colrapi 0.1.0
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- checksums.yaml +7 -0
- data/.github/workflows/main.yml +19 -0
- data/.gitignore +10 -0
- data/CHANGELOG.md +5 -0
- data/CODE_OF_CONDUCT.md +84 -0
- data/Gemfile +12 -0
- data/Gemfile.lock +75 -0
- data/LICENSE.txt +21 -0
- data/README.md +44 -0
- data/Rakefile +14 -0
- data/bin/console +15 -0
- data/bin/setup +8 -0
- data/colrapi.gemspec +56 -0
- data/lib/colrapi/faraday.rb +74 -0
- data/lib/colrapi/helpers/configuration.rb +26 -0
- data/lib/colrapi/request.rb +169 -0
- data/lib/colrapi/utils.rb +38 -0
- data/lib/colrapi/version.rb +5 -0
- data/lib/colrapi.rb +1026 -0
- metadata +209 -0
data/lib/colrapi.rb
ADDED
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# frozen_string_literal: true
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require "erb"
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require_relative "colrapi/version"
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require_relative "colrapi/request"
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require "colrapi/helpers/configuration"
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module Colrapi
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extend Configuration
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define_setting :base_url, "https://api.checklistbank.org/"
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define_setting :mailto, ENV["COL_API_EMAIL"]
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# Get assembly status
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#
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# @param dataset_id [String] The dataset id
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#
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# @return [Hash] A result hash of the assembly queue
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def self.assembly(dataset_id, verbose: false)
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endpoint = "dataset/#{dataset_id}/assembly"
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Request.new(endpoint: endpoint, verbose: verbose).perform
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end
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# Get a dataset's original archive
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#
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# @param dataset_id [String] The dataset id
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#
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# @return [Binary] An archive of the original dataset
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def self.archive(dataset_id, verbose: false)
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endpoint = "dataset/#{dataset_id}/archive"
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Request.new(endpoint: endpoint, verbose: verbose).perform
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end
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# Get dataset metadata
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#
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# For a specific dataset:
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# @param dataset_id [String] The dataset id
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# @param attempt [Integer] Returns archived metadata for a past import attempt number
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#
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# Search datasets:
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# @param q [String] A search query for datasets
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# @param short_title [String] A dataset alias
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# @param code [String] The nomenclatural code (bacterial, botanical, cultivars, phytosociological, virus, zoological)
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# @param private [Boolean] Whether the dataset is private or not
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# @param released_from [Integer] Filter by a project id that a dataset was released from
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# @param contributes_to [Integer] Filter by a project id that a dataset contributes to
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# @param has_source_dataset [Boolean] Filter by if source datasets contribute to the project dataset
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# @param has_gbif_id [Boolean] Whether the dataset has a GBIF registry id
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# @param gbif_id [String] The GBIF registry id
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# @param gbif_publisher_id [String] Filter by a GBIF publisher's id
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# @param editor [Integer] Filter by an editor's user id
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# @param reviewer [Integer] Filter by a reviewer's user id
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# @param modified_by [Integer] Filter by a user id on last modified by
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# @param origin [Array, String] Filter by the origin of a dataset (external, project, release, xrelease)
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# @param type [Array, String] Filter by the dataset type (nomenclatural, taxonomic, phylogenetic, article, legal, thematic, other)
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# @param license [Array, String] Filter by the license type (cc0, cc_by, cc_by_sa, cc_by_nc, cc_by_nd, cc_by_nc_sa, cc_by_nc_nd, unspecified, other)
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# @param row_type [Array, String] Filter by datasets that include a row type (e.g., acef:AcceptedSpecies, col:Taxon, dwc:Taxon)
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# @param created_after [Date] Filter by created after date
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# @param created_before [Date] Filter by created before date
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# @param issued_after [Date] Filter by issued after date
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# @param issued_before [Date] Filter by issued before date
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# @param modified_after [Date] Filter by modified after date
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# @param modified_before [Date] Filter by modified before date
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# @param min_size [Integer] Filter by minimum record size
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#
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# @param sort_by [String] Sort by (key, alias, title, creator, relevance, created, modified, imported, size)
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# @param reverse [Boolean] Sort in reverse
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# @param offset [Integer] Offset for pagination
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# @param limit [Integer] Limit for pagination
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# @param verbose [Boolean] Print headers to STDOUT
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#
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# @return [Array, Boolean] An array of hashes
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def self.dataset(dataset_id: nil, attempt: nil, q: nil, short_title: nil, code: nil, private: nil, released_from: nil,
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contributes_to: nil, has_source_dataset: nil, has_gbif_id: nil, gbif_id: nil, gbif_publisher_id: nil,
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editor: nil, reviewer: nil, modified_by: nil, origin: nil, type: nil, license: nil, row_type: nil,
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created_after: nil, created_before: nil, issued_after: nil, issued_before: nil, modified_after: nil,
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modified_before: nil, min_size: nil, sort_by: nil, reverse: nil, offset: nil, limit: nil,
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verbose: false)
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endpoint = "dataset"
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unless dataset_id.nil?
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endpoint = "#{endpoint}/#{dataset_id}"
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unless attempt.nil?
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endpoint = "#{endpoint}/#{attempt}"
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end
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endpoint = "#{endpoint}.json"
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Request.new(endpoint: endpoint, verbose: verbose).perform
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else
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Request.new(endpoint: endpoint, q: q, short_title: short_title, code: code, private: private,
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released_from: released_from, contributes_to: contributes_to, has_source_dataset: has_source_dataset,
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has_gbif_id: has_gbif_id, gbif_id: gbif_id, gbif_publisher_id: gbif_publisher_id, editor: editor,
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reviewer: reviewer, modified_by: modified_by, origin: origin, type: type, license: license,
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row_type: row_type, created_after: created_after, created_before: created_before,
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issued_after: issued_after, issued_before: issued_before, modified_after: modified_after,
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modified_before: modified_before, min_size: min_size, sort_by: sort_by, reverse: reverse,
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offset: offset, limit: limit, verbose: verbose).perform
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end
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end
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# Get project decisions
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#
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# @param dataset_id [String] The dataset id
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# @param decision_id [Integer, nil] The decision id
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# @param name [String, nil] The scientific name to match
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# @param rank [String, nil] The rank of the scientific name
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# @param modified_by [Integer, nil] Filter by a user id on last modified by
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# @param broken [Boolean, nil] Whether the decision is broken or not
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# @param subject_dataset_id [String, nil] The source dataset id
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# @param mode [String, nil] The type of decision (block, reviewed, update, update_recursive, ignore)
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# @param subject [Boolean, nil] TODO: what does this do? All decisions with subject=true are bare names, so maybe it checks if the subject taxon exists?
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#
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# @param offset [Integer] Offset for pagination
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# @param limit [Integer] Limit for pagination
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# @param verbose [Boolean] Print headers to STDOUT
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#
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# @return [Hash, Boolean] A result hash
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def self.decision(dataset_id, decision_id: nil, name: nil, rank: nil, modified_by: nil, broken: nil,
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subject_dataset_id: nil, mode: nil, subject: nil, offset: nil, limit: nil, verbose: false)
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if decision_id.nil?
