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

11:00 - 11:30 am CST Release team sync
by brettin＠mcs.anl.gov 03 Jun '13

03 Jun '13

The following meeting has been modified: Subject: 11:00 - 11:30 am CST Release team sync [MODIFIED] 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, June 3, 2013, 11:00:00 AM - 11:30:00 AM GMT -06:00 US/Canada Central [MODIFIED] Invitees: release-team(a)kbase.us *~*~*~*~*~*~*~*~*~* we should meet next week to sync and tie up loose ends. India, can you schedule something for us. Phone is fine. To keep the meeting short, can everyone send me any outstanding issues/tasks/etc? I know of some right now. 1) ubuntu image needs to be made 2) iris production server needs to be finished 3) public communication The things that I think are done, but we should verify new dmg testing of the dmg testing of production services testing of iris

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1:00 - 1:30 pm CST Release team sync
by brettin＠mcs.anl.gov 03 Jun '13

03 Jun '13

The following is a new meeting request: Subject: 1:00 - 1:30 pm CST Release team sync 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, June 3, 2013, 1:00:00 PM - 1:30:00 PM GMT -06:00 US/Canada Central Invitees: release-team(a)kbase.us *~*~*~*~*~*~*~*~*~* we should meet next week to sync and tie up loose ends. India, can you schedule something for us. Phone is fine. To keep the meeting short, can everyone send me any outstanding issues/tasks/etc? I know of some right now. 1) ubuntu image needs to be made 2) iris production server needs to be finished 3) public communication The things that I think are done, but we should verify new dmg testing of the dmg testing of production services testing of iris

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sync up next week to tie up loose ends
by Thomas Brettin 31 May '13

31 May '13

we should meet next week to sync and tie up loose ends. India, can you schedule something for us. Phone is fine. To keep the meeting short, can everyone send me any outstanding issues/tasks/etc? I know of some right now. 1) ubuntu image needs to be made 2) iris production server needs to be finished 3) public communication The things that I think are done, but we should verify new dmg testing of the dmg testing of production services testing of iris

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Re: [Release-team] Release
by Nomi Harris 29 May '13

29 May '13

Maybe today at the developer meeting you could ask each developer to summarize the significant changes in their service(s) since the Feb release? (But someone else will have to take notes--I unfortunately have a conflicting meeting.) For future releases, it would be good to have a less interventional way to collect this information, like maybe release notes or something similar. Nomi On May 29, 2013, at 9:42 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > Right, I don't plan on going through the commits either. I don't have a change list. It would have to be constructed by talking with each developer. > > > On May 29, 2013, at 11:41 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> Sure, I can put together an announcement if you send me a change list. (Combing the git commits is not a useful way to get that. There have been thousands of commits since Feb., most of which are not interesting to anyone outside of KBase.) >> Nomi >> >> On May 29, 2013, at 9:39 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: >> >>> I was wondering last night if you are going to prepare the text for the updates to the public site? >>> >>> >>> On May 29, 2013, at 11:36 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>>> How is the release coming along? Have the updated services been pushed to production? Do we need to update some of the downloads on https://www.kbase.us/developer-zone/downloads/ ? >>>> >>>> Any changes needed on https://www.kbase.us/developer-zone/services/ ? (BTW, I just noticed that something funny has happened with the fonts on that page--the service names are now in a different font, and no longer bold.) >>>> >>>> When the release is ready, I'd like to put up an announcement on kbase.us. How can I get a summary of what's changed in this release? >>>> >>>> Thanks, >>>> Nomi Harris >>>> Project Manager, KBase

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Re: [Release-team] Release
by Thomas Brettin 29 May '13

