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

Re: [Release-team] When will IRIS be updated?
by Thomas Brettin 25 Sep '13

25 Sep '13

Did Functional Ortholog make it through the Aug Build? On Sep 25, 2013, at 6:42 AM, "Land, Miriam L." <landml(a)ornl.gov> wrote: > Invocation is one of the modules in the current mini build. > > Miriam > > On 9/25/13 12:38 AM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: > >> Dear Release Team, >> >> I just checked IRIS to see if the one (!?) script for Functional Ortholog >> Predictor was there, and it was not. I don't see any way to see when IRIS >> was last updated. (I filed a new JIRA ticket about this.) >> >> Does anyone know when IRIS will be updated? Is this something that has to >> be done manually? >> >> When IRIS is updated, will the FOP script, fop-rank-pgene.pl, then be >> accessible from IRIS? It should be, right? >> >> I am asking because the updated Services page (which includes the new >> service, Functional Ortholog Predictor) is basically ready to push to the >> public site but I don't want to push it out until the release is complete. >> >> Thanks, >> Nomi >> _______________________________________________ >> 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

1 0

Re: [Release-team] When will IRIS be updated?
by Land, Miriam L. 25 Sep '13

25 Sep '13

Invocation is one of the modules in the current mini build. Miriam On 9/25/13 12:38 AM, "Nomi Harris" <nlharris(a)lbl.gov> wrote: >Dear Release Team, > >I just checked IRIS to see if the one (!?) script for Functional Ortholog >Predictor was there, and it was not. I don't see any way to see when IRIS >was last updated. (I filed a new JIRA ticket about this.) > >Does anyone know when IRIS will be updated? Is this something that has to >be done manually? > >When IRIS is updated, will the FOP script, fop-rank-pgene.pl, then be >accessible from IRIS? It should be, right? > >I am asking because the updated Services page (which includes the new >service, Functional Ortholog Predictor) is basically ready to push to the >public site but I don't want to push it out until the release is complete. > >Thanks, > Nomi >_______________________________________________ >Release-team mailing list >Release-team(a)lists.kbase.us >https://lists.kbase.us/mailman/listinfo/release-team

1 0

When will IRIS be updated?
by Nomi Harris 24 Sep '13

24 Sep '13

Dear Release Team, I just checked IRIS to see if the one (!?) script for Functional Ortholog Predictor was there, and it was not. I don't see any way to see when IRIS was last updated. (I filed a new JIRA ticket about this.) Does anyone know when IRIS will be updated? Is this something that has to be done manually? When IRIS is updated, will the FOP script, fop-rank-pgene.pl, then be accessible from IRIS? It should be, right? I am asking because the updated Services page (which includes the new service, Functional Ortholog Predictor) is basically ready to push to the public site but I don't want to push it out until the release is complete. Thanks, Nomi

1 0

Re: [Release-team] Tutorial links from Services page all broken
by Neal Conrad 24 Sep '13

