dina 0.1.0.0

data/lib/dina/models/identifier.rb

@@ -0,0 +1,67 @@
+require_rel 'base_model'
+
+module Dina
+  class Identifier < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :namespace, type: :string
+    property :value, type: :string
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    def self.endpoint_path
+      "agent-api/"
+    end
+
+    def self.table_name
+      "identifier"
+    end
+
+=begin
+    TODO: fix because identifier has independent model now
+
+    def self.find_by_orcid(orcid)
+      if orcid.include? "http"
+        orcid = orcid.orcid_from_url
+      end
+      if orcid.is_orcid?
+        orcid = "https://orcid.org/#{orcid}"
+        where("identifiers.uri": orcid).all.first
+      else
+        nil
+      end
+    end
+
+    def self.find_by_wikidata(wikidata)
+      if wikidata.include? "http"
+        wikidata = wikidata.wiki_from_url
+      end
+      if wikidata.is_wiki_id?
+        wikidata = "http://www.wikidata.org/entity/#{wikidata}"
+        where("identifiers.uri": wikidata).all.first
+      else
+        nil
+      end
+      where("identifiers.uri": wikidata).all.first
+    end
+
+    def orcid
+      identifiers.select{|o| o[:type] == "ORCID"}.first[:uri]
+    end
+
+    def orcid=(uri)
+      identifiers.delete_if{|o| o[:type] == "ORCID"}
+      identifiers << { type: "ORCID", uri: uri }
+    end
+
+    def wikidata
+      identifiers.select{|o| o[:type] == "WIKIDATA"}.first[:uri]
+    end
+
+    def wikidata=(id)
+      identifiers.delete_if{|o| o[:type] == "WIKIDATA"}
+      identifiers << { type: "WIKIDATA", uri: uri }
+    end
+=end
+
+  end
+end

data/lib/dina/models/institution.rb

@@ -0,0 +1,25 @@
+require_rel 'base_model'
+
+module Dina
+  class Institution < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :name, type: :string
+    property :multilingualDescription, type: :multilingual_description
+    property :webpage, type: :string
+    property :address, type: :string
+    property :remarks, type: :string
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    has_many :collections, class_name: "Collection"
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "institution"
+    end
+
+  end
+end

data/lib/dina/models/managed_attribute.rb

@@ -0,0 +1,43 @@
+require_rel 'base_model'
+
+module Dina
+  class ManagedAttribute < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+    property :name, type: :string
+    property :key, type: :string
+    property :managedAttributeType, type: :string #values = STRING or INTEGER
+    property :managedAttributeComponent, type: :string #values = COLLECTING_EVENT, MATERIAL_SAMPLE, or DETERMINATION
+    property :acceptedValues, type: :array
+    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
+      "managed-attribute"
+    end
+
+    def english_description=(desc)
+      description[:en] = desc
+    end
+
+    def english_description
+      description[:en]
+    end
+
+    def french_description=(desc)
+      description[:fr] = desc
+    end
+
+    def french_description
+      description[:fr]
+    end
+
+  end
+end

data/lib/dina/models/material_sample.rb

@@ -0,0 +1,62 @@
+require_rel 'base_model'
+
+module Dina
+  class MaterialSample < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :dwcCatalogNumber, type: :string
+    property :materialSampleName, type: :string
+    property :materialSampleType, type: :string
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+    property :barcode, type: :string
+    property :group, type: :string
+    property :managedAttributes, type: :object
+    property :dwcOtherCatalogNumbers, type: :array
+    property :preparationMethod, type: :string
+    property :preservationType, type: :string
+    property :preparationFixative, type: :string
+    property :preparationMaterials, type: :string
+    property :preparationSubstrate, type: :string
+    property :preparationDate, type: :time
+    property :preparationRemarks, type: :string
+    property :dwcDegreeOfEstablishment, type: :string
+    property :materialSampleState, type: :string
+    property :stateChangedOn, type: :time
+    property :stateChangeRemarks, type: :string
+    property :materialSampleRemarks, type: :string
+    property :materialSampleChildren, type: :array
+    property :associations, type: :array, default: []
+    property :tags, type: :array, default: []
+    property :publiclyReleasable, type: :boolean
+    property :notPubliclyReleasableReason, type: :string
+    property :hostOrganism, type: :object, default: { name: nil, remarks: nil }
+    property :scheduledActions, type: :object
+    property :hierarchy, type: :object
+    property :allowDuplicateName, type: :boolean
+
+    has_one :collection
+    has_one :parent_material_sample, class_name: "MaterialSample"
+    has_one :collecting_event, class_name: "CollectingEvent"
+    has_one :preparation_type
+    has_one :prepared_by, class_name: "Person"
+    has_one :storage_unit
+    has_one :acquisition_event
+
+    has_many :assemblages, class_name: "Assemblage"
+    has_many :projects, class_name: "Project"
+    has_many :attachment, class_name: "Attachment" #TODO: error requesting Dina::MaterialSample::Metadatum
+    has_many :preparation_attachment, class_name: "Attachment" #TODO: error requesting Dina::MaterialSample::Metadatum
+    has_many :organism, class_name: "Organism"
+
+    validates_presence_of :group, :materialSampleName
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "material-sample"
+    end
+
+  end
+end

data/lib/dina/models/object_store.rb

@@ -0,0 +1,50 @@
+require_rel 'base_model'
+
+module Dina
+  class ObjectStore < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+    property :dcType, type: :string
+    property :originalFilename, type: :string
+    property :bucket, type: :string
+    property :dateTimeDigitized, type: :string
+    property :fileIdentifier, type: :string
+    property :fileExtension, type: :string
+    property :dcFormat, type: :string
+    property :dcType, type: :string
+    property :acDigitizationDate, type: :time
+    property :acCaption, type: :string
+    property :xmpMetadataDate, type: :time
+    property :xmpRightsWebStatement, type: :string, default: "https://open.canada.ca/en/open-government-licence-canada"
+    property :dcRights, type: :string, default: "© Her Majesty The Queen in Right of Canada, as represented by the Minister of Agriculture and