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endpoint = "dataset/#{dataset_id}/decision"
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Request.new(endpoint: endpoint, name: name, rank: rank, modified_by: modified_by, broken: broken,
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subject_dataset_id: subject_dataset_id, mode: mode, subject: subject, offset: offset,
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limit: limit, verbose: verbose).perform
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else
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endpoint = "dataset/#{dataset_id}/decision/#{decision_id}"
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Request.new(endpoint: endpoint, verbose: verbose).perform
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end
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end
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# Get duplicate names
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#
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# @param dataset_id [String] The dataset id
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#
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# @param offset [Integer] Offset for pagination
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# @param limit [Integer] Limit for pagination
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# @param verbose [Boolean] Print headers to STDOUT
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def self.duplicate(dataset_id, offset: nil, limit: nil, verbose: false)
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endpoint = "dataset/#{dataset_id}/duplicate"
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Request.new(endpoint: endpoint, offset: offset, limit: limit, verbose: verbose).perform
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end
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# Get names diff between 2 datasets
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#
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# @param dataset_id [String] The first dataset id
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# @param dataset2_id [String] The second dataset id
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# @param root_id [Array, String, nil] The root taxon for the first dataset
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# @param root2_id [Array, String, nil] The root taxon for the second dataset
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# @param min_rank [String, nil] The minimum taxonomic rank
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# @param authorship [Boolean, nil] Include authorship
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# @param include_synonyms [Boolean, nil] Include synonyms
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# @param include_parent [Boolean, nil] Include parent
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# @param parent_rank [String, nil] Filter by parent rank
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# @param token [String, nil] An authentication token from Colrapi.user_login()
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#
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# @param offset [Integer] Offset for pagination
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# @param limit [Integer] Limit for pagination
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# @param verbose [Boolean] Print headers to STDOUT
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#
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# @return [String, Boolean] A text diff of names
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def self.diff(dataset_id, dataset2_id, root_id: nil, root2_id: nil, min_rank: nil,
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authorship: nil, include_synonyms: nil, include_parent: nil, parent_rank: nil,
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offset: nil, limit: nil, token: nil, verbose: false)
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endpoint = "dataset/#{dataset_id}/diff/#{dataset2_id}"
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Request.new(endpoint: endpoint, root_id: root_id, root2_id: root2_id, min_rank: min_rank,
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authorship: authorship, include_synonyms: include_synonyms,
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include_parent: include_parent, parent_rank: parent_rank,
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offset: offset, limit: limit, token: token, verbose: verbose).perform
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end
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# Get editor info
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#
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# @param dataset_id [String] The dataset id
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# @param token [String, nil] The authentication token from retrieved with Colrapi.user_login(user, password)
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#
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# # @return [Array, Hash, Boolean] An array of hashes
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def self.editor(dataset_id, token, verbose: false)
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endpoint = "dataset/#{dataset_id}/editor"
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Request.new(endpoint: endpoint, token: token, verbose: verbose).perform
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end
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# Get estimates
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# @param dataset_id [String] The dataset id
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# @param estimate_id [Integer, nil] The estimate ID
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# @param name [String] The scientific name
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# @param rank [String, nil] taxonomic rank
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# @param modified_by [Integer, nil] Filter by a user id on last modified by
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# @param broken [Boolean, nil] Whether the estimate is broken or not
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# @param min [Integer, nil] Filter by the minimum estimate
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# @param max [Integer, nil] Filter by the maximum estimate
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#
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# @param offset [Integer] Offset for pagination
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# @param limit [Integer] Limit for pagination
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# @param verbose [Boolean] Print headers to STDOUT
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#
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# @return [Hash, Boolean] A results hash
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def self.estimate(dataset_id, estimate_id: nil, name: nil, rank: nil, modified_by: nil, broken: nil, min: nil,
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max: nil, offset: nil, limit: nil, verbose: false)
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endpoint = "dataset/#{dataset_id}/estimate"
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if estimate_id.nil?
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Request.new(endpoint: endpoint, name: name, rank: rank, modified_by: modified_by, broken: broken,
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min: min, max: max, offset: offset, limit: limit, verbose: verbose).perform
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else
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endpoint = "dataset/#{dataset_id}/estimate/#{estimate_id}"
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Request.new(endpoint: endpoint, verbose: verbose).perform
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end
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end
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# TODO: /dataset/{key}/export is covered, but /export and /export/{id} are not
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# Get a dataset export
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#
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# @param dataset_id [String] The dataset id
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# @param show_id [Boolean, nil] TODO: not implemented because it doesn't seem to do anything?
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# @param verbose [Boolean] Print headers to STDOUT
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#
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# @return [Hash, Boolean] An export hash
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def self.export(dataset_id, show_id: nil, verbose: false)
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endpoint = "dataset/#{dataset_id}/export"
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Request.new(endpoint: endpoint, verbose: verbose).perform
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end
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# Get data quality issues
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#
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# @param dataset_id [String] The dataset id
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# @param issue [String] Filter by data quality issue (e.g., ACCEPTED_NAME_MISSING, DUPLICATE_NAME, URL_INVALID)
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# @param mode [String] Verbatim (default) or interpreted
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#
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# @param offset [Integer] Offset for pagination
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# @param limit [Integer] Limit for pagination
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# @param verbose [Boolean] Print headers to STDOUT
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#
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# @return [Array, Hash, Boolean] An array of hashes
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def self.issues(dataset_id, issue: nil, mode: 'verbatim', offset: nil, limit: nil, verbose: false)
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if issue.nil?
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metrics = Request.new(endpoint: "/dataset/#{dataset_id}/import?state=finished").perform
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return {"issuesCount" => metrics[0]['issuesCount']}
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else
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if mode == 'interpreted'
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issues = self.vocab(term: 'issue')
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record_type = 'any'
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issues.each do |i|
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if i['name'] == issue.downcase
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record_type = i['group']
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end
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end
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# TODO: so far issues are only filterable on nameusage/search and /reference
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# for other record_types, may need to add other endpoints in the future
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if record_type == 'reference'
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self.reference(dataset_id, issue: issue, offset: offset, limit: limit, verbose: verbose)
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else
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self.nameusage_search(dataset_id: dataset_id, issue: issue, facet: 'issue', offset: offset, limit: limit,
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verbose: verbose)
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end
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else
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self.verbatim(dataset_id, issue: issue, offset: offset, limit: limit, verbose: verbose)
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end
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end
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end
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# Get importer status
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#
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# @param dataset_id [String] Calls the dataset_id endpoint /importer/{dataset_id}
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# @param dataset_id_filter [String] Filters the importer queue by dataset_id
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# @param state [Array, String] The import status (e.g., waiting, preparing, downloading, processing, inserting, ...)
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# @param running [Boolean] Filter by actively importing datasets
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#
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# @param offset [Integer] Offset for pagination
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# @param limit [Integer] Limit for pagination
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# @param verbose [Boolean] Print headers to STDOUT
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#
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# @return [Array, Boolean] An array of hashes
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def self.importer(dataset_id: nil, dataset_id_filter: nil, state: nil, running: nil, offset: nil, limit: nil,
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verbose: false)
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endpoint = "importer"
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if dataset_id.nil?
