Download with geometry parameter

[nmtarr]

Hello,

I can't seem to figure out how to run occurrences.download() with a geometry parameter successfully. I've tried enough tweaks to get to the point of wondering if there's a bug. Anyone got any advice?

I'm using Python 3.7.10 and pygbif 0.5.0. Here is my code; it works without the geometry parameter:

------------------------------------------------

from pygbif import occurrences

username = 'xxxxxx'
password = 'xxxxxx'
email = 'xxxxxx'

download_filters = ["taxonKey = 2496287",
"geometry within 'POLYGON ((-82.7 36.9, -85.0 35.6, -81.0 33.5, -79.4 36.3, -79.4 36.3, -82.7 36.9))'"]

download = occurrences.download(download_filters,
pred_type='and',
user = username,
pwd = password,
email = email)
#-------------------------------------------------

And here is the error message:

Exception: error: JSON parse error: Cannot construct instance of org.gbif.api.model.occurrence.predicate.WithinPredicate, problem: may not be null; nested exception is com.fasterxml.jackson.databind.exc.ValueInstantiationException: Cannot construct instance of org.gbif.api.model.occurrence.predicate.WithinPredicate, problem: may not be null
at [Source: UNKNOWN; line: -1, column: -1] (through reference chain: org.gbif.api.model.occurrence.predicate.ConjunctionPredicate["predicates"]->java.util.ArrayList[1]), with error status code 400check your number of active downloads.

Regards,

Nathan

[sckott]

thanks, on leave until may 3, will have a look then

[sckott]

Wasn't quite sure, had to look this one up, see https://github.com/sckott/pygbif/blob/master/test/test-occurrences-download_request.py#L83

Seems a little bit different from other queries, have to use GbifDownload to construct a class first, then add_geometry

e.g.,

req = GbifDownload("name", "email")
req.add_geometry(
    "POLYGON((-14.06 42.55, 9.84 38.27, -7.03 26.43, -14.06 42.55))"
)
req.post_download()

[nmtarr]

Scott, Thank you for looking into this. This is my first time submitting an issue that required edits on the part of a contributor. How should I proceed? Download and test the development version and confirm that the error was fixed for my application? Nathan

…

On Thu, May 6, 2021 at 7:52 PM Scott Chamberlain ***@***.***> wrote: Wasn't quite sure, had to look this one up, see https://github.com/sckott/pygbif/blob/master/test/test-occurrences-download_request.py#L83 Seems a little bit different from other queries, have to use GbifDownload to construct a class first, then add_geometry e.g., req = GbifDownload("name", "email")req.add_geometry( "POLYGON((-14.06 42.55, 9.84 38.27, -7.03 26.43, -14.06 42.55))" )req.post_download() — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#81 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEMYMOGPKHJED7VTBEEYTSLTMMTSHANCNFSM43NL7V7Q> .

-- *Nathan Tarr* Research Scholar NC Cooperative Fish and Wildlife Research Unit | Department of Applied Ecology NC State University website <https://nmtarr.wordpress.ncsu.edu/> All electronic mail messages in connection with State business which are sent to or received by this account are subject to the NC Public Records Law and may be disclosed to third parties.

[sckott]

@nmtarr Yes, download dev version from github pip install git+git://github.com/sckott/pygbif.git#egg=pygbif

[nmtarr]

@sckott I downloaded the dev version, but I'm still getting the error as described above. Can someone please confirm that my geometry parameter should indeed be formatted like this:

"geometry within 'POLYGON ((-82.7 36.9, -85.0 35.6, -81.0 33.5, -79.4 36.3, -79.4 36.3, -82.7 36.9))'"

I'm not confident that I've got it right.

Thanks for the help.

[sckott]

The string you supply to add_geometry should just be the WKT itself, without the geometry within part - the geometry within gets added internally. Does that make sense?

[nmtarr]

@sckott Thanks. That makes sense for use of add_geometry. I would really like to be able to include a geometry parameter with occurrences.download. The documentation for that function states that geometry can be included. Is that not actually the case?

[sckott]

Got it now, thanks for clarifying.

Okay, just pushed a change on branch geometry-predicate. The download predicate logic was splitting strings on spaces, which doesn't work for geometry predicate since you can't remove spaces from a WKT string. Should work now after reinstalling from github. Let me know if works.

[nmtarr]

It is working for me now. Thanks for addressing the issue!

[sckott]

Awesome, glad it works now.

i'll PR the change to the main branch and seek a bit of feedback first from other contribs