sckott/gbifrb

GBIF Ruby client; docs: http://www.rubydoc.info/gems/gbifrb/0.1.0

gbifrb

gbifrb is a low level client for the GBIF API

Other GBIF API clients:

• Python: pygbif
• R: rgbif
• PHP: php-gbif

Changes

For changes see the Changelog

API

Methods in relation to GBIF API routes

registry

• /node - Gbif::Registry.nodes
• /network - Gbif::Registry.networks
• /installations - Gbif::Registry.installations
• /organizations - Gbif::Registry.organizations
• /dataset_metrics - Gbif::Registry.dataset_metrics
• /datasets - Gbif::Registry.datasets
• /dataset_suggest - Gbif::Registry.dataset_suggest
• /dataset_search - Gbif::Registry.dataset_search

species

• /species/match - Gbif::Species.name_backbone
• /species/suggest - Gbif::Species.name_suggest
• /species/search - Gbif::Species.name_lookup
• /species - Gbif::Species.name_usage

occurrences

• /search - Gbif::Occurrences.search
• /get - Gbif::Occurrences.get
• /get_verbatim - Gbif::Occurrences.get_verbatim
• /get_fragment - Gbif::Occurrences.get_fragment

Install

Release version

gem install gbifrb

Development version

git clone [email protected]:sckott/gbifrb.git
cd gbifrb
rake install

Examples, in Ruby repl

Registry module

Nodes

require 'gbifrb'
registry = Gbif::Registry
registry.nodes(limit: 5)

Networks

registry.networks(uuid: '16ab5405-6c94-4189-ac71-16ca3b753df7')

Species module

GBIF backbone

species = Gbif::Species
species.name_backbone(name: "Helianthus")

Suggester

species.name_suggest(q: "Helianthus")

Lookup

species.name_lookup(q: "Helianthus")

Lookup example with more parameters: name usages of plants where accepted scientific name includes 'reptans':

species.name_lookup(q: 'reptans', higherTaxonKey: 6, nameType: 'SCIENTIFIC', status: 'ACCEPTED')

Name usage (/species)

species.name_usage(name: "Helianthus")

Name usage example with more parameters: name usages of 'Andropogon' in Database of Vascular Plants of Canada (VASCAN) checklist:

species.name_usage(name: 'Andropogon', datasetKey: '3f8a1297-3259-4700-91fc-acc4170b27ce')

Occurrences

occ = Gbif::Occurrences
occ.search(taxonKey: 3329049)
occ.search(taxonKey: 3329049, limit: 2)
occ.search(scientificName: 'Ursus americanus')

curl options

species = Gbif::Species
species.name_backbone("Helianthus", verbose: true)

Todo

• CLI interface
• occurrence metrics methods
• occurrence downloads methods
• OAI-PMH interface

Meta

• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
• License: MIT

gbifrb's Issues

Dependabot can't resolve your Ruby dependency files

Dependabot can't resolve your Ruby dependency files.

As a result, Dependabot couldn't update your dependencies.

The error Dependabot encountered was:

Bundler::VersionConflict with message: Bundler found conflicting requirements for the Ruby version:
  In Gemfile:
    Ruby (~> 2.0.0.0)

    faraday (~> 1.1) was resolved to 1.4.1, which depends on
      Ruby (>= 2.4)

If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.

View the update logs.

Dependabot can't resolve your Ruby dependency files

Dependabot can't resolve your Ruby dependency files.

As a result, Dependabot couldn't update your dependencies.

The error Dependabot encountered was:

Bundler::VersionConflict with message: Bundler found conflicting requirements for the Ruby version:
  In Gemfile:
    Ruby (~> 2.0.0.0)

    faraday (~> 1.1) was resolved to 1.4.0, which depends on
      Ruby (>= 2.4)

If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.

View the update logs.

Support for /grscicoll/collection

As a developer I want a wrapper for the collections endpoint. API

Params:

• q
• institution
• contact
• code
• name

Personal priorities:

• /grscicoll/collection
• /grscicoll/collection/suggest
• /grscicoll/collection/{UUID}/identifier
• /grscicoll/collection/deleted
• /grscicoll/collection/{UUID}/tag

Species `name_usage` params include unsupported parameters

The following params on the Species name_usage method are not supported and do not work:

• key
• data
• uuid
• rank
• shortname

These parameters are not listed for this search method on https://www.gbif.org/developer/species

Details on each below, and a PR forthcoming.

key

I cannot seem to find any key that has any effect when passed in here. The result set always begins with taxonID=>gbif:0 and seems to include everything.

data
I saved the results for:

https://api.gbif.org/v1/species?name=Puma%20concolor

and

https://api.gbif.org/v1/species?name=Puma%20concolor&data=all

The files were identical when diffed.

uuid

The comments in the code say this should work the same as datasetKey

test = species.name_usage(name: 'Andropogon', datasetKey: '3f8a1297-3259-4700-91fc-acc4170b27ce')
test['results'].length
=> 2
test['results'].each{ |r| puts r['key'] }
100015804
100015805

But it does not:

test = species.name_usage(name: 'Andropogon', uuid: '3f8a1297-3259-4700-91fc-acc4170b27ce')
test['results'].length
=> 89
test['results'].first['key']
=> 2706077
test['results'].last['key']
=> 181589405

It has no effect, and produces the same results as passing only the name parameter:

test = species.name_usage(name: 'Andropogon')
test['results'].length
=> 89
test['results'].first['key']
=> 2706077
test['results'].last['key']
=> 181589405

rank

Does not seem to have any effect:

test = species.name_usage(name: 'Helianthus', rank: 'SPECIES')
test['results'].map{ |t| t['rank'] }.tally
=> {"GENUS"=>64, nil=>2, "SPECIES"=>2}

test = species.name_usage(name: 'Helianthus')
test['results'].length
=> 68

shortname

The comments in the code say: A short name..need more info on this?

I'm not seeing it documented in the Species API at all. It's referenced in terms of the /species/root/{uuid|shortname} route, but that is not the root being used by this name_usage method.

Dependabot can't resolve your Ruby dependency files

Dependabot can't resolve your Ruby dependency files.

As a result, Dependabot couldn't update your dependencies.

The error Dependabot encountered was:

Bundler::VersionConflict with message: Bundler found conflicting requirements for the Ruby version:
  In Gemfile:
    Ruby (~> 2.0.0.0)

    rake (~> 13.0, >= 13.0.1) was resolved to 13.0.3, which depends on
      Ruby (>= 2.2)

If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.

View the update logs.

Dependabot can't resolve your Ruby dependency files

Dependabot can't resolve your Ruby dependency files.

As a result, Dependabot couldn't update your dependencies.

The error Dependabot encountered was:

Bundler::VersionConflict with message: Bundler found conflicting requirements for the Ruby version:
  In Gemfile:
    Ruby (~> 2.0.0.0)

    faraday (~> 1.1) was resolved to 1.4.1, which depends on
      Ruby (>= 2.4)

If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.

View the update logs.

Dependabot can't resolve your Ruby dependency files

Dependabot can't resolve your Ruby dependency files.

As a result, Dependabot couldn't update your dependencies.

The error Dependabot encountered was:

Bundler::VersionConflict with message: Bundler found conflicting requirements for the Ruby version:
  In Gemfile:
    Ruby (~> 2.0.0.0)

    faraday (~> 1.1) was resolved to 1.3.0, which depends on
      Ruby (>= 2.4)

If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.

View the update logs.

cli tools?