Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-07-15

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Time Nick Message
00:29 kcranstn joined #opentreeoflife
01:47 ilbot3 joined #opentreeoflife
01:47 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
14:20 kcranstn joined #opentreeoflife
14:42 jar286 joined #opentreeoflife
14:42 jar286 I was watching someone browse the opentree tree yesterday… it was very fast, very nice
14:43 jar286 he had a very fast computer
14:43 kcranstn yay
14:43 jar286 so I think we’re javascript-bound.  it’s very slow when I look at it
14:43 kcranstn hmm
14:44 jar286 many variables at play here, could be something else
14:44 jar286 he was using linux, for example
15:07 kcranstn jimallman?
15:08 jimallman kcranstn: hi!
15:08 kcranstn documentation pretty good. I made a few minor changes.
15:08 kcranstn I think it is missing stuff about web2py setup, though
15:08 kcranstn is that somewhere else?
15:09 kcranstn (I am doing this on a brand new machine)
15:09 jimallman new machine is good. do you recall the web2py stumbling blocks?
15:09 kcranstn there is something I need to setup to tell web2py to run application ‘opentree’, right?
15:09 kcranstn I am getting the default web2py page
15:10 jimallman feel free to add notes to the issue:  https://github.com/OpenTreeOfLife/opentree/issues/676
15:10 jimallman hm, we do need to symlink our web apps into the web2py directory
15:11 kcranstn yes, that’s the step I am missing
15:11 kcranstn vague recollections of doing this once before
15:12 jimallman and possibly some routing tweaks in a web2py config file… but let’s start with the symlinks (i’ll add this to wiki page now)
15:12 kcranstn cool, thanks
15:12 jimallman this might be documented elsewhere, but i think this page should give all the steps if possible
15:13 kcranstn I agree
15:21 kcranstn the instructions are in the readme
15:21 kcranstn for the symlinks
15:23 kcranstn we should homogenize the readme and the wiki page (or put all of the instructiosn in one place)
15:24 jimallman yes, just realized the prior documentation is in https://github.com/OpenTreeOfLife/opentree/blob/51a96f3885c5eecc3a14547d6c664a0e714d49b8/README.md#installation
15:24 jimallman homogenize = combine, with generic instructions?
15:25 kcranstn I’d rather have the instructions in the repo
15:25 kcranstn than on a wiki page
15:26 jimallman it’s tempting to use the standard deployment tools for local test setup, since this catches numerous quirks (noted in the issue). but my original intent was to support a minimal app server, without using apache/etc. maybe that’s no longer realistic with the complexity of our setup.
15:27 kcranstn let’s push through with the minimal app server and see if that becomes unwieldy
15:28 jimallman will do. this setup certainly works for me and supports nimble tweaking/testing without commits. so for now, it’s OK to have some repetition in the README and a wiki page?
15:28 kcranstn for now
15:28 * jimallman nods
15:39 kcranstn not too worried right now about *where* the documentation lives, just that it is accurate and sufficient
15:41 jar286 joined #opentreeoflife
15:52 kcranstn ok, now getting errors related to https
15:53 jar286 joined #opentreeoflife
15:57 jar286 maybe I need to set JAVA_HOME
15:57 kcranstn jar286?
15:57 jar286 yes
15:58 kcranstn I didn’t understand that comment
15:58 jar286 you mean in IRC?
15:58 jar286 talking to myself
15:58 jar286 or you mean 10:43 am?
15:58 kcranstn you lonely there in Boston?
15:59 jar286 sort of
15:59 kcranstn Duke Bio also very quiet over the summer
15:59 kcranstn jimallman, looking at this: https://github.com/OpenTreeOfLife/opentree/blob/master/webapp/models/db.py
16:00 kcranstn seems to be defaulting to SSL/HTTPS unless there is a localconfig
16:01 jar286 I think he’s away from keyboard
16:03 jimallman i’m here, reviewing code and issues...