24 Sep '13

Yes, thank you very much, Bill! -Neal ----- Original Message ----- From: "Nomi Harris" <nlharris(a)lbl.gov> To: "William Riehl" <wjriehl(a)lbl.gov> Cc: "Thomas Brown" <tbrown(a)cels.anl.gov>, "Sarah Poon" <sspoon(a)lbl.gov>, "Thomas Brettin" <brettin(a)mcs.anl.gov>, "Dan Olson" <dolson(a)mcs.anl.gov>, "Elizabeth Marie Marland Glass" <marland(a)mcs.anl.gov>, release-team(a)kbase.us, "Neal Conrad" <nconrad(a)mcs.anl.gov>, "Stephen Chan" <sychan(a)lbl.gov> Sent: Tuesday, September 24, 2013 7:53:59 PM Subject: Re: [Release-team] Tutorial links from Services page all broken Bill, thanks so much for fixing it! Nomi On Sep 24, 2013, at 3:44 PM, William Riehl < wjriehl(a)lbl.gov > wrote: Okay, here's what I did. (Thanks for the pointers, Steve!) We wanted to revert the commit that caused problems, so I dug up the commit id through the git page: https://git.kbase.us/docs.git (this commit, in particular: https://git.kbase.us/docs.git/commit/45afaddde56463c2718ea85482e6d023761ec3… ). Then: > git revert <commit id> This command is essentially an undo for a commit, and sets the HEAD to the state of the repo right before that commit. Then, it was a matter of adding that new release notes file that was about to be staged: > git add networks/release-notes.txt Then a usual commit and push. It's going to take a couple minutes, though to go through, apparently it wants to update everything. And any commits after that will likely be wiped out, but it shouldn't be too much work to restore them, since the changes are still part of the git logs. Not a big deal, and that's why we use version control. :) Hope this helps! - Bill On Tue, Sep 24, 2013 at 2:57 PM, Thomas Brown < tbrown(a)cels.anl.gov > wrote: Please let me know how it ws done. ----- Original Message ----- From: "Sarah Poon" < sspoon(a)lbl.gov > To: "Neal Conrad" < nconrad(a)mcs.anl.gov >, "William Riehl" < wjriehl(a)lbl.gov > Cc: "Thomas Brown" < tbrown(a)cels.anl.gov >, "Thomas Brettin" < brettin(a)mcs.anl.gov >, "Dan Olson" < dolson(a)mcs.anl.gov >, "Nomi Harris" < nlharris(a)lbl.gov >, "Elizabeth Marie Marland Glass" < marland(a)mcs.anl.gov >, release-team(a)kbase.us Sent: Tuesday, September 24, 2013 4:53:41 PM Subject: Re: [Release-team] Tutorial links from Services page all broken Bill is going to help fix the git repo, if that's ok On Tue, Sep 24, 2013 at 2:51 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: I would have ran this by now, but i screwed up my working local repo... and to reclone involves downloading 2gig of data. On Sep 24, 2013, at 4:50 PM, Thomas Brown wrote: > I'm looking at: > http://stackoverflow.com/questions/9764288/git-reset-to-previous-commit > > > ----- Original Message ----- > From: "Thomas Brettin" < brettin(a)mcs.anl.gov > > To: "Neal Conrad" < nconrad(a)mcs.anl.gov > > Cc: "Dan Olson" < dolson(a)mcs.anl.gov >, "Nomi Harris" < nlharris(a)lbl.gov >, "Elizabeth Marie Marland Glass" < marland(a)mcs.anl.gov >, "Thomas Brown" < tbrown(a)cels.anl.gov >, "Sarah Poon" < sspoon(a)lbl.gov >, release-team(a)kbase.us > Sent: Tuesday, September 24, 2013 4:48:18 PM > Subject: Re: [Release-team] Tutorial links from Services page all broken > > Not sure, but it seems plausible. You'll need to push the changes to git.kbase.us , > > > t > > > On Sep 24, 2013, at 4:46 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: > > > > Tom Brown accidently removed all the docs from the repo. > > > Anybody know how to easily revert? is it git revert -n master~3 to go back 3 commits? > > > > > Thanks, > > > Neal > > > > > On Sep 24, 2013, at 4:42 PM, Thomas Brettin wrote: > > > Looping Elizabeth in on this. Please include her. > > > On Sep 24, 2013, at 4:41 PM, Nomi Harris < nlharris(a)lbl.gov > wrote: > > > > All of the tutorials seem to have disappeared from kbase.us . If you go to http://www.kbase.us/developer-zone/services/ and click on any of the Tutorial links (e.g., http://www.kbase.us/for-users/tutorials/analyzing-data/plant-genome-analysi… ) you get an error message: > > > Warning: readfile(docs/ontology_service/tutorials/ontology_tutorial.html): failed to open stream: No such file or directory in /var/www/ksite3/blocks/basic_test/view.php on line 4 > > > > > > Tom Brown, can you fix this ASAP? (I will also create a JIRA ticket.) > > > > > > Thanks, > > > Nomi > > > _______________________________________________ > > > Release-team mailing list > > > Release-team(a)lists.kbase.us > > > https://lists.kbase.us/mailman/listinfo/release-team > >

1 0

Re: [Release-team] Tutorial links from Services page all broken
by Neal Conrad 24 Sep '13

