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Counts per degree cell
by Scott Chamberlain 29 Oct '15

29 Oct '15

Hi all! AFAIK, what the route http://data.gbif.org/ws/rest/density/list used to provide is gone, right? If so, I imagine that it was too expensive computationally? If not, might it come back? Some users requesting that kind of data. Thanks! Scott

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dateline queries
by jorrit poelen 29 Oct '15

29 Oct '15

Hi! When searching for occurrences by geometry I am using the following WKT polygon: POLYGON((116.71875 55.7765730186677,116.71875 90,87.1875 90,87.1875 55.7765730186677,116.71875 55.7765730186677)) This polygon is intended to cover parts of eastern Russia, Alaska, northern Canada and Greenland. For some reason, the GBIF results include the inverted longitudinal selection. Does GBIF support dateline wrapping for it’s spatial queries? If so, how should I form the geometry to capture this? thx, -jorrit PS1 Is there a github issue list than I can post this at? PS2 For context, please see a working prototype at: http://www.effechecka.org/#geometry=POLYGON%28%28116.71875%2055.77657301866…

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Get a '400 Bad Request'
by Maria Cubillos 22 Oct '15

22 Oct '15

Hi, when I try to sent a request to http://api.gbif.org/v1/species?name=Allium%20Sativum&limit=1&callback=jQuer… from browser which has Language option in español(Latinoamerica) this send Accept-Language: en-US,en;q=0.8,es;q=0.6,es-419;q=0.4 in the headers, then I recive a 400 Bad Request. This only happend when I have this language option. With español(Latinoamerica) General 1. Request URL: http://api.gbif.org/v1/species?name=Allium%20Sativum&limit=1&callback=jQuer… 2. Request Method: GET 3. Status Code: 400 Bad Request 4. Remote Address: 130.226.238.135:80 1. Response Headersview source 1. Accept-Ranges: bytes 2. Access-Control-Allow-Origin: * 3. Age: 0 4. Connection: keep-alive 5. Content-Length: 72 6. Content-Type: text/plain 7. Date: Thu, 22 Oct 2015 14:59:13 GMT 8. Server: Jetty(9.2.z-SNAPSHOT) 9. Via: 1.1 varnish 10. x-api-url: /v1/species?name=Allium%20Sativum&limit=1&callback=jQuery214020442963019013405_1445525943637&_=1445525943638 11. X-Varnish: 282045222 2. Request Headersview source 1. Accept: */* 2. Accept-Encoding: gzip, deflate, sdch 3. Accept-Language: en-US,en;q=0.8,es;q=0.6,es-419;q=0.4 4. Connection: keep-alive 5. Host: api.gbif.org 6. Referer: http://192.168.206.86:7000/?taxonRecordName=Allium+Sativum&abstract= 7. User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/48.0.2537.0 Safari/537.36 3. Query String Parametersview sourceview URL encoded 1. name: Allium Sativum 2. limit: 1 3. callback: jQuery214020442963019013405_1445525943637 4. _: 1445525943638 Without español(Latinoamerica) General Remote Address:130.226.238.135:80 Request URL: http://api.gbif.org/v1/species?name=Allium%20Sativum&limit=1&callback=jQuer… Request Method:GET Status Code:200 OK Response Headers view source Accept-Ranges:bytes Access-Control-Allow-Origin:* Age:0 Connection:keep-alive Content-Length:1031 Content-Type:application/javascript Date:Thu, 22 Oct 2015 16:46:26 GMT Server:Jetty(9.2.z-SNAPSHOT) Via:1.1 varnish x-api-url:/v1/species?name=Allium%20Sativum&limit=1&callback=jQuery21406685116644948721_1445532365523&_=1445532365524 X-Varnish:282682159 Request Headers view source Accept:*/* Accept-Encoding:gzip, deflate, sdch Accept-Language:en-US,en;q=0.8,es;q=0.6 Connection:keep-alive Host:api.gbif.org Referer:http://localhost:7000/ User-Agent:Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/41.0.2272.76 Chrome/41.0.2272.76 Safari/537.36 Query String Parameters view source view URL encoded name:Allium Sativum limit:1 callback:jQuery21406685116644948721_1445532365523 _:1445532365524 -- *María Fernanda Cubillos Vargas*Investigadora Asistente - Sistema de Información sobre Biodiversidad de Colombia (SIB Colombia) *Instituto de Investigación de Recursos BiológicosAlexander von Humboldt**Avenida Paseo Bolivar (Circunvalar) 16-20 * *PBX: (57) 1 320 2767 Ext. 1154Bogotá, D.C., Colombia* Antes de imprimir este mensaje, piensa si realmente necesitas hacerlo. ¡Gracias!

