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()

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[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