Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-02-17

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All times shown according to UTC.

Time Nick Message
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15:50 * jimallman is checking for netsplit or other outages on Freenode
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15:51 kcranstn mornin!
15:51 blackrim towodo: made it
15:52 towodo tried many times to join #opentreeoflife, no luck… then joined a different room, then tried opentreeoflife, success
15:52 towodo add that one to your bag of tricks
15:53 blackrim done
15:53 jimallman towodo: i do find that Colloquy is weird about recognizing selection of a channel or user.
15:53 towodo same behavior in adium though
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16:02 PEM Checking my client, please ignore
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16:05 kcranstn what happened to this page:
16:05 kcranstn http://dev.opentreeoflife.org/ott/
16:06 blackrim i think it is files.opentreeoflife.org/ott
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16:10 blackrim is phylografter down ?
16:11 blackrim looks like it is back. nevermind
16:17 kcranstn is there anything that I can do to push through the deployment of changes to http://dev.opentreeoflife.org/about/developer-resources ?
16:17 kcranstn 11 days since the updates to the source, and still haven't appeared in the app
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16:32 blackrim kcranstn: by the way, if you are wondering where the fungi are in the analyses that i was doing, they are going now. romina didn't give me tree ids, so i had to get those for all the studies and it delayed things for those
16:34 towodo Jim has been managing the deployment. You have two options: (a) wait for him to do a push, (b) sneak the file in the side door using scp.  The host is ot3, and the path will be repo/opentree/webapp/views/about/developer_resources.html
16:34 towodo I can give you the ssh key if you don't already have it
16:34 towodo s/Jim/jimallman/
16:38 towodo ooops, forgot to prefix that answer with 'kcransn,'
16:38 towodo s/'kcransn',/'kcranstn,'/
16:38 jimallman towodo: kcranstn: apologies, i've been working in isolation. i'll push new stuff to ot3 now.
16:40 jimallman http://dev.opentreeoflife.org/about/developer_resources.html
16:40 jimallman kcranstn: better?
16:42 blackrim towodo: loading taxonomy and rerunning things. will let you know if there are issues
16:43 jimallman hm, newick link ("newicks of the tree") looks good in jar's changes, but fails on the site
16:43 * jimallman is chasing this now
16:46 jimallman towodo: kcranstn: OK, i believe this is up to date now - http://dev.opentreeoflife.org/about/developer_resources.html
16:46 towodo jimallman, thanks
16:47 kcranstn yes, thanks jimallman!
16:48 towodo blackrim: darn, forgot to fix Heterolobosea. oh well, next round
16:48 towodo oops, did fix it and forgot *that* never mind
16:49 blackrim ha, sounds good
16:49 towodo Heterolobosea   |       class   |       silva:M98050/#5,ncbi:5752,gbif:116,irmng:1308
16:59 kcranstn @jimallman - details on what you did to update?
17:02 jimallman sure, local shift to master (git checkout master)... then cd opentree/deploy... then './push.sh -c ot3.config opentree' to update just the main web apps...
17:03 jimallman the sever-config file is the hard part, can send mine if you like
17:03 kcranstn ok, so it just needed a manual push
17:03 kcranstn yes, please do send (would be good to have multiple folks who can work the required magic)
17:03 jimallman agreed. maybe we need a *secure* shared repository for server-config files?
17:05 kcranstn FYI, I am going through and updating the help messages in the curator app
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17:19 towodo jimallman, I don't think the config files need to be secure…
17:19 towodo you'd be amazed by the http server logs… continuous lock-rattling
17:20 kcranstn towodo: according to http://files.opentreeoflife.org/ott/, GBIF already had low priority relative to the other sources. What did you change in response to Laura's email?
17:20 towodo I just eliminated (rather, hid) it entirely, as she asked
17:21 towodo just as I did for Fungi
17:21 kcranstn so we don't see the GBIF backbone at all?
17:21 kcranstn but still get tips?
17:21 towodo not for microbes
17:21 kcranstn ah, ok
17:21 towodo nope, no gbif microbe tips
17:22 kcranstn ok
17:22 towodo there's a command to selectively hide any specified subtree for any specified input taxonomy
17:24 kcranstn cool
17:24 jimallman towodo: i suppose the .pem files are the real secrets, but ot3.config does include our GITHUB_CLIENT_SECRET.
17:36 towodo jimallman: ah. there shouldn't be secrets in the config files. need to rework that
17:39 jimallman in other cases (like Janrain) we've isolated secrets as one-line files.
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18:42 kcranstn1 can we get timestamps on the files on this page?
18:42 kcranstn1 http://files.opentreeoflife.org/other/curnewicks/index.html
18:46 towodo kcranstn1, I can put the file write dates on the index page… that's the best I can do without blackrim's help
18:50 towodo the files are very stale
18:51 towodo as usual putting "cur" ("current") in the name of something is a guarantee that it will be false in the future
18:52 kcranstn1 I suppose hooking those up to the relevant curl calls would be much better
18:53 mtholder we could use http://files.opentreeoflife.org/other/the-newicks-formerly-known-as-current/index.html as the URL
18:53 kcranstn1 getting an increasingly frequent number of "where can I download all / part of the current tree" requests
19:05 towodo I respect people who won't commit to dates, but they are darned frustrating
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21:58 blackrim towodo kcranstn: i will add dates. we hadn't been updating in a while. I will time stamp them
21:59 towodo I already put them on the index page
22:00 blackrim i see. so i don't need to do it at all ever?
22:00 towodo well keeping the dates up to date would be nice
22:01 blackrim right. so we will do that starting with our synths now. they were mostly there to communicate within the project which is why they were not anymore formal
22:03 towodo that's fine but there are enough people involved now that someone is likely to be confused if some care isn't taken
22:03 blackrim for sure
22:03 towodo the links were on the 'developer resources' page so likely to be found by someone, who would be confused
22:04 towodo my "I respect" comment was snarky, sorry. and it wasn't about the curnewicks
22:04 * blackrim hangs head in shame
22:05 blackrim no problems. where do i put these files now that we have moved to the amazon
22:05 towodo they are still on norbert.csail.mit.edu, same as before
22:06 towodo I worked recently with a fantastic software guy who refused to ever say when he was going to have anything done
22:06 towodo I completely understand why
22:06 blackrim ok, will be a bit before a new one comes up since we are running through a bunch of tests with the new taxonomy (rerunning the monophyly and other things as well as synth now)
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