colrapi 0.1.4 → 0.1.6

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 28f0950d39f06e58346fc3a84ab0db4675dbc7c3b19d4c05e538999133b72d88
+  metadata.gz: 07aa378c2254f300d7086a0a2679e36a594a99a939d4487adb8745f96abe50b6
+  data.tar.gz: ada0fe3d028b8a20be01c229165fdff97ee67fd0684d078989891e067d68a862
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data/CHANGELOG.md

@@ -1,5 +1,24 @@
 ## [Unreleased]
 
+## [0.1.6] - 2025-03-25
+ - Added more nameusage_search parameters:
+    - authorship
+    - authorship_year
+    - extinct
+    - field
+    - name_type
+    - nomenclatural_code
+    - nomenclatural_status
+    - origin
+    - secondary_source
+    - sector_dataset_id
+    - sector_mode
+    - status
+    - taxonomic_group
+
+## [0.1.5] - 2025-03-25
+ - Added usage_id to nameusage_search
+
 ## [0.1.4] - 2025-03-05
  - Fixed authentication
  - Kept depreciated ChecklistBank preview endpoint functionality by using /dataset/{dataset_id}LRC.json instead (now requires a token)

data/lib/colrapi/faraday.rb

@@ -20,7 +20,7 @@ module Faraday
           when 502
             raise Colrapi::BadGateway, error_message_500(response, "The server returned an invalid or incomplete response.")
           when 503
-            raise Colrapi::ServiceUnavailable, error_message_500(response, "Crossref is rate limiting your requests.")
+            raise Colrapi::ServiceUnavailable, error_message_500(response, "The service is unavailable.")
           when 504
             raise Colrapi::GatewayTimeout, error_message_500(response, "504 Gateway Time-out")
           end

data/lib/colrapi/request.rb

@@ -1,15 +1,11 @@
-require_relative "faraday" # !! Potential ruby 3.0 difference in module loading? relative differs from Serrano
+require_relative "faraday"
 require "faraday/follow_redirects"
 require_relative "utils"
 require "colrapi/error"
 
 module Colrapi
   class Request
-    attr_accessor :endpoint
-    attr_accessor :q
-    attr_accessor :verbose
-
-    attr_accessor :options
+    attr_accessor :endpoint, :q, :verbose, :options
 
     def initialize(**args)
       @endpoint = args[:endpoint]
@@ -22,15 +18,20 @@ module Colrapi
       @regexp = args[:regexp]
       @content = Array(args[:content]) if args[:content]
       @name = args[:name]
-      @authorship = args[:authorship]
-      @code = args[:code]
+      @authorship = Array(args[:authorship]) if args[:authorship]
+      @authorship_year = Array(args[:authorship_year]) if args[:authorship_year]
+      @code = Array(args[:code]) if args[:code]
+      @nomenclatural_code = Array(args[:nomenclatural_code]) if args[:nomenclatural_code]  # unfortunately code and nom_code get used on different endpoints
+      @field = Array(args[:field]) if args[:field]
       @type = Array(args[:type]) if args[:type]
       @rank = Array(args[:rank]) if args[:rank]
       @facet = Array(args[:facet]) if args[:facet]
+      @extinct = Array(args[:extinct]) if args[:extinct]
       @min_rank = args[:min_rank]
       @max_rank = args[:max_rank]
-      @environment = args[:environment]
+      @environment = Array(args[:environment]) if args[:environment]
       @highest_taxon_id = args[:highest_taxon_id]
+      @usage_id = args[:usage_id]
       @parent_rank = args[:parent_rank]
       @root_id = Array(args[:root_id]) if args[:root_id]
       @root2_id = Array(args[:root2_id]) if args[:root2_id]
@@ -46,6 +47,7 @@ module Colrapi
       @has_gbif_id = args[:has_gbif_id]
       @gbif_id = args[:gbif_id]
       @gbif_publisher_id = args[:gbif_publisher_id]
+      @taxonomic_group = Array(args[:taxonomic_group]) if args[:taxonomic_group]
       @editor = args[:editor]
       @reviewer = args[:reviewer]
       @modified_by = args[:modified_by]
@@ -61,12 +63,18 @@ module Colrapi
       @term_operator = args[:term_operator]
       @issued = args[:issued]
       @issued_before = args[:issued]
-      @modified_after =  args[:modified_after]
+      @modified_after = args[:modified_after]
       @modified_before = args[:modified_before]
       @last_synced_before = args[:last_synced_before]
       @min = args[:min]
       @max = args[:max]
       @min_size = args[:min_size]
+      @name_type = Array(args[:name_type]) if args[:name_type]
+      @nomenclatural_status = Array(args[:nomenclatural_status]) if args[:nomenclatural_status]
+      @status = Array(args[:status]) if args[:status]
+      @sector_mode = Array(args[:sector_mode]) if args[:sector_mode]
+      @sector_dataset_id = Array(args[:sector_dataset_id]) if args[:sector_dataset_id]
+      @secondary_source = Array(args[:secondary_source]) if args[:secondary_source]
       @size = args[:size]
       @within_superkingdom = args[:within_superkingdom]
       @within_kingdom = args[:within_kingdom]
@@ -111,16 +119,19 @@ module Colrapi
 