24 Sep '13

Yes, thank you very much, Bill! On Sep 24, 2013, at 7:53 PM, Nomi Harris wrote: > Bill, thanks so much for fixing it! > Nomi > > On Sep 24, 2013, at 3:44 PM, William Riehl <wjriehl(a)lbl.gov> wrote: > >> Okay, here's what I did. (Thanks for the pointers, Steve!) >> >> We wanted to revert the commit that caused problems, so I dug up the commit id through the git page: https://git.kbase.us/docs.git (this commit, in particular: https://git.kbase.us/docs.git/commit/45afaddde56463c2718ea85482e6d023761ec3…) Then: >> >> > git revert <commit id> >> >> This command is essentially an undo for a commit, and sets the HEAD to the state of the repo right before that commit. Then, it was a matter of adding that new release notes file that was about to be staged: >> >> > git add networks/release-notes.txt >> >> Then a usual commit and push. >> >> It's going to take a couple minutes, though to go through, apparently it wants to update everything. And any commits after that will likely be wiped out, but it shouldn't be too much work to restore them, since the changes are still part of the git logs. >> >> Not a big deal, and that's why we use version control. :) Hope this helps! >> >> - Bill >> >> >> On Tue, Sep 24, 2013 at 2:57 PM, Thomas Brown <tbrown(a)cels.anl.gov> wrote: >> Please let me know how it ws done. >> >> ----- Original Message ----- >> From: "Sarah Poon" <sspoon(a)lbl.gov> >> To: "Neal Conrad" <nconrad(a)mcs.anl.gov>, "William Riehl" <wjriehl(a)lbl.gov> >> Cc: "Thomas Brown" <tbrown(a)cels.anl.gov>, "Thomas Brettin" <brettin(a)mcs.anl.gov>, "Dan Olson" <dolson(a)mcs.anl.gov>, "Nomi Harris" <nlharris(a)lbl.gov>, "Elizabeth Marie Marland Glass" <marland(a)mcs.anl.gov>, release-team(a)kbase.us >> Sent: Tuesday, September 24, 2013 4:53:41 PM >> Subject: Re: [Release-team] Tutorial links from Services page all broken >> >> >> Bill is going to help fix the git repo, if that's ok >> >> >> >> On Tue, Sep 24, 2013 at 2:51 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: >> >> >> I would have ran this by now, but i screwed up my working local repo... and to reclone involves downloading 2gig of data. >> >> >> >> >> On Sep 24, 2013, at 4:50 PM, Thomas Brown wrote: >> >> > I'm looking at: >> > http://stackoverflow.com/questions/9764288/git-reset-to-previous-commit >> > >> > >> > ----- Original Message ----- >> > From: "Thomas Brettin" < brettin(a)mcs.anl.gov > >> > To: "Neal Conrad" < nconrad(a)mcs.anl.gov > >> > Cc: "Dan Olson" < dolson(a)mcs.anl.gov >, "Nomi Harris" < nlharris(a)lbl.gov >, "Elizabeth Marie Marland Glass" < marland(a)mcs.anl.gov >, "Thomas Brown" < tbrown(a)cels.anl.gov >, "Sarah Poon" < sspoon(a)lbl.gov >, release-team(a)kbase.us >> > Sent: Tuesday, September 24, 2013 4:48:18 PM >> > Subject: Re: [Release-team] Tutorial links from Services page all broken >> > >> > Not sure, but it seems plausible. You'll need to push the changes to git.kbase.us , >> > >> > >> > t >> > >> >> > >> > On Sep 24, 2013, at 4:46 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: >> > >> > >> > >> > Tom Brown accidently removed all the docs from the repo. >> > >> > >> > Anybody know how to easily revert? is it git revert -n master~3 to go back 3 commits? >> > >> > >> > >> > >> > Thanks, >> > >> > >> > Neal >> > >> > >> > >> > >> > On Sep 24, 2013, at 4:42 PM, Thomas Brettin wrote: >> > >> > >> > Looping Elizabeth in on this. Please include her. >> > >> > >> > On Sep 24, 2013, at 4:41 PM, Nomi Harris < nlharris(a)lbl.gov > wrote: >> > >> > >> > >> > All of the tutorials seem to have disappeared from kbase.us . If you go to http://www.kbase.us/developer-zone/services/ and click on any of the Tutorial links (e.g., http://www.kbase.us/for-users/tutorials/analyzing-data/plant-genome-analysi… ) you get an error message: >> > >> > >> > Warning: readfile(docs/ontology_service/tutorials/ontology_tutorial.html): failed to open stream: No such file or directory in /var/www/ksite3/blocks/basic_test/view.php on line 4 >> > >> > >> > >> > >> > >> > Tom Brown, can you fix this ASAP? (I will also create a JIRA ticket.) >> > >> > >> > >> > >> > >> > Thanks, >> > >> > >> > Nomi >> > >> > >> > _______________________________________________ >> > >> > >> > Release-team mailing list >> > >> > >> > Release-team(a)lists.kbase.us >> > >> > >> > https://lists.kbase.us/mailman/listinfo/release-team >> > >> > >> >> >