16:04 jimallman some context for HTTPS-everywhere: https://github.com/OpenTreeOfLife/opentree/pull/307
16:06 jimallman kcranstn: you can disable HTTPS (if desired) with this config setting (in both app config files): https://github.com/OpenTreeOfLife/opentree/blob/51a96f3885c5eecc3a14547d6c664a0e714d49b8/curator/private/config.example#L9
16:07 kcranstn should that be what we what people to do for local install?
16:07 jimallman hm, not sure about private/localconfig vs. private/config (the latter should suffice)
16:07 jimallman i haven’t run my local setup w/o HTTPS in a long time, so i’m not sure what changes.
16:08 kcranstn I can’t get mine running with HTTPS
16:08 kcranstn I’d like to debug that
16:08 jimallman symptoms?
16:08 kcranstn line 62 of db.py
16:08 kcranstn Traceback (most recent call last):
16:08 kcranstn File "/Users/karen/Documents/code/web2py/gluon/restricted.py", line 227, in restricted
16:08 kcranstn exec ccode in environment
16:08 kcranstn File "/Users/karen/Documents/code/web2py/applications/opentree/models/db.py", line 62, in <module>
16:08 kcranstn SECURE_SESSIONS_WITH_HTTPS = conf.getboolean("security", "secure_sessions_with_HTTPS")
16:08 kcranstn File "/Users/karen/anaconda/lib/python2.7/ConfigParser.py", line 368, in getboolean
16:08 kcranstn v = self.get(section, option)
16:08 kcranstn File "/Users/karen/anaconda/lib/python2.7/ConfigParser.py", line 607, in get
16:08 kcranstn raise NoSectionError(section)
16:08 kcranstn NoSectionError: No section: 'security'
16:09 jimallman gotcha. maybe this is missing from config.example
16:09 jimallman hm, i see it there:  https://github.com/OpenTreeOfLife/opentree/blob/master/webapp/private/config.example#L8
16:09 jimallman does your local private/config have this section and setting?
16:11 jimallman (check both apps, so webapp/private/config and curator/private/config)
16:12 jimallman kcranstn: ^
16:13 kcranstn I had an old copy of config, which I just modified based on the wiki page
16:13 kcranstn so, the [security] section missing
16:14 kcranstn now loading the opentree webapp, but getting a 500
16:18 kcranstn just a sec, debugging
16:22 kcranstn ok, got past the 500
16:23 kcranstn now getting the dreaded “Whoops!” error
16:24 kcranstn ah, the CACHED_* links
16:30 jimallman fyi, i’ve updated the wiki page to specify web2py 2.8.2 (incl. new download URL from deployment scripts).
16:33 kcranstn in the config file, I am confused abotu the method_urls, e.g. getDraftTreeID_url = {treemachine_domain}/getDraftTreeID
16:33 kcranstn because treemachine_domain not defined anywhere?
16:34 kcranstn or does it come from outside the file?
16:35 kcranstn I was hoping to be able to set http://devapi.opentreeoflife.org once in the config file, rather than 6 times but can’t figure out the syntax
16:36 kcranstn tried treemachine={baseURL}/treemachine/v2 but that didn’t work
16:38 jimallman i’ve added the correct version of web2py and our patched files that fix some web2py bugs (OAuth, URL rewriting):  https://github.com/OpenTreeOfLife/opentree/wiki/Installing-a-local-curator-and-tree-browser-test-server#install-and-patch-web2py
16:39 jimallman kcranstn: apologies, these substitutions are done on-the-fly, using the values in the [domains] section.
16:40 kcranstn ok
16:40 jimallman … so “{CACHED_treemachine_domain}/getSyntheticTree” becomes “//devapi.opentreeoflife.org/cached/treemachine/v1/getSyntheticTree”
16:40 kcranstn so it’s not a variable expansion at all, just a text placeholder
16:41 jimallman kinda, sorta? the footer shows what’s literally in the config file, but the running app knows the “expanded” versions
16:41 jimallman substitutions happen on the server side, and the full URLs (sans scheme) are passed to the client in JS
16:42 kcranstn where does web2py log ticket info?