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Request.new(endpoint: endpoint, dataset_id_filter: dataset_id_filter, state: state, running: running,
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offset: offset, limit: limit, verbose: verbose).perform
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else
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endpoint = "#{endpoint}/#{dataset_id}"
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Request.new(endpoint: endpoint, verbose: verbose).perform
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end
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end
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# Get a dataset's logo
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#
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# @param dataset_id [String] The dataset id
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# @param size [String] The size of the logo (original, large, medium, small)
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#
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# @return [Binary] The dataset logo
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def self.logo(dataset_id, size: nil, verbose: false)
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endpoint = "dataset/#{dataset_id}/logo"
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Request.new(endpoint: endpoint, size: size, verbose: verbose).perform
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end
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# Get names or a name from a dataset
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#
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# @param dataset_id [String] The dataset id
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# @param name [String] The scientific name to match
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# @param authorship [String] The authorship string for the scientific name
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# @param code [String] The nomenclatural code (bacterial, botanical, cultivars, phytosociological, virus, zoological)
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# @param rank [String] The rank of the scientific name
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# @param within_superkingdom [String] Restricts query to within a superkingdom
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302
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+
# @param within_kingdom [String] Restricts query to within a kingdom
|
303
|
+
# @param within_subkingdom [String] Restricts query to within a subkingdom
|
304
|
+
# @param within_superphylum [String] Restricts query to within a superphylum
|
305
|
+
# @param within_phylum [String] Restricts query to within a phylum
|
306
|
+
# @param within_subphylum [String] Restricts query to within a subphylum
|
307
|
+
# @param within_superclass [String] Restricts query to within a superclass
|
308
|
+
# @param within_class [String] Restricts query to within a class
|
309
|
+
# @param within_subclass [String] Restricts query to within a subclass
|
310
|
+
# @param within_superorder [String] Restricts query to within a superorder
|
311
|
+
# @param within_order [String] Restricts query to within a order
|
312
|
+
# @param within_suborder [String] Restricts query to within a suborder
|
313
|
+
# @param within_superfamily [String] Restricts query to within a superfamily
|
314
|
+
# @param within_family [String] Restricts query to within a family
|
315
|
+
# @param within_subfamily [String] Restricts query to within a subfamily
|
316
|
+
# @param within_tribe [String] Restricts query to within a tribe
|
317
|
+
# @param within_subtribe [String] Restricts query to within a subtribe
|
318
|
+
# @param within_genus [String] Restricts query to within a genus
|
319
|
+
# @param within_subgenus [String] Restricts query to within a subgenus
|
320
|
+
# @param within_section [String] Restricts query to within a section
|
321
|
+
# @param within_species [String] Restricts query to within a species
|
322
|
+
#
|
323
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
324
|
+
#
|
325
|
+
# @return [Array, Boolean] An array of hashes
|
326
|
+
# def self.matching(dataset_id, name: nil, authorship: nil, code: nil, rank: nil, within_superkingdom: nil,
|
327
|
+
# within_kingdom: nil, within_subkingdom: nil, within_superphylum: nil, within_phylum: nil,
|
328
|
+
# within_subphylum: nil, within_superclass: nil, within_class: nil, within_subclass: nil,
|
329
|
+
# within_superorder: nil, within_order: nil, within_suborder: nil, within_superfamily: nil,
|
330
|
+
# within_family: nil, within_subfamily: nil, within_tribe: nil, within_subtribe: nil,
|
331
|
+
# within_genus: nil, within_subgenus: nil, within_section: nil, within_species: nil,
|
332
|
+
# verbose: false)
|
333
|
+
# endpoint = "dataset/#{dataset_id}/matching"
|
334
|
+
# Request.new(endpoint: endpoint, name: name, authorship: authorship, code: code, rank: rank,
|
335
|
+
# within_superkingdom: within_superkingdom, within_kingdom: within_kingdom,
|
336
|
+
# within_subkingdom: within_subkingdom, within_superphylum: within_superphylum,
|
337
|
+
# within_phylum: within_phylum, within_subphylum: within_subphylum, within_superclass: within_superclass,
|
338
|
+
# within_class: within_class, within_subclass: within_subclass, within_superorder: within_superorder,
|
339
|
+
# within_order: within_order, within_suborder: within_suborder, within_superfamily: within_superfamily,
|
340
|
+
# within_family: within_family, within_subfamily: within_subfamily, within_tribe: within_tribe,
|
341
|
+
# within_subtribe: within_subtribe, within_genus: within_genus, within_subgenus: within_subgenus,
|
342
|
+
# within_section: within_section, within_species: within_species, verbose: verbose).perform
|
343
|
+
# end
|
344
|
+
|
345
|
+
# Get metrics for the *last successful* import of a dataset or a specific import_attempt
|
346
|
+
#
|
347
|
+
# @param dataset_id [String] The dataset id
|
348
|
+
# @param import_attempt [Integer] The import attempt
|
349
|
+
#
|
350
|
+
# @return [Array, Hash, Boolean] An array of hashes
|
351
|
+
def self.metrics(dataset_id, import_attempt: nil, verbose: false)
|
352
|
+
|
353
|
+
import = self.importer(dataset_id: dataset_id)
|
354
|
+
unless %w[unchanged finished].include? import['state']
|
355
|
+
return {"code" => 400, 'message' => 'Dataset has not finished importing or failed to import'}
|
356
|
+
end
|
357
|
+
|
358
|
+
# it's necessary to get the last finished import attempt because status=unchanged import results don't have metrics
|
359
|
+
# project release datasets do not seem to have import_attempts or should be taken from the project dataset, e.g.:
|
360
|
+
# https://api.checklistbank.org/dataset/3/import/107 == https://api.checklistbank.org/dataset/9837/import
|
361
|
+
if import_attempt.nil?
|
362
|
+
import = self.importer(dataset_id_filter: dataset_id, state: 'finished')
|
363
|
+
if import['total'] > 0
|
364
|
+
import_attempt = import['result'][0]['attempt']
|
365
|
+
end
|
366
|
+
end
|
367
|
+
|
368
|
+
endpoint = "dataset/#{dataset_id}/import"
|
369
|
+
if !import_attempt.nil?
|
370
|
+
endpoint = "#{endpoint}/#{import_attempt}"
|
371
|
+
Request.new(endpoint: endpoint, verbose: verbose).perform
|
372
|
+
else
|
373
|
+
# /dataset/{id}/import returns an array of 1 item while /dataset/{id}/import/{attempt} doesn't
|
374
|
+
res = Request.new(endpoint: endpoint, verbose: verbose).perform
|
375
|
+
res[0]
|
376
|
+
end
|
377
|
+
end
|
378
|
+
|
379
|
+
# Get names or a name from a dataset
|
380
|
+
#
|
381
|
+
# @param dataset_id [String] The dataset id
|
382
|
+
# @param name_id [String] The name id
|
383
|
+
# @param subresource [String] The name subresource endpoint (relations, synonyms, types, or orphans)
|
384
|
+
#
|
385
|
+
# @param offset [Integer] Offset for pagination
|
386
|
+
# @param limit [Integer] Limit for pagination
|
387
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
388
|
+
#
|
389
|
+
# @return [Array, Boolean] An array of hashes
|
390
|
+
def self.name(dataset_id, name_id: nil, subresource: nil, offset: nil, limit: nil, verbose: false)
|
391
|
+
endpoint = "dataset/#{dataset_id}/name"
|
392
|
+
unless name_id.nil?
|
393
|
+
endpoint = "#{endpoint}/#{name_id}"
|
394
|
+
offset = nil
|
395
|
+
limit = nil
|
396
|
+
end
|
397
|
+
if !subresource.nil? and %w[relations synonyms types orphans].include? subresource
|
398
|
+
endpoint = "#{endpoint}/#{subresource}"
|
399
|
+
end
|
400
|
+
Request.new(endpoint: endpoint, offset: offset, limit: limit, verbose: verbose).perform
|
401
|
+
end
|
402
|
+
|
403
|
+
# Get a text list of names for a dataset
|
404
|
+
#
|
405
|
+
# @param dataset_id [String] The dataset id
|
406
|
+
# @param import_attempt [Integer] The import attempt number
|
407
|
+
#
|
408
|
+
def self.name_list(dataset_id, import_attempt: nil, verbose: nil)
|
409
|
+
|
410
|
+
# get last import attempt number if none given
|
411
|
+
if import_attempt.nil?