1 0

Re: [Release-team] Tutorial links from Services page all broken
by Nomi Harris 24 Sep '13

24 Sep '13

Bill, thanks so much for fixing it! Nomi On Sep 24, 2013, at 3:44 PM, William Riehl <wjriehl(a)lbl.gov> wrote: > Okay, here's what I did. (Thanks for the pointers, Steve!) > > We wanted to revert the commit that caused problems, so I dug up the commit id through the git page: https://git.kbase.us/docs.git (this commit, in particular: https://git.kbase.us/docs.git/commit/45afaddde56463c2718ea85482e6d023761ec3…) Then: > > > git revert <commit id> > > This command is essentially an undo for a commit, and sets the HEAD to the state of the repo right before that commit. Then, it was a matter of adding that new release notes file that was about to be staged: > > > git add networks/release-notes.txt > > Then a usual commit and push. > > It's going to take a couple minutes, though to go through, apparently it wants to update everything. And any commits after that will likely be wiped out, but it shouldn't be too much work to restore them, since the changes are still part of the git logs. > > Not a big deal, and that's why we use version control. :) Hope this helps! > > - Bill > > > On Tue, Sep 24, 2013 at 2:57 PM, Thomas Brown <tbrown(a)cels.anl.gov> wrote: > Please let me know how it ws done. > > ----- Original Message ----- > From: "Sarah Poon" <sspoon(a)lbl.gov> > To: "Neal Conrad" <nconrad(a)mcs.anl.gov>, "William Riehl" <wjriehl(a)lbl.gov> > Cc: "Thomas Brown" <tbrown(a)cels.anl.gov>, "Thomas Brettin" <brettin(a)mcs.anl.gov>, "Dan Olson" <dolson(a)mcs.anl.gov>, "Nomi Harris" <nlharris(a)lbl.gov>, "Elizabeth Marie Marland Glass" <marland(a)mcs.anl.gov>, release-team(a)kbase.us > Sent: Tuesday, September 24, 2013 4:53:41 PM > Subject: Re: [Release-team] Tutorial links from Services page all broken > > > Bill is going to help fix the git repo, if that's ok > > > > On Tue, Sep 24, 2013 at 2:51 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: > > > I would have ran this by now, but i screwed up my working local repo... and to reclone involves downloading 2gig of data. > > > > > On Sep 24, 2013, at 4:50 PM, Thomas Brown wrote: > > > I'm looking at: > > http://stackoverflow.com/questions/9764288/git-reset-to-previous-commit > > > > > > ----- Original Message ----- > > From: "Thomas Brettin" < brettin(a)mcs.anl.gov > > > To: "Neal Conrad" < nconrad(a)mcs.anl.gov > > > Cc: "Dan Olson" < dolson(a)mcs.anl.gov >, "Nomi Harris" < nlharris(a)lbl.gov >, "Elizabeth Marie Marland Glass" < marland(a)mcs.anl.gov >, "Thomas Brown" < tbrown(a)cels.anl.gov >, "Sarah Poon" < sspoon(a)lbl.gov >, release-team(a)kbase.us > > Sent: Tuesday, September 24, 2013 4:48:18 PM > > Subject: Re: [Release-team] Tutorial links from Services page all broken > > > > Not sure, but it seems plausible. You'll need to push the changes to git.kbase.us , > > > > > > t > > > > > > > On Sep 24, 2013, at 4:46 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: > > > > > > > > Tom Brown accidently removed all the docs from the repo. > > > > > > Anybody know how to easily revert? is it git revert -n master~3 to go back 3 commits? > > > > > > > > > > Thanks, > > > > > > Neal > > > > > > > > > > On Sep 24, 2013, at 4:42 PM, Thomas Brettin wrote: > > > > > > Looping Elizabeth in on this. Please include her. > > > > > > On Sep 24, 2013, at 4:41 PM, Nomi Harris < nlharris(a)lbl.gov > wrote: > > > > > > > > All of the tutorials seem to have disappeared from kbase.us . If you go to http://www.kbase.us/developer-zone/services/ and click on any of the Tutorial links (e.g., http://www.kbase.us/for-users/tutorials/analyzing-data/plant-genome-analysi… ) you get an error message: > > > > > > Warning: readfile(docs/ontology_service/tutorials/ontology_tutorial.html): failed to open stream: No such file or directory in /var/www/ksite3/blocks/basic_test/view.php on line 4 > > > > > > > > > > > > Tom Brown, can you fix this ASAP? (I will also create a JIRA ticket.) > > > > > > > > > > > > Thanks, > > > > > > Nomi > > > > > > _______________________________________________ > > > > > > Release-team mailing list > > > > > > Release-team(a)lists.kbase.us > > > > > > https://lists.kbase.us/mailman/listinfo/release-team > > > > > >