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eventDate parameter in occurrence/search?
by Kumiko Totsu 16 Oct '15

16 Oct '15

Hi all, I found a problem using 'eventDate' in the occurrence API. I could only get results by range queries but not with a date. 14 results between 2014-03-10 and 2014-03-11 http://api.gbif.org/v1/occurrence/search?institutionCode=NIES&eventDate=201… 0 result on 2014-03-11 (It should be 14 results) http://api.gbif.org/v1/occurrence/search?institutionCode=NIES&eventDate=201… 0 result on 2014-03-10 http://api.gbif.org/v1/occurrence/search?institutionCode=NIES&eventDate=201… The example below is totally fine, so it seems that not all data have this problem. 14 results between 2015-03-17 and 2015-03-18 http://api.gbif.org/v1/occurrence/search?institutionCode=NIES&eventDate=201… 14 results on 2015-03-18 http://api.gbif.org/v1/occurrence/search?institutionCode=NIES&eventDate=201… 0 result on 2015-03-17 http://api.gbif.org/v1/occurrence/search?institutionCode=NIES&eventDate=201… Is there anything wrong with data or API? Cheers, Kumiko -------------------------------------------------------- Kumiko Totsu Center for Environmental Biology and Ecosystem Studies National Institute for Environmental Studies, Japan totsu.kumiko(a)nies.go.jp --------------------------------------------------------

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API Changelog?
by Scott Chamberlain 29 Sep '15

29 Sep '15

Hi all, Is there a changelog somewhere with noteable changes in the API? I could follow the Issue tracker I suppose, but curious if there's something like this https://developers.digitalocean.com/documentation/changelog/ for this API meant for human consumption. Thanks! Scott

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Some questions from a begginer
by Eduardo Dalcin 16 Sep '15

16 Sep '15

Hi folks, This is my first message to the list. So, please, be nice :) I'm working here at Rio de Janeiro Botanical Garden, together with the guys at the National Center for Flora Conservation. We are doing the risk assessment of the Brazilian flora to the government. We assess, so far, the risk of ca. 6.000 species <https://mailtrack.io/trace/link/453c7d453a2da4e332a97aeca082eb5547d8191b?ur…>, but we still have to assess ca. 35.000. Access occurrence records for Brazil is crucial, and every occurrence is important. That means that we have to put together occurrence data from different sources and, after the first batch of the risk assessment, we realize that we need to build up our aggregator. We are planning to do this with the Lontra-harvester, with the help of the guys at Brazilian GBIF Node. So, the one of the firsts steps was to list the available resources to understand the dimension of the task and, that brings me to my questions. First: The request: http://api.gbif.org/v1/occurrence/count?country=BR&taxonKey=6&basisOfRecord… <https://mailtrack.io/trace/link/a74c129abf8bbfa4b19b1e189b34df8e0487feca?ur…> returns 4.982.689 records And the request: http://api.gbif.org/v1/occurrence/counts/datasets?country=BR&taxonKey=6&bas… <https://mailtrack.io/trace/link/9d992e7b6733894b7f83de11d178c1437080224b?ur…> returns (here <https://mailtrack.io/trace/link/f15b92c6e49e193b58c96df93026b672d630a4fd?ur…>) 7.406.310 records Comments? Second: The request: http://api.gbif.org/v1/occurrence/count?country=BR&taxonKey=6&basisOfRecord… <https://mailtrack.io/trace/link/a74c129abf8bbfa4b19b1e189b34df8e0487feca?ur…> return things like this: "197908d0-5565-11d8-b290-b8a03c50a862":27629 But the consult of the same dataset: http://www.gbif.org/occurrence/search?TAXON_KEY=6&DATASET_KEY=197908d0-5565… <https://mailtrack.io/trace/link/6b3dbf4bfc7f45d67d05057979f1e72e2617ca68?ur…> Returns "null" (of course, is a FishBase!) I have plenty of examples like this, on yellow here (not finished!): https://docs.google.com/spreadsheets/d/1msUjwMLoKwnXxJFzF20SeN_C65RIkGLbwaY… <https://mailtrack.io/trace/link/21008349e3704f943677730af8f5afdc6cd3cc7b?ur…> Comments? I think those two questions is a good start. Please, let me know if I'm doing something wrong. Cheers, Eduardo -------------------------------- *Eduardo Dalcin <https://mailtrack.io/trace/link/0013f9d54db6dace53d2df17834b697a7abd50cc?ur…>* Instituto de Pesquisas Jardim Botânico do Rio de Janeiro - JBRJ e-mail: edalcin(a)jbrj.gov.br Trabalho / Work: +55 21 3204 2116 -------------------------------- *e-mail alternativo / * *alternate email:** edalcin(a)jbrj.org <edalcin(a)jbrj.org>* -------------------------------- Agendar reunião / Schedule a meeting: http://agendar.dalc.in <https://mailtrack.io/trace/link/0307534e3500b69d419aa6594a8e7baed96be03e?ur…>

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Dataset search on keyword broken?
by Peter Desmet 15 Sep '15