|
412
|
+
import = self.importer(dataset_id: dataset_id)
|
413
|
+
import_attempt = import['attempt']
|
414
|
+
end
|
415
|
+
|
416
|
+
endpoint = "dataset/#{dataset_id}/import/#{import_attempt}/names"
|
417
|
+
Request.new(endpoint: endpoint, verbose: verbose).perform
|
418
|
+
end
|
419
|
+
|
420
|
+
# Get a text tree of names for a dataset
|
421
|
+
#
|
422
|
+
# @param dataset_id [String] The dataset id
|
423
|
+
# @param import_attempt [Integer] The import attempt number
|
424
|
+
#
|
425
|
+
def self.name_tree(dataset_id, import_attempt: nil, verbose: nil)
|
426
|
+
|
427
|
+
# get last import attempt number if none given
|
428
|
+
if import_attempt.nil?
|
429
|
+
import = self.importer(dataset_id: dataset_id)
|
430
|
+
import_attempt = import['attempt']
|
431
|
+
end
|
432
|
+
|
433
|
+
endpoint = "dataset/#{dataset_id}/import/#{import_attempt}/tree"
|
434
|
+
Request.new(endpoint: endpoint, verbose: verbose).perform
|
435
|
+
end
|
436
|
+
|
437
|
+
# Get name usages or a nameusage from a dataset
|
438
|
+
# Note: Queries the PSQL database, whereas nameusage_search uses Elastic Search
|
439
|
+
#
|
440
|
+
# @param dataset_id [String] The dataset id
|
441
|
+
# @param nameusage_id [String] The nameusage id
|
442
|
+
# @param q [String] The scientific name or authorship search query
|
443
|
+
# @param rank [Array, String] The rank of the taxon in the search query q
|
444
|
+
# @param nidx_id [String] The name index id
|
445
|
+
# @param subresource [String] The name subresource endpoint (relations, synonyms, types, or orphans)
|
446
|
+
#
|
447
|
+
# @param offset [Integer] Offset for pagination
|
448
|
+
# @param limit [Integer] Limit for pagination
|
449
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
450
|
+
#
|
451
|
+
# @return [Array, Boolean] An array of hashes
|
452
|
+
def self.nameusage(dataset_id, nameusage_id: nil, q: nil, rank: nil, nidx_id: nil, subresource: nil,
|
453
|
+
offset: nil, limit: nil, verbose: false)
|
454
|
+
endpoint = "dataset/#{dataset_id}/nameusage"
|
455
|
+
unless nameusage_id.nil?
|
456
|
+
endpoint = "#{endpoint}/#{nameusage_id}"
|
457
|
+
offset = nil
|
458
|
+
limit = nil
|
459
|
+
end
|
460
|
+
unless subresource.nil?
|
461
|
+
endpoint = "#{endpoint}/#{subresource}"
|
462
|
+
end
|
463
|
+
Request.new(endpoint: endpoint, q: q, rank: rank, nidx_id: nidx_id, offset: offset, limit: limit,
|
464
|
+
verbose: verbose).perform
|
465
|
+
end
|
466
|
+
|
467
|
+
# TODO: /dataset/{key}/nameusage/{id}/related not covered
|
468
|
+
# TODO: /dataset/{key}/nameusage/{id}/source not covered
|
469
|
+
|
470
|
+
# Get names or a name from a dataset
|
471
|
+
#
|
472
|
+
# @param dataset_id [String] The dataset id
|
473
|
+
# @param name [String] The scientific name to match
|
474
|
+
# @param authorship [String] The authorship string for the scientific name
|
475
|
+
# @param code [String] The nomenclatural code (bacterial, botanical, cultivars, phytosociological, virus, zoological)
|
476
|
+
# @param rank [String] The rank of the scientific name
|
477
|
+
# @param within_superkingdom [String] Restricts query to within a superkingdom
|
478
|
+
# @param within_kingdom [String] Restricts query to within a kingdom
|
479
|
+
# @param within_subkingdom [String] Restricts query to within a subkingdom
|
480
|
+
# @param within_superphylum [String] Restricts query to within a superphylum
|
481
|
+
# @param within_phylum [String] Restricts query to within a phylum
|
482
|
+
# @param within_subphylum [String] Restricts query to within a subphylum
|
483
|
+
# @param within_superclass [String] Restricts query to within a superclass
|
484
|
+
# @param within_class [String] Restricts query to within a class
|
485
|
+
# @param within_subclass [String] Restricts query to within a subclass
|
486
|
+
# @param within_superorder [String] Restricts query to within a superorder
|
487
|
+
# @param within_order [String] Restricts query to within a order
|
488
|
+
# @param within_suborder [String] Restricts query to within a suborder
|
489
|
+
# @param within_superfamily [String] Restricts query to within a superfamily
|
490
|
+
# @param within_family [String] Restricts query to within a family
|
491
|
+
# @param within_subfamily [String] Restricts query to within a subfamily
|
492
|
+
# @param within_tribe [String] Restricts query to within a tribe
|
493
|
+
# @param within_subtribe [String] Restricts query to within a subtribe
|
494
|
+
# @param within_genus [String] Restricts query to within a genus
|
495
|
+
# @param within_subgenus [String] Restricts query to within a subgenus
|
496
|
+
# @param within_section [String] Restricts query to within a section
|
497
|
+
# @param within_species [String] Restricts query to within a species
|
498
|
+
#
|
499
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
500
|
+
#
|
501
|
+
# @return [Array, Boolean] An array of hashes
|
502
|
+
def self.matching(dataset_id, name: nil, authorship: nil, code: nil, rank: nil, within_superkingdom: nil,
|
503
|
+
within_kingdom: nil, within_subkingdom: nil, within_superphylum: nil, within_phylum: nil,
|
504
|
+
within_subphylum: nil, within_superclass: nil, within_class: nil, within_subclass: nil,
|
505
|
+
within_superorder: nil, within_order: nil, within_suborder: nil, within_superfamily: nil,
|
506
|
+
within_family: nil, within_subfamily: nil, within_tribe: nil, within_subtribe: nil,
|
507
|
+
within_genus: nil, within_subgenus: nil, within_section: nil, within_species: nil,
|
508
|
+
verbose: false)
|
509
|
+
endpoint = "dataset/#{dataset_id}/nameusage/match"
|
510
|
+
Request.new(endpoint: endpoint, name: name, authorship: authorship, code: code, rank: rank,
|
511
|
+
within_superkingdom: within_superkingdom, within_kingdom: within_kingdom,
|
512
|
+
within_subkingdom: within_subkingdom, within_superphylum: within_superphylum,
|
513
|
+
within_phylum: within_phylum, within_subphylum: within_subphylum, within_superclass: within_superclass,
|
514
|
+
within_class: within_class, within_subclass: within_subclass, within_superorder: within_superorder,
|
515
|
+
within_order: within_order, within_suborder: within_suborder, within_superfamily: within_superfamily,
|
516
|
+
within_family: within_family, within_subfamily: within_subfamily, within_tribe: within_tribe,
|
517
|
+
within_subtribe: within_subtribe, within_genus: within_genus, within_subgenus: within_subgenus,
|
518
|
+
within_section: within_section, within_species: within_species, verbose: verbose).perform
|
519
|
+
end
|
520
|
+
|
521
|
+
# Search for a name usage with a regex pattern
|
522
|
+
#
|
523
|
+
# @param dataset_id [String, nil] restricts name usage pattern search within a dataset
|
524
|
+
# @param regexp [String] The regular expression pattern
|
525
|
+
# @param status [String, nil] The taxonomic status (accepted, provisionally_accepted, synonym, ambiguous_synonym, misapplied, bare_name)
|
526
|
+
# @param rank [String, nil] The taxonomic rank
|
527
|
+
# @param project_id [String, nil] Filter to names from project_id, required if decision_mode used
|
528
|
+
# @param decision_mode [String, nil] The type of decision (block, reviewed, update, update_recursive, ignore)
|
529
|
+
#
|
530
|
+
# @param offset [Integer] Offset for pagination
|
531
|
+
# @param limit [Integer] Limit for pagination
|
532
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
533
|
+
def self.nameusage_pattern(dataset_id, regexp, status: nil, rank: nil, project_id: nil, decision_mode: nil,
|
534
|
+
offset: nil, limit: nil, verbose: false)
|
535
|
+
endpoint = "dataset/#{dataset_id}/nameusage/pattern"
|
536
|
+
Request.new(endpoint: endpoint, regexp: regexp, project_id: project_id, status: status, rank: rank,
|
537
|
+
decision_mode: decision_mode, offset: offset, limit: limit, verbose: verbose).perform
|
538
|
+
end
|
539
|
+
|
540
|
+
# Search the nameusage route, which uses Elastic Search
|
541
|
+
#
|
542
|
+
# @param q [String] A query string
|
543
|
+
# @param dataset_id [String, nil] restricts name usage search within a dataset
|
544
|
+
# @param endpoint [String, nil] some endpoints have nested options
|
545
|
+
# @param content [Array, String, nil] restrict search to SCIENTIFIC_NAME, or AUTHORSHIP
|
546
|
+
# @param issue [Array, String, nil] the data quality issue
|
547
|
+
# @param type [String, nil] sets the type of search to PREFIX, WHOLE_WORDS, or EXACT
|
548
|
+
# @param rank [String, nil] taxonomic rank of name usages
|
549
|
+
# @param min_rank [String, nil] minimum taxonomic rank of name usages
|
550
|
+
# @param max_rank [String, nil] maximum taxonomic rank of name usages
|
551
|
+
# @param facet [Array, String, nil] the search facet
|
552
|
+
#
|
553
|
+
# @param sort_by [String, nil] sort results by NAME, TAXONOMIC, INDEX_NAME_ID, NATIVE, or RELEVANCE
|
554
|
+
# @param reverse [Boolean] sort in reverse order
|
555
|
+
# @param offset [Integer] Offset for pagination
|
556
|
+
# @param limit [Integer] Limit for pagination
|
557
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
558
|
+
#
|
559
|
+
# @return [Array, Boolean] An array of hashes
|
560
|
+
def self.nameusage_search(q: nil, dataset_id: nil, endpoint: 'nameusage/search', content: nil, issue: nil,
|
561
|
+
type: nil, rank: nil, min_rank: nil, max_rank: nil, facet: nil,
|
562
|
+
sort_by: nil, reverse: nil, offset: nil, limit: nil,
|
563
|
+
verbose: false)
|
564
|
+
|
565
|
+
# a nil dataset_id will search name usages from all datasets in ChecklistBank
|
566
|
+
unless dataset_id.nil?
|
567
|
+
endpoint = "dataset/#{dataset_id}/nameusage/search"
|
568
|
+
end
|
569
|
+
|
570
|
+
Request.new(endpoint: endpoint, q: q, content: content, issue: issue, type: type,
|
571
|
+
rank: rank, min_rank: min_rank, max_rank: max_rank, facet: facet,
|
572
|
+
sort_by: sort_by, reverse: reverse, offset: offset, limit: limit, verbose: verbose).perform
|
573
|
+
end
|
574
|
+
|
575
|
+
# Get a name usage suggestion
|
576
|
+
#
|
577
|
+
# @param dataset_id [String] restricts name usage search within a dataset
|
578
|
+
# @param q [String] A suggestion search query
|
579
|
+
# @param fuzzy [Boolean, nil] Whether to include fuzzy matches for misspellings (TODO: might not actually work?)
|
580
|
+
# @param min_rank [String, nil] The minimum rank to suggest
|
581
|
+
# @param max_rank [String, nil] The maximum rank to suggest
|
582
|
+
# @param sort_by [String, nil] The sorting order (name, taxonomic, index_name_id, native, relevance)
|
583
|
+
# @param reverse [Boolean, nil] Sort in opposite order
|
584
|
+
# @param accepted [Boolean, nil] Suggest only accepted names
|
585
|
+
#
|
586
|
+
# @limit [Integer, nil] Limit the suggestion number (offset not available)
|
587
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
588
|
+
#
|
589
|
+
# @return [Hash, Boolean] A a hash of name usage suggestions
|
590
|
+
def self.nameusage_suggest(dataset_id, q, fuzzy: nil, min_rank: nil, max_rank: nil, sort_by: nil, reverse: nil,
|
591
|
+
accepted: nil, limit: nil, verbose: false)
|
592
|
+
endpoint = "dataset/#{dataset_id}/nameusage/suggest"
|
593
|
+
Request.new(endpoint: endpoint, q: q, fuzzy: fuzzy, min_rank: min_rank, max_rank: max_rank, sort_by: sort_by,
|
594
|
+
reverse: reverse, accepted: accepted, limit: limit, verbose: verbose).perform
|
595
|
+
end
|
596
|
+
|
597
|
+
# Get names index info
|
598
|
+
#
|
599
|
+
# @param nidx_id [Integer] a names index ID
|
600
|
+
# @param subresource [String, nil] the subresource (group)
|
601
|
+
def self.nidx(nidx_id, subresource: nil, verbose: false)
|
602
|
+
endpoint = "nidx/#{nidx_id}"
|
603
|
+
endpoint = "nidx/#{nidx_id}/#{subresource}" unless subresource.nil?
|
604
|
+
Request.new(endpoint: endpoint, verbose: verbose).perform
|
605
|
+
end
|
606
|
+
|
607
|
+
# Get names index matches
|
608
|
+
# @param q [String, nil] A match query
|
609
|
+
# @param authorship [String, nil] An authorship string
|
610
|
+
# @param rank [String, nil] The taxonomic rank
|
611
|
+
# @param code [String, nil] The nomenclatural code
|
612
|
+
#
|
613
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
614
|
+
#
|
615
|
+
# @return [Hash, Boolean] A match hash
|
616
|
+
def self.nidx_match(q, authorship: nil, rank: nil, code: nil, verbose: false)
|
617
|
+
endpoint = "nidx/match"
|
618
|
+
Request.new(endpoint: endpoint, q: q, authorship: authorship, rank: rank, code: code, verbose: verbose).perform
|
619
|
+
end
|
620
|
+
|
621
|
+
# Parse a {subresource}
|
622
|
+
#
|
623
|
+
# This is the generic parser wrapper. For specialized parsers, like the names, homoglyphs, idconverter, metadata,
|
624
|
+
# use the specialized parsers below like Colrapi.parser_name(). Returns a list of parsers if no subresource given.
|
625
|
+
#
|
626
|
+
# @param subresource [String] the type of parser to use
|
627
|
+
# @param q [Array, String] a query string or array of query strings to parse
|
628
|
+
#
|
629
|
+
# @return [Array, Hash, Boolean] An array of parsers, or a parser result hash
|
630
|
+
def self.parser(subresource: nil, q: nil, verbose: false)
|
631
|
+
endpoint = "parser"
|
632
|
+
endpoint = "#{endpoint}/#{subresource}" unless subresource.nil?
