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

Re: [Release-team] Deployments
by Thomas Brettin 11 Feb '13

11 Feb '13

Hey guys, want me to do some deployments? Tom On Feb 11, 2013, at 12:17 PM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > Will there be any deployments today? I haven't seen any changes since I added modules to be deployed on Friday morning. > > Miriam > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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Deployments
by Land, Miriam L. 11 Feb '13

11 Feb '13

Will there be any deployments today? I haven't seen any changes since I added modules to be deployed on Friday morning. Miriam

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Re: [Release-team] Some API docs missing that were there before
by Thomas Brettin 11 Feb '13

11 Feb '13

Glassfish is a web server. Is it taking the nginx port? On Feb 11, 2013, at 10:56 AM, Nomi Harris <nlharris(a)lbl.gov> wrote: > > On Feb 11, 2013, at 8:47 AM, Shane Canon <scanon(a)lbl.gov> wrote: > >> These are all fixed now. These were mostly an issue with deployment. > > Thanks! > >> Two remarks: >> * Regulation still needs to fix the docs to show the right thing. > > Yeah, I don't see their api doc--I just see a Glassfish default page. > >> * It would be nice if there was an index.html for all of the services so that following the doc link takes you to a formatted page. > > Well, this is not something that's needed for getting the API docs onto kbase.us, so I'm not sure it's a good use of developers' time (or are you suggesting that the tech doc team produce these?). The automated process that most repos use to make the API docs (typespec -> type compiler -> perl libraries -> pod2html -> html API doc) does not produce an index.html. > >> I'm especially keen on this last point. > > Why? > > Nomi > >> >> --Shane >> >> >> On Feb 9, 2013, at 4:48 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> Still missing: >>> aux_store >>> jnomics >>> protein_info_service >>> regprecise (aka Regulation) (just shows some generic Glassfish page) >>> >>> Newly missing (was there yesterday): >>> genotype_phenotype_api >>> >>> Nomi >>> >>> On Feb 8, 2013, at 1:26 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >>> >>>> Here's a list of modules for which API docs are not showing up or there's some issue (weird self-referential webroot symlink?). >>>> If not otherwise indicated, then the issue is that the API docs were there at some point but are missing now. >>>> >>>> auth_service >>>> (aux_store--but I don't think that was deployed) >>>> file_type_service >>>> genome_annotation >>>> genotype_phenotype_api (doc there but has funky webroot symlink) >>>> invocation (doc there but has funky webroot symlink) >>>> jnomics (should have javadocs and user guide--Dan will try to figure out what happened to them) >>>> networks (doc was there yesterday in KBaseNetworksService--today there is no such dir, there is a networks dir, but empty) >>>> protein_info_service >>>> regprecise (aka Regulation) >>>> trees >>>> workspace_service (workspaceService) >>>> registry >>>> >>>> >>>> Begin forwarded message: >>>> >>>>> From: Nomi Harris <nlharris(a)lbl.gov> >>>>> Subject: Some API docs missing that were there before >>>>> Date: February 7, 2013 5:38:26 PM PST >>>>> To: "release-team(a)lists.kbase.us" <release-team(a)lists.kbase.us> >>>>> Cc: Nomi Harris <nlharris(a)lbl.gov> >>>>> >>>>> I'm checking API docs at http://140.221.84.191/services/docs/ >>>>> Some were there after the first deploy but are not now. They are yellow in column M of https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0Ana5oznWypH2dFppaEJz… >>>>> One of them--Regulation--is particularly odd since I saw the API docs there an hour or two before and now I don't. >>>>> Nomi Harris >>>>> Project Manager, KBase >>>>> >>>> >>> >> > > _______________________________________________ > Release-team mailing list > Release-team(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/release-team Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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Re: [Release-team] Some API docs missing that were there before
by Nomi Harris 11 Feb '13

