dina 0.1.0.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: fb9d082cc5779c2164cc62c37dc96ccb9518172dd7d4906e5e7de7ca9270af35
+  data.tar.gz: 0fe67de260e7fab5f9167175dfc85bd8fe64f000887941648d7b003bbab16ab5
+SHA512:
+  metadata.gz: b1bc2b324d1c9d970aaba2703f347734dff1624f55104c924779e1ddf5a8f3cc0244403cd18c4de355e13dd7949251db844fc992414fb9652329b6d0e09afcae
+  data.tar.gz: c3e36505634d44f74c9068988a90ccdd41bf4a9d8462491131665ffb53af15bfd1fc9d64d2527bf43dd2e352457de4a7f8bf228e29f72cb6069a5717e7e6cf0d

data/lib/dina/authentication/authentication.rb

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+# encoding: utf-8
+
+module Dina
+  module Authentication
+
+    def self.config(options = {})
+      @token_store_file = options[:token_store_file]
+      @user = options[:user]
+      @password = options[:password]
+      @server_name = options[:server_name]
+      @client_id = options[:client_id]
+      @endpoint_url = options[:endpoint_url]
+      @authorization_url = options[:authorization_url]
+      @realm = options[:realm]
+      Keycloak.auth_server_url = @authorization_url
+      Keycloak.realm = @realm
+    end
+
+    def self.header
+      if access_token.nil? || refresh_token.nil?
+        set_token
+      end
+
+      if Time.now >= Time.parse(auth_expiry)
+        renew_token
+      end
+
+      "Bearer " + access_token
+    end
+
+    class << self
+      attr_accessor :token_store_file, :authorization_url, :endpoint_url, :client_id, :realm, :server_name
+
+      private
+
+      def get_token
+        response = Keycloak::Client.get_token(
+          @user,
+          @password,
+          client_id= @client_id,
+          secret='')
+        JSON.parse(response, symbolize_names: true)
+      end
+
+      def set_token
+        json = get_token
+        auth_expiry = (Time.now + json[:expires_in].seconds).to_s
+        save_token(access_token: json[:access_token], refresh_token: json[:refresh_token], auth_expiry: auth_expiry)
+      end
+
+      def renew_token
+        begin
+          response = Keycloak::Client.get_token_by_refresh_token(
+            refresh_token,
+            client_id= @client_id,
+            secret='')
+          json = JSON.parse(response, symbolize_names: true)
+          auth_expiry = (Time.now + json[:expires_in].seconds).to_s
+          save_token(access_token: json[:access_token], refresh_token: json[:refresh_token], auth_expiry: auth_expiry)
+        rescue
+          set_token
+        end
+      end
+
+      def access_token
+        read_token[:access_token] rescue nil
+      end
+
+      def refresh_token
+        read_token[:refresh_token] rescue nil
+      end
+
+      def auth_expiry
+        read_token[:auth_expiry] rescue "9999-01-01 00:00:00 -0500"
+      end
+
+      def read_token
+        raise TokenStoreFileNotFound unless @token_store_file.instance_of?(String) && ::File.exist?(@token_store_file)
+        JSON.parse(::File.read(@token_store_file), symbolize_names: true)[@server_name.to_sym] rescue default_token
+      end
+
+      def default_token
+        { access_token: nil, refresh_token: nil, auth_expiry: "9999-01-01 00:00:00 -0500" }
+      end
+
+      def save_token(access_token:, refresh_token:, auth_expiry:)
+        raise TokenStoreFileNotFound unless @token_store_file.instance_of?(String) && ::File.exist?(@token_store_file)
+        data_hash = JSON.parse(::File.read(@token_store_file), symbolize_names: true) rescue {}
+        data_hash[@server_name.to_sym] = {
+          access_token: access_token,
+          refresh_token: refresh_token,
+          auth_expiry: auth_expiry
+        }
+        ::File.write(@token_store_file, JSON.dump(data_hash))
+      end
+
+    end
+
+  end
+end

data/lib/dina/casters/array_caster.rb

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+
+module Dina
+  class ArrayCaster
+    def self.cast(value, default)
+      if value.is_a?(String)
+        [value]
+      elsif value.is_a?(Array)
+        value
+      else
+        default
+      end
+    end
+  end
+end