29 May '13

Right, I don't plan on going through the commits either. I don't have a change list. It would have to be constructed by talking with each developer. On May 29, 2013, at 11:41 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Sure, I can put together an announcement if you send me a change list. (Combing the git commits is not a useful way to get that. There have been thousands of commits since Feb., most of which are not interesting to anyone outside of KBase.) > Nomi > > On May 29, 2013, at 9:39 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > >> I was wondering last night if you are going to prepare the text for the updates to the public site? >> >> >> On May 29, 2013, at 11:36 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> How is the release coming along? Have the updated services been pushed to production? Do we need to update some of the downloads on https://www.kbase.us/developer-zone/downloads/ ? >>> >>> Any changes needed on https://www.kbase.us/developer-zone/services/ ? (BTW, I just noticed that something funny has happened with the fonts on that page--the service names are now in a different font, and no longer bold.) >>> >>> When the release is ready, I'd like to put up an announcement on kbase.us. How can I get a summary of what's changed in this release? >>> >>> Thanks, >>> Nomi Harris >>> Project Manager, KBase >>> >>> _______________________________________________ >>> 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] Release
by Nomi Harris 29 May '13

29 May '13

Sure, I can put together an announcement if you send me a change list. (Combing the git commits is not a useful way to get that. There have been thousands of commits since Feb., most of which are not interesting to anyone outside of KBase.) Nomi On May 29, 2013, at 9:39 AM, Thomas Brettin <brettin(a)mcs.anl.gov> wrote: > I was wondering last night if you are going to prepare the text for the updates to the public site? > > > On May 29, 2013, at 11:36 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> How is the release coming along? Have the updated services been pushed to production? Do we need to update some of the downloads on https://www.kbase.us/developer-zone/downloads/ ? >> >> Any changes needed on https://www.kbase.us/developer-zone/services/ ? (BTW, I just noticed that something funny has happened with the fonts on that page--the service names are now in a different font, and no longer bold.) >> >> When the release is ready, I'd like to put up an announcement on kbase.us. How can I get a summary of what's changed in this release? >> >> Thanks, >> Nomi Harris >> Project Manager, KBase >> >> _______________________________________________ >> 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] Release
by Thomas Brettin 29 May '13

29 May '13

I was wondering last night if you are going to prepare the text for the updates to the public site? On May 29, 2013, at 11:36 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > How is the release coming along? Have the updated services been pushed to production? Do we need to update some of the downloads on https://www.kbase.us/developer-zone/downloads/ ? > > Any changes needed on https://www.kbase.us/developer-zone/services/ ? (BTW, I just noticed that something funny has happened with the fonts on that page--the service names are now in a different font, and no longer bold.) > > When the release is ready, I'd like to put up an announcement on kbase.us. How can I get a summary of what's changed in this release? > > Thanks, > Nomi Harris > Project Manager, KBase > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team

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Release
by Nomi Harris 29 May '13

29 May '13

How is the release coming along? Have the updated services been pushed to production? Do we need to update some of the downloads on https://www.kbase.us/developer-zone/downloads/ ? Any changes needed on https://www.kbase.us/developer-zone/services/ ? (BTW, I just noticed that something funny has happened with the fonts on that page--the service names are now in a different font, and no longer bold.) When the release is ready, I'd like to put up an announcement on kbase.us. How can I get a summary of what's changed in this release? Thanks, Nomi Harris Project Manager, KBase

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Re: [Release-team] auto generation of command -h output
by Land, Miriam L. 22 May '13

22 May '13

FYI - Behavior with -h and --help 3 modules (idserver, kb_seed, and phispy) have one or more scripts that state that these are unknown options. A usage message is sent and an error code is returned. The user gets the information they need but there is no contribution to the auto-generation of documentation. There is a total of 8 affected scripts. 2 modules (kb_seed and KBaseFBAModeling) have one or more scripts that return an error code and an error message but no usage information. These have been reported in JIRA. There is a total of 5 affected scripts. 1 module (KBaseFBAModeling) has one script that returns an error code but the text on the screen looks like normal usage information. Auto-generation of documentation would probably miss this one. Miriam On 5/22/13 4:41 PM, "Land, Miriam L." <landml(a)ornl.gov> wrote: >How much of a nag should I be when h and ‹help are not valid options? >For example: > >----------TEST idserver external_ids_to_kbase_ids with --help option >Unknown option: help >usage: external_ids_to_kbase_ids [-c column] DB-name < input > output > >It contains usage information but it is non-standard. > >Miriam > >From: Tom Brettin <brettin(a)mcs.anl.gov<mailto:[email protected]>> >Date: Wednesday, May 22, 2013 4:37 PM >To: Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]>> >Cc: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>>, Elizabeth >Glass <marland(a)mcs.anl.gov<mailto:[email protected]>>, 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: Re: [Release-team] auto generation of command -h output > >Please tell the module owner to fix the problem, > >Also, we're seeing errors from the gen-comand-docs.pl program while >deploying invocation service in production. > >Tom >On May 22, 2013, at 12:33 PM, Michael Sneddon ><mwsneddon(a)lbl.gov<mailto:[email protected]>> wrote: > >It appears that there are problems with processing the COMMANDS file. > >For "communities_api" and "communities_qc", the COMMANDS file is not >properly formed- the module authors have used "group-set" as a keyword >instead of "command-set", so no scripts are recognized by invocation. > >For "jnomics" and "assembly", the COMMANDS file looks like it was parsed >correctly, but the files were not located by the "gen-valid-commands" >script. It could be a problem with the regex provided in COMMANDS, or >with handling the regex in the gen-valid-commands script, but I'm not >sure. > >Therefore none of these scripts will appear in the command-docs listing >or in the IRIS deploy as well... > >I've attached output from 'gen-valid-commands' which I modified slightly >to print out the files that are detected. This may help in solving the >problem. > >-michael > > > > >On Wed, May 22, 2013 at 6:26 AM, Land, Miriam L. ><landml(a)ornl.gov<mailto:[email protected]>> 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 >-------- > >Michael, > >The following have a COMMANDS file: > >assembly/COMMANDS >:::::::::::::: >#group-name arast Assembly-RAST scripts >#command-set scripts/(.*).pl arast > > communities_api/COMMANDS >:::::::::::::: >#group-name mgapi Metagenomics Scripts >#group-set scripts/(.*).pl mgapi > >communities_qc/COMMANDS >:::::::::::::: >#group-name qc Sequence QC >#group-set scripts/(.*) qc > >jnomics/COMMANDS >:::::::::::::: >#group-name variation Variation Detection Scripts >#command-set bin/(jk_*) variation ****************** Nothing actually here > >Miriam > >From: Tom Brettin ><brettin(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected] >v<mailto:[email protected]>>> >Date: Tuesday, May 21, 2013 5:55 PM >To: Michael Sneddon ><mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mail >to:[email protected]>>> >Cc: Miriam Land ><landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:lan >dml(a)ornl.gov>>>, Elizabeth Glass ><marland(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected] >v<mailto:[email protected]>>>, Keith Keller ><kkeller(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:kke >ller(a)lbl.gov>>>, >"release-team(a)kbase.us<mailto:[email protected]><mailto:release-team@k >base.us<mailto:[email protected]>>" ><release-team(a)kbase.us<mailto:[email protected]><mailto:release-team@k >base.us<mailto:[email protected]>>> >Subject: Re: [Release-team] auto generation of command -h output > >Not exactly sure what you guys are seeing, but for now I think we should >take the position that we are only documenting those commands listed in >COMMANDS files. IRIS users see these commands, and presumably these >commands are our user facing CLI > >t > > >On May 21, 2013, at 2:18 PM, Michael Sneddon ><mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mail >to:[email protected]>>> wrote: > >Hmm, it should have picked up all of them. I checked out the repos that >contain non-empty COMMANDS files, and our code relies on an invocation >service script to assemble the list of commands. One of these steps >could have an error. What modules/scripts seem to be missing? > >-michael > > >On Tue, May 21, 2013 at 11:46 AM, Land, Miriam L. ><landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:lan >dml(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 >-------- > >There are other modules with a COMMANDS file. Were only certain modules >picked for this demonstration? > >Miriam > >From: Michael Sneddon ><mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mail >to:[email protected]>><mailto:[email protected]<mailto:[email protected]>< >mailto:[email protected]<mailto:[email protected]>>>> >Date: Tuesday, May 21, 2013 2:32 PM >To: Miriam Land ><landml(a)ornl.gov<mailto:[email protected]><mailto:[email protected]<mailto:lan >dml(a)ornl.gov>><mailto:[email protected]<mailto:[email protected]><mailto:landm >l(a)ornl.gov<mailto:[email protected]>>>> >Cc: Tom Brettin ><brettin(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected] >v<mailto:[email protected]>><mailto:[email protected]<mailto:brettin@m >cs.anl.gov><mailto:[email protected]<mailto:[email protected]>>>>, >Elizabeth Glass ><marland(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected] >v<mailto:[email protected]>><mailto:[email protected]<mailto:marland@m >cs.anl.gov><mailto:[email protected]<mailto:[email protected]>>>>, >Keith Keller ><kkeller(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:kke >ller(a)lbl.gov>><mailto:[email protected]<mailto:[email protected]><mailto:kkell >er(a)lbl.gov<mailto:[email protected]>>>>, >"release-team(a)kbase.us<mailto:[email protected]><mailto:release-team@k >base.us<mailto:[email protected]>><mailto:[email protected]<mailto >:[email protected]><mailto:[email protected]<mailto:release-team@k >base.us>>>" ><release-team(a)kbase.us<mailto:[email protected]><mailto:release-team@k >base.us<mailto:[email protected]>><mailto:[email protected]<mailto >:[email protected]><mailto:[email protected]<mailto:release-team@k >base.us>>>> >Subject: Re: [Release-team] auto generation of command -h output > >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<mailto:[email protected]><mailto:[email protected]<mailto:lan >dml(a)ornl.gov>><mailto:[email protected]<mailto:[email protected]><mailto:landm >l(a)ornl.gov<mailto:[email protected]>>>> 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]><mailto:[email protected]<mail >to:[email protected]>><mailto:[email protected]<mailto:[email protected]>< >mailto:[email protected]<mailto:[email protected]>>><mailto:mwsneddon@lbl. >gov<mailto:[email protected]><mailto:[email protected]<mailto:mwsneddon@lb >l.gov>><mailto:[email protected]<mailto:[email protected]><mailto:mwsneddo >n(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]><mailto:[email protected] >v<mailto:[email protected]>><mailto:[email protected]<mailto:brettin@m >cs.anl.gov><mailto:[email protected]<mailto:[email protected]>>><mailt >o:[email protected]<mailto:[email protected]><mailto:[email protected] >ov<mailto:[email protected]>><mailto:[email protected]<mailto:brettin@ >mcs.anl.gov><mailto:[email protected]<mailto:[email protected]>>>>>, >Elizabeth Glass ><marland(a)mcs.anl.gov<mailto:[email protected]><mailto:[email protected] >v<mailto:[email protected]>><mailto:[email protected]<mailto:marland@m >cs.anl.gov><mailto:[email protected]<mailto:[email protected]>>><mailt >o:[email protected]<mailto:[email protected]><mailto:[email protected] >ov<mailto:[email protected]>><mailto:[email protected]<mailto:marland@ >mcs.anl.gov><mailto:[email protected]<mailto:[email protected]>>>>> >Cc: Keith Keller ><kkeller(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto:kke >ller(a)lbl.gov>><mailto:[email protected]<mailto:[email protected]><mailto:kkell >er(a)lbl.gov<mailto:[email protected]>>><mailto:[email protected]<mailto:kkeller >@lbl.gov><mailto:[email protected]<mailto:[email protected]>><mailto:kkeller@l >bl.gov<mailto:[email protected]><mailto:[email protected]<mailto:[email protected] >ov>>>>>, >"release-team(a)kbase.us<mailto:[email protected]><mailto:release-team@k >base.us<mailto:[email protected]>><mailto:[email protected]<mailto >:[email protected]><mailto:[email protected]<mailto:release-team@k >base.us>>><mailto:[email protected]<mailto:[email protected]><mail >to:[email protected]<mailto:[email protected]>><mailto:release-tea >m(a)kbase.us<mailto:[email protected]><mailto:[email protected]<mail >to:[email protected]>>>>" ><release-team(a)kbase.us<mailto:[email protected]><mailto:release-team@k >base.us<mailto:[email protected]>><mailto:[email protected]<mailto >:[email protected]><mailto:[email protected]<mailto:release-team@k >base.us>>><mailto:[email protected]<mailto:[email protected]><mail >to:[email protected]<mailto:[email protected]>><mailto:release-tea >m(a)kbase.us<mailto:[email protected]><mailto:[email protected]<mail >to:[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 > > > > > > > ><gen-valid-commands-output.txt> > >_______________________________________________ >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] auto generation of command -h output
by Michael Sneddon 22 May '13

