- API-users - lists.gbif.org

extinct taxa in GBIF API
by Dröge, Gabriele 09 Feb '21

09 Feb '21

Hello GBIF team, I was wondering if there is a way to flag extinct taxa in the GBIF backbone api? e.g. http://api.gbif.org/v1/species?name=Amplibuteo%20concordatus is marked as extinct in the CoL (coming originally from PalaeoDB). For using the backbone it would be very useful to distinguish between extinct and recent taxa. Best, Gabi

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Small change to retrieving GBIF download files
by Matthew Blissett 11 Nov '20

11 Nov '20

Hi all, We've made a small change to the way files are downloaded from GBIF.org. People retrieving GBIF downloads using a web browser will not notice any difference. There will also be no difference for many command line download programs, like "wget". API clients will notice that download links like https://api.gbif.org/v1/occurrence/download/request/0001649-180925134338326… now return an HTTP 302 redirect to a different location. The client will need to follow the redirect to retrieve the file. Users of "curl" on the command line can add the "-L" argument to follow redirects automatically. The change was necessary to improve stability and performance of api.gbif.org, following the change by Google Chrome to block non-HTTPS downloads. The default for download links is now HTTPS, but files (and all of api.gbif.org) can still be accessed using only HTTP if preferred. Thanks, Matt Blissett

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GBIF.org supports recordedByID and identifiedByID
by Tim Robertson 06 Apr '20

06 Apr '20

Dear all Last week GBIF.org enabled two new filters to allow search using recordedByID and identifiedByID fields. Datasets such as iNaturalist support the use of ORCID IDs for people. Those users who have linked their account in iNaturalist can now find records in GBIF using their ORCID - e.g.: https://www.gbif.org/occurrence/search?recorded_by_id=https:~2F~2Forcid.org… Similarly, users in the Danish SvampeAtlas can find records they've submitted but were identified by a particular user: https://www.gbif.org/occurrence/taxonomy?recorded_by_id=https:~2F~2Forcid.o… We recommend using well-controlled identifiers for people / agents, such as ORCID and WikiData identifiers, but will index any value filled in. The fields are included in the DwC-A downloads from GBIF.org searches. We now plan to enable this for data publishers using the IPT. I have made a new release of the Occurrence core schema and enabled it for IPTs in TEST mode only [1]. I would appreciate if an IPT user could help test this with me. Using an IPT that is in test mode: 1) In Admin / Core and Extensions you should be able to hit "update" 2) Following update, you should see a note on "Occurrence" stating that the fields are available 3) You can then map occurrence records using this term 4) If you register the test dataset in GBIF it should index on https://www.gbif-uat.org and the searches can be done in the test environment. If someone is able to test this, please can you reply to all so we know it is underway? Many thanks, Tim [1] http://rs.gbif.org/sandbox/core/dwc_occurrence_2020-03-30.xml

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Points appear/dissapear with zoom levels (Maps API)
by 戸津久美子 06 Mar '20

06 Mar '20

Hi, I am using Maps API v2 with Mapbox GL JS to map occurrence data with two parameters; taxonKey and country. When I zoom in on the map, some points (hex in my case) dissappear and appear. Could you think of any idea why this happens? GBIF Maps API https://api.gbif.org/v2/map/occurrence/density/{z}/{x}/{y}@1x.png?style=cla… Base map https://tile.gbif.org/3857/omt/{z}/{x}/{y}@1x.png?style=gbif-dark Image of the map with different zoom levels and the source file https://nieseicmg-my.sharepoint.com/:f:/g/personal/totsu_kumiko_nies_go_jp/… Best regards, 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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understanding download status (specially FILE_ERASED)
by Herbario SANT 21 Jan '20