|
633
|
+
Request.new(endpoint: endpoint, q: q, verbose: verbose).perform
|
634
|
+
end
|
635
|
+
|
636
|
+
# Encode or decode identifiers to different formats (e.g., proquints are used as stable identifiers in ChecklistBank)
|
637
|
+
# @param mode [String] encode or decode
|
638
|
+
# @param id [String] the identifier to convert
|
639
|
+
# @param format [String] the format (proquint, hex, latin29, latin32, latin36, base64)
|
640
|
+
#
|
641
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
642
|
+
#
|
643
|
+
# @return [String, Integer, Boolean] A parser result hash
|
644
|
+
def self.parser_idconverter(mode, id, format, verbose: false)
|
645
|
+
endpoint = "parser/idconverter/#{mode}"
|
646
|
+
Request.new(endpoint: endpoint, id: id, format: format, verbose: verbose).perform
|
647
|
+
end
|
648
|
+
|
649
|
+
# Parse metadata
|
650
|
+
# @param url [String] The url to a metadata file
|
651
|
+
# @param format [String] The format of the metadata (yaml, json, eml, datacite, zenodo)
|
652
|
+
#
|
653
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
654
|
+
#
|
655
|
+
# @return [String, Integer, Boolean] A parser result hash
|
656
|
+
def self.parser_metadata(url, format: nil, verbose: false)
|
657
|
+
endpoint = 'parser/metadata'
|
658
|
+
Request.new(endpoint: endpoint, url: url, format: format, verbose: verbose).perform
|
659
|
+
end
|
660
|
+
|
661
|
+
# Parse a scientific name
|
662
|
+
#
|
663
|
+
# @param name [String] The scientific name to parse
|
664
|
+
# @param authorship [String, nil] The authorship string for the scientific name
|
665
|
+
# @param rank [String, nil] The rank of the scientific name to parse
|
666
|
+
# @param code [String] The nomenclatural code (bacterial, botanical, cultivars, phytosociological, virus, zoological)
|
667
|
+
#
|
668
|
+
# @return [Hash, Boolean] A hash with the parsed scientific name
|
669
|
+
def self.parser_name(name, authorship: nil, rank: nil, code: nil, verbose: false)
|
670
|
+
endpoint = 'parser/name'
|
671
|
+
Request.new(endpoint: endpoint, name: name, authorship: authorship, rank: rank, code: code,
|
672
|
+
verbose: verbose).perform
|
673
|
+
end
|
674
|
+
|
675
|
+
# Get metadata patch
|
676
|
+
#
|
677
|
+
# @param dataset_id [String] The dataset id
|
678
|
+
# @param token [String, nil] The authentication token from retrieved with Colrapi.user_login(user, password)
|
679
|
+
def self.patch(dataset_id, patch_id: nil, token: nil, verbose: false)
|
680
|
+
endpoint = "dataset/#{dataset_id}/patch"
|
681
|
+
unless patch_id.nil?
|
682
|
+
endpoint = "#{endpoint}/#{patch_id}"
|
683
|
+
end
|
684
|
+
Request.new(endpoint: endpoint, token: token, verbose: verbose).perform
|
685
|
+
end
|
686
|
+
|
687
|
+
# Get the latest preview release metadata (or points to the project draft dataset after the preview is released?)
|
688
|
+
# (Note: you can also use 3LRC where 3 is the project_id as an ID on any endpoint with dataset_id or project_id
|
689
|
+
# to get data from the latest release candidate, or 3LR gets the latest release)
|
690
|
+
# @param project_id [String] The project id
|
691
|
+
#
|
692
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
693
|
+
# @return [Array, Boolean] An array of hashes
|
694
|
+
def self.preview(project_id, verbose: false)
|
695
|
+
Request.new(endpoint: "dataset/#{project_id}/preview", verbose: verbose).perform
|
696
|
+
end
|
697
|
+
|
698
|
+
# Get a reference with @reference_id from dataset @dataset_id via the reference route
|
699
|
+
#
|
700
|
+
# @param dataset_id [String] The dataset id
|
701
|
+
# @param reference_id [String] The reference id
|
702
|
+
# @param subresource [String] The reference subresource endpoint (orphans)
|
703
|
+
# @param issue [Array, String] The data quality issue (https://api.checklistbank.org/vocab/issue)
|
704
|
+
#
|
705
|
+
# @param offset [Integer] Offset for pagination
|
706
|
+
# @param limit [Integer] Limit for pagination
|
707
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
708
|
+
#
|
709
|
+
# @return [Array, Boolean] An array of hashes
|
710
|
+
def self.reference(dataset_id, reference_id: nil, subresource: nil, issue: nil, offset: nil, limit: nil,
|
711
|
+
verbose: false)
|
712
|
+
endpoint = "dataset/#{dataset_id}/reference"
|
713
|
+
if subresource == 'orphans'
|
714
|
+
reference_id = nil
|
715
|
+
endpoint = "#{endpoint}/orphans"
|
716
|
+
end
|
717
|
+
unless reference_id.nil?
|
718
|
+
endpoint = "#{endpoint}/#{reference_id}"
|
719
|
+
end
|
720
|
+
Request.new(endpoint: endpoint, issue: issue, offset: offset, limit: limit, verbose: verbose).perform
|
721
|
+
end
|
722
|
+
|
723
|
+
# Get reviewer info
|
724
|
+
#
|
725
|
+
# @param dataset_id [String] The dataset id
|
726
|
+
# @param token [String, nil] The authentication token from retrieved with Colrapi.user_login(user, password)
|
727
|
+
#
|
728
|
+
# # @return [Array, Hash, Boolean] An array of hashes
|
729
|
+
def self.reviewer(dataset_id, token, verbose: false)
|
730
|
+
endpoint = "dataset/#{dataset_id}/reviewer"
|
731
|
+
Request.new(endpoint: endpoint, token: token, verbose: verbose).perform
|
732
|
+
end
|
733
|
+
|
734
|
+
# Get sector metadata, which allows importing datasets into project subtrees
|
735
|
+
#
|
736
|
+
# @param dataset_id [String] The dataset id
|
737
|
+
# @param sector_id [Integer, nil] The sector id
|
738
|
+
# @param name [String] The scientific name to query
|
739
|
+
# @param rank [String, nil] The rank of the scientific name
|
740
|
+
# @param modified_by [Integer, nil] Filter by a user id on last modified by
|
741
|
+
# @param broken [Boolean, nil] Whether the decision is broken or not
|
742
|
+
# @param subject_dataset_id [String, nil] The source dataset id
|
743
|
+
# @param last_synced_before [Date, nil] Filter by sectors synced before this date
|
744
|
+
# @param mode [String, nil] Filter by type of sector (attach, union, merge)
|
745
|
+
# @param subject [Boolean, nil] TODO: what does this do? All decisions with subject=true are bare names, so maybe it checks if the subject taxon exists?
|
746
|
+
# @param min_size [Integer, nil] The minimum number of records in the sector
|
747
|
+
# @param without_data [Boolean, nil] Filters to empty sectors with no data synced into the project yet
|
748
|
+
#
|
749
|
+
# @param offset [Integer] Offset for pagination
|
750
|
+
# @param limit [Integer] Limit for pagination
|
751
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
752
|
+
#
|
753
|
+
# @return [Hash, Boolean] An hash of results
|
754
|
+
def self.sector(dataset_id, sector_id: nil, name: nil, rank: nil, modified_by: nil, broken: nil,
|
755
|
+
subject_dataset_id: nil, last_synced_before: nil, mode: nil, subject: nil, min_size: nil, without_data: nil,
|
756
|
+
offset: nil, limit: nil, verbose: false)
|
757
|
+
endpoint = "dataset/#{dataset_id}/sector"
|
758
|
+
if sector_id.nil?
|
759
|
+
Request.new(endpoint: endpoint, name: name, rank: rank, modified_by: modified_by, broken: broken,
|
760
|
+
subject_dataset_id: subject_dataset_id, last_synced_before: last_synced_before, mode: mode,
|
761
|
+
subject: subject, min_size: min_size, without_data: without_data,
|
762
|
+
offset: offset, limit: limit, verbose: verbose).perform
|
763
|
+
else
|
764
|
+
endpoint = "#{endpoint}/#{sector_id}"
|
765
|
+
Request.new(endpoint: endpoint, verbose: verbose).perform
|
766
|
+
end
|
767
|
+
end
|
768
|
+
|
769
|
+
# Get sector sync info
|
770
|
+
#
|
771
|
+
# @param dataset_id [String] The dataset id
|
772
|
+
# @param sector_id [Integer, nil] The sector id
|
773
|
+
# @param state [Array, String, nil] The sector sync state (e.g., waiting, processing, inserting, indexing, finished, etc.)
|
774
|
+
# @param running [Boolean, nil] Filter to sector syncs that are only running
|
775
|
+
# @param attempt [Integer, nil] The sync attempt number for sector_id
|
776
|
+
# @param subresource [String, nil] The subresource for attempt (names or tree)
|
777
|
+
#
|
778
|
+
# @param offset [Integer] Offset for pagination
|
779
|
+
# @param limit [Integer] Limit for pagination
|
780
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
781
|
+
#
|
782
|
+
# @return [Hash, Boolean] An hash of results
|
783
|
+
def self.sector_sync(dataset_id, sector_id: nil, attempt: nil, subresource: nil, state: nil, running: nil, offset: nil, limit: nil, verbose: false)
|
784
|
+
endpoint = "dataset/#{dataset_id}/sector/sync"
|
785
|
+
if sector_id.nil?
|
786
|
+
Request.new(endpoint: endpoint, state: state, running: running, offset: offset, limit: limit,
|
787
|
+
verbose:verbose).perform
|
788
|
+
else
|
789
|
+
if attempt.nil?
|
790
|
+
endpoint = "dataset/#{dataset_id}/sector/#{sector_id}/sync"
|
791
|
+
else
|
792
|
+
endpoint = "dataset/#{dataset_id}/sector/#{sector_id}/sync/#{attempt}"
|
793
|
+
endpoint = "#{endpoint}/#{subresource}" unless subresource.nil?
|
794
|
+
end
|
795
|
+
Request.new(endpoint: endpoint, verbose:verbose).perform
|
796
|
+
end
|
797
|
+
end
|
798
|
+
|
799
|
+
# Get source metadata for datasets assembled into a project dataset
|
800
|
+
#
|
801
|
+
# @param dataset_id [String] The project dataset id
|
802
|
+
# @param source_id [String] The source dataset id
|
803
|
+
# @param not_current_only [String] Return only not current sources
|
804
|
+
# @param original [String] TODO: what does this do?
|
805
|
+
#
|
806
|
+
# @return [Array, Hash, Boolean] An array of source hashes, or a hash of a source
|
807
|
+
def self.source(dataset_id, source_id: nil, not_current_only: nil, original: nil, verbose: false)
|
808
|
+
endpoint = "dataset/#{dataset_id}/source"
|
809
|
+
if source_id.nil?
|
810
|
+
Request.new(endpoint: endpoint, not_current_only: not_current_only, verbose: verbose).perform
|
811
|
+
else
|
812
|
+
endpoint = "dataset/#{dataset_id}/source/#{source_id}"
|
813
|
+
Request.new(endpoint: endpoint, original: original, verbose: verbose).perform
|
814
|
+
end
|
815
|
+
end
|
816
|
+
|
817
|
+
|
818
|
+
# Get the dataset settings
|
819
|
+
# @param dataset_id [String] The dataset id
|
820
|
+
#
|
821
|
+
# @return [Hash, Boolean] A hash including the dataset settings
|
822
|
+
def self.settings(dataset_id)
|
823
|
+
Request.new(endpoint: "dataset/#{dataset_id}/settings").perform
|
824
|
+
end
|
825
|
+
|
826
|
+
# Get a synonym with @synonym_id from dataset @dataset_id via the synonym route
|
827
|
+
#
|
828
|
+
# @param dataset_id [String] The dataset id
|
829
|
+
# @param synonym_id [String] The synonym id
|
830
|
+
# @param subresource [String] The synonym subresource endpoint (source)
|
831
|
+
#
|
832
|
+
# @param offset [Integer] Offset for pagination
|
833
|
+
# @param limit [Integer] Limit for pagination
|
834
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
835
|
+
#
|
836
|
+
# @return [Array, Boolean] An array of hashes
|
837
|
+
def self.synonym(dataset_id, synonym_id: nil, subresource: nil, offset: nil, limit: nil, verbose: false)
|
838
|
+
endpoint = "dataset/#{dataset_id}/synonym"
|
839
|
+
unless synonym_id.nil?
|
840
|
+
endpoint = "#{endpoint}/#{synonym_id}"
|
841
|
+
end
|
842
|
+
if subresource == 'source'
|
843
|
+
endpoint = "#{endpoint}/source"
|
844
|
+
end
|
845
|
+
Request.new(endpoint: endpoint, offset: offset, limit: limit, verbose: verbose).perform
|
846
|
+
end
|
847
|
+
|
848
|
+
# Get the full list of taxon IDs for a dataset (returns 1 ID string per line, not JSON)
|
849
|
+
#
|
850
|
+
# @param dataset_id [String] The dataset id
|
851
|
+
#
|
852
|
+
# @return [Array, Boolean] An array of hashes
|
853
|
+
def self.taxon_ids(dataset_id, verbose: false)
|
854
|
+
Request.new(endpoint: "dataset/#{dataset_id}/taxon/ids", verbose: verbose).perform
|
855
|
+
end
|
856
|
+
|
857
|
+
# Get a taxon with @id from dataset @dataset_id via the taxon route
|
858
|
+
#
|
859
|
+
# @param dataset_id [String] The dataset id
|
860
|
+
# @param taxon_id [String] The taxon id
|
861
|
+
# @param subresource [String] The taxon subresource endpoint (classification, distribution, info, interaction, media,
|
862
|
+
# relation, source, synonyms, treatment, or vernacular)
|
863
|
+
# @param format [String] The format of the treatment (plain_text, markdown, xml, html, tax_pub, taxon_x, rdf)
|
864
|
+
#
|
865
|
+
# @param offset [Integer] Offset for pagination
|
866
|
+
# @param limit [Integer] Limit for pagination
|
867
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
868
|
+
#
|
869
|
+
# @return [Array, Boolean] An array of hashes
|
870
|
+
def self.taxon(dataset_id, taxon_id: nil, subresource: nil, format: nil, offset: nil, limit: nil, verbose: false)
|
871
|
+
endpoint = "dataset/#{dataset_id}/taxon"
|
872
|
+
unless taxon_id.nil?
|
873
|
+
endpoint = "#{endpoint}/#{taxon_id}"
|
874
|
+
end
|
875
|
+
|
876
|
+
if !subresource.nil?
|
877
|
+
endpoint = "#{endpoint}/#{subresource}"
|
878
|
+
end
|
879
|
+
Request.new(endpoint: endpoint, offset: offset, format: format, limit: limit, verbose: verbose).perform
|
880
|
+
end
|
881
|
+
|
882
|
+
# Get the root taxa
|
883
|
+
#
|
884
|
+
# @param dataset_id [String] The dataset id
|
885
|
+
# @param taxon_id [String] The taxon id
|
886
|
+
# @param children [Boolean] Display the children of taxon_id
|
887
|
+
#
|
888
|
+
# @param offset [Integer] Offset for pagination
|
889
|
+
# @param limit [Integer] Limit for pagination
|
890
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
891
|
+
#
|
892
|
+
# @return [Array, Boolean] An array of hashes
|
893
|
+
def self.tree(dataset_id, taxon_id: nil, children: false, offset: nil, limit: nil, verbose: false)
|
894
|
+
endpoint = "dataset/#{dataset_id}/tree"
|
895
|
+
endpoint = "#{endpoint}/#{taxon_id}" unless taxon_id.nil?