11 Feb '13

On Feb 11, 2013, at 8:47 AM, Shane Canon <scanon(a)lbl.gov> wrote: > These are all fixed now. These were mostly an issue with deployment. Thanks! > Two remarks: > * Regulation still needs to fix the docs to show the right thing. Yeah, I don't see their api doc--I just see a Glassfish default page. > * It would be nice if there was an index.html for all of the services so that following the doc link takes you to a formatted page. Well, this is not something that's needed for getting the API docs onto kbase.us, so I'm not sure it's a good use of developers' time (or are you suggesting that the tech doc team produce these?). The automated process that most repos use to make the API docs (typespec -> type compiler -> perl libraries -> pod2html -> html API doc) does not produce an index.html. > I'm especially keen on this last point. Why? Nomi > > --Shane > > > On Feb 9, 2013, at 4:48 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> Still missing: >> aux_store >> jnomics >> protein_info_service >> regprecise (aka Regulation) (just shows some generic Glassfish page) >> >> Newly missing (was there yesterday): >> genotype_phenotype_api >> >> Nomi >> >> On Feb 8, 2013, at 1:26 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: >> >>> Here's a list of modules for which API docs are not showing up or there's some issue (weird self-referential webroot symlink?). >>> If not otherwise indicated, then the issue is that the API docs were there at some point but are missing now. >>> >>> auth_service >>> (aux_store--but I don't think that was deployed) >>> file_type_service >>> genome_annotation >>> genotype_phenotype_api (doc there but has funky webroot symlink) >>> invocation (doc there but has funky webroot symlink) >>> jnomics (should have javadocs and user guide--Dan will try to figure out what happened to them) >>> networks (doc was there yesterday in KBaseNetworksService--today there is no such dir, there is a networks dir, but empty) >>> protein_info_service >>> regprecise (aka Regulation) >>> trees >>> workspace_service (workspaceService) >>> registry >>> >>> >>> Begin forwarded message: >>> >>>> From: Nomi Harris <nlharris(a)lbl.gov> >>>> Subject: Some API docs missing that were there before >>>> Date: February 7, 2013 5:38:26 PM PST >>>> To: "release-team(a)lists.kbase.us" <release-team(a)lists.kbase.us> >>>> Cc: Nomi Harris <nlharris(a)lbl.gov> >>>> >>>> I'm checking API docs at http://140.221.84.191/services/docs/ >>>> Some were there after the first deploy but are not now. They are yellow in column M of https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0Ana5oznWypH2dFppaEJz… >>>> One of them--Regulation--is particularly odd since I saw the API docs there an hour or two before and now I don't. >>>> Nomi Harris >>>> Project Manager, KBase >>>> >>> >> >

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Re: [Release-team] Some API docs missing that were there before
by Shane Canon 11 Feb '13

11 Feb '13

These are all fixed now. These were mostly an issue with deployment. Two remarks: * Regulation still needs to fix the docs to show the right thing. * It would be nice if there was an index.html for all of the services so that following the doc link takes you to a formatted page. I'm especially keen on this last point. --Shane On Feb 9, 2013, at 4:48 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > Still missing: > aux_store > jnomics > protein_info_service > regprecise (aka Regulation) (just shows some generic Glassfish page) > > Newly missing (was there yesterday): > genotype_phenotype_api > > Nomi > > On Feb 8, 2013, at 1:26 PM, Nomi Harris <nlharris(a)lbl.gov> wrote: > >> Here's a list of modules for which API docs are not showing up or there's some issue (weird self-referential webroot symlink?). >> If not otherwise indicated, then the issue is that the API docs were there at some point but are missing now. >> >> auth_service >> (aux_store--but I don't think that was deployed) >> file_type_service >> genome_annotation >> genotype_phenotype_api (doc there but has funky webroot symlink) >> invocation (doc there but has funky webroot symlink) >> jnomics (should have javadocs and user guide--Dan will try to figure out what happened to them) >> networks (doc was there yesterday in KBaseNetworksService--today there is no such dir, there is a networks dir, but empty) >> protein_info_service >> regprecise (aka Regulation) >> trees >> workspace_service (workspaceService) >> registry >> >> >> Begin forwarded message: >> >>> From: Nomi Harris <nlharris(a)lbl.gov> >>> Subject: Some API docs missing that were there before >>> Date: February 7, 2013 5:38:26 PM PST >>> To: "release-team(a)lists.kbase.us" <release-team(a)lists.kbase.us> >>> Cc: Nomi Harris <nlharris(a)lbl.gov> >>> >>> I'm checking API docs at http://140.221.84.191/services/docs/ >>> Some were there after the first deploy but are not now. They are yellow in column M of https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0Ana5oznWypH2dFppaEJz… >>> One of them--Regulation--is particularly odd since I saw the API docs there an hour or two before and now I don't. >>> Nomi Harris >>> Project Manager, KBase >>> >> >

