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

Re: [Release-team] auto generation of command -h output
by Michael Sneddon 21 May '13

21 May '13

Yeah, getting everyone to follow the same conventions is going to be a challenge, but at least we have something to work with. One of the goals of this exercise is to provide Outreach with at least an index of what commands are available in KBase so that we can start checking for accuracy/completeness and post some of this reference information to the website. -michael On Tue, May 21, 2013 at 11:20 AM, Land, Miriam L. <landml(a)ornl.gov> wrote: > -------- > WARNING: At least one of the links in the message below goes to an IP > address (e.g. > 10.1.1.1), which could be malicious. To learn how to protect yourself, > please go here: > http://www.lbl.gov/cyber/services/suspicious-links.html > -------- > > I noticed that there are differences between the modules. There are some > that: > > * Are empty (phispy) > * Are one line and difficult to read (genopheno) > * Try to download a file instead of displaying content (sr) > * Are much more elaborate and complete than others ( > http://140.221.85.77/command-docs/pe/coex_cluster.txt vs > http://140.221.85.77/command-docs/genome_annotation/a_and_b.txt) > > It is going to be difficult for a script to compensate for all the > variation. Otherwise, good place to start. > > Miriam > > From: Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]>> > Date: Tuesday, May 21, 2013 2:06 PM > To: Tom Brettin <brettin(a)mcs.anl.gov<mailto:[email protected]>>, > Elizabeth Glass <marland(a)mcs.anl.gov<mailto:[email protected]>> > Cc: Keith Keller <kkeller(a)lbl.gov<mailto:[email protected]>>, " > release-team(a)kbase.us<mailto:[email protected]>" < > release-team(a)kbase.us<mailto:[email protected]>> > Subject: [Release-team] auto generation of command -h output > > During this last build meeting, Keith and I put together, using some of > Bob's invocation code, a method for capturing the help output of the > command-line scripts which service owners have declared using the COMMANDS > file. I put up an example of the output here: > http://140.221.85.77/command-docs/ > > The commands are grouped into folders which are named with the > "group-name" declared in the COMMANDS files. In each of these folders, > there is an 'index.txt' file which includes the verbose name of the set of > commands on the first line, followed by a list of all the commands that > were declared. For each of these commands, there is a text file in the > folder with the actual commands '-h' help output. > > If the text file for a command is empty, then for some reason the script > with the '-h' option did not run successfully or no help was printed. > > Let me know if you have questions. The format of this output is fairly > easy to change. > > For those on the release team, this help output generation can be invoked > from the invocation service Makefile with the "deploy-command-docs" target. > This output is placed in /kb/deployment/services/invocation/webroot/. > Perhaps we should start including this step by default whenever the > invocation service is deployed? > > -michael > >

1 0

Re: [Release-team] auto generation of command -h output
by Land, Miriam L. 21 May '13

21 May '13

I noticed that there are differences between the modules. There are some that: * Are empty (phispy) * Are one line and difficult to read (genopheno) * Try to download a file instead of displaying content (sr) * Are much more elaborate and complete than others (http://140.221.85.77/command-docs/pe/coex_cluster.txt vs http://140.221.85.77/command-docs/genome_annotation/a_and_b.txt) It is going to be difficult for a script to compensate for all the variation. Otherwise, good place to start. Miriam From: Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]>> Date: Tuesday, May 21, 2013 2:06 PM To: Tom Brettin <brettin(a)mcs.anl.gov<mailto:[email protected]>>, Elizabeth Glass <marland(a)mcs.anl.gov<mailto:[email protected]>> Cc: Keith Keller <kkeller(a)lbl.gov<mailto:[email protected]>>, "release-team(a)kbase.us<mailto:[email protected]>" <release-team(a)kbase.us<mailto:[email protected]>> Subject: [Release-team] auto generation of command -h output During this last build meeting, Keith and I put together, using some of Bob's invocation code, a method for capturing the help output of the command-line scripts which service owners have declared using the COMMANDS file. I put up an example of the output here: http://140.221.85.77/command-docs/ The commands are grouped into folders which are named with the "group-name" declared in the COMMANDS files. In each of these folders, there is an 'index.txt' file which includes the verbose name of the set of commands on the first line, followed by a list of all the commands that were declared. For each of these commands, there is a text file in the folder with the actual commands '-h' help output. If the text file for a command is empty, then for some reason the script with the '-h' option did not run successfully or no help was printed. Let me know if you have questions. The format of this output is fairly easy to change. For those on the release team, this help output generation can be invoked from the invocation service Makefile with the "deploy-command-docs" target. This output is placed in /kb/deployment/services/invocation/webroot/. Perhaps we should start including this step by default whenever the invocation service is deployed? -michael

