>>>>> >>>>> >>>>> >>>> >>> _______________________________________________ >>> Release-team mailing list >>> Release-team(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/release-team >>> >>> >>> >>> >>> >> >> >> > >

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