Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-07-03

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Time Nick Message
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14:03 codiferous so there is some interest in having the study id, tree id, and commit sha all stored and returned separately by treemachine services, yes?
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14:37 codiferous @josephwb, do you still use pgloadind to load nexsons into treemachine?
14:37 josephwb yes
14:38 codiferous ok
14:53 josephwb codiferous: in gcmdr, we get the sha from the downloaded nexson
14:54 josephwb https://github.com/OpenTreeOfLife/gcmdr/blob/master/general_tm_utils.py#L34-38
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15:43 codiferous is the updateGraphFromPhylografter service ever called by anything?
15:44 josephwb don't believe so
15:44 codiferous it's in the plugin PhylografterUpdater in treemachine
15:44 codiferous ok
15:46 codiferous can you give me an example command for gcmdr to import some things so i can see if my edits are working
15:49 josephwb it's a little involved
15:49 josephwb need to set up a bunch of variables
15:49 josephwb like in stephen_laptop_conf.py
15:51 josephwb what are you trying to do?
15:52 codiferous test loading of studies and make sure the properties are getting set the way i want in the graph
15:52 codiferous i can replicate that conf file and set the variables. assuming i do that and have a file called cody_laptop_conf.py, how do i load some studies?
15:53 josephwb load_studies.py
15:53 josephwb using your conf
15:53 josephwb studytreelist is a, well, list of studies.
15:54 josephwb there are lists in "files_for_submission_v2.0"
15:54 josephwb casn import one of those
15:54 josephwb or just type a few into load_studies.py
15:55 josephwb e.g. studytreelist=["pg_244_3855", "pg_2879_6673"]
15:56 josephwb load_studies.py assumes you already have the studies downloaded
15:56 josephwb in studyloc, defined in conf
15:57 codiferous ok
15:58 josephwb you can put the following in load_studies.py
15:58 josephwb download = True
15:58 josephwb if download:
15:58 josephwb import general_tm_utils
15:58 josephwb general_tm_utils.get_all_studies_opentreeapi(studytreelist,studyloc)
15:58 josephwb that will download the studies in studytreelist in the directory studyloc
16:01 codiferous ok
16:01 codiferous gcmdr is a 900mb repo
16:01 codiferous apparently
16:02 josephwb huh
16:02 josephwb we purged a lot of stuff
16:02 josephwb might want to start it over again
16:03 codiferous i just cloned it
16:03 josephwb right. as this was the workhorse of the Science synthesis, all files have spent some time in there
16:04 codiferous ok
16:05 josephwb where are you getting 900 MB from?
16:05 josephwb i have 247 MB
16:06 josephwb codiferous: ^
16:08 codiferous while cloning
16:08 codiferous 4% (472/10979), 40.85 MiB
16:09 josephwb yeah, that ain't right
16:09 codiferous in any event, even 240mb is too big for airplane wifi
16:09 codiferous i'll get it later
16:09 josephwb https://api.github.com/repos/OpenTreeOfLife/gcmdr
16:10 josephwb search for "size"
16:10 josephwb seems like the repo is 141.7 MB (I must have a lot of uncommited junk in mine)
16:10 codiferous i see that
16:11 codiferous dk
16:13 josephwb "size" from the github api is in kilobytes
16:13 josephwb why isn't the size of repos just displayed on the repo site itself?
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18:03 josephwb make me a pie
18:04 josephwb *wrong window*
18:13 josephwb towodo: do you prefer edits in the form of ott.taxon('Some taxon')…
18:13 josephwb like here: https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/doc/scripting.md#surgery
18:13 josephwb or tsv
18:13 josephwb like her: https://github.com/OpenTreeOfLife/reference-taxonomy/tree/master/feed/ott/edits
18:13 towodo hmm.  nobody has asked this before
18:13 towodo the python form is much richer and more robust
18:14 josephwb you mentioned the ott.taxon('Some taxon')… to me some time before
18:14 josephwb ok
18:14 towodo so I guess python.  I'm planning some changes but I guess I can maintain backward compatibility
18:14 towodo see more examples in make-ott.py in reference-taxonomy
18:14 josephwb but i don't see any files containing such commands in https://github.com/OpenTreeOfLife/reference-taxonomy/tree/master/feed/ott/edits
18:15 josephwb another question: do any of these take ottIDs?
18:15 towodo they're not in that directory.  the only commands so far are in make-ott.py
18:15 towodo you can say ott.taxon('ottid') or ncbi.taxon('ncbiid')
18:15 towodo there are some examples in make-ott.py
18:16 towodo and you can test these out by running smasher, loading in ott, and running the patches.
18:16 towodo testing catches problems like misspellings and undisambiguated homonyms
18:18 josephwb i don't see any string "ott.taxon('ottid')" in the repo
18:18 josephwb you mean, e.g., ottid = ott12345?
18:18 towodo no
18:19 josephwb ott.taxon('ott12345')
18:19 josephwb ok, i missed soemthing then
18:19 towodo see e.g. ids.taxon('67952')     ids = previous ott version
18:20 towodo there are no examples of ott.taxon('123') but it works
18:20 josephwb ok
18:20 towodo fire up smasher and play around.  it's fun
18:21 josephwb if i have a bunch of edits in this form, where should i put it?
18:22 towodo I would say in feed/misc/, then edit make-ott.py to add an import - for precedent see 'fixChromista(ott)'
18:22 josephwb got it. thanks.
18:23 towodo you're a pioneer, what are you doing?
18:23 josephwb just minor taxonomy edits
18:23 josephwb we are testing all of the synthesis sources trees in the new taxonomy
18:24 josephwb so, the following should be copacetic?
18:24 towodo one thing that's missing is provenance. currently I'm putting it in comments.
18:24 josephwb ott.taxon('12345').take(ott.taxon('6789'))
18:24 towodo yes
18:24 towodo that will move 6789
18:25 towodo I've taken a stab at a successor language - it's in the ievobio2014 branch of the repo
18:25 josephwb i see provenance in this example: ott.taxon('Parentia').add(ott.newTaxon('Parentia daughtera',
18:25 josephwb 'species', 'http://www.marinespecies.org/aphia.php?p=taxdetails&id=557120'))
18:25 towodo yes there's a field for new taxa, but not for classification edits
18:26 josephwb oh, okay. so just a comment at the moment?
18:26 towodo url for new taxa,  # python comment for 'take' and other edits - be as verbose as you're willing to be
18:27 towodo link to issue is nice
18:27 towodo oh, and the date
18:27 towodo and your name
18:30 josephwb for each change? or can i just put this at the top of the document
18:31 josephwb all changes look like they are reflected on the IOC bird list
18:31 towodo if the info is the same, put at top. I'm going to have to go back over all the comments at some point
18:31 towodo you could just do a bird list import.  very similar to amphibiaweb, for which I have the code
18:33 josephwb yes, i'll do that then
18:34 towodo that would be great.  the columns in the bird spreadsheet aren't exactly the same as in the amphibia one.  you could load both and compare, and copy and modify the amphibia script
18:37 josephwb you are talking about "process_amphibiaweb.py"
18:37 towodo yes
18:37 josephwb ok, looks straightforward
18:38 josephwb i don't see "amphib_names.txt" in the repo
18:39 towodo it's downloaded on build.  see Makefile
18:39 josephwb right
18:39 towodo you can try using 'make amphibiaweb' (I think, or something similar) to make the amphibiaweb converted taxonomy
18:40 josephwb hmm, don't see amphi* in the makefile
18:41 towodo oh, you're right.  never made a rule for it. sorry
18:41 josephwb regardless, i see how things work
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