1 0

auto generation of command -h output
by Michael Sneddon 21 May '13

21 May '13

During this last build meeting, Keith and I put together, using some of Bob's invocation code, a method for capturing the help output of the command-line scripts which service owners have declared using the COMMANDS file. I put up an example of the output here: http://140.221.85.77/command-docs/ The commands are grouped into folders which are named with the "group-name" declared in the COMMANDS files. In each of these folders, there is an 'index.txt' file which includes the verbose name of the set of commands on the first line, followed by a list of all the commands that were declared. For each of these commands, there is a text file in the folder with the actual commands '-h' help output. If the text file for a command is empty, then for some reason the script with the '-h' option did not run successfully or no help was printed. Let me know if you have questions. The format of this output is fairly easy to change. For those on the release team, this help output generation can be invoked from the invocation service Makefile with the "deploy-command-docs" target. This output is placed in /kb/deployment/services/invocation/webroot/. Perhaps we should start including this step by default whenever the invocation service is deployed? -michael

1 0

initial tech doc review complete
by Michael Sneddon 20 May '13

20 May '13

Nearly all services passed the API tech doc review. Two services (matR and assembly) do not have actual API documentation (just a combination of tutorials and readme style descriptions), but I think this is ok because these modules do not have an actual service API. Is this correct? One service (KBaseFbaModeling) has documentation deployed correctly, but it is not appearing here: http://140.221.84.191/services/docs/fbaModelServices/ The Search service failed because documentation was not deployed to the proper webroot location, but this is a minor problem given this was the first deploy for Search. Documentation was instead available here: http://140.221.84.191/services/search-doc/ Finally, feature_selection failed and I could not find any deployed documentation. This may be because deployment failed for this module? All in all, pretty good across the board API documentation deployment for this round. -michael

1 0

Fwd: Notebook in build
by Nomi Harris 07 May '13

07 May '13

I was just wondering if the KBNB iPython notebook is now in the build process? Nomi Begin forwarded message: > From: Thomas Brettin <Brettin(a)mcs.anl.gov> > Subject: Re: [Release-team] Notebook in build > Date: March 29, 2013 7:05:34 AM PDT > To: Andreas Wilke <andreas.wilke(a)me.com> > Cc: Travis Harrison <teharrison(a)anl.gov>, Folker Meyer <folker(a)anl.gov>, "release-team(a)lists.kbase.us" <release-team(a)lists.kbase.us> > > Hey Guys, > > I'm digging out of email from vacation. I'll get this on the next schedule. > > In general, emailing the release-team(a)lists.kbase.us is a more sure way, but usually sending me the email would work, except when vacation is involved … > > > t > > > > On Mar 25, 2013, at 9:00 AM, Andreas Wilke <andreas.wilke(a)me.com> wrote: > >> Hi Tom, >> >> Can you add the KBNB iPython notebook to the build process? Travis did the Make file a while ago and I looked at it. Seems ok. >> >> Thanks, >> >> Andreas >> >> >> Sent en route > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

1 0

Re: [Release-team] Fwd: 3:30 - 4:30 pm CST Webmaster Candidate Telecon
by Dan Olson 07 May '13

