Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-08-07

| Channels | #opentreeoflife index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
10:49 josephwb joined #opentreeoflife
10:49 7GHAAU603 joined #opentreeoflife
11:58 kcranstn joined #opentreeoflife
12:27 kcranstn joined #opentreeoflife
13:34 kcranstn joined #opentreeoflife
14:18 josephwb wassup ilbot3? feel like we haven't connected in a while.
14:27 josephwb ok, catch you later then
14:40 kcranstn joined #opentreeoflife
15:04 jimallman joined #opentreeoflife
15:07 kcranstn joined #opentreeoflife
15:17 josephwb joined #opentreeoflife
15:18 josephwb hey jimallman
15:20 josephwb did anything ever get done about purging unused tip labels from the OTU mapping?
15:20 josephwb e.g. upload a tree with bad labels, delete tree, but bad labels remain
15:20 jimallman hm, not sure i got the memo on that one
15:20 kcranstn was there an issue?
15:21 josephwb see here (A_fasciatus and M_migrans are not used in any tree): https://tree.opentreeoflife.org/curator/study/view/ot_305/?tab=otu-mapping
15:21 jimallman oh yes, i remember now
15:21 * jimallman is checking issue tracker...
15:21 josephwb not sure if there is an issue. i thin kso...
15:21 josephwb think so...
15:22 kcranstn https://github.com/OpenTreeOfLife/opentree/issues/618
15:24 kcranstn unfortunately, I think this is lower priority for jimallman than other things...
15:24 jimallman true, but possibly an easy fix if it’s a pain point for curators
15:25 jimallman (like 30 minutes with testing)
15:25 josephwb right, not a high priority. if too many such labels are involved, it is easy enough to delete the study and start anew
15:27 josephwb i updated the issue with this example: https://github.com/OpenTreeOfLife/opentree/issues/618
15:27 josephwb thanks
15:43 jimallman thankYOU, examples are always helpful!
16:08 kcranstn about to make some changes to feedback form
16:08 kcranstn might have questions :)
16:25 travis-ci joined #opentreeoflife
16:25 travis-ci OpenTreeOfLife/phylesystem-api#807 (support-tree-collections - b387a65 : Jim Allman): The build passed.
16:25 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/8f76125207e2...b387a6564fc9
16:25 travis-ci Build details : https://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/74597870
16:25 travis-ci left #opentreeoflife
17:26 kcranstn joined #opentreeoflife
18:10 kcranstn joined #opentreeoflife
18:31 kcranstn can someone else try and load tree.opentreeoflife.org ?
18:36 kcranstn forget it - figured out what happened
18:36 * jimallman is checking it now..
18:36 jimallman oh, what was it? local HOSTS?
18:37 kcranstn when you first authorize github for opentree, it takes you to github.com, not back to opentree
18:37 kcranstn if you try and test this by revoking access, you get a 500 error until you clear browser cache
18:38 kcranstn https://github.com/OpenTreeOfLife/opentree/issues/685
18:38 kcranstn not sure if we have control over this
18:57 jimallman hmm
18:58 jimallman yes, probably a session cookie that expects the auth to be working
18:58 kcranstn that’s not what the issue is about
18:58 kcranstn I think we need to set a callback URL after authentication
18:59 jimallman OK, i’ll follow the OAuth dance and see if there’s a way
18:59 kcranstn https://developer.github.com/guides/basics-of-authentication/
19:01 kcranstn our callbacks are set to the login page, not the main URL
19:01 kcranstn is that the problem?
19:03 kcranstn and the user login page http://tree.opentreeoflife.org/opentree/user/login forwards to github
19:03 kcranstn I am going to modify for dev and test
19:12 kcranstn ah, but we override the redirect uri in the config file
19:13 kcranstn I think the redirect URLs should be /opentree and /curator not opentree/user/login and curator/user/login
19:13 kcranstn and we don’t need to define these in the config, because the default is what is defined on github
19:13 kcranstn (which, right now, is the same)
19:14 kcranstn does that make sense?
19:16 kcranstn http://thechiselgroup.org/2013/11/14/using-oauth-to-authenticate-users-with-github/
19:20 jimallman sorry, lost track of this conversation… i believe our redirect_uri needs to be to the login page (to establish a logged-in session in web2py), but we usually bounce directly to our desired destination after that.
19:21 jimallman we can probably just add this final bounce URL (on the query-string? i’ll need to review) to get the behavior that you want.
19:24 kcranstn so this is a strange web2py quirk?
19:28 kcranstn just tested locally
19:28 kcranstn my fix works
19:34 jimallman sounds good! can we put this on a branch (or PR) for review?
19:35 kcranstn neither change involves files under version control
19:36 kcranstn one github UI change for each application, and one config file change for each application
19:36 jimallman of course. sorry, my head is elsewhere today (collections)
19:37 kcranstn want to test by changing private/webapp/config and private/curator/config on devtree
19:37 kcranstn I’ve made the two UI changes for devtree
19:39 jimallman test plan sounds good.
19:39 kcranstn ot16 is devtree, right?
19:39 jimallman yes (confirmed with ‘dig’)
19:39 jimallman i can never keep these straight otherwise
19:40 kcranstn will we need to redeploy after modifying the config files?
19:40 jimallman just restart apache
19:41 jimallman $ ssh admin@ot16 sudo apache2ctl graceful
19:42 kcranstn ok
19:42 kcranstn trying now
19:43 kcranstn I only have access for user opentree, not admin
19:46 kcranstn and I think these URLs might also be specificed in the deploy scripts
19:47 kcranstn not sure why
19:47 jimallman OK, restarted apache from here.
19:47 kcranstn ok, I’ll test
19:48 jimallman yes, TREEVIEW_GITHUB_REDIRECT_URI and CURATION_GITHUB_REDIRECT_URI are in the server-config files
19:48 jimallman https://github.com/OpenTreeOfLife/deployed-systems/blob/master/development/devtree.config#L17-L26
19:49 jimallman we don’t want to hard-code these, since they change on each deployed server (based on domain name)
19:49 kcranstn also in push.sh
19:49 jimallman !
19:50 kcranstn does devtree not ask for login for comments?
19:50 kcranstn (worked in curator, BTW. Got redirected back to curator, not github)
19:52 jimallman i see, push.sh uses a default ridirect_uri if one wasn’t specified in the server-config file. we should update this to reflect your new URL:  https://github.com/OpenTreeOfLife/opentree/blob/51a96f3885c5eecc3a14547d6c664a0e714d49b8/deploy/push.sh#L101
19:52 kcranstn worked for webapp too
19:52 jimallman devtree does prompt for login, once the user starts to add a thread.
19:55 kcranstn ok, I’ll PR those other changes
20:21 travis-ci joined #opentreeoflife
20:21 travis-ci OpenTreeOfLife/phylesystem-api#809 (support-tree-collections - 5e6beb7 : Jim Allman): The build passed.
20:21 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/b387a6564fc9...5e6beb7d9d0f
20:21 travis-ci Build details : https://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/74627755
20:21 travis-ci left #opentreeoflife
21:13 jar286 joined #opentreeoflife
23:29 jar286 joined #opentreeoflife

| Channels | #opentreeoflife index | Today | | Search | Google Search | Plain-Text | summary