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Re: [Release-team] [Kbase-ui] prizes for this week
by Syed, Mustafa H. 11 Feb '13

11 Feb '13

Thanks for the appreciation!! I want to acknowledge Miriam, Ranjan and Shinjae for their help & guidance. Cheers, Mustafa. -----Original Message----- From: Land, Miriam L. Sent: Monday, February 11, 2013 10:04 AM To: Nomi Harris; Thomas Brettin Cc: release-team(a)lists.kbase.us; Syed, Mustafa H. Subject: Re: [Release-team] [Kbase-ui] prizes for this week I've decided that the prize for best test coverage should go to Mustafa Syed for his contribution to the genotype_phenotype_api test. He did not get a set of sample tests from the testing team, there was nothing automated to help generate hundreds of tests, the tests were more than the base minimum (test using sample data), and the first attempt included client, server, and script tests. The Chewbacca MimoMicro USB Drive & Reader goes to Mustafa. Miriam On 2/7/13 11:55 PM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: >I decided that Chris Henry has the best API documentation >(http://140.221.84.191/services/docs/workspaceService/workspaceService. >htm l). He gives a good overview of the services, including *why* you >might use it as well as how. He included an example of how you'd use >the API from a perl program. And he documented every variable and >method. >Furthermore, he generated his API docs in the currently approved >standard KBase way, by putting comments in the typespec. I looked at a >few API docs that were very nice-looking, but were not generated the standard way. > >Overall, the API docs are looking pretty good. There are a few that are >not showing up on http://140.221.84.191/services/docs that should be, >which seems like it may be due to some sort of deploy issue. But a lot >more services have API docs now than did in November. > >I gave the Star Wars X-Wing Ice Cube Tray to Andreas to bring back to >ANL for Chris. > > Nomi > >On Feb 3, 2013, at 2:39 PM, Thomas Brettin <brettint(a)gmail.com> wrote: > >> Elizabeth was so kind as to pony up some prizes on behalf of outreach >>for this build :-) >> >> Here is what we came up with for categories-- >> >> The module that has the best test coverage of their service as >>determined by Miriam >>> Prize: Chewbacca MimoMicro USB Drive & Reader >> >> >> Best technical API documentation as determined by Nomi >>> Star Wars X-Wing Ice Cube Tray >> >> Best command line user documentation as determined by Paramvir >>> Doctor Who Dalek Tumbler >> >> >> 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] [Kbase-ui] prizes for this week
by Thomas Brettin 11 Feb '13

11 Feb '13

Paramvir, you ok with this? t On Feb 11, 2013, at 9:07 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > I suggested Mike Sneddon last week. > > Miriam > > On 2/11/13 10:06 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: > >> I would like to write up a note and post to kbase devel. >> >> We just need an award for best command help documentation. I don't know >> if Paramvir is going to do this. Miriam, can you suggest someone? Or >> Keith suggest someone? >> >> Tom >> >> >> On Feb 11, 2013, at 9:03 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: >> >>> I've decided that the prize for best test coverage should go to Mustafa >>> Syed for his contribution to the genotype_phenotype_api test. He did >>> not >>> get a set of sample tests from the testing team, there was nothing >>> automated to help generate hundreds of tests, the tests were more than >>> the >>> base minimum (test using sample data), and the first attempt included >>> client, server, and script tests. >>> >>> The Chewbacca MimoMicro USB Drive & Reader goes to Mustafa. >>> >>> Miriam >>> >>> On 2/7/13 11:55 PM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: >>> >>>> I decided that Chris Henry has the best API documentation >>>> >>>> (http://140.221.84.191/services/docs/workspaceService/workspaceService.h >>>> tm >>>> l). He gives a good overview of the services, including *why* you might >>>> use it as well as how. He included an example of how you'd use the API >>>> from a perl program. And he documented every variable and method. >>>> Furthermore, he generated his API docs in the currently approved >>>> standard >>>> KBase way, by putting comments in the typespec. I looked at a few API >>>> docs that were very nice-looking, but were not generated the standard >>>> way. >>>> >>>> Overall, the API docs are looking pretty good. There are a few that are >>>> not showing up on http://140.221.84.191/services/docs that should be, >>>> which seems like it may be due to some sort of deploy issue. But a lot >>>> more services have API docs now than did in November. >>>> >>>> I gave the Star Wars X-Wing Ice Cube Tray to Andreas to bring back to >>>> ANL >>>> for Chris. >>>> >>>> Nomi >>>> >>>> On Feb 3, 2013, at 2:39 PM, Thomas Brettin <brettint(a)gmail.com> wrote: >>>> >>>>> Elizabeth was so kind as to pony up some prizes on behalf of outreach >>>>> for this build :-) >>>>> >>>>> Here is what we came up with for categories-- >>>>> >>>>> The module that has the best test coverage of their service as >>>>> determined by Miriam >>>>>> Prize: Chewbacca MimoMicro USB Drive & Reader >>>>> >>>>> >>>>> Best technical API documentation as determined by Nomi >>>>>> Star Wars X-Wing Ice Cube Tray >>>>> >>>>> Best command line user documentation as determined by Paramvir >>>>>> Doctor Who Dalek Tumbler >>>>> >>>>> >>>>> Tom >>>> >>>> _______________________________________________ >>>> Release-team mailing list >>>> Release-team(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/release-team >>> >> >> Thomas Brettin >> 865-603-7760 (cell) >> brettin(a)mcs.anl.gov >> >> >> > Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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Re: [Release-team] [Kbase-ui] prizes for this week
by Land, Miriam L. 11 Feb '13