07 May '13

It looks like updates we're made just yesterday to that module. I'll push it to test now. Thanks for catching this Miriam. ----- Original Message ----- > From: "Miriam L. Land" <landml(a)ornl.gov> > To: "Dan Olson" <dolson(a)mcs.anl.gov>, "Thomas Brettin" <brettin(a)mcs.anl.gov> > Cc: release-team(a)lists.kbase.us > Sent: Tuesday, May 7, 2013 9:56:00 AM > Subject: Re: [Release-team] Fwd: 3:30 - 4:30 pm CST Webmaster Candidate Telecon > > I can't find any evidence that the genome_annotation was redeployed > into > the test VM and retested with all the updates. Are we skipping that > step? > > Miriam > > On 5/4/13 7:38 PM, "Dan Olson" <dolson(a)mcs.anl.gov> wrote: > > > > >There will be an updated vm, likely tuesday. > >---- > >Daniel Murphy-Olson > >Systems Administrator > >Mathematics & Computer Science Division > >Argonne National Laboratory > >630-252-0055 > > > >----- Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> Hey Guys, > >> > >> I got the approval to send Susan Gregurick a laptop preloaded with > >>KBase. I have Virtual Box installed. I'm blocking on an ubuntu > >>image and > >>a dmg. Will there be a new ubuntu image and/or dmg this week? About > >>all > >>I imagine is auth and genome annotation modules would be redeployed > >>on > >>the vm and dmg. > >> > >> Let me know what you think. Otherwise, I;ll just preload the old > >> image > >>and dmg and ship it to her. > >> > >> Thanks, > >> Tom > >> > >

1 0

Re: [Release-team] Fwd: 3:30 - 4:30 pm CST Webmaster Candidate Telecon
by Land, Miriam L. 07 May '13

07 May '13

I can't find any evidence that the genome_annotation was redeployed into the test VM and retested with all the updates. Are we skipping that step? Miriam On 5/4/13 7:38 PM, "Dan Olson" <dolson(a)mcs.anl.gov> wrote: > >There will be an updated vm, likely tuesday. >---- >Daniel Murphy-Olson >Systems Administrator >Mathematics & Computer Science Division >Argonne National Laboratory >630-252-0055 > >----- Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> Hey Guys, >> >> I got the approval to send Susan Gregurick a laptop preloaded with >>KBase. I have Virtual Box installed. I'm blocking on an ubuntu image and >>a dmg. Will there be a new ubuntu image and/or dmg this week? About all >>I imagine is auth and genome annotation modules would be redeployed on >>the vm and dmg. >> >> Let me know what you think. Otherwise, I;ll just preload the old image >>and dmg and ship it to her. >> >> Thanks, >> Tom >>

1 0

Re: [Release-team] Fwd: 3:30 - 4:30 pm CST Webmaster Candidate Telecon
by Thomas Brettin 06 May '13

