Hi Mauro

Oh ...
No way to set it unlimited?
The 'manual via browser' option and parsing the returning csv is the current status.
or any alternative to pygbif?

If I understood it correctly, GBIF database is organized as Web Server, so I gues there should be a way to connect to the birdhouse WPS, am I right? 

(put the web-dev list in copy)

Merci
Nils

On 02/06/2016 12:40, Mauro Cavalcanti wrote:

Nils,

That's a limit imposed (for good operational reasons) by the GBIF API. If you want a larger number of records, you'll have to download them "manually" (that is, via browser) and then parse locally the csv file returned from the GBIF server.

Hope this helps.

Best regards,

--
Dr. Mauro J. Cavalcanti
E-mail: maurobio@gmail.com
Web: http://sites.google.com/site/maurobio

Em 02/06/2016 04:48, "Nils Hempelmann" <info@nilshempelmann.de> escreveu:

Hi Scott

works fine. Thanks a lot. Just have a question for the search limits:

The maximal records seems to be limited to 300. Is that on purpose?
And requesting more than 200000 gives a 'bad request'

Merci
Nils


In [68]: len( occurrences.search(taxonKey=key, limit=100)['results'])
Out[68]: 100

In [69]: len( occurrences.search(taxonKey=key, limit=300)['results'])
Out[69]: 300

In [70]: len( occurrences.search(taxonKey=key, limit=3000)['results'])
Out[70]: 300

In [71]: len( occurrences.search(taxonKey=key, limit=200000)['results'])
Out[71]: 300

In [72]: len( occurrences.search(taxonKey=key, limit=200001)['results'])
---------------------------------------------------------------------------
HTTPError                                 Traceback (most recent call last)
<ipython-input-72-2f7d7b4ccba0> in <module>()
----> 1 len( occurrences.search(taxonKey=key, limit=200001)['results'])

/home/nils/.conda/envs/birdhouse/lib/python2.7/site-packages/pygbif/occurrences/search.pyc in search(taxonKey, scientificName, country, publishingCountry, hasCoordinate, typeStatus, recordNumber, lastInterpreted, continent, geometry, recordedBy, basisOfRecord, datasetKey, eventDate, catalogNumber, year, month, decimalLatitude, decimalLongitude, elevation, depth, institutionCode, collectionCode, hasGeospatialIssue, issue, q, mediatype, limit, offset, **kwargs)
    251         'collectionCode': collectionCode, 'hasGeospatialIssue': hasGeospatialIssue,
    252         'issue': issue, 'q': q, 'mediatype': mediatype, 'limit': limit,
--> 253         'offset': offset}, **kwargs)
    254     return out

/home/nils/.conda/envs/birdhouse/lib/python2.7/site-packages/pygbif/gbifutils.pyc in gbif_GET(url, args, **kwargs)
     17 def gbif_GET(url, args, **kwargs):
     18   out = requests.get(url, params=args, headers=make_ua(), **kwargs)
---> 19   out.raise_for_status()
     20   stopifnot(out.headers['content-type'])
     21   return out.json()

/home/nils/.conda/envs/birdhouse/lib/python2.7/site-packages/requests/models.pyc in raise_for_status(self)
    842
    843         if http_error_msg:
--> 844             raise HTTPError(http_error_msg, response=self)
    845
    846     def close(self):

HTTPError: 400 Client Error: Bad Request for url: http://api.gbif.org/v1/occurrence/search?taxonKey=2882316&limit=200001&offset=0

In [73]:

On 02/06/2016 02:22, Scott Chamberlain wrote:

Fixes to docs and fix to download_get are up on Github now. Will push new version to pypi soon. Let me know if some thing still don't work for you after reinstalling from github

S

On Wed, Jun 1, 2016 at 4:51 PM Nils Hempelmann <info@nilshempelmann.de> wrote:

Hi Scott and Mauro

Mauro sended me a snipped of code which worked fine:
https://github.com/bird-house/flyingpigeon/blob/develop/scripts/pygbif_occurence.py

I found the example here:
https://github.com/maurobio/pygbif#occurrence-data

and here:
https://github.com/sckott/pygbif#occurrences-module

Thanks a lot very great. That enables a lot ;-)
I ll keep you posted

merci

Nils

On 02/06/2016 01:45, Scott Chamberlain wrote:

And where are those example from exactly? I don't see those examples searching the repo (which includes all docs). 

`pygbif.name_suggest` wouldn't work because `name_suggest` is a method in the `species` module, so you'd have to do pygbif.species.name_suggest, or `from pygbif import species`, then `species.name_suggest`

Looks like occ.get(taxonKey = 252408386)  is a documentation bug, that should be `key` instead of `taxonKey`, a copy paste error. will fix that. 

The `occ.download_get` call has a small bug, will fix that

All other calls work for me

S 

On Wed, Jun 1, 2016 at 4:34 PM Scott Chamberlain <myrmecocystus@gmail.com> wrote:

Hi, 

What version of pygbif are you on? And what version of Python>

Best, Scott

On Wed, Jun 1, 2016 at 4:02 PM Nils Hempelmann <info@nilshempelmann.de> wrote:

Hi Mauro and Scott

Was checking out pygbif. seems to be a very useful tool.

Can you help me with the syntax (or forward me to the appropriate person
;-) )
The given snippets of code are outdated.

I am basically just looking for the occurrence coordinates:
here is my first try :

import pygbif
occ = pygbif.occurrences.search(scientificName='Fagus sylvatica')
occ['count']

... and further? ;-)

the examples in the docu are throwing errors:

key=  pygbif.name_suggest(q='Helianthus annuus',rank='species')['key']
pygbif.search(taxonKey=key[0]['key'],limit=2)

from pygbif import occurrences as occ occ.search(taxonKey = 3329049)
occ.get(taxonKey = 252408386) occ.count(isGeoreferenced = True)
occ.download_list(user  =  "sckott",  limit  =  5)
occ.download_meta(key  =  "0000099-140929101555934")
occ.download_get("0000099-140929101555934")


Thanks
Nils