|
896
|
+
endpoint = "#{endpoint}/children" unless taxon_id.nil? or !children
|
897
|
+
Request.new(endpoint: endpoint, offset: offset, limit: limit, verbose: verbose).perform
|
898
|
+
end
|
899
|
+
|
900
|
+
# Get user data
|
901
|
+
#
|
902
|
+
# @param user_id [Integer, nil] The user id
|
903
|
+
# @param q [String, nil] The search query
|
904
|
+
# @param role [String, nil] The user role (admin, editor, or reviewer)
|
905
|
+
#
|
906
|
+
# @param offset [Integer] Offset for pagination
|
907
|
+
# @param limit [Integer] Limit for pagination
|
908
|
+
# @param token [String, nil] The authentication token from retrieved with Colrapi.user_login(user, password)
|
909
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
910
|
+
#
|
911
|
+
# @return [Array, Boolean] An array of hashes
|
912
|
+
def self.user(user_id: nil, q: nil, role: nil, offset: nil, limit: nil, token: nil, verbose: false)
|
913
|
+
if user_id.nil?
|
914
|
+
endpoint = "user"
|
915
|
+
Request.new(endpoint: endpoint, q: q, role: role, offset: offset, limit: limit, token: token,
|
916
|
+
verbose: verbose).perform
|
917
|
+
else
|
918
|
+
endpoint = "user/#{user_id}"
|
919
|
+
Request.new(endpoint: endpoint, token: token, verbose: verbose).perform
|
920
|
+
end
|
921
|
+
end
|
922
|
+
|
923
|
+
# Get datasets user can access
|
924
|
+
# @param token [String] The access token from Colrapi.user_login()
|
925
|
+
# @param dataset_id [String, nil] A dataset id to check
|
926
|
+
# @param origin [Array, String, nil] Filter by the origin of a dataset (external, project, release, xrelease)
|
927
|
+
#
|
928
|
+
# @return [Array, Boolean] An array of datasets, or returns a boolean if dataset_id is provided
|
929
|
+
def self.user_dataset(token, dataset_id: nil, origin: nil, verbose: false)
|
930
|
+
endpoint = "user/dataset"
|
931
|
+
if dataset_id.nil?
|
932
|
+
Request.new(endpoint: endpoint, token: token, origin: origin, verbose: verbose).perform
|
933
|
+
else
|
934
|
+
endpoint = "user/dataset/#{dataset_id}"
|
935
|
+
Request.new(endpoint: endpoint, token: token, verbose: verbose).perform
|
936
|
+
end
|
937
|
+
end
|
938
|
+
|
939
|
+
# Authenticate user and get authentication token
|
940
|
+
def self.user_login(user, password, verbose: false)
|
941
|
+
Request.new(endpoint: "user/login", user: user, password: password, verbose: verbose).perform
|
942
|
+
end
|
943
|
+
|
944
|
+
# Get the authenticated user
|
945
|
+
#
|
946
|
+
# @param token [String, nil] The authentication token from retrieved with Colrapi.user_login(user, password)
|
947
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
948
|
+
#
|
949
|
+
# @return [Array, Boolean] An array of hashes
|
950
|
+
def self.user_me(token, verbose: false)
|
951
|
+
Request.new(endpoint: "user/me", token: token, verbose: verbose).perform
|
952
|
+
end
|
953
|
+
|
954
|
+
# Get verbatim data
|
955
|
+
#
|
956
|
+
# @param dataset_id [String] The dataset id
|
957
|
+
# @param verbatim_id [String] The verbatim id
|
958
|
+
# @param q [String] The search query string
|
959
|
+
# @param issue [Array, String] Filter by data quality issue (e.g., ACCEPTED_NAME_MISSING, DUPLICATE_NAME, URL_INVALID)
|
960
|
+
# @param type [Array, String] The file type (e.g., acef:AcceptedSpecies, col:Taxon, dwc:Taxon)
|
961
|
+
#
|
962
|
+
# TODO: May not work yet: https://github.com/CatalogueOfLife/backend/issues/1201
|
963
|
+
# @param term [Array, String] Filter by term (http://api.checklistbank.org/vocab/term)
|
964
|
+
# @param term_operator [String] The operator to use with term ('and' or 'or')
|
965
|
+
#
|
966
|
+
# @param offset [Integer] Offset for pagination
|
967
|
+
# @param limit [Integer] Limit for pagination
|
968
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
969
|
+
#
|
970
|
+
# @return [Array, Boolean] An array of hashes
|
971
|
+
def self.verbatim(dataset_id, verbatim_id: nil, q: nil, issue: nil, type: nil, term: nil, term_operator: nil,
|
972
|
+
offset: nil, limit: nil, verbose: false)
|
973
|
+
endpoint = "dataset/#{dataset_id}/verbatim"
|
974
|
+
if verbatim_id.nil?
|
975
|
+
Request.new(endpoint: endpoint, q: q, issue: issue, type: type, term: term, term_operator: term_operator,
|
976
|
+
offset: offset, limit: limit, verbose: verbose).perform
|
977
|
+
else
|
978
|
+
endpoint = "#{endpoint}/#{verbatim_id}"
|
979
|
+
Request.new(endpoint: endpoint, verbose: verbose).perform
|
980
|
+
end
|
981
|
+
end
|
982
|
+
|
983
|
+
# Get vernacular names
|
984
|
+
#
|
985
|
+
# @param dataset_id [String, nil] The dataset id
|
986
|
+
# @param q [String] A vernacular name search query
|
987
|
+
# @param language [String, nil] The language of the vernacular name (see: http://api.checklistbank.org/vocab/language)
|
988
|
+
#
|
989
|
+
# @param offset [Integer] Offset for pagination
|
990
|
+
# @param limit [Integer] Limit for pagination
|
991
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
992
|
+
#
|
993
|
+
# @return [Hash] A hash of vernacular results
|
994
|
+
def self.vernacular(dataset_id: nil, q: nil, language: nil, offset: nil, limit: nil, verbose: false)
|
995
|
+
if dataset_id.nil?
|
996
|
+
endpoint = 'vernacular'
|
997
|
+
Request.new(endpoint: endpoint, q: q, language: language, offset: offset, limit: limit, verbose: verbose).perform
|
998
|
+
else
|
999
|
+
endpoint = "dataset/#{dataset_id}/vernacular"
|
1000
|
+
Request.new(endpoint: endpoint, q: q, language: language, offset: offset, limit: limit, verbose: verbose).perform
|
1001
|
+
end
|
1002
|
+
end
|
1003
|
+
|
1004
|
+
# Get backend version
|
1005
|
+
#
|
1006
|
+
# @return [String] A version string
|
1007
|
+
def self.version(verbose: false)
|
1008
|
+
Request.new(endpoint: 'version', verbose: verbose).perform
|
1009
|
+
end
|
1010
|
+
|
1011
|
+
# Get vocab
|
1012
|
+
# @param term [String] The vocab term
|
1013
|
+
# @param subresource [String] The subresource which is usually the id, code, or name
|
1014
|
+
# @param children [Boolean] Returns the geotime's children if true
|
1015
|
+
#
|
1016
|
+
# @param verbose [Boolean] Print headers to STDOUT
|
1017
|
+
#
|
1018
|
+
# @return [Array]
|
1019
|
+
def self.vocab(term: nil, subresource: nil, children: false, verbose: false)
|
1020
|
+
endpoint = "vocab"
|
1021
|
+
endpoint = "#{endpoint}/#{term}" unless term.nil?
|
1022
|
+
endpoint = "#{endpoint}/#{subresource}" unless term.nil? or subresource.nil?
|
1023
|
+
endpoint = "#{endpoint}/children" if children and term == "geotime"
|
1024
|
+
Request.new(endpoint: endpoint, verbose: verbose).perform
|
1025
|
+
end
|
1026
|
+
end
|