TPL1_1_synonymy_list
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I've been making some minor edits to this to get it to work with TPL v1.0 (don't ask...). I think I'm being stupid, but could someone (maybe @ejforrestel ) tell me where the file data/theplantlist1.1/TPL1_1_synonymy_list comes from? I'm trying to re-build it for 1.0, but I want to make sure I do the same thing (...and hopefully script it...)
I've made some minor edits to get stuff to run without using the desktop (and a new 'v1.0' folder), which I can put on a new branch here if anyone wants. @dschwilk you probably don't want the repo becoming a holding ground for everyone's code :p
Thanks! Sorry (if) I'm being dumb!
Hi Will~
The list comes from The Plant List website -- do you need the specifics of
how it was scraped (the script is posted--don't expect the most streamlined
code, but it works)? I guess I'm not clear on exactly what you are
asking. You can just reformat your v1.0 to match that of the 1.1, right?
Sorry if I am missing something!
Best,
Beth
On Thu, Nov 20, 2014 at 2:46 PM, Will Pearse notifications@github.com
wrote:
I've been making some minor edits to this to get it to work with TPL v1.0
(don't ask...). I think I'm being stupid, but could someone (maybe
@ejforrestel https://github.com/ejforrestel ) tell me where the file
data/theplantlist1.1/TPL1_1_synonymy_list comes from? I'm trying to
re-build it for 1.0, but I want to make sure I do the same thing (...and
hopefully script it...)I've made some minor edits to get stuff to run without using the desktop
(and a new 'v1.0' folder), which I can put on a new branch here if anyone
wants. @dschwilk https://github.com/dschwilk you probably don't want
the repo becoming a holding ground for everyone's code :pThanks! Sorry (if) I'm being dumb!
Reply to this email directly or view it on GitHub
#8.
No, I'm sure you're not missing something, I think I'm not being clear. I've grep-ed the source code, and I can't seem to find where that file is created. I'm sure it is in the script, but I don't know where it gets created - could you point me to a file/line-number where it's created?
I hope that makes sense! Thank you!...
Hi @willpearse
The file name is declared at https://github.com/schwilklab/taxon-name-utils/blob/master/data/theplantlist1.1/R_scripts/getsynonymsTPL.R#L17 and each line written at https://github.com/schwilklab/taxon-name-utils/blob/master/data/theplantlist1.1/R_scripts/getsynonymsTPL.R#L62
Note that these scripts of Beth's were just dropped here and the relative paths probably need to be cleaned up. I did not re-run them in place but used the created files Beth sent (three files in https://github.com/schwilklab/taxon-name-utils/tree/master/data/theplantlist1.1).
@willpearse : if you cleaned up the relative paths so this all runs, either issue a pull request or just merge into master, that is fine.
Thanks; I can confirm I was being stupid! Thank you for pointing me to the lines; if/when I get this all merged in, I'll issue a request. Thank you both!