15 Sep '15

Hi, I'm trying to search for datasets with a certain keyword. Every query I try though returns 0 results: http://api.gbif.org/v1/dataset/search?keyword=lifewatch Some datasets do have that keyword though, e.g. http://data.inbo.be/ipt/resource?r=bird-tracking-gull-occurrences, but I noticed keywords are not displayed on GBIF dataset pages: http://www.gbif.org/dataset/83e20573-f7dd-4852-9159-21566e1e691e, though they are available via the API: http://api.gbif.org/v1/dataset/83e20573-f7dd-4852-9159-21566e1e691e According to the documentation: keyword parameter = Filters datasets by a case insensitive plain text keyword. The search is done on the merged collection of tags, the dataset keywordCollections and temporalCoverages. Searching for the machineTag "13" (value for key "crawl_attempt") or temporalCoverage "breeding season 2013" which are both available in the above dataset, doesn't return anything either: http://api.gbif.org/v1/dataset/search?keyword=13 http://api.gbif.org/v1/dataset/search?keyword=breeding%20season%202013 Am I doing something wrong or is this a bug? Peter

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204 response
by Scott Chamberlain 31 Jul '15

31 Jul '15

Hi all, I am curious as to the reasoning behind the 204 response for some API requests. For example: curl -v ' http://api.gbif.org/v1/dataset/3f8a1297-3259-4700-91fc-acc4170b27ce/metrics' < HTTP/1.1 204 No Content < Content-Type: application/json < Access-Control-Allow-Origin: * * Server Jetty(9.2.z-SNAPSHOT) is not blacklisted < Server: Jetty(9.2.z-SNAPSHOT) < x-api-url: /v1/dataset/3f8a1297-3259-4700-91fc-acc4170b27ce/metrics < Accept-Ranges: bytes < Date: Fri, 31 Jul 2015 17:46:32 GMT < X-Varnish: 1108784184 < Age: 0 < Via: 1.1 varnish < Connection: keep-alive I assume this means that that dataset ID is not found? If so, I would have expected a 404 perhaps. There's no other info in the headers, so I'm not sure what other reason there is for no data returned (I realize a 204 should not return a body). I know this dataset ID used to return data, as I used it in examples for hitting the /dataset/*/metrics route In other APIs I get a 204 on a successful DELETE request - that's the only context I'm familiar with wrt 204's Thanks! Scott

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Patch to fix Deserialisation failure of BoundingBox
by Nozomi James Ytow 30 Jul '15

30 Jul '15

Hi, I might report it previously, the Java web service client code fails to deserialise Dataset because of BoundingBox code. org.gbif.api.model.registry.eml.geospatial.BoundingBox does not have setGlobalCoverage(boolean) method while JSON response has globalCoverage of boolean. Here is a fix patch. James --- org/gbif/api/model/registry/eml/geospatial/BoundingBox.java.orig 2014-06-27 00:00:00.000000000 +0900 +++ org/gbif/api/model/registry/eml/geospatial/BoundingBox.java 2015-07-30 23:22:18.962696356 +0900 @@ -18,6 +18,7 @@ import java.io.Serializable; import java.util.Locale; +import org.codehaus.jackson.annotate.JsonIgnore; /** * Geographic coverage geometry in the form of 4 sided bounding box. @@ -103,6 +104,15 @@ } /** + * Set whether this binding box represents global coverage or not. + * + * @param globalCoverage global coverage status to set + */ + public void setGlobalCoverage(boolean globalCoverage) { + isGlobalCoverage = globalCoverage; + } + + /** * Set whether this binding box represents global coverage or not. Setter ensures all 4 required params are provided. * * @param minLatitude min latitude @@ -110,6 +120,7 @@ * @param minLongitude min longitude * @param maxLongitude max longitude */ + @JsonIgnore public void setGlobalCoverage(double minLatitude, double maxLatitude, double minLongitude, double maxLongitude) { isGlobalCoverage = checkIsGlobalCoverage(minLatitude, maxLatitude, minLongitude, maxLongitude); }

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numDescendants in species/?name response
by Nozomi James Ytow 30 Jul '15

30 Jul '15

Hi, is there any modification made in numDescendants in species/?name response? For example, http://api.gbif.org/v1/species/?name=Lembus returened one record with 2 descendants (I remember it as http://api.gbif.org/v1/species/102321492 ) and two records with 16 descendatns arournt 2015-07-29 04:00 UTC (ish) but now only one record of GBIF Backborn Taxonomy with 16 descendants and others have no descendants. http://api.gbif.org/v1/species/?name=Lembus%20infusionum was shered lower name in there three records. http://api.gbif.org/v1/species/102321493 is one of Lembus infusionum which has parentKey 102321492. The parent key is the record had two descandants. The modified implementation requires to try /species/{int}/children even if numDescendants is zero, because there may be descendants. I prefer to the previous implementation to navigate classifications. James

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