- API-users - lists.gbif.org

[External] occurrenceID as a search parameter
by Steve Baskauf 24 Jul '14

24 Jul '14

Both I and the programmer I'm working with have looked through the API documentation and we don't see occurrenceID as a search parameter. That surprised me, since I thought it was a required field. If we could search for it, we could map any assigned occurrenceID to the GBIFID. I'm sure that there is probably some more indirect way to accomplish this (such as retrieving all records that we have provided, but it seems like this ought to be a simple thing to facilitate. Am I missing something? Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu http://vanderbilt.edu/trees

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Dataset registration change in API v1
by Markus Döring 23 Jul '14

23 Jul '14

Hi all, Pensoft has discovered an issue when migrating to the v1 API to programmatically register new datasets. The dataset property "owningOrganizationKey" is now called "publishingOrganizationKey" and still posting the owningOrganizationKey will result in an exception. Please update your registration code to use publishingOrganizationKey instead. For example a simple json post could look like this: curl -i --user USERNAME:PASSWORD -H "Content-Type: application/json" -H "Accept: application/json" -X POST -d '{"installationKey":"d5b61ace-f25c-43bd-9dd0-03486850f90b","publishingOrganizationKey":"750a8724-fa66-4c27-b645-bd58ac5ee010","title":"Saproxylic beetles of the Po plain woodlands, Italy","type":"OCCURRENCE"}' http://api.gbif.org/v1/dataset If you also want to start to automatically register new datasets please get in touch with us and we will setup the right permissions for your GBIF account Thanks to Pensoft for spotting the problem! best, Markus

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GBIF taxon page URLs by scientific name?
by Ken-ichi 22 Jul '14

22 Jul '14

Is there a way to link to a scientific name on the new GBIF? The old one would (and still does) let you link to taxon pages like this http://data.gbif.org/species/Rhus_typhina but the new GBIF seems to require an identifier in the URL. I could just link to http://www.gbif.org/species/search?q=Rhus%20typhina, but I'd rather link directly to the taxon page. Possible?

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download request for with predicate in taxon_keys throws exception
by jorrit poelen 19 Jul '14