data/lib/dina/casters/multilingual_description.rb

@@ -0,0 +1,42 @@
+module Dina
+  class MultilingualDescription
+    attr_accessor :descriptions
+
+    def initialize(opts = {})
+      @descriptions = []
+      if opts[:descriptions]
+        @descriptions = opts[:descriptions]
+      end
+      if opts[:english]
+        self.english_description = opts[:english]
+      end
+      if opts[:french]
+        self.french_description = opts[:french]
+      end
+    end
+
+    def english_description=(desc)
+      descriptions.delete_if{|o| o[:lang] == "en"}
+      descriptions << { lang: "en", desc: desc }
+    end
+
+    def english_description
+      descriptions.select{|o| o[:lang] == "en"}.first[:desc]
+    end
+
+    def french_description=(desc)
+      descriptions.delete_if{|o| o[:lang] == "fr"}
+      descriptions << { lang: "fr", desc: desc }
+    end
+
+    def french_description
+      descriptions.select{|o| o[:lang] == "fr"}.first[:desc]
+    end
+
+    def to_hash
+      hash = {}
+      instance_variables.each { |var| hash[var.to_s.delete('@')] = instance_variable_get(var) }
+      hash
+    end
+  end
+end

data/lib/dina/casters/multilingual_description_caster.rb

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+require_relative 'multilingual_description'
+
+module Dina
+  class MultilingualDescriptionCaster
+    def self.cast(value, default)
+      begin
+        Dina::MultilingualDescription.new(value).to_hash
+      rescue ArgumentError
+        { descriptions: [] }
+      end
+    end
+  end
+end

data/lib/dina/casters/multilingual_title.rb

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+module Dina
+  class MultilingualTitle
+    attr_accessor :titles
+
+    def initialize(opts = {})
+      @titles = []
+      if opts[:titles]
+        @descriptions = opts[:titles]
+      end
+      if opts[:english]
+        self.english_title = opts[:english]
+      end
+      if opts[:french]
+        self.french_title = opts[:french]
+      end
+    end
+
+    def english_title=(title)
+      titles.delete_if{|o| o[:lang] == "en"}
+      titles << { lang: "en", title: desc }
+    end
+
+    def english_title
+      titles.select{|o| o[:lang] == "en"}.first[:title]
+    end
+
+    def french_title=(title)
+      titles.delete_if{|o| o[:lang] == "fr"}
+      titles << { lang: "fr", title: title }
+    end
+
+    def french_title
+      titles.select{|o| o[:lang] == "fr"}.first[:title]
+    end
+
+    def to_hash
+      hash = {}
+      instance_variables.each { |var| hash[var.to_s.delete('@')] = instance_variable_get(var) }
+      hash
+    end
+  end
+end

data/lib/dina/casters/multilingual_title_caster.rb

@@ -0,0 +1,13 @@
+require_relative 'multilingual_title'
+
+module Dina
+  class MultilingualTitleCaster
+    def self.cast(value, default)
+      begin
+        Dina::MultilingualTitle.new(value).to_hash
+      rescue ArgumentError
+        { titles: [] }
+      end
+    end
+  end
+end

data/lib/dina/casters/object_caster.rb

@@ -0,0 +1,11 @@
+module Dina
+  class ObjectCaster
+    def self.cast(value, default)
+      if value.is_a?(Hash)
+        value
+      else
+        default
+      end
+    end
+  end
+end

data/lib/dina/components/determination.rb

@@ -0,0 +1,31 @@
+module Dina
+  class Determination
+    attr_accessor :verbatimScientificName
+    attr_accessor :verbatimDeterminer
+    attr_accessor :verbatimDate
+    attr_accessor :scientificName
+    attr_accessor :transcriberRemarks
+    attr_accessor :verbatimRemarks
+    attr_accessor :determinationRemarks
+    attr_accessor :typeStatus
+    attr_accessor :typeStatusEvidence
+    attr_accessor :determiner #A known UUID for a Person
+    attr_accessor :determinedOn
+    attr_accessor :qualifier
+    attr_accessor :scientificNameSource
+    attr_accessor :scientificNameDetails #in the form { classificationPath: "", classificationRanks: "" }
+    attr_accessor :isPrimary
+    attr_accessor :isFiledAs
+    attr_accessor :managedAttributes
+
+    def initialize
+    end
+
+    def to_hash
+      hash = {}
+      instance_variables.each { |var| hash[var.to_s.delete('@')] = instance_variable_get(var) }
+      hash
+    end
+
+  end
+end

