R help - Sep 2016 - Opening or activating a URL to access data, alternative to browseURL

Hi all,

I've got a situation that involves activating a URL so that a link to some
data becomes available for download. I can easily use 'browseURL' to do
so,
but I'm hoping to make this batch-process-able, and I would prefer to not
have 100s of browser windows open when I go to download multiple data sets.

Here's the example:

#1
browseURL('
http://pick18.discoverlife.org/mp/20m?plot=2&kind=Hypoprepia+fucosa&site=33.9+-83.3&date1=2011,2012,2013&flags=build_txt:
')
# This opens the URL and creates a link to machine-readable data on the
page, which I can then download by simply doing this:

#2
read.delim('
http://pick18.discoverlife.org/tmp/Hypoprepia_fucosa_33.9_-83.3_2011,2012,2013.txt
')

However, I can only get the second line above to work if the thing in line
#1 has been opened in a browser already. Is there any way to allow me to
either 1) close the browser after it's been opened or 2) execute the line
#2 above without having to open a browser? We have hundreds of species that
you can see after the '&kind=' bit of the URL, so I'm trying to
keep the
browsing situation sane.

Thanks!
R

-- 

Ryan Utz, Ph.D.
Assistant professor of water resources
*chatham**UNIVERSITY*
Home/Cell: (724) 272-7769

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On 29/09/2016 3:29 PM, Ryan Utz wrote:
> Hi all,
>
> I've got a situation that involves activating a URL so that a link to
some
> data becomes available for download. I can easily use 'browseURL'
to do so,
> but I'm hoping to make this batch-process-able, and I would prefer to
not
> have 100s of browser windows open when I go to download multiple data sets.
>
> Here's the example:
>
> #1
> browseURL('
>
http://pick18.discoverlife.org/mp/20m?plot=2&kind=Hypoprepia+fucosa&site=33.9+-83.3&date1=2011,2012,2013&flags=build_txt:
> ')
> # This opens the URL and creates a link to machine-readable data on the
> page, which I can then download by simply doing this:
>
> #2
> read.delim('
>
http://pick18.discoverlife.org/tmp/Hypoprepia_fucosa_33.9_-83.3_2011,2012,2013.txt
> ')
>
> However, I can only get the second line above to work if the thing in line
> #1 has been opened in a browser already. Is there any way to allow me to
> either 1) close the browser after it's been opened or 2) execute the
line
> #2 above without having to open a browser? We have hundreds of species that
> you can see after the '&kind=' bit of the URL, so I'm
trying to keep the
> browsing situation sane.
>
> Thanks!
> R
>
You'll need to figure out what happens when you open the first page. 
Does it set a cookie?  Does it record your IP address?  Does it just 
build the file but record nothing about you?

If it's one of the simpler versions, you can just read the first page, 
wait a bit, then read the second one.

If you need to manage cookies, you'll need something more complicated. 
I don't know the easiest way to do that.

Duncan Murdoch

The rvest/httr/curl trio can do the cookie management pretty well. Make the
initial connection via rvest::html_session() and then hopefully be able to
use other rvest function calls, but curl and httr calls will use the cached
in-memory handle info seamlessly. You'd need to store and retrieve cookies
if you need them preserved between R sessions.

Failing the above and assuming this would not need to be lightning fast,
use the phantomjs or firefox web driver (either with RSelenium or some new
stuff rOpenSci is cooking up) which will then do what browsers do best and
maintain all this state for you. You can still slurp the page contents up
with xml2::read_html() and use the super handy processing idioms in the
scraping tidyverse (it needs it's own name).

A concrete example (assuming the URLs aren't sensitive) would enable me or
someone else to mock up something for you.


On Thu, Sep 29, 2016 at 4:59 PM, Duncan Murdoch <murdoch.duncan at
gmail.com>
wrote:
> On 29/09/2016 3:29 PM, Ryan Utz wrote:
>
>> Hi all,
>>
>> I've got a situation that involves activating a URL so that a link
to some
>> data becomes available for download. I can easily use
'browseURL' to do
>> so,
>> but I'm hoping to make this batch-process-able, and I would prefer
to not
>> have 100s of browser windows open when I go to download multiple data
>> sets.
>>
>> Here's the example:
>>
>> #1
>> browseURL('
>> http://pick18.discoverlife.org/mp/20m?plot=2&kind=Hypoprepia
>>
+fucosa&site=33.9+-83.3&date1=2011,2012,2013&flags=build_txt:
>> ')
>> # This opens the URL and creates a link to machine-readable data on the
>> page, which I can then download by simply doing this:
>>
>> #2
>> read.delim('
>> http://pick18.discoverlife.org/tmp/Hypoprepia_fucosa_33.9_-
>> 83.3_2011,2012,2013.txt
>> ')
>>
>> However, I can only get the second line above to work if the thing in
line
>> #1 has been opened in a browser already. Is there any way to allow me
to
>> either 1) close the browser after it's been opened or 2) execute
the line
>> #2 above without having to open a browser? We have hundreds of species
>> that
>> you can see after the '&kind=' bit of the URL, so I'm
trying to keep the
>> browsing situation sane.
>>
>> Thanks!
>> R
>>
>>
> You'll need to figure out what happens when you open the first page.
Does
> it set a cookie?  Does it record your IP address?  Does it just build the
> file but record nothing about you?
>
> If it's one of the simpler versions, you can just read the first page,
> wait a bit, then read the second one.
>
> If you need to manage cookies, you'll need something more complicated.
I
> don't know the easiest way to do that.
>
> Duncan Murdoch
>
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
>
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