06 May '13

OK, thanks. I need to send Susan the laptop. I got the paperwork approved and told her such. If I could have by the end of the week we could call it done. t On May 4, 2013, at 6:38 PM, Dan Olson <dolson(a)mcs.anl.gov> wrote: > > There will be an updated vm, likely tuesday. > ---- > Daniel Murphy-Olson > Systems Administrator > Mathematics & Computer Science Division > Argonne National Laboratory > 630-252-0055 > > ----- Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> Hey Guys, >> >> I got the approval to send Susan Gregurick a laptop preloaded with KBase. I have Virtual Box installed. I'm blocking on an ubuntu image and a dmg. Will there be a new ubuntu image and/or dmg this week? About all I imagine is auth and genome annotation modules would be redeployed on the vm and dmg. >> >> Let me know what you think. Otherwise, I;ll just preload the old image and dmg and ship it to her. >> >> Thanks, >> Tom >> >> Begin forwarded message: >> >>> From: Nomi Harris <nlharris(a)lbl.gov> >>> Subject: Re: 3:30 - 4:30 pm CST Webmaster Candidate Telecon >>> Date: May 2, 2013 11:37:45 AM CDT >>> To: Thomas Brettin <brettin(a)mcs.anl.gov> >>> >>> I guess we just disagree about this. At any rate, we both have bigger things to worry about. >>> I hope the Bootcamp is going well. Let's touch base at some point about the minor release. I have not been monitoring that as closely as perhaps I should. >>> Nomi >>> >>> On May 2, 2013, at 8:48 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >>> >>>> >>>>> I'm not willing >>>> >>>> >>>> Am I missing something here? I'm sorry if my position upset you. This doesn't make sense to me. What is the harm in this. It could only be productive regardless if it is by your design or not. >>>> >>>> >>>> >>>> On May 2, 2013, at 10:37 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>>> >>>>> I really do have another meeting at 3:30 CT (sorry for not communicating that), but at any rate, I'm not willing to talk to Tom Brown with Tom Brettin listening in, so let's just forget it. Go ahead and hire him, I'm sure he'll be fine. >>>>> Nomi >>>>> >>>>> On May 2, 2013, at 8:32 AM, India Gordon <igordon(a)cels.anl.gov> wrote: >>>>> >>>>>> Good morning Nomi, >>>>>> >>>>>> I'm sorry. In your original e-mail you said you were available. Will you please let me know what time works for you? >>>>>> >>>>>> Thank you, >>>>>> India >>>>>> >>>>>> On May 2, 2013, at 10:22 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >>>>>> >>>>>> India, >>>>>> >>>>>> My proposal is to make my participation in the call optional when it comes to scheduling. While I would like to be on the call and would find it valuable, I think it's more important from a scheduling perspective to have the call with Nomi. >>>>>> >>>>>> Thanks, >>>>>> Tom >>>>>> >>>>>> On May 2, 2013, at 10:18 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>>>>> >>>>>>> I'm sorry, I already have a meeting at this time. >>>>>>> Tom Brettin, I know you're busy with the Bootcamp--why don't we find a time to talk when that's over. >>>>>>> Nomi >>>>>>> >>>>>>> On May 1, 2013, at 8:21 PM, brettin(a)mcs.anl.gov wrote: >>>>>>> >>>>>>>> The following is a new meeting request: >>>>>>>> >>>>>>>> Subject: 3:30 - 4:30 pm CST Webmaster Candidate 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: Friday, May 3, 2013, 3:30:00 PM - 4:30:00 PM GMT -06:00 US/Canada Central >>>>>>>> Invitees: nlharris(a)lbl.gov; tomasbrown(a)gmail.com >>>>>>>> *~*~*~*~*~*~*~*~*~* >>>>>>>> >>>>>>>> <meeting.ics> >>> >> >

1 0

Re: [Release-team] Fwd: 3:30 - 4:30 pm CST Webmaster Candidate Telecon
by Dan Olson 04 May '13