11 Feb '13

I suggested Mike Sneddon last week. Miriam On 2/11/13 10:06 AM, "Thomas Brettin" <brettin(a)mcs.anl.gov> wrote: >I would like to write up a note and post to kbase devel. > >We just need an award for best command help documentation. I don't know >if Paramvir is going to do this. Miriam, can you suggest someone? Or >Keith suggest someone? > >Tom > > >On Feb 11, 2013, at 9:03 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > >> I've decided that the prize for best test coverage should go to Mustafa >> Syed for his contribution to the genotype_phenotype_api test. He did >>not >> get a set of sample tests from the testing team, there was nothing >> automated to help generate hundreds of tests, the tests were more than >>the >> base minimum (test using sample data), and the first attempt included >> client, server, and script tests. >> >> The Chewbacca MimoMicro USB Drive & Reader goes to Mustafa. >> >> Miriam >> >> On 2/7/13 11:55 PM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: >> >>> I decided that Chris Henry has the best API documentation >>> >>>(http://140.221.84.191/services/docs/workspaceService/workspaceService.h >>>tm >>> l). He gives a good overview of the services, including *why* you might >>> use it as well as how. He included an example of how you'd use the API >>> from a perl program. And he documented every variable and method. >>> Furthermore, he generated his API docs in the currently approved >>>standard >>> KBase way, by putting comments in the typespec. I looked at a few API >>> docs that were very nice-looking, but were not generated the standard >>>way. >>> >>> Overall, the API docs are looking pretty good. There are a few that are >>> not showing up on http://140.221.84.191/services/docs that should be, >>> which seems like it may be due to some sort of deploy issue. But a lot >>> more services have API docs now than did in November. >>> >>> I gave the Star Wars X-Wing Ice Cube Tray to Andreas to bring back to >>>ANL >>> for Chris. >>> >>> Nomi >>> >>> On Feb 3, 2013, at 2:39 PM, Thomas Brettin <brettint(a)gmail.com> wrote: >>> >>>> Elizabeth was so kind as to pony up some prizes on behalf of outreach >>>> for this build :-) >>>> >>>> Here is what we came up with for categories-- >>>> >>>> The module that has the best test coverage of their service as >>>> determined by Miriam >>>>> Prize: Chewbacca MimoMicro USB Drive & Reader >>>> >>>> >>>> Best technical API documentation as determined by Nomi >>>>> Star Wars X-Wing Ice Cube Tray >>>> >>>> Best command line user documentation as determined by Paramvir >>>>> Doctor Who Dalek Tumbler >>>> >>>> >>>> Tom >>> >>> _______________________________________________ >>> Release-team mailing list >>> Release-team(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/release-team >> > >Thomas Brettin >865-603-7760 (cell) >brettin(a)mcs.anl.gov > > >

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Re: [Release-team] [Kbase-ui] prizes for this week
by Thomas Brettin 11 Feb '13