21 Jan '20

I have a question about the results returned by the api when requesting the download activity of a dataset. /occurrence/download/dataset/{datasetKey} <https://www.gbif.org/developer/occurrence#download> Where can I find a description of the possible "status" of a given download? (I found at least 6 different values in our datasets activity). I understand that KILLED, FAILED, RUNNING, PREPARING ... can all be interpreted as "nobody has (still) used that information". Whereas a "SUCCEEDED" download means the opposite. But what about "FILE_ERASED <http://api.gbif.org/v1/occurrence/download/0000316-140429114108248>"? Does it mean the download was "SUCCEEDED" in the past, and some time later the info was deleted? (when looking at old downloads, the percentage of FILE_ERASED is much higher). If I want to evaluate real usage of a dataset along years, should I better use the sum of "SUCCEEDED + FILE_ERASED". Right? Also, I understand that the sum of SUCCEEDED + FILE_ERASED downloads for a given dataset and year, should be the same if somebody repeats the query in the future (whereas the sum of SUCCEEDED downloads will decrease). Thanks a lot for your help David

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(1) error in downloads activity api response + (2) proposed enhancement
by Herbario SANT 16 Jan '20

16 Jan '20

Hello. I am using the api to retrieve information about downloads, and compare usage of my institution datasets from year to year. I use the last option in occurrence downloads <https://www.gbif.org/developer/occurrence#download> section, which lists the downloads activity of a certain dataset: /occurrence/download/dataset/{datasetKey} I have a couple of questions (a bug and a request) (1) BUG: For one of our datasets, I was delaying a few seconds between page requests until I got this error at a certain offset: http://api.gbif.org/v1/occurrence/download/dataset/1c334170-7ed1-11df-8c4a-… Oddly, if I increased or decreased the offset a little bit, I got no errors. So it seemed to me a problem related to a certain download event record. Then I changed the offset and limit and I was able to find the single event using this url: http://api.gbif.org/v1/occurrence/download/dataset/1c334170-7ed1-11df-8c4a-… This download event was on 2016-03-01 (date reported in the events after and before that offset). Unfortunately, when you read this message the number of download events will already be higher. So you will need to change the above url and increase the offset value to see the same event record (because the api offset count begins with the last download event instead of beginning with the first one). I created this copy of the error page for you: http://archive.is/5UNAy Or you can substract the current number of downloads count minus 18918 to find the offset for the problematic record. (2) ENHANCEMENT: I take the opportunity to encourage you to introduce a "sort" parameter in this kind of api requests. So that limit=1&offset=0&sort=asc will return the oldest event (instead of the newest one). You can keep the current sorting as default (i.e. sort=desc) so you don't break any applications which are already using this api. This option will make the above url more permanent (so you keep getting the same event records when you repeat the same offset/limit values using sort=asc). It would be much easier to track historical usage of datasets: if I store the offset of my last report, I can resume it from that point the next time I want to see activity of this dataset (i.e., if year 2018 events begin at offset 3333 and end at 3567, I will be able to make my next report starting at offset 3568) Another option would be to let use filter events by date (BTW, the api shows a "created" and a "modified" date, but I don't understand the meaning of "modified" for a download event). Thanks a lot in advance for your help -- David

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GBIF occurence index - get all indexed fields
by Felicitas Löffler 19 Nov '19

19 Nov '19

Dear GBIF API users, I would like to get some GBIF index statistics, e.g., Is it possible to obtain all indexed fields in the elasticsearch occurrence index? I already tried to get the mapping http://api.gbif.org/v1/_mapping?pretty and http://api.gbif.org/v1/occurence/_mapping?pretty and I also tried it with the search (http://api.gbif.org/v1/occurrence/search) and a facet on _field_names. { "query": { "match_all": {} }, "aggs": { "Field Names": { "terms": { "field": "_field_names" }} } } Unfortunately, both doesn't work. Is there any other opportunity to get all indexed fields? Thank you and best regards, Felicitas Löffler -- ------------------------------------------------------------------- Felicitas Löffler Wissenschaftliche Mitarbeiterin/ Promotionsstudentin Heinz-Nixdorf-Professur für verteilte Informationssysteme Institut für Informatik Friedrich-Schiller-Universität Jena Leutragraben 1, Jentower, R17N02 07743 Jena Germany Telefon: +49 (0)3641 946413 http://fusion.cs.uni-jena.de felicitas.loeffler(a)uni-jena.de