1 0

Re: [Release-team] Tutorial links from Services page all broken
by Thomas Brown 24 Sep '13

24 Sep '13

Thanks much ----- Original Message ----- From: "William Riehl" <wjriehl(a)lbl.gov> To: "Thomas Brown" <tbrown(a)cels.anl.gov> Cc: "Sarah Poon" <sspoon(a)lbl.gov>, "Thomas Brettin" <brettin(a)mcs.anl.gov>, "Dan Olson" <dolson(a)mcs.anl.gov>, "Nomi Harris" <nlharris(a)lbl.gov>, "Elizabeth Marie Marland Glass" <marland(a)mcs.anl.gov>, release-team(a)kbase.us, "Neal Conrad" <nconrad(a)mcs.anl.gov>, "Stephen Chan" <sychan(a)lbl.gov> Sent: Tuesday, September 24, 2013 5:44:27 PM Subject: Re: [Release-team] Tutorial links from Services page all broken Okay, here's what I did. (Thanks for the pointers, Steve!) We wanted to revert the commit that caused problems, so I dug up the commit id through the git page: https://git.kbase.us/docs.git (this commit, in particular: https://git.kbase.us/docs.git/commit/45afaddde56463c2718ea85482e6d023761ec3… ). Then: > git revert <commit id> This command is essentially an undo for a commit, and sets the HEAD to the state of the repo right before that commit. Then, it was a matter of adding that new release notes file that was about to be staged: > git add networks/release-notes.txt Then a usual commit and push. It's going to take a couple minutes, though to go through, apparently it wants to update everything. And any commits after that will likely be wiped out, but it shouldn't be too much work to restore them, since the changes are still part of the git logs. Not a big deal, and that's why we use version control. :) Hope this helps! - Bill On Tue, Sep 24, 2013 at 2:57 PM, Thomas Brown < tbrown(a)cels.anl.gov > wrote: Please let me know how it ws done. ----- Original Message ----- From: "Sarah Poon" < sspoon(a)lbl.gov > To: "Neal Conrad" < nconrad(a)mcs.anl.gov >, "William Riehl" < wjriehl(a)lbl.gov > Cc: "Thomas Brown" < tbrown(a)cels.anl.gov >, "Thomas Brettin" < brettin(a)mcs.anl.gov >, "Dan Olson" < dolson(a)mcs.anl.gov >, "Nomi Harris" < nlharris(a)lbl.gov >, "Elizabeth Marie Marland Glass" < marland(a)mcs.anl.gov >, release-team(a)kbase.us Sent: Tuesday, September 24, 2013 4:53:41 PM Subject: Re: [Release-team] Tutorial links from Services page all broken Bill is going to help fix the git repo, if that's ok On Tue, Sep 24, 2013 at 2:51 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: I would have ran this by now, but i screwed up my working local repo... and to reclone involves downloading 2gig of data. On Sep 24, 2013, at 4:50 PM, Thomas Brown wrote: > I'm looking at: > http://stackoverflow.com/questions/9764288/git-reset-to-previous-commit > > > ----- Original Message ----- > From: "Thomas Brettin" < brettin(a)mcs.anl.gov > > To: "Neal Conrad" < nconrad(a)mcs.anl.gov > > Cc: "Dan Olson" < dolson(a)mcs.anl.gov >, "Nomi Harris" < nlharris(a)lbl.gov >, "Elizabeth Marie Marland Glass" < marland(a)mcs.anl.gov >, "Thomas Brown" < tbrown(a)cels.anl.gov >, "Sarah Poon" < sspoon(a)lbl.gov >, release-team(a)kbase.us > Sent: Tuesday, September 24, 2013 4:48:18 PM > Subject: Re: [Release-team] Tutorial links from Services page all broken > > Not sure, but it seems plausible. You'll need to push the changes to git.kbase.us , > > > t > > > > > > > On Sep 24, 2013, at 4:46 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: > > > > Tom Brown accidently removed all the docs from the repo. > > > Anybody know how to easily revert? is it git revert -n master~3 to go back 3 commits? > > > > > Thanks, > > > Neal > > > > > On Sep 24, 2013, at 4:42 PM, Thomas Brettin wrote: > > > Looping Elizabeth in on this. Please include her. > > > On Sep 24, 2013, at 4:41 PM, Nomi Harris < nlharris(a)lbl.gov > wrote: > > > > All of the tutorials seem to have disappeared from kbase.us . If you go to http://www.kbase.us/developer-zone/services/ and click on any of the Tutorial links (e.g., http://www.kbase.us/for-users/tutorials/analyzing-data/plant-genome-analysi… ) you get an error message: > > > Warning: readfile(docs/ontology_service/tutorials/ontology_tutorial.html): failed to open stream: No such file or directory in /var/www/ksite3/blocks/basic_test/view.php on line 4 > > > > > > Tom Brown, can you fix this ASAP? (I will also create a JIRA ticket.) > > > > > > Thanks, > > > Nomi > > > _______________________________________________ > > > Release-team mailing list > > > Release-team(a)lists.kbase.us > > > https://lists.kbase.us/mailman/listinfo/release-team > > >