data/lib/dina/components/georeference_assertion.rb

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+module Dina
+  class GeoreferenceAssertion
+    attr_accessor :dwcDecimalLatitude
+    attr_accessor :dwcDecimalLongitude
+    attr_accessor :dwcCoordinateUncertaintyInMeters
+    attr_accessor :dwcGeoreferencedDate
+    attr_accessor :georeferencedBy
+    attr_accessor :literalGeoreferencedBy
+    attr_accessor :dwcGeoreferenceProtocol
+    attr_accessor :dwcGeoreferenceSources
+    attr_accessor :dwcGeoreferenceRemarks
+    attr_accessor :dwcGeodeticDatum #A known UUID for a Person
+    attr_accessor :isPrimary
+    attr_accessor :dwcGeoreferenceVerificationStatus
+
+    def initialize
+    end
+
+    def to_hash
+      hash = {}
+      instance_variables.each { |var| hash[var.to_s.delete('@')] = instance_variable_get(var) }
+      hash
+    end
+
+  end
+end

data/lib/dina/exceptions.rb

@@ -0,0 +1,4 @@
+module Dina
+  class DinaException < StandardError; end
+  class TokenStoreFileNotFound < DinaException; end
+end

data/lib/dina/models/acquisition_event.rb

@@ -0,0 +1,24 @@
+require_rel 'base_model'
+
+module Dina
+  class AcquisitionEvent < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+    property :receivedDate, type: :string
+    property :receptionRemarks, type: :string
+    property :isolatedOn, type: :string
+    property :isolationRemarks, type: :string
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    validates_presence_of :group
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "acquisition-event"
+    end
+  end
+end

data/lib/dina/models/assemblage.rb

@@ -0,0 +1,27 @@
+require_rel 'base_model'
+
+module Dina
+  class Assemblage < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+    property :name, type: :string
+    property :multilingualTitle, type: :multilingual_title
+    property :multilingualDescription, type: :multilingual_description
+    property :managedAttributes, type: :object
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    has_many :attachment, class_name: "ObjectStore"
+
+    validates_presence_of :group, :name
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "assemblage"
+    end
+
+  end
+end

data/lib/dina/models/attachment.rb

@@ -0,0 +1,19 @@
+require_rel 'base_model'
+
+module Dina
+  class Attachment < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+
+    belongs_to :material_sample, shallow_path: true
+    belongs_to :project, shallow_path: true
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "attachment"
+    end
+
+  end
+end

data/lib/dina/models/base_model.rb

@@ -0,0 +1,45 @@
+module Dina
+  class BaseModel < JsonApiClient::Resource
+    include JsonApiClient::Helpers::Callbacks
+
+    self.json_key_format = :camelized_key
+    self.paginator = JsonApiClient::Paginating::NestedParamPaginator
+
+    before_create :on_before_create
+
+    def self.endpoint_path
+    end
+
+    def self.site
+      Dina::Authentication.endpoint_url + endpoint_path
+    end
+
+    def self.custom_headers
+      { content_type: "application/vnd.api+json", authorization: Dina::Authentication.header }
+    end
+
+    def self.find_by_group(group, page: 1, per: 50)
+      self.where("group.groupName": group).page(page).per(per)
+    end
+
+    def english_description
+      if self.respond_to?(:multilingualDescription)
+        multilingualDescription[:descriptions].select{|o| o[:lang] == "en"}.first[:desc]
+      end
+    end
+
+    def french_description
+      if self.respond_to?(:multilingualDescription)
+        multilingualDescription[:descriptions].select{|o| o[:lang] == "fr"}.first[:desc]
+      end
+    end
+
+    private
+
+    def on_before_create
+      self.attributes.delete_if { |k, v| v.nil? || v == "" }
+      self.attributes = self.attributes.deep_symbolize_keys
+    end
+
+  end
+end

data/lib/dina/models/bucket.rb

@@ -0,0 +1,8 @@
+require_rel 'base_model'
+require_rel 'file'
+
+module Dina
+  class Bucket < File
+    property :id, type: :string, default: SecureRandom.uuid
+  end
+end