11 Feb '13

I would like to write up a note and post to kbase devel. We just need an award for best command help documentation. I don't know if Paramvir is going to do this. Miriam, can you suggest someone? Or Keith suggest someone? Tom On Feb 11, 2013, at 9:03 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > I've decided that the prize for best test coverage should go to Mustafa > Syed for his contribution to the genotype_phenotype_api test. He did not > get a set of sample tests from the testing team, there was nothing > automated to help generate hundreds of tests, the tests were more than the > base minimum (test using sample data), and the first attempt included > client, server, and script tests. > > The Chewbacca MimoMicro USB Drive & Reader goes to Mustafa. > > Miriam > > On 2/7/13 11:55 PM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: > >> I decided that Chris Henry has the best API documentation >> (http://140.221.84.191/services/docs/workspaceService/workspaceService.htm >> l). He gives a good overview of the services, including *why* you might >> use it as well as how. He included an example of how you'd use the API >> from a perl program. And he documented every variable and method. >> Furthermore, he generated his API docs in the currently approved standard >> KBase way, by putting comments in the typespec. I looked at a few API >> docs that were very nice-looking, but were not generated the standard way. >> >> Overall, the API docs are looking pretty good. There are a few that are >> not showing up on http://140.221.84.191/services/docs that should be, >> which seems like it may be due to some sort of deploy issue. But a lot >> more services have API docs now than did in November. >> >> I gave the Star Wars X-Wing Ice Cube Tray to Andreas to bring back to ANL >> for Chris. >> >> Nomi >> >> On Feb 3, 2013, at 2:39 PM, Thomas Brettin <brettint(a)gmail.com> wrote: >> >>> Elizabeth was so kind as to pony up some prizes on behalf of outreach >>> for this build :-) >>> >>> Here is what we came up with for categories-- >>> >>> The module that has the best test coverage of their service as >>> determined by Miriam >>>> Prize: Chewbacca MimoMicro USB Drive & Reader >>> >>> >>> Best technical API documentation as determined by Nomi >>>> Star Wars X-Wing Ice Cube Tray >>> >>> Best command line user documentation as determined by Paramvir >>>> Doctor Who Dalek Tumbler >>> >>> >>> Tom >> >> _______________________________________________ >> Release-team mailing list >> Release-team(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/release-team > Thomas Brettin 865-603-7760 (cell) brettin(a)mcs.anl.gov

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Re: [Release-team] [Kbase-ui] prizes for this week
by Land, Miriam L. 11 Feb '13

11 Feb '13

I've decided that the prize for best test coverage should go to Mustafa Syed for his contribution to the genotype_phenotype_api test. He did not get a set of sample tests from the testing team, there was nothing automated to help generate hundreds of tests, the tests were more than the base minimum (test using sample data), and the first attempt included client, server, and script tests. The Chewbacca MimoMicro USB Drive & Reader goes to Mustafa. Miriam On 2/7/13 11:55 PM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: >I decided that Chris Henry has the best API documentation >(http://140.221.84.191/services/docs/workspaceService/workspaceService.htm >l). He gives a good overview of the services, including *why* you might >use it as well as how. He included an example of how you'd use the API >from a perl program. And he documented every variable and method. >Furthermore, he generated his API docs in the currently approved standard >KBase way, by putting comments in the typespec. I looked at a few API >docs that were very nice-looking, but were not generated the standard way. > >Overall, the API docs are looking pretty good. There are a few that are >not showing up on http://140.221.84.191/services/docs that should be, >which seems like it may be due to some sort of deploy issue. But a lot >more services have API docs now than did in November. > >I gave the Star Wars X-Wing Ice Cube Tray to Andreas to bring back to ANL >for Chris. > > Nomi > >On Feb 3, 2013, at 2:39 PM, Thomas Brettin <brettint(a)gmail.com> wrote: > >> Elizabeth was so kind as to pony up some prizes on behalf of outreach >>for this build :-) >> >> Here is what we came up with for categories-- >> >> The module that has the best test coverage of their service as >>determined by Miriam >>> Prize: Chewbacca MimoMicro USB Drive & Reader >> >> >> Best technical API documentation as determined by Nomi >>> Star Wars X-Wing Ice Cube Tray >> >> Best command line user documentation as determined by Paramvir >>> Doctor Who Dalek Tumbler >> >> >> Tom > >_______________________________________________ >Release-team mailing list >Release-team(a)lists.kbase.us >https://lists.kbase.us/mailman/listinfo/release-team

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