1 0

Re: [Release-team] Tutorial links from Services page all broken
by William Riehl 24 Sep '13

24 Sep '13

Okay, here's what I did. (Thanks for the pointers, Steve!) We wanted to revert the commit that caused problems, so I dug up the commit id through the git page: https://git.kbase.us/docs.git (this commit, in particular: https://git.kbase.us/docs.git/commit/45afaddde56463c2718ea85482e6d023761ec3…) Then: > git revert <commit id> This command is essentially an undo for a commit, and sets the HEAD to the state of the repo right before that commit. Then, it was a matter of adding that new release notes file that was about to be staged: > git add networks/release-notes.txt Then a usual commit and push. It's going to take a couple minutes, though to go through, apparently it wants to update everything. And any commits after that will likely be wiped out, but it shouldn't be too much work to restore them, since the changes are still part of the git logs. Not a big deal, and that's why we use version control. :) Hope this helps! - Bill On Tue, Sep 24, 2013 at 2:57 PM, Thomas Brown <tbrown(a)cels.anl.gov> wrote: > Please let me know how it ws done. > > ----- Original Message ----- > From: "Sarah Poon" <sspoon(a)lbl.gov> > To: "Neal Conrad" <nconrad(a)mcs.anl.gov>, "William Riehl" <wjriehl(a)lbl.gov> > Cc: "Thomas Brown" <tbrown(a)cels.anl.gov>, "Thomas Brettin" < > brettin(a)mcs.anl.gov>, "Dan Olson" <dolson(a)mcs.anl.gov>, "Nomi Harris" < > nlharris(a)lbl.gov>, "Elizabeth Marie Marland Glass" <marland(a)mcs.anl.gov>, > release-team(a)kbase.us > Sent: Tuesday, September 24, 2013 4:53:41 PM > Subject: Re: [Release-team] Tutorial links from Services page all broken > > > Bill is going to help fix the git repo, if that's ok > > > > On Tue, Sep 24, 2013 at 2:51 PM, Neal Conrad < nconrad(a)mcs.anl.gov > > wrote: > > > I would have ran this by now, but i screwed up my working local repo... > and to reclone involves downloading 2gig of data. > > > > > On Sep 24, 2013, at 4:50 PM, Thomas Brown wrote: > > > I'm looking at: > > http://stackoverflow.com/questions/9764288/git-reset-to-previous-commit > > > > > > ----- Original Message ----- > > From: "Thomas Brettin" < brettin(a)mcs.anl.gov > > > To: "Neal Conrad" < nconrad(a)mcs.anl.gov > > > Cc: "Dan Olson" < dolson(a)mcs.anl.gov >, "Nomi Harris" < nlharris(a)lbl.gov>, "Elizabeth Marie Marland Glass" < > marland(a)mcs.anl.gov >, "Thomas Brown" < tbrown(a)cels.anl.gov >, "Sarah > Poon" < sspoon(a)lbl.gov >, release-team(a)kbase.us > > Sent: Tuesday, September 24, 2013 4:48:18 PM > > Subject: Re: [Release-team] Tutorial links from Services page all broken > > > > Not sure, but it seems plausible. You'll need to push the changes to > git.kbase.us , > > > > > > t > > > > > > > > > > > > > > On Sep 24, 2013, at 4:46 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: > > > > > > > > Tom Brown accidently removed all the docs from the repo. > > > > > > Anybody know how to easily revert? is it git revert -n master~3 to go > back 3 commits? > > > > > > > > > > Thanks, > > > > > > Neal > > > > > > > > > > On Sep 24, 2013, at 4:42 PM, Thomas Brettin wrote: > > > > > > Looping Elizabeth in on this. Please include her. > > > > > > On Sep 24, 2013, at 4:41 PM, Nomi Harris < nlharris(a)lbl.gov > wrote: > > > > > > > > All of the tutorials seem to have disappeared from kbase.us . If you go > to http://www.kbase.us/developer-zone/services/ and click on any of the > Tutorial links (e.g., > http://www.kbase.us/for-users/tutorials/analyzing-data/plant-genome-analysi…) you get an error message: > > > > > > Warning: > readfile(docs/ontology_service/tutorials/ontology_tutorial.html): failed to > open stream: No such file or directory in > /var/www/ksite3/blocks/basic_test/view.php on line 4 > > > > > > > > > > > > Tom Brown, can you fix this ASAP? (I will also create a JIRA ticket.) > > > > > > > > > > > > Thanks, > > > > > > Nomi > > > > > > _______________________________________________ > > > > > > Release-team mailing list > > > > > > Release-team(a)lists.kbase.us > > > > > > https://lists.kbase.us/mailman/listinfo/release-team > > > > > > > > > >