data/lib/dina/models/collecting_event.rb

@@ -0,0 +1,76 @@
+require_rel 'base_model'
+
+module Dina
+  class CollectingEvent < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+    property :version, type: :integer
+    property :dwcVerbatimCoordinates, type: :string
+    property :dwcRecordedBy, type: :string
+    property :startEventDateTime, type: :string
+    property :endEventDateTime, type: :string
+    property :verbatimEventDateTime, type: :string
+    property :dwcVerbatimLocality, type: :string
+    property :host, type: :string
+    property :dwcVerbatimLatitude, type: :string
+    property :dwcVerbatimLongitude, type: :string
+    property :dwcVerbatimCoordinateSystem, type: :string, default: "decimal degrees"
+    property :dwcVerbatimSRS, type: :string, default: "WGS84 (EPSG:4326)"
+    property :dwcVerbatimElevation, type: :string
+    property :dwcVerbatimDepth, type: :string
+    property :dwcOtherRecordNumbers, type: :array, default: []
+    property :dwcRecordNumber, type: :string
+    property :dwcCountry, type: :string
+    property :dwcCountryCode, type: :string
+    property :dwcStateProvince, type: :string
+    property :habitat, type: :string
+    property :dwcMinimumElevationInMeters, type: :float
+    property :dwcMinimumDepthInMeters, type: :float
+    property :dwcMaximumElevationInMeters, type: :float
+    property :dwcMaximumDepthInMeters, type: :float
+    property :substrate, type: :string
+    property :remarks, type: :string
+    property :publiclyReleasable, type: :boolean
+    property :notPubliclyReleasableReason, type: :string, default: nil
+    property :tags, type: :array, default: []
+    property :geographicPlaceNameSource, type: :string
+    property :geographicPlaceNameSourceDetail, type: :array, default: [{ sourceID: nil, sourceIdType: nil, sourceURL: nil }]
+    property :managedAttributes, type: :array, default: []
+    property :geoReferenceAssertions, type: :array, default: []
+    property :eventGeom, type: :string
+    property :extensionValues, type: :array, default: []
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    has_many :collectors, class_name: "Person"
+    has_many :attachment, class_name: "Attachment"
+
+    validates_presence_of :group
+
+    before_save :on_before_save
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "collecting-event"
+    end
+
+    private
+
+    def on_before_save
+      if self.dwcVerbatimLatitude.nil? && self.dwcVerbatimLongitude.nil?
+        self.dwcVerbatimCoordinateSystem = nil
+        self.dwcVerbatimSRS = nil
+      end
+      if self.geographicPlaceNameSource.nil?
+        self.geographicPlaceNameSourceDetail = nil
+      end
+      if !self.geoReferenceAssertions.empty? && self.geoReferenceAssertions[0][:dwcDecimalLatitude].nil?
+        self.geoReferenceAssertions = nil
+      end
+    end
+
+  end
+end

data/lib/dina/models/collecting_method.rb

@@ -0,0 +1,23 @@
+require_rel 'base_model'
+
+module Dina
+  class CollectingMethod < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+    property :name, type: :string
+    property :multilingualDescription, type: :multilingual_description
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    validates_presence_of :group
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "collection-method"
+    end
+
+  end
+end

data/lib/dina/models/collection.rb

@@ -0,0 +1,40 @@
+require_rel 'base_model'
+
+module Dina
+  class Collection < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+    property :name, type: :string
+    property :code, type: :string
+    property :multilingualDescription, type: :multilingual_description
+    property :webpage, type: :string
+    property :contact, type: :string
+    property :address, type: :string
+    property :remarks, type: :string
+    property :identifiers, type: :array, default: []
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    has_one :institution, class_name: "Institution"
+    has_one :parent_collection, class_name: "Collection"
+
+    validates_presence_of :group
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "collection"
+    end
+
+    def self.find_by_name(name)
+      where(name: name).all.first
+    end
+
+    def self.find_by_code(code)
+      where(code: code).all.first
+    end
+
+  end
+end

data/lib/dina/models/derivative.rb

@@ -0,0 +1,26 @@
+require_rel 'base_model'
+
+module Dina
+  class Derivative < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :bucket, type: :string
+    property :fileIdentifier, type: :string
+    property :fileExtension, type: :string
+    property :dcType, type: :string
+    property :cdFormat, type: :string
+    property :acHashFunction, type: :string, default: "SHA-1"
+    property :acHashValue, type: :string
+    property :derivativeType, type: :string
+
+    belongs_to :object_store, shallow_path: true
+
+    def self.endpoint_path
+      "objectstore-api/"
+    end
+
+    def self.table_name
+      "derivative"
+    end
+
+  end
+end

data/lib/dina/models/file.rb

@@ -0,0 +1,40 @@
+require_rel 'base_model'
+
+module Dina
+  class File < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+
+    def self.endpoint_path
+      "objectstore-api/"
+    end
+
+    def self.table_name
+      "file"
+    end
+
+    #TODO: a "bucket" as part of the path (=table_name) to permit POST with necessary permissions
+    #TODO: body not JSON but an asset
+
+=begin
+
+    def initialize(bucket:, file:)
+      if !file.is_a?(::File) || !::File.exist?(file)
+        raise Exception.new "file is not of class File or does not exist"
+      end
+      super
+      set_headers
+    end
+
+    private
+
+    def set_headers
+      headers = {
+        content_type: "application/octet-stream",
+        content_disposition: "form-data; name=file; filename=#{::File.basename(file.path)}"
+      }
+      self.custom_headers.merge(headers)
+    end
+=end
+
+  end
+end