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Re: [API-users] Intermittent outages??
by Tim Robertson 05 Nov '19

05 Nov '19

Hi William I am very sorry to you (and everyone) that you are experiencing this. We have an unusual load coming on GBIF.org which is causing us some issues, and we are doing all we can to address this. I hope things will be back to normal later today. Please feel free to contact me directly if you continue to have issue (trobertson(a)gbif.org<mailto:trobertson@gbif.org>) after today. Thanks, Tim From: API-users <api-users-bounces(a)lists.gbif.org> on behalf of William Gearty <wgearty(a)unl.edu> Date: Monday, 4 November 2019 at 23.41 To: "API-users(a)lists.gbif.org" <API-users(a)lists.gbif.org> Subject: [API-users] Intermittent outages?? Hi all, I've noticed some intermittent outages lately, specifically with the occurrences API. I'm trying to query the occurrences API via rgbif for a bunch of taxa in a loop, and I keep getting "Error: 500 - Server error" and I have to restart my loop. Any idea when the resource will be permanently stable again? Thanks, Will [Image removed by sender.] William Gearty Postdoctoral Research Fellow University of Nebraska–Lincoln School of Biological Sciences williamgearty.com<http://williamgearty.com>

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Re: [API-users] Intermittent outages??
by Marie Grosjean 05 Nov '19

05 Nov '19

Hi William, It seems that a lot of users have been querying the search API lately, which puts a strain on the GBIF backend (especially it comes to deep paging) and makes it slow for everyone. The solution is to use the download API instead. In other words, use the occ_download()<https://www.rdocumentation.org/packages/rgbif/versions/1.3.0/topics/occ_dow…> function instead of the occ_search()<https://www.rdocumentation.org/packages/rgbif/versions/1.3.0/topics/occ_sea…> function. Using the download API would also allow you to get all your species in one download making it more convenient for citations later on because you would have only one DOI to cite. This blogpost give an example of R code to generate a download of a long list of species: https://data-blog.gbif.org/post/downloading-long-species-lists-on-gbif/ I hope this helps! Cheers Marie From: API-users <api-users-bounces(a)lists.gbif.org> on behalf of William Gearty <wgearty(a)unl.edu> Date: Monday, 4 November 2019 at 23.41 To: "API-users(a)lists.gbif.org" <API-users(a)lists.gbif.org> Subject: [API-users] Intermittent outages?? Hi all, I've noticed some intermittent outages lately, specifically with the occurrences API. I'm trying to query the occurrences API via rgbif for a bunch of taxa in a loop, and I keep getting "Error: 500 - Server error" and I have to restart my loop. Any idea when the resource will be permanently stable again? Thanks, Will [https://ucomm.unl.edu/images/email-signature/Nebraska_N_RGB_small_on_white.…] William Gearty Postdoctoral Research Fellow University of Nebraska–Lincoln School of Biological Sciences williamgearty.com<http://williamgearty.com>

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Intermittent outages??
by William Gearty 05 Nov '19

05 Nov '19

Hi all, I've noticed some intermittent outages lately, specifically with the occurrences API. I'm trying to query the occurrences API via rgbif for a bunch of taxa in a loop, and I keep getting "Error: 500 - Server error" and I have to restart my loop. Any idea when the resource will be permanently stable again? Thanks, Will [https://ucomm.unl.edu/images/email-signature/Nebraska_N_RGB_small_on_white.…] William Gearty Postdoctoral Research Fellow University of Nebraska–Lincoln School of Biological Sciences williamgearty.com<http://williamgearty.com>

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