- API-users - lists.gbif.org

Re: [API-users] Occurrence search API limitations
by ptrans2004es 24 Apr '15

24 Apr '15

Hello, Thank you very much, Markus, for your answer. For me a callback URL is not really needed. Actively poll the download request status may be an acceptable solution as well. The problem is more in interactivity: as I understand, using asynchronous service does not allow us to show some kind of "progress" to the user, which seems to us convenient particularly on large downloads. Using synchronous paging service, we can show to the user the download progress. Maybe using the call /occurrence/download/{key} iteratively we could obtain some kind of "percent of completion" information, until the request is completed? (Sorry, I still don't tested the asynchronous service; only the synchronous one). Thank you very much. E. Garcia

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Occurrence search API limitations
by ptrans2004es 24 Apr '15

24 Apr '15

Hello, I know there is a limit of 200000 records when using the occurrence search API, and also that this limit can be avoided using the asynchronous download service instead. The problem is that this asynchronous service will send a link to a file to an email. That method seems not really convenient for programmatic downloads to be made from an interactive application, for example. There is another mechanism that allows downloading more than 200000 records? Removal of this limitation is expected? Thank you very much. Best regards, E.Gracia

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Parameter name changes?
by Scott Chamberlain 14 Apr '15

14 Apr '15

Hi again, Just noticed that spatialIssues parameter has bee changed to hasGeospatialIssue. But the documentation http://www.gbif.org/developer/occurrence#p_spatialIssues still has spatialIssues . Can the docs be updated? Are there any other parameters that have been changed but are not updated in the docs? Thanks! Scott Chamberlain

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Any changes in the download API?
by Scott Chamberlain 13 Apr '15

13 Apr '15

Hi all, Any news on the download API? More users of our R client are asking about this (e.g., "I want data for 15,000 species, and it takes sooo long with your R package, but using the web interface for so many species is a bit cumbersome"), so I am curious if you think it's now okay to expose download functions in our R client `rgbif`? If not, any idea when? If it is still a concern to allow programmatic access to the download API, I wonder if you can simply rate limit usage of the download API? Thanks! Scott

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Difference between /occurrence/search and /occurrence/count?
by Scott Chamberlain 09 Apr '15

09 Apr '15

Hi, A user of the R client we make for GBIF reports different number of occurrences for the /occurrence/search endpoint and the /occurrence/count endpoint with the same taxonkey, and limiting to georeferenced data only. See https://discuss.ropensci.org/t/rgbif-occ-count-and-occ-search-results-diffe… for the discussion. I imagine there's a good explanation for this, but I'm not sure what it is right now. Thanks! Scott

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geometry string length
by Scott Chamberlain 31 Mar '15

31 Mar '15

Hi all, Any known way to get around the URI string length for GET requests to the `/occurrence/search` endpoint? E.g., are POST requests supported for passing in parameters? I ask because a user of an R client I work on wants to pass in a polygon that is 40K characters long. Of course precision could be reduced, so the string is shorter, but that doesn't seem ideal. Also not ideal is converting to a bounding box approach that approximates the polygon, then converting that to WKT. Any thoughts? I know it's not standard, but maybe you allow body to be passed to a GET request for `/occurrence/search`? Thanks! Scott

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interaction for the maps api
by Ken-ichi 19 Mar '15

19 Mar '15

Hi all, We just added GBIF tiles as an optional overlay to many of our maps at iNaturalist.org, e.g. http://www.inaturalist.org/taxa/27818-Taricha-torosa/map. They're great and the API works perfectly, but the first thing people want to do when they see this data is click on those points! Has anyone at GBIF or elsewhere given some thought to how to implement that? The easiest way to do this from our perspective would be for GBIF to implement a UTFGrid endpoint for their tiles (https://github.com/mapbox/utfgrid-spec). The corresponding JSON wouldn't have to include all the occurrences (which would probably be a lot) but it could include 1 page of occurrences, or just a bounding box clients could use to generate a link to retrieve the corresponding data on GBIF. Another method I was thinking about was to make a custom tile overlay composed of HTML canvas elements, load the tile image onto the canvas, and use clicks to get the RGBA values of the corresponding pixel at the click coordinates to see if there was any color there. If alpha == 1, then retrieve corresponding occurrences from the GBIF occurrences API using the bounding box implied by the pixel at that zoom level. Canvases have been used as overlays in Google Maps, at least (e.g. https://github.com/brendankenny/CanvasLayer), and I'm sure in other frontend map frameworks as well, but I'm not sure what the performance would be like. Other ideas? -ken-ichi

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A question about the Maps API
by Mauro Cavalcanti 19 Mar '15

19 Mar '15

Dear ALL, Before the implementation of the new GBIF Portal, it was possible to generate distribution maps for a given species using an API call as follows: http://data.gbif.org/species/taxonName/ajax/returnType/concept/view/ajaxMap… where the value of the "query parameter" was a species name. This API call has been used by Roderick Page in his "iSpecies" web biodiversity data aggregator, as well as in my own "eSpecies" (sort of a clone of Page's iSpecies, written in Python, see sourceforge.net/projects/especies). Unfortunately, with the new GBIF Portal is seems that all API calls have changed and I got lost attempting to find out how to reproduce the previous behaviour using the new API. I presume it is still possible to generate distribution maps with the new API, but could not find out how. Can anyone offer some hints? Thanks in advance for any assistance you can provide. With warmest regards, -- Dr. Mauro J. Cavalcanti E-mail: maurobio(a)gmail.com Web: http://sites.google.com/site/maurobio

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Limits on the occurrence search API
by Nicolas Noé 26 Feb '15

26 Feb '15

Hi, I'm having some doubts about how the hard limits work when using the occurrence search API. I think this is a documentation/error message issue rather than a technical one: Here is what the doc says: - max value for "limit" = 300 - max total records = 1.000.000 (does that means limit * offset?) What my tests says: - http://api.gbif.org/v1/occurrence/search?hasCoordinate=true&limit=300&offse… => works, but shouldn't since 300*3335 = 1000500 total records - http://api.gbif.org/v1/occurrence/search?hasCoordinate=true&limit=1&offset=… => "maximum offset allowed is 200000", but offset IS 200000 (message should be "less than"? 199999 works) Also, this limit on the offset parameter should be stated in the doc page. - http://api.gbif.org/v1/occurrence/search?hasCoordinate=true&limit=300&offse… => "maximum offset allowed is 200000": here, we probably hit the 1.000.000 total limit, but the error message refer to the undocumented (and not hit here) max offset limit. Could you clarify a bit ? All the best, Nico

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yesterdays GBIF portal problems resolved
by Markus Döring 13 Feb '15

13 Feb '15

Dear all, we deployed some updated components of our portal yesterday and had troubles especially with species related pages for almost the entire day. We are sorry for this and this should be solved now. Thanks all for reporting issues. If you still experience unexpected behavior or even Oops pages please let us know! Regards, GBIF Dev Team

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