- API-users - lists.gbif.org

Re: [API-users] GBIF Occurrence Detail URLs
by Keith Bornhorst 14 Dec '17

14 Dec '17

Perfect! Thank you so much!

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GBIF Occurrence Detail URLs
by Bornhorst, Keith 13 Dec '17

13 Dec '17

Hello all, My question concerns both the API and the GBIF website... GBIF is aware of and ingests all of my specimen/occurrence data via a Darwin Core archive on our IPT instance. The information flow is one-way, however, so I don't know GBIF's internal, unique identifier (e.g. gbifID = 1503266467) which I need to know if I want to create a direct link to the occurrence page (e.g. https://www.gbif.org/occurrence/1503266467). Using the API, I can obtain the gbifID via an API query such as http://api.gbif.org/v1/occurrence/search?occurrenceId=urn:catalog:USF:Herb:… (the UUID we're currently using, soon to be replaced with a GUID) and I could batch process all of my occurrence records and store these ids (or do a real-time API lookup and redirect users). And using the Advanced Search I can link to https://www.gbif.org/occurrence/search?occurrence_id=urn:catalog:USF:Herb:2… and get the single record in the search result. I'm curious to know if the GBIF website has any hidden (to me) auto-redirect capabilities that will send users to the matching occurrence page? Possibly a "redirectOnSingleResult=true" query string value that performs a redirect? Thanks, Keith Keith Bornhorst (bornhorst(a)usf.edu<mailto:bornhorst@usf.edu>) Web Development Team Leader, USF Water Institute School of Geosciences University of South Florida 4202 East Fowler Ave, CHE 304, Tampa, FL 33620 Phone: (813) 974-7406 WaterInstitute.usf.edu<http://waterinstitute.usf.edu/> - WaterAtlas.org<http://wateratlas.usf.edu/> - PlantAtlas.org<http://plantatlas.usf.edu/> - TampaTreeMap.org<http://tampatreemap.usf.edu/> - ButterflyAtlas.org<http://butterflyatlas.usf.edu/>

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Clarification on limit defaults and max values for some routes
by Scott Chamberlain 06 Dec '17

06 Dec '17

Hi all, I don't remember what API behavior and documentation used to be like, but for some routes the behavior and docs don't seem ideal. For example, for name usages, I don't see any docs on default and max limit/offset values. As far as I can tell, only occurrences routes have that information. Could docs be added for what default and max limit/offset values are for each route or each set of routes? About behavior: If you put in a very large number to limit param like 20,000 I would think that's bigger than what's allowed, but perhaps not? If I do a curl request with a very high limit value I was expecting to quickly get an error about the limit parameter being too high. If it's too high perhaps it's simply dropped and a default value is used (just like the /occurrences/search)? If that was the case I would expect some round default value like 1000 or so. Or is there no max value for limit on some routes? If so, that seems like it'd leave the API open to abuse? (p.s., I was testing what a request with very large limit does and I hope I didn't break anything on your end, apologies if I did) Best, Scott

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GBIF API requests limit
by Akshat Pant 06 Dec '17

06 Dec '17

Hi all, I am new to this mailing list. Can someone please tell me what is the maximum requests per second allowed on the GBIF API ? I was not able to find this on the GBIF website's API section. I hope that the API guru members on this list will be able to help. Thanks in advance, Akshat

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/occurrence/download route sometimes give size: 0
by Scott Chamberlain 13 Nov '17

13 Nov '17

Hi, Just ran into this, not sure how often it happens, but sometimes size value is zero when at least I don't think it should be: ➜ curl https://api.gbif.org/v1/occurrence/download/0000739-171109162308116 | jq . { "key": "0000739-171109162308116", "doi": "doi:10.15468/dl.jmachn", "license": "http://creativecommons.org/licenses/by/4.0/legalcode", "request": { "predicate": { "type": "greaterThanOrEquals", "key": "ELEVATION", "value": "11000" }, "format": "DWCA", "sendNotification": false }, "created": "2017-11-10T18:37:35.542+0000", "modified": "2017-11-10T18:38:54.444+0000", "status": "SUCCEEDED", "downloadLink": " http://api.gbif.org/v1/occurrence/download/request/0000739-171109162308116.… ", "size": 0, "totalRecords": 14064, "numberDatasets": 105 } The file ends up having data in it, so it's not size 0. Best, Scott Chamberlain

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How to query genus names with the GBIF API
by Szlamka József 08 Sep '17

08 Sep '17

Hello to all list members, I'm new on this list and also new to the GBIF API. I'd like to get a list of all the genus names occuring in the GBIF database. After several hours of trying with the API, and no success, I found this mailing list. I hope that API guru members on the list can show me the right way or tell if this is not possible at all. Thank you in advance.

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Registry API and authentication
by Christian Svindseth 14 Aug '17

14 Aug '17

Hello, We have a number of datasets we'd like to publish to GBIF directly through the registry APIs, bypassing our IPT completely. I've been looking through the documentation, but got stuck trying to figure out how to authenticate against the registry API. I suppose the organization name/password pairs used in the IPT might come into play at some point, but this isn't obvious from the documentation..? Or maybe my own account needs to be authorized to access the registry? Would love to get some input on this, and if anyone else is doing something similar code samples would be much appreciated! Thanks, Christian Svindseth GBIF Norway

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Broken Endpoint?
by Sandy Cheeks 24 Jul '17

24 Jul '17

Hi, the /species/{int}/media endpoint seems to be broken. The result set is alway empty, even for the ID linked in the examples under http://www.gbif.org/developer/species . In December 2016, I was able to get plenty of Images for different bird-species through the API, but now this is not possible anymore. I need to do this because I am trying to train an AI used for image classification in context of my master's thesis. Could somebody tell me if anything changed and I'm doing something wrong or I am right and the empty result really is caused by an error on the server-side? Thanks you in advance, Dayzd

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Planned outages of GBIF.org / TDWG.org
by Tim Robertson 05 Jul '17

05 Jul '17

Dear all, Our apologies in advance, but we expect disruptions in both GBIF and TDWG services next week, Thursday and Friday, 22-23 June 2017. Partial outages may occur while we relocate the servers for GBIF's and TDWG's systems to a new data centre within the University of Copenhagen. During this move, we anticipate that GBIF.org, demo.GBIF.org and the GBIF API will continue to operate on temporary servers, though user account creation, dataset registration and dataset crawling will all be temporarily suspended. The TDWG website and all TDWG mailing lists are likely to remain offline throughout the outage. We apologize for any inconvenience and will strive to reduce the disruption and its duration as much as possible. Best wishes, Tim

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Planned outages of GBIF.org / TDWG.org
by Tim Robertson 14 Jun '17

14 Jun '17

Dear all, Our apologies in advance, but we expect disruptions in both GBIF and TDWG services next week, Thursday and Friday, 22-23 June 2017. Partial outages may occur while we relocate the servers for GBIF's and TDWG's systems to a new data centre within the University of Copenhagen. During this move, we anticipate that GBIF.org, demo.GBIF.org and the GBIF API will continue to operate on temporary servers, though user account creation, dataset registration and dataset crawling will all be temporarily suspended. The TDWG website and all TDWG mailing lists are likely to remain offline throughout the outage. We apologize for any inconvenience and will strive to reduce the disruption and its duration as much as possible. Best wishes, Tim

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