1 0

Re: [Release-team] Tutorial links from Services page all broken
by Shane Canon 24 Sep '13

24 Sep '13

I can revert on the host? Is this apache2? --Shane On Sep 24, 2013, at 2:52 PM, Thomas Brown <tbrown(a)cels.anl.gov> wrote: > I can add/commit/push from my end > ... > > ----- Original Message ----- > From: "Neal Conrad" <nconrad(a)mcs.anl.gov> > To: "Thomas Brown" <tbrown(a)cels.anl.gov> > Cc: "Thomas Brettin" <brettin(a)mcs.anl.gov>, "Dan Olson" <dolson(a)mcs.anl.gov>, "Nomi Harris" <nlharris(a)lbl.gov>, "Elizabeth Marie Marland Glass" <marland(a)mcs.anl.gov>, "Sarah Poon" <sspoon(a)lbl.gov>, release-team(a)kbase.us > Sent: Tuesday, September 24, 2013 4:51:02 PM > Subject: Re: [Release-team] Tutorial links from Services page all broken > > I would have ran this by now, but i screwed up my working local repo... and to reclone involves downloading 2gig of data. > > > On Sep 24, 2013, at 4:50 PM, Thomas Brown wrote: > >> I'm looking at: >> http://stackoverflow.com/questions/9764288/git-reset-to-previous-commit >> >> >> ----- Original Message ----- >> From: "Thomas Brettin" <brettin(a)mcs.anl.gov> >> To: "Neal Conrad" <nconrad(a)mcs.anl.gov> >> Cc: "Dan Olson" <dolson(a)mcs.anl.gov>, "Nomi Harris" <nlharris(a)lbl.gov>, "Elizabeth Marie Marland Glass" <marland(a)mcs.anl.gov>, "Thomas Brown" <tbrown(a)cels.anl.gov>, "Sarah Poon" <sspoon(a)lbl.gov>, release-team(a)kbase.us >> Sent: Tuesday, September 24, 2013 4:48:18 PM >> Subject: Re: [Release-team] Tutorial links from Services page all broken >> >> Not sure, but it seems plausible. You'll need to push the changes to git.kbase.us , >> >> >> t >> >> >> >> >> >> >> On Sep 24, 2013, at 4:46 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: >> >> >> >> Tom Brown accidently removed all the docs from the repo. >> >> >> Anybody know how to easily revert? is it git revert -n master~3 to go back 3 commits? >> >> >> >> >> Thanks, >> >> >> Neal >> >> >> >> >> On Sep 24, 2013, at 4:42 PM, Thomas Brettin wrote: >> >> >> Looping Elizabeth in on this. Please include her. >> >> >> On Sep 24, 2013, at 4:41 PM, Nomi Harris < nlharris(a)lbl.gov > wrote: >> >> >> >> All of the tutorials seem to have disappeared from kbase.us . If you go to http://www.kbase.us/developer-zone/services/ and click on any of the Tutorial links (e.g., http://www.kbase.us/for-users/tutorials/analyzing-data/plant-genome-analysi… ) you get an error message: >> >> >> Warning: readfile(docs/ontology_service/tutorials/ontology_tutorial.html): failed to open stream: No such file or directory in /var/www/ksite3/blocks/basic_test/view.php on line 4 >> >> >> >> >> >> Tom Brown, can you fix this ASAP? (I will also create a JIRA ticket.) >> >> >> >> >> >> Thanks, >> >> >> Nomi >> >> >> _______________________________________________ >> >> >> 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