22 May '13

The gen-command-docs can take some time to run, because certain commands will attempt to take input from stdin even if -h is given. It may appear to hang, but gen-command-docs should detect this case and will still complete. That said, it looks like the version that was tagged for test at the beginning of last week was advanced to include gen-command-docs, but is not pointing to the latest version. The latest version as of a couple days ago will not run the gen-command-docs script on make deploy by default (because it can take a few minutes). It is probably worth bumping the test-tag again to the latest version. Keith and I thought it was safe to start work since the new updates would not be tagged for release this cycle, but perhaps we were wrong since the test tags can be updated mid-build. Sorry if this has created problems! Please let us know if there is something further we can do to help, but removing the deployment dependency on gen-command-docs should be trivial. -michael On Wed, May 22, 2013 at 1:37 PM, Thomas Brettin <Brettin(a)mcs.anl.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 > -------- > Please tell the module owner to fix the problem, > > Also, we're seeing errors from the gen-comand-docs.pl program while > deploying invocation service in production. > > Tom > On May 22, 2013, at 12:33 PM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > > It appears that there are problems with processing the COMMANDS file. > > For "communities_api" and "communities_qc", the COMMANDS file is not > properly formed- the module authors have used "group-set" as a keyword > instead of "command-set", so no scripts are recognized by invocation. > > For "jnomics" and "assembly", the COMMANDS file looks like it was parsed > correctly, but the files were not located by the "gen-valid-commands" > script. It could be a problem with the regex provided in COMMANDS, or with > handling the regex in the gen-valid-commands script, but I'm not sure. > > Therefore none of these scripts will appear in the command-docs listing or > in the IRIS deploy as well... > > I've attached output from 'gen-valid-commands' which I modified slightly > to print out the files that are detected. This may help in solving the > problem. > > -michael > > > > > On Wed, May 22, 2013 at 6:26 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 >> -------- >> >> Michael, >> >> The following have a COMMANDS file: >> >> assembly/COMMANDS >> :::::::::::::: >> #group-name arast Assembly-RAST scripts >> #command-set scripts/(.*).pl arast >> >> communities_api/COMMANDS >> :::::::::::::: >> #group-name mgapi Metagenomics Scripts >> #group-set scripts/(.*).pl mgapi >> >> communities_qc/COMMANDS >> :::::::::::::: >> #group-name qc Sequence QC >> #group-set scripts/(.*) qc >> >> jnomics/COMMANDS >> :::::::::::::: >> #group-name variation Variation Detection Scripts >> #command-set bin/(jk_*) variation ****************** Nothing actually here >> >> Miriam >> >> From: Tom Brettin <brettin(a)mcs.anl.gov<mailto:[email protected]>> >> Date: Tuesday, May 21, 2013 5:55 PM >> To: Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected]>> >> Cc: Miriam Land <landml(a)ornl.gov<mailto:[email protected]>>, Elizabeth >> Glass <marland(a)mcs.anl.gov<mailto:[email protected]>>, Keith Keller < >> kkeller(a)lbl.gov<mailto:[email protected]>>, "release-team(a)kbase.us<mailto: >> release-team(a)kbase.us>" <release-team(a)kbase.us<mailto: >> release-team(a)kbase.us>> >> Subject: Re: [Release-team] auto generation of command -h output >> >> Not exactly sure what you guys are seeing, but for now I think we should >> take the position that we are only documenting those commands listed in >> COMMANDS files. IRIS users see these commands, and presumably these >> commands are our user facing CLI >> >> t >> >> >> On May 21, 2013, at 2:18 PM, Michael Sneddon <mwsneddon(a)lbl.gov<mailto: >> mwsneddon(a)lbl.gov>> wrote: >> >> Hmm, it should have picked up all of them. I checked out the repos that >> contain non-empty COMMANDS files, and our code relies on an invocation >> service script to assemble the list of commands. One of these steps could >> have an error. What modules/scripts seem to be missing? >> >> -michael >> >> >> On Tue, May 21, 2013 at 11:46 AM, Land, Miriam L. <landml(a)ornl.gov >> <mailto:[email protected]>> 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 >> -------- >> >> There are other modules with a COMMANDS file. Were only certain modules >> picked for this demonstration? >> >> Miriam >> >> From: Michael Sneddon <mwsneddon(a)lbl.gov<mailto:[email protected] >> ><mailto:[email protected]<mailto:[email protected]>>> >> Date: Tuesday, May 21, 2013 2:32 PM >> To: Miriam Land <landml(a)ornl.gov<mailto:[email protected]><mailto: >> landml(a)ornl.gov<mailto:[email protected]>>> >> Cc: Tom Brettin <brettin(a)mcs.anl.gov<mailto:[email protected]><mailto: >> brettin(a)mcs.anl.gov<mailto:[email protected]>>>, Elizabeth Glass < >> marland(a)mcs.anl.gov<mailto:[email protected]><mailto: >> marland(a)mcs.anl.gov<mailto:[email protected]>>>, Keith Keller < >> kkeller(a)lbl.gov<mailto:[email protected]><mailto:[email protected]<mailto: >> kkeller(a)lbl.gov>>>, "release-team(a)kbase.us<mailto:[email protected] >> ><mailto:[email protected]<mailto:[email protected]>>" < >> release-team(a)kbase.us<mailto:[email protected]><mailto: >> release-team(a)kbase.us<mailto:[email protected]>>> >> Subject: Re: [Release-team] auto generation of command -h output >> >> 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 >> <mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> >> 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] >> ><mailto:[email protected]<mailto:[email protected]>><mailto: >> mwsneddon(a)lbl.gov<mailto:[email protected]><mailto:[email protected] >> <mailto:[email protected]>>>> >> Date: Tuesday, May 21, 2013 2:06 PM >> To: Tom Brettin <brettin(a)mcs.anl.gov<mailto:[email protected]><mailto: >> brettin(a)mcs.anl.gov<mailto:[email protected]>><mailto: >> brettin(a)mcs.anl.gov<mailto:[email protected]><mailto: >> brettin(a)mcs.anl.gov<mailto:[email protected]>>>>, Elizabeth Glass < >> marland(a)mcs.anl.gov<mailto:[email protected]><mailto: >> marland(a)mcs.anl.gov<mailto:[email protected]>><mailto: >> marland(a)mcs.anl.gov<mailto:[email protected]><mailto: >> marland(a)mcs.anl.gov<mailto:[email protected]>>>> >> Cc: Keith Keller <kkeller(a)lbl.gov<mailto:[email protected]><mailto: >> kkeller(a)lbl.gov<mailto:[email protected]>><mailto:[email protected]<mailto: >> kkeller(a)lbl.gov><mailto:[email protected]<mailto:[email protected]>>>>, " >> release-team(a)kbase.us<mailto:[email protected]><mailto: >> release-team(a)kbase.us<mailto:[email protected]>><mailto: >> release-team(a)kbase.us<mailto:[email protected]><mailto: >> release-team(a)kbase.us<mailto:[email protected]>>>" < >> release-team(a)kbase.us<mailto:[email protected]><mailto: >> release-team(a)kbase.us<mailto:[email protected]>><mailto: >> release-team(a)kbase.us<mailto:[email protected]><mailto: >> 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 >> >> >> >> >> >> >> > <gen-valid-commands-output.txt> > > >

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