19 Jul '14

Hi! When using: curl -i --user USER:PASSWORD -H "Content-Type: application/json" -H "Accept: application/json" -X POST -d @filter.json http://api.gbif.org/v1/occurrence/download/request with —— filter.json { "creator”:”USERNAME", "notification_address": [“EMAIL"], "predicate": { "type":"in", "key":"TAXON_KEY", "values":["2440447","5166399", "2269484"] } } —— I am getting a 500 status (see stack trace below). Am I using a valid predicate? thx, -jorrit http://globalbioticinteractions.org — stacktrace — HTTP/1.1 500 Internal Server Error Server: Apache-Coyote/1.1 Content-Type: text/html;charset=utf-8 x-api-url: /v1/occurrence/download/request Transfer-Encoding: chunked Date: Fri, 18 Jul 2014 20:21:20 GMT X-Varnish: 626777577 Age: 0 Via: 1.1 varnish Connection: keep-alive <html><head><title>Apache Tomcat/7.0.39 - Error report</title><style></style> </head><body><h1>HTTP Status 500 - Error building the hive query, attempting to continue</h1><HR size="1" noshade="noshade">type Exception reportmessage Error building the hive query, attempting to continuedescription The server encountered an internal error that prevented it from fulfilling this request.exception <pre>org.gbif.api.exception.ServiceUnavailableException: Error building the hive query, attempting to continue org.gbif.occurrence.download.service.DownloadRequestServiceImpl.create(DownloadRequestServiceImpl.java:207) org.gbif.occurrence.ws.resources.DownloadResource.startDownload(DownloadResource.java:107) org.apache.bval.guice.ValidateMethodInterceptor.invoke(ValidateMethodInterceptor.java:92) sun.reflect.GeneratedMethodAccessor2784.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185) com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1483) com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1414) com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1363) com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1353) com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:414) com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:708) javax.servlet.http.HttpServlet.service(HttpServlet.java:728) com.google.inject.servlet.ServletDefinition.doService(ServletDefinition.java:263) com.google.inject.servlet.ServletDefinition.service(ServletDefinition.java:178) com.google.inject.servlet.ManagedServletPipeline.service(ManagedServletPipeline.java:91) com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:62) com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:118) com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:113) </pre>root cause <pre>org.gbif.occurrence.download.service.QueryBuildingException: java.lang.reflect.InvocationTargetException org.gbif.occurrence.download.service.HiveQueryVisitor.visit(HiveQueryVisitor.java:355) org.gbif.occurrence.download.service.HiveQueryVisitor.getHiveQuery(HiveQueryVisitor.java:151) org.gbif.occurrence.download.service.DownloadRequestServiceImpl.create(DownloadRequestServiceImpl.java:204) org.gbif.occurrence.ws.resources.DownloadResource.startDownload(DownloadResource.java:107) org.apache.bval.guice.ValidateMethodInterceptor.invoke(ValidateMethodInterceptor.java:92) sun.reflect.GeneratedMethodAccessor2784.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185) com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1483) com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1414) com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1363) com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1353) com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:414) com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:708) javax.servlet.http.HttpServlet.service(HttpServlet.java:728) com.google.inject.servlet.ServletDefinition.doService(ServletDefinition.java:263) com.google.inject.servlet.ServletDefinition.service(ServletDefinition.java:178) com.google.inject.servlet.ManagedServletPipeline.service(ManagedServletPipeline.java:91) com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:62) com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:118) com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:113) </pre>root cause <pre>java.lang.reflect.InvocationTargetException sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) org.gbif.occurrence.download.service.HiveQueryVisitor.visit(HiveQueryVisitor.java:348) org.gbif.occurrence.download.service.HiveQueryVisitor.getHiveQuery(HiveQueryVisitor.java:151) org.gbif.occurrence.download.service.DownloadRequestServiceImpl.create(DownloadRequestServiceImpl.java:204) org.gbif.occurrence.ws.resources.DownloadResource.startDownload(DownloadResource.java:107) org.apache.bval.guice.ValidateMethodInterceptor.invoke(ValidateMethodInterceptor.java:92) sun.reflect.GeneratedMethodAccessor2784.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185) com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1483) com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1414) com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1363) com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1353) com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:414) com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:708) javax.servlet.http.HttpServlet.service(HttpServlet.java:728) com.google.inject.servlet.ServletDefinition.doService(ServletDefinition.java:263) com.google.inject.servlet.ServletDefinition.service(ServletDefinition.java:178) com.google.inject.servlet.ManagedServletPipeline.service(ManagedServletPipeline.java:91) com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:62) com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:118) com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:113) </pre>root cause <pre>java.lang.IllegalArgumentException: Search parameter TAXON_KEY is not mapped to Hive org.gbif.occurrence.download.service.HiveQueryVisitor.toHiveField(HiveQueryVisitor.java:137) org.gbif.occurrence.download.service.HiveQueryVisitor.visit(HiveQueryVisitor.java:199) sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) org.gbif.occurrence.download.service.HiveQueryVisitor.visit(HiveQueryVisitor.java:348) org.gbif.occurrence.download.service.HiveQueryVisitor.getHiveQuery(HiveQueryVisitor.java:151) org.gbif.occurrence.download.service.DownloadRequestServiceImpl.create(DownloadRequestServiceImpl.java:204) org.gbif.occurrence.ws.resources.DownloadResource.startDownload(DownloadResource.java:107) org.apache.bval.guice.ValidateMethodInterceptor.invoke(ValidateMethodInterceptor.java:92) sun.reflect.GeneratedMethodAccessor2784.invoke(Unknown Source) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60) com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185) com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75) com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288) com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108) com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147) com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84) com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1483) com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1414) com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1363) com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1353) com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:414) com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537) com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:708) javax.servlet.http.HttpServlet.service(HttpServlet.java:728) com.google.inject.servlet.ServletDefinition.doService(ServletDefinition.java:263) com.google.inject.servlet.ServletDefinition.service(ServletDefinition.java:178) com.google.inject.servlet.ManagedServletPipeline.service(ManagedServletPipeline.java:91) com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:62) com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:118) com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:113) </pre>note The full stack trace of the root cause is available in the Apache Tomcat/7.0.39 logs.<HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.39</h3></body></html> ----

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Dataset contacts
by "Holetschek, Jörg" 10 Jul '14

10 Jul '14

Hi guys, I'm using the API to get dataset metadata from the registry (http://api.gbif.org/v0.9/dataset). Each dataset entry has a 'contact' element, which is a list of contacts. Usually, each contact has a certain type. In the given example in the documentation, there are two contacts, each of type ADMINISTRATIVE_POINT_OF_CONTACT: http://api.gbif.org/v0.9/dataset/4fa7b334-ce0d-4e88-aaae-2e0c138d049e/conta… However, paging through the datasets, I hit contacts that somehow look different. For example, they don't have a type, which breaks a script if you want to find the primary administrative contact, for example: http://api.gbif.org/v0.9/dataset/570489ac-e114-4a17-9340-2e01ee7d9ee3/conta… Is that intended? Or is it leftovers from the old registry? Cheers, Jörg ---//------------------------------------------------------------ Jörg Holetschek Coordinator Biodiversity Data Networks Botanic Garden & Botanical Museum Berlin-Dahlem Dept. Biodiversity Informatics Königin-Luise-Str. 6-8, D-14195 Berlin +49 (0)30 838-50150, j.holetschek(a)bgbm.org ------------------------------------------------------------//---