16:43 kcranstn I am getting one of those “Internal error” pages with a ticket link, but clicking on the link merely opens up another ticket
16:46 kcranstn I am being beaten into “never try and edit the web application” submission
16:47 kcranstn I suspect that those patch files broke my web2py, which I installed before the note about using v 2.8.2
16:56 kcranstn ok, moving onto weekly hangout
17:02 kcranstn jat286?
17:02 kcranstn jar286?
17:03 jar286 yes looking for url
17:03 kcranstn in google doc
17:03 kcranstn and calendar item
17:03 jar286 yes
17:03 jar286 ahh… doesn’t show up my cal client
18:43 kcranstn jar286 - have you had a change to look at oti?
18:43 jar286 I’ve started to.
18:43 kcranstn jimallman and I were discussing this issue: https://github.com/OpenTreeOfLife/opentree/issues/674
18:43 kcranstn and wondering if you had any input
18:43 kcranstn (he’s gone to get coffee)
18:45 jar286 wasn’t thinking about that.  focusing on the study indexing issue
18:46 jar286 looks like I won’t be able to do debugging on my laptop.  going to try on varela
18:49 kcranstn do you have any initial thoughts about trying to put collections into oti vs a Plan B (!oti)
18:50 jar286 success - http://stackoverflow.com/questions/1348842/what-should-i-set-java-home-to-on-osx
18:51 jar286 my initial thought is still that it would be nicer to have a rdb
18:51 jar286 then direct access from python, r, java, etc. , mature tech, etc
18:51 jar286 as long as the db can be rebuilt from primary sources
18:52 kcranstn my initial thought was that loading collections (JSON) into Couch and building a few trivial views would get us going pretty quickly
18:53 jar286 I wasn’t impressed by couch, and my consultant (@tdanford) said to avoid it.  but I could learn more
18:53 kcranstn I like how you have your own consultant
18:54 jar286 yeah, that’s where I am friday afternoons from 3 to 4 alternate weeks. vry nice
18:54 jimallman jar286 has a posse
18:54 kcranstn I like the ease of input without having to design a model, but I still have a hard time wrapping my brain around MapReduce
18:55 jar286 mapreduce is just another way to write a cursor iteration
18:55 kcranstn of course!
18:55 kcranstn :P
18:56 kcranstn my concern with RDB is time - are we going to be ok with getting the collections going right away and wait to design the rest of the model?
18:57 jar286 yes, that’s why reload from sources is so important.  can change schema and ingest, and then ready to go (maybe use views for compatibility patches?)
18:57 kcranstn ok
18:57 jar286 do you have a good couch example to look at?
18:58 jar286 I found it to be sort of propaganda heavy
18:58 kcranstn not off the top of my head
18:58 jar286 maybe rod page’s stuff?
18:58 jar286 isn’t bionames couch?…
18:59 jar286 he has 94 repositories
18:59 jar286 on github
18:59 kcranstn yes, bionames is couch
18:59 kcranstn http://iphylo.blogspot.com/search?q=couchdb&amp;max-results=20&amp;by-date=true
19:00 jar286 https://github.com/rdmpage/bionames
19:01 kcranstn oh, look at all of that php
19:01 jar286 hmm.
19:04 jar286 I think my short-term focus has to be on the indexing bug.  it screwed my demo yesterday
19:04 kcranstn agreed
19:04 jar286 so I was going to put off this investigation a little bit… expecting just 1-3 days on the indexing bug
19:04 kcranstn and when the paper comes out, people are going to (hopefully) be looking at the site, and that’s a big bug
19:05 kcranstn cody is no longer travelling, so don’t be afraid to bug him on the issues: https://github.com/OpenTreeOfLife/oti/issues
19:14 kcranstn my gut feeling here is that we are *not* going to use oti for collections

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