1 0

Re: [Release-team] Tutorial links from Services page all broken
by Thomas Brown 24 Sep '13

24 Sep '13

Please let me know how it ws done. ----- Original Message ----- From: "Sarah Poon" <sspoon(a)lbl.gov> To: "Neal Conrad" <nconrad(a)mcs.anl.gov>, "William Riehl" <wjriehl(a)lbl.gov> Cc: "Thomas Brown" <tbrown(a)cels.anl.gov>, "Thomas Brettin" <brettin(a)mcs.anl.gov>, "Dan Olson" <dolson(a)mcs.anl.gov>, "Nomi Harris" <nlharris(a)lbl.gov>, "Elizabeth Marie Marland Glass" <marland(a)mcs.anl.gov>, release-team(a)kbase.us Sent: Tuesday, September 24, 2013 4:53:41 PM Subject: Re: [Release-team] Tutorial links from Services page all broken Bill is going to help fix the git repo, if that's ok On Tue, Sep 24, 2013 at 2:51 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: I would have ran this by now, but i screwed up my working local repo... and to reclone involves downloading 2gig of data. On Sep 24, 2013, at 4:50 PM, Thomas Brown wrote: > I'm looking at: > http://stackoverflow.com/questions/9764288/git-reset-to-previous-commit > > > ----- Original Message ----- > From: "Thomas Brettin" < brettin(a)mcs.anl.gov > > To: "Neal Conrad" < nconrad(a)mcs.anl.gov > > Cc: "Dan Olson" < dolson(a)mcs.anl.gov >, "Nomi Harris" < nlharris(a)lbl.gov >, "Elizabeth Marie Marland Glass" < marland(a)mcs.anl.gov >, "Thomas Brown" < tbrown(a)cels.anl.gov >, "Sarah Poon" < sspoon(a)lbl.gov >, release-team(a)kbase.us > Sent: Tuesday, September 24, 2013 4:48:18 PM > Subject: Re: [Release-team] Tutorial links from Services page all broken > > Not sure, but it seems plausible. You'll need to push the changes to git.kbase.us , > > > t > > > > > > > On Sep 24, 2013, at 4:46 PM, Neal Conrad < nconrad(a)mcs.anl.gov > wrote: > > > > Tom Brown accidently removed all the docs from the repo. > > > Anybody know how to easily revert? is it git revert -n master~3 to go back 3 commits? > > > > > Thanks, > > > Neal > > > > > On Sep 24, 2013, at 4:42 PM, Thomas Brettin wrote: > > > Looping Elizabeth in on this. Please include her. > > > On Sep 24, 2013, at 4:41 PM, Nomi Harris < nlharris(a)lbl.gov > wrote: > > > > All of the tutorials seem to have disappeared from kbase.us . If you go to http://www.kbase.us/developer-zone/services/ and click on any of the Tutorial links (e.g., http://www.kbase.us/for-users/tutorials/analyzing-data/plant-genome-analysi… ) you get an error message: > > > Warning: readfile(docs/ontology_service/tutorials/ontology_tutorial.html): failed to open stream: No such file or directory in /var/www/ksite3/blocks/basic_test/view.php on line 4 > > > > > > Tom Brown, can you fix this ASAP? (I will also create a JIRA ticket.) > > > > > > Thanks, > > > Nomi > > > _______________________________________________ > > > Release-team mailing list > > > Release-team(a)lists.kbase.us > > > https://lists.kbase.us/mailman/listinfo/release-team > > >

1 0