04 May '13

There will be an updated vm, likely tuesday. ---- Daniel Murphy-Olson Systems Administrator Mathematics & Computer Science Division Argonne National Laboratory 630-252-0055 ----- Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Hey Guys, > > I got the approval to send Susan Gregurick a laptop preloaded with KBase. I have Virtual Box installed. I'm blocking on an ubuntu image and a dmg. Will there be a new ubuntu image and/or dmg this week? About all I imagine is auth and genome annotation modules would be redeployed on the vm and dmg. > > Let me know what you think. Otherwise, I;ll just preload the old image and dmg and ship it to her. > > Thanks, > Tom > > Begin forwarded message: > > > From: Nomi Harris <nlharris(a)lbl.gov> > > Subject: Re: 3:30 - 4:30 pm CST Webmaster Candidate Telecon > > Date: May 2, 2013 11:37:45 AM CDT > > To: Thomas Brettin <brettin(a)mcs.anl.gov> > > > > I guess we just disagree about this. At any rate, we both have bigger things to worry about. > > I hope the Bootcamp is going well. Let's touch base at some point about the minor release. I have not been monitoring that as closely as perhaps I should. > > Nomi > > > > On May 2, 2013, at 8:48 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > > > >> > >>> I'm not willing > >> > >> > >> Am I missing something here? I'm sorry if my position upset you. This doesn't make sense to me. What is the harm in this. It could only be productive regardless if it is by your design or not. > >> > >> > >> > >> On May 2, 2013, at 10:37 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> > >>> I really do have another meeting at 3:30 CT (sorry for not communicating that), but at any rate, I'm not willing to talk to Tom Brown with Tom Brettin listening in, so let's just forget it. Go ahead and hire him, I'm sure he'll be fine. > >>> Nomi > >>> > >>> On May 2, 2013, at 8:32 AM, India Gordon <igordon(a)cels.anl.gov> wrote: > >>> > >>>> Good morning Nomi, > >>>> > >>>> I'm sorry. In your original e-mail you said you were available. Will you please let me know what time works for you? > >>>> > >>>> Thank you, > >>>> India > >>>> > >>>> On May 2, 2013, at 10:22 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >>>> > >>>> India, > >>>> > >>>> My proposal is to make my participation in the call optional when it comes to scheduling. While I would like to be on the call and would find it valuable, I think it's more important from a scheduling perspective to have the call with Nomi. > >>>> > >>>> Thanks, > >>>> Tom > >>>> > >>>> On May 2, 2013, at 10:18 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >>>> > >>>>> I'm sorry, I already have a meeting at this time. > >>>>> Tom Brettin, I know you're busy with the Bootcamp--why don't we find a time to talk when that's over. > >>>>> Nomi > >>>>> > >>>>> On May 1, 2013, at 8:21 PM, brettin(a)mcs.anl.gov wrote: > >>>>> > >>>>>> The following is a new meeting request: > >>>>>> > >>>>>> Subject: 3:30 - 4:30 pm CST Webmaster Candidate 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: Friday, May 3, 2013, 3:30:00 PM - 4:30:00 PM GMT -06:00 US/Canada Central > >>>>>> Invitees: nlharris(a)lbl.gov; tomasbrown(a)gmail.com > >>>>>> *~*~*~*~*~*~*~*~*~* > >>>>>> > >>>>>> <meeting.ics> > > >

1 0

Re: [Release-team] 3:30 - 4:30 pm CST Webmaster Candidate Telecon
by Nomi Harris 04 May '13

04 May '13

Automating the dmg and app creation would be great, but I know how fiddly that kind of thing can be. I agree with Bob that our first goal should be to at least make it possible for someone else to also be able to build them. Nomi On May 4, 2013, at 9:41 AM, Robert Olson <olson(a)mcs.anl.gov> wrote: > it's mostly just a stock deployment with some additional scripts to build the app and dmg. What we need is a standard platform to do it on, other than my laptop. > > --bob > > On May 4, 2013, at 10:40 AM, Shane Canon wrote: > >> >> Bob, >> >> How labor intensive is the process right now and what do you think the hurdles are to automating it? I think Tom and Dan captured >> this on a list of todos for infrastructure. Do you have the current steps documented anywhere? If so, we could use that to start >> moving towards automating it. We need to make similar strides on building the virtual machine images, tar balls, etc. I think Dan or Tom >> has made some progress on the later. >> >> --Shane >> >> >> On May 4, 2013, at 6:26 AM, Robert Olson <olson(a)mcs.anl.gov> wrote: >> >>> I started doing the dmg work when we started this build but got distracted along the way somehow. I'll shoot for doing one early this week. >>> >>> >>> >>> On May 4, 2013, at 7:46 AM, Thomas Brettin wrote: >>> >>>> Hey Guys, >>>> >>>> I got the approval to send Susan Gregurick a laptop preloaded with KBase. I have Virtual Box installed. I'm blocking on an ubuntu image and a dmg. Will there be a new ubuntu image and/or dmg this week? About all I imagine is auth and genome annotation modules would be redeployed on the vm and dmg.

1 0