2 2

API v1.0 release
by Markus Döring 08 Jul '14

08 Jul '14

Dear GBIF API users, we are getting close to releasing the final version 1.0 of the GBIF API. If all goes well we will go live later this week. There will be minor changes in the API compared to what is live today, please see below for more details. With the arrival of version 1.0 we will also change the base URL of the API to finally become: http://api.gbif.org/v1/ To give you some time to adapt we will also keep the v0.9 URL running up to the end of August, serving the exact same content. With v1 existing we also promise to keep the API stable. This means we won't rename or remove any REST resources or response properties to be backwards compatible, but we might add new resources to the API to be announced in this list. Bug fixes and additions will result in minor version changes which are not reflected in the API URL, only in the documentation and our Java client code. As usual if you notice problems or need help with the API feel invited to post questions in this list. with thanks, GBIF dev team Version 1.0 changes: ---------------------------- - remove all underscores from URLs and replace them with camelCase (mainly species & metrics API) - dataset.owningOrganizationKey renamed to dataset.publishingOrganizationKey - use of lists instead of simple strings for email, phone, homepage, position and address for contacts, organization and node in the registry - include issue column in dwca download - search facets use country iso 2letter codes - species & dataset suggest returns minimal information now: http://api.gbif-uat.org/v0.9/species/suggest?q=Dracul - remove reverse geocode & mendeley GBIF articles from our API

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Error 503 with Species Web Service
by Urbanowski, Shayne 08 Jul '14

08 Jul '14

Hello- I have a list of 348782 taxonKeys for which I need the canonicalName. I'm using the species web service (http://api.gbif.org/v0.9/species) within a script to get this data. The web service works well for the first 3000 or 4000 records and then throws the following error. Can you assist me in resolving (or working around) this issue. The list of taxonKeys is posted at: ftp://bison.ornl.gov/pub/bison/out/outspecies1of2.txt http://api.gbif.org/v0.9/species/5278064 Error 503 Service Unavailable Service Unavailable Guru Meditation: XID: 1016539404 Varnish cache server Thanks in advance, -- Shayne Urbanowski COMSO - USGS CSAS surbanowski(a)usgs.gov o: 303-202-4299 m: 720-280-3210 http://www.usgs.gov/core_science_systems/csas/

2 1

ISO country code
by David.Martin＠csiro.au 01 Jul '14

01 Jul '14

Hello, This query was previously working: http://api.gbif.org/v0.9/dataset/search?publishingCountry=SPAIN&type=OCCURR… But now returns: "Value SPAIN invalid for filter parameter PUBLISHING_COUNTRY" We've switched to using the 2 letter iso country code (which works fine): http://api.gbif.org/v0.9/dataset/search?publishingCountry=ES&type=OCCURRENC…<http://api.gbif.org/v0.9/dataset/search?publishingCountry=SPAIN&type=OCCURR…> but just thought I'd flag this in case it wasn't an intended change. This JIRA issue [1] suggests that the intention is to support both. Cheers Dave Martin ALA [1] http://dev.gbif.org/issues/browse/POR-43

2 1

mediatype json formatting
by Scott Chamberlain 30 Jun '14

30 Jun '14

Hi, Thanks for adding media content to the occurrence endpoint output. I am curious if the below is the intended behavior. It appears as though the "references" field associated with an array of "type", "format", and "identifier" is in the next array. Does it not make more sense to have the "references" field within the same array so when parsed we can easily tell that they go together? I can tell by seeing that the photo ID is the same, but I wonder if that is the best approach since then we need to make sure a "references" field goes with an arry of type/format/identifier by e.g. regex-ing. Sorry if I am misunderstanding why this is the way it is :) [ { type: "StillImage", format: "image/jpeg", identifier: "http://static.inaturalist.org/photos/696339/medium.JPG?1393473140" }, { references: "http://conabio.inaturalist.org/photos/696339" }, { type: "StillImage", format: "image/jpeg", identifier: "http://static.inaturalist.org/photos/696341/medium.JPG?1393473245" }, { references: "http://conabio.inaturalist.org/photos/696341" } ] Thanks! Scott Chamberlain

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lastInterpreted query param not working?
by Ken-ichi 27 Jun '14

27 Jun '14

GET http://api.gbif.org/v0.9/occurrence/search?institutioncode=iNaturalist&last… { offset: 0, limit: 20, endOfRecords: true, count: 0, results: [ ] } I'm pretty sure you guys have indexed more than zero records from us since 2014-01-01. Am I doing something wrong? Also, does "interpreted" here mean the last time you *changed* or *added* the record on GBIF or the last time you verified that the source and the GBIF record were in sync? -ken-ichi

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