     def perform
 
-      args = { q: @q, regex: @regexp, attempt: @attempt, content: @content, name: @name, authorship: @authorship, code: @code, type: @type,
+      args = { q: @q, regex: @regexp, attempt: @attempt, content: @content, name: @name, authorship: @authorship, 
+               authorshipYear: @authorship_year, code: @code, nomCode: @nomenclatural_code, field: @field, extinct: @extinct, type: @type,
                rank: @rank, minRank: @min_rank, maxRank: @max_rank, parentRank: @parent_rank, projectKey: @project_id,
                term: @term, termOp: @term_operator, status: @status, decisionMode: @decision_mode,
                alias: @short_title, private: @private, releasedFrom: @released_from, contributesTo: @contributes_to,
-               hasSourceDataset: @has_source_dataset, hasGbifKey: @has_gbif_id, gbifKey: @gbif_id,
+               hasSourceDataset: @has_source_dataset, hasGbifKey: @has_gbif_id, group: @taxonomic_group, gbifKey: @gbif_id,
                gbifPublisherKey: @gbif_publisher_id, editor: @editor, reviewer: @reviewer, modifiedBy: @modified_by,
                id: @id, format: @format, root: @root_id, root2: @root2_id, synonyms: @include_synonyms,
                showParent: @include_parent, origin: @origin, original: @original, license: @license, rowType: @row_type,
                created: @created_after, createdBefore: @created_before, issued: @issued, issuedBefore: @issued_before,
                modified: @modified_after, modifiedBefore: @modified_before, lastSync: @last_synced_before,
+               status: @status, nomStatus: @nomenclatural_status, nameType: @name_type,
+               sectorMode: @sector_mode, sectorDatasetKey: @sector_dataset_id, secondarySourceGroup: @secondary_source,
                minSize: @min_size, size: @size, issue: @issue, min: @min, max: @max, datasetKey: @dataset_id_filter,
                withoutData: @without_data, superkingdom: @within_superkingdom, kingdom: @within_kingdom,
                subkingdom: @within_subkingdom, superphylum: @within_superphylum, phylum: @within_phylum,
@@ -132,30 +143,18 @@ module Colrapi
                subgenus: @within_subgenus, section: @within_section, species: @within_species,
                nidx: @nidx_id, state: @state, running: @running, notCurrentOnly: @not_current_only,
                broken: @broken, subjectDatasetKey: @subject_dataset_id, mode: @mode, subject: @subject,
-               TAXON_ID: @highest_taxon_id, environment: @environment,
-               sortBy: @sort_by, reverse: @reverse, url: @url, offset: @offset, limit: @limit}
+               TAXON_ID: @highest_taxon_id, USAGE_ID: @usage_id, environment: @environment,
+               sortBy: @sort_by, reverse: @reverse, url: @url, body: @body, offset: @offset, limit: @limit }
       opts = args.delete_if { |_k, v| v.nil? }
 
-      conn = if verbose
-               Faraday.new(url: Colrapi.base_url, request: { params_encoder: Faraday::FlatParamsEncoder }) do |f|
-                 if !@user.nil? and !@password.nil?
-                   f.request :authorization, :basic, @user, @password
-                 end
-                 f.response :logger
-                 f.use Faraday::ColrapiErrors::Middleware
-                 f.adapter Faraday.default_adapter
-               end
-             else
-               Faraday.new(url: Colrapi.base_url, request: { params_encoder: Faraday::FlatParamsEncoder }) do |f|
-                 if !@user.nil? and !@password.nil?
-                   f.request :authorization, :basic, @user, @password
-                 end
-                 f.use Faraday::ColrapiErrors::Middleware
-                 f.adapter Faraday.default_adapter
-               end
-             end
+      conn = Faraday.new(url: Colrapi.base_url, request: { params_encoder: Faraday::FlatParamsEncoder }) do |f|
+        f.request :authorization, :basic, @user, @password if @user && @password
+        f.response :logger if @verbose
+        f.use Faraday::ColrapiErrors::Middleware
+        f.adapter Faraday.default_adapter
+      end
 
-      conn.headers['Authorization'] = "Bearer #{@token}" unless @token.nil?
+      conn.headers['Authorization'] = "Bearer #{@token}" if @token
       conn.headers['Accept'] = 'application/json,*/*'
       conn.headers[:user_agent] = make_user_agent
       conn.headers["X-USER-AGENT"] = make_user_agent
@@ -168,7 +167,6 @@ module Colrapi
       rescue MultiJson::ParseError
         res.body
       end
-      
     end
   end
 end

data/lib/colrapi/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Colrapi
-  VERSION = "0.1.4"
+  VERSION = "0.1.6"
 end

data/lib/colrapi.rb

@@ -42,6 +42,7 @@ module Colrapi
   # Search datasets:
   #   @param q [String] A search query for datasets
   #   @param short_title [String] A dataset alias
+  #   @param title [String] A dataset title
   #   @param code [String] The nomenclatural code (bacterial, botanical, cultivars, phytosociological, virus, zoological)
   #   @param private [Boolean] Whether the dataset is private or not
   #   @param released_from [Integer] Filter by a project id that a dataset was released from
@@ -64,6 +65,7 @@ module Colrapi
   #   @param modified_after [Date] Filter by modified after date
   #   @param modified_before [Date] Filter by modified before date
   #   @param min_size [Integer] Filter by minimum record size
+  #   @param token [String, nil] An authentication token from Colrapi.user_login()
   #
   #   @param sort_by [String] Sort by (key, alias, title, creator, relevance, created, modified, imported, size)
   #   @param reverse [Boolean] Sort in reverse
@@ -76,7 +78,7 @@ module Colrapi
                    contributes_to: nil, has_source_dataset: nil, has_gbif_id: nil, gbif_id: nil, gbif_publisher_id: nil,
                    editor: nil, reviewer: nil, modified_by: nil, origin: nil, type: nil, license: nil, row_type: nil,
                    created_after: nil, created_before: nil, issued_after: nil, issued_before: nil, modified_after: nil,
-                   modified_before: nil, min_size: nil, sort_by: nil, reverse: nil, offset: nil, limit: nil,
+                   modified_before: nil, min_size: nil, sort_by: nil, token: nil, reverse: nil, offset: nil, limit: nil,
                    verbose: false)
     endpoint = "dataset"
     unless dataset_id.nil?
@@ -94,7 +96,7 @@ module Colrapi
                   row_type: row_type, created_after: created_after, created_before: created_before,
                   issued_after: issued_after, issued_before: issued_before, modified_after: modified_after,
                   modified_before: modified_before, min_size: min_size, sort_by: sort_by, reverse: reverse,
-                  offset: offset, limit: limit, verbose: verbose).perform
+                  offset: offset, limit: limit, token: token, verbose: verbose).perform
     end
   end
 
@@ -541,19 +543,33 @@ module Colrapi
 
   # Search the nameusage route, which uses Elastic Search
   #
-  # @param q [String] A query string
+  # @param authorship [Array, String, nil] filters by authorship
+  # @param authorship_year [Array, String, nil] filters by authorship year
+  # @param content [Array, String, nil] restrict search to SCIENTIFIC_NAME, or AUTHORSHIP
   # @param dataset_id [String, nil] restricts name usage search within a dataset
   # @param endpoint [String, nil] some endpoints have nested options
-  # @param content [Array, String, nil] restrict search to SCIENTIFIC_NAME, or AUTHORSHIP
-  # @param issue [Array, String, nil] the data quality issue
-  # @param type [String, nil] sets the type of search to PREFIX, WHOLE_WORDS, or EXACT
-  # @param rank [String, nil] taxonomic rank of name usages
-  # @param min_rank [String, nil] minimum taxonomic rank of name usages
-  # @param max_rank [String, nil] maximum taxonomic rank of name usages
-  # @param facet [Array, String, nil] the search facet
   # @param environment [Array, String, nil] filter by environment (MARINE, TERRESTRIAL, FRESHWATER, BRACKISH)
+  # @param extinct [Array, int, nil] filter by extinct status (0, 1)
+  # @param facet [Array, String, nil] the search facet
+  # @param field [Array, String, nil] filter by name field (see: http://api.checklistbank.org/vocab/namefield)
   # @param highest_taxon_id [String, nil] Filter by highest taxon ID
-  #
+  # @param issue [Array, String, nil] the data quality issue
+  # @param max_rank [String, nil] maximum taxonomic rank of name usages
+  # @param min_rank [String, nil] minimum taxonomic rank of name usages
+  # @param name_type [Array, String, nil] filter by name type (hybrid formula, informal, no name, otu, placeholder, scientific, virus)
+  # @param nomenclatural_code [Array, String, nil] filter by nomenclatural code (botanical, zoological, bacterial, viral, phytosociological, cultivars)
+  # @param nomenclatural_status [Array, String, nil] filter by nomenclatural status (acceptable, conserved, doubtful, established, manuscript, not established, rejected, unacceptable)
+  # @param origin [Array, String, nil] filter by origin of the name usage (see: http://api.checklistbank.org/vocab/origin)
+  # @param q [String] A query string
+  # @param rank [Array, String, nil] taxonomic rank of name usages
+  # @param secondary_source [Array, String, nil] filter by secondary source (authorship, basionym, extinct, holotype, parent, published in, rank, temporal range)
+  # @param sector_dataset_id [Array, String, nil] filter by the sector source dataset ID
+  # @param sector_mode [Array, String, nil] filter by the sector mode (attach, merge, union)
+  # @param status [Array, String, nil] filter by taxonomic status (accepted, ambiguous synonym, misapplied, provisionally accepted, synonym)
+  # @param taxonomic_group [Array, String, nil] filter by taxonomic group (see: http://api.checklistbank.org/vocab/taxgroup)
+  # @param type [String, nil] sets the type of search to PREFIX, WHOLE_WORDS, or EXACT
+  # @param usage_id [String, nil] Filter by usage ID
+  # 
   # @param sort_by [String, nil] sort results by NAME, TAXONOMIC, INDEX_NAME_ID, NATIVE, or RELEVANCE
   # @param reverse [Boolean] sort in reverse order
   # @param offset [Integer] Offset for pagination
@@ -561,20 +577,29 @@ module Colrapi
   # @param verbose [Boolean] Print headers to STDOUT
   #
   # @return [Array, Boolean] An array of hashes
-  def self.nameusage_search(q: nil, dataset_id: nil, endpoint: 'nameusage/search', content: nil, issue: nil,
+  def self.nameusage_search(q: nil, authorship: nil, authorship_year: nil, dataset_id: nil, 
+                            endpoint: 'nameusage/search', extinct: nil, field: nil, content: nil, issue: nil,
                             type: nil, rank: nil, min_rank: nil, max_rank: nil, environment: nil, facet: nil,
-                            highest_taxon_id: nil, sort_by: nil, reverse: nil, offset: nil, limit: nil, 
-                            verbose: false)
+                            nomenclatural_code: nil, highest_taxon_id: nil, usage_id: nil, nomenclatural_status: nil, 
+                            name_type: nil, origin: nil, secondary_source: nil, 
+                            sector_mode: nil, sector_dataset_id: nil, status: nil, taxonomic_group: nil,
+                            sort_by: nil, reverse: nil, offset: nil, limit: nil, verbose: false)
 
     # a nil dataset_id will search name usages from all datasets in ChecklistBank
     unless dataset_id.nil?
       endpoint = "dataset/#{dataset_id}/nameusage/search"
     end
 
-    Request.new(endpoint: endpoint, q: q, content: content, issue: issue, type: type,
-                rank: rank, min_rank: min_rank, max_rank: max_rank, facet: facet, environment: environment,
-                highest_taxon_id: highest_taxon_id, sort_by: sort_by, reverse: reverse,
-                offset: offset, limit: limit, verbose: verbose).perform
+    Request.new(endpoint: endpoint, q: q, authorship: authorship, authorship_year: authorship_year, 
+                extinct: extinct, field: field, content: content, issue: issue, type: type,
+                rank: rank, min_rank: min_rank, max_rank: max_rank, facet: facet, 
+                nomenclatural_code: nomenclatural_code,environment: environment, 
+                highest_taxon_id: highest_taxon_id, usage_id: usage_id, 
+                name_type: name_type, nomenclatural_status: nomenclatural_status, origin: origin,
+                secondary_source: secondary_source, sector_mode: sector_mode, 
+                sector_dataset_id: sector_dataset_id, status: status, taxonomic_group: taxonomic_group, 
+                sort_by: sort_by, reverse: reverse,  offset: offset, limit: limit, 
+                verbose: verbose).perform
   end
 
   # Get a name usage suggestion

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: colrapi
 version: !ruby/object:Gem::Version
-  version: 0.1.4
+  version: 0.1.6
 platform: ruby
 authors:
 - Matt Yoder, Geoff Ower
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2025-03-05 00:00:00.000000000 Z
+date: 2025-04-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -198,7 +198,7 @@ licenses:
 metadata:
   homepage_uri: https://github.com/SpeciesFileGroup/colrapi
   source_code_uri: https://github.com/SpeciesFileGroup/colrapi
-  changelog_uri: https://github.com/SpeciesFileGroup/colrapi/releases/tag/v0.1.4
+  changelog_uri: https://github.com/SpeciesFileGroup/colrapi/releases/tag/v0.1.6
 post_install_message:
 rdoc_options: []
 require_paths: