Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-01-16

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

All times shown according to UTC.

Time Nick Message
23:18 ilbot3 joined #opentreeoflife
23:18 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
23:39 dukeleto joined #opentreeoflife
01:04 towodo joined #opentreeoflife
01:57 dukeleto joined #opentreeoflife
02:41 towodo joined #opentreeoflife
03:57 jimallman joined #opentreeoflife
04:15 lcoghill joined #opentreeoflife
12:07 josephwb joined #opentreeoflife
12:09 josephwb just a note that i refreshed both AVATOL_nexsons and phylesystem yesterday
12:18 towodo joined #opentreeoflife
13:34 blackrim joined #opentreeoflife
13:38 josephwb joined #opentreeoflife
13:52 josephwb joined #opentreeoflife
13:53 josephwb joined #opentreeoflife
14:14 PEM joined #opentreeoflife
14:24 kcranstn joined #opentreeoflife
14:24 kcranstn anyone have suggestions for the all-hands this afternoon? (since Gordon didn't realize he was leading)
14:25 kcranstn I was thinking about doing a tour through the curation interface, but if there are more pressing concerns... would tackle taxonomy, but stephen won't be there
14:26 kcranstn actually, I see that Keith stepped up. Yay!
14:39 blackrim that is great. curation interface would also be nice. when is that scheduled for
14:42 kcranstn it isn't at this point (might be a separate meeting)
14:59 josephwb joined #opentreeoflife
14:59 josephwb not sure my earlier message got through: phylografter appears to be down again.
15:12 kcranstn thanks, joseph
15:12 kcranstn sent mail
15:15 kcranstn joanthan - what do we have for monitoring right now?
15:15 kcranstn should we look into setting up nagios (or something similar) and adding phylografter?
15:26 lcoghill joined #opentreeoflife
15:26 towodo nothing yet, it's on my to do list.
15:27 towodo I already have a nagios client running on norbert.csail.mit.edu ...
15:27 towodo (kcranstn, to get my attention put my screen name 'towodo' in a message)
15:28 towodo i mean, the client is set up to monitor other systems, could be set up for opentree purposes
15:28 towodo haven't done it before but i don't think it's too hard
15:31 jimallman joined #opentreeoflife
16:10 lcoghill joined #opentreeoflife
16:29 blackrim towodo: didn't realize this was you jonathan. anyway, just got the email about my taxonomy issue. let me know if there is something i can do to help investigate
16:31 towodo it sure looks like a bug.  The GBIF family is incertae sedis in Plantae.  I don't know why the NCBI genus got placed in it. Just writing code to help me out with looking at nodes and synonyms
16:32 towodo the parent of the ncbi genus should only change if the gbif classification is a 'refinement' of the ncbi one. so i'm looking to see if there's a bug in the 'is refinement' predicate.  thanks for finding this
16:34 blackrim there is a synonym for that genus (looks like a mispelling to me) that has the single r in the name and then would point to the bad family (who is just a child of Plantae)
16:34 towodo i could easily patch this but that wouldn't identify the real bug.
16:36 blackrim right
16:43 towodo I must have been very tired when I wrote that code. Need to rethink it from first principles
16:44 blackrim ok
16:54 towodo I can see the problem, am trying out a fix.  it's sort of shooting in the dark without test cases but I don't know how to manage test cases.  I guess they could go in the build script. what do you do for synthesis regression testing?
16:59 blackrim I don't have anything formal other than a set of important studies and output of where they map. we have discussed formal test cases, but that discussion didn't get far (waiting on some empirical feedback on reliable monophyletic groups we can verify are present)
17:05 kcranstn joined #opentreeoflife
17:37 josephwb phylografter still down
17:48 PEM josephwb - yes, Rick responded pretty quickly yesterday.  Are you exporting a lot of Nexsons?
17:48 PEM (yes it is still down)
17:54 josephwb no rush, just noting it.
18:02 dukeleto joined #opentreeoflife
18:03 lcoghill I'm curious why it keeps going down at about the same time each day.
18:18 towodo python question for anyone: how do I run a script from a script? like 'load' in LISP?
18:18 towodo or maybe 'include'
18:20 josephwb maybe 'import'?
18:20 towodo I want it to run in the same lexical scope as the loading file
18:22 towodo I guess I can abstract over the needed variables, define a function, and call it
18:22 towodo but was wondering if there was something more direct
18:23 towodo I've used 'import sys' and such for libraries, not for my own files, guess i need to read about it
18:26 josephwb for file 'foo.py':
18:26 josephwb from foo import *
18:26 towodo can i say from foo/bar import *?
18:26 towodo does it search in same directory as the script first?
18:27 towodo I see https://github.com/OpenTreeOfLife/gcmdr/blob/master/life.py  as a model
18:27 josephwb eek. i don't know.
18:27 josephwb yes, gcmdr is where i use import
18:30 lcoghill yep, you can import it, and then access any of the pieces inside the calling script, and then call those objects or functions locally in your primary script.
18:31 lcoghill ala: "import script2"
18:31 lcoghill script2.function()
18:32 towodo need to look up how to do:  from foo/bar import x
18:35 josephwb import sys
18:35 lcoghill do you mean like: "from script2 import desired_function as function_call_name"
18:35 josephwb sys.path.append("directory")
18:36 josephwb from file_in_directory import *
18:37 towodo what gcmdr does is fine with me, now i just have to figure out how to specify that the imported script is in the same directory as the running script (which is not the current directory)
18:37 josephwb what i put above works for me
18:38 josephwb sys.path.append("directory_path")
18:39 josephwb anything in "directory_path" can be imported
18:39 kcranstn joined #opentreeoflife
18:40 towodo seems ugly, but it will do.  directory containing script ought to automatically be on the directory path
18:42 PEM lcoghill - I don't think the phylografter crashes are due to time of day - Rick says it's running out of memory and may be related to heavy use of the nexson export.  I spent some time last summer looking for the memory leak and resolved some of the problem, but there is still some leakage.
18:43 lcoghill PEM: good to know. the FM network seems... less than reliable some days so I just wanted to make sure.
18:45 josephwb definitely ugly
18:46 josephwb probably a much more elegant way, but i just don't know python
18:48 dukeleto towodo: you can also modify PYTHONPATH, which are prepended to sys.path
18:49 towodo yes that might be better… since the Makefile will know the directory structure
19:13 towodo argh, now i make a change to foo, do import foo, and nothing happens because the older version is already imported!
19:13 towodo what kind of interactive language is this?
19:13 towodo (well, could be a jython only problem)
19:14 josephwb stephen is back: he will be able to help
19:15 blackrim i am looking back at the bits here to get a handle as to what the issue is.
19:16 blackrim towodo: you can do reload(foo)
19:16 towodo it's not that significant, i'm just being lazy by asking irc instead of RTFMing
19:18 dukeleto towodo: beware of *.pyc files
19:19 towodo this is jython, i doubt there are any, but i will
19:22 towodo blackrim, i'm giving up on the chromista spreadsheet, half the corrections fail because they use taxa not known to OTT.  there's got to be a better way to solicit fixes from the curators
19:22 towodo whose idea was it to make that spreadsheet?
19:23 towodo a tool of the sort cody was talking about last august would be much better
19:24 blackrim towodo: yeah, i don't know. it is a little confusing why the names would not be in ott. where are they coming from? anyway, not worth pursuing.
19:24 blackrim is there a new taxonomy up now?
19:27 towodo just building it now. give me 7 minutes
19:29 blackrim you have 6
19:34 towodo ok, draft8 is up now in the usual place
19:34 towodo enjoy
19:34 towodo blackrim, ping
19:36 blackrim getting it now
19:36 blackrim look at all that organization!
19:46 kcranstn joined #opentreeoflife
19:46 kcranstn joined #opentreeoflife
19:48 PEM left #opentreeoflife
20:04 towodo blackrim: going on errand now. let me know how it goes by email
20:09 kcranstn joined #opentreeoflife
20:22 PEM joined #opentreeoflife
20:59 blackrim left #opentreeoflife
21:02 PEM left #opentreeoflife
21:14 towodo joined #opentreeoflife
21:20 PEM joined #opentreeoflife
21:31 towodo_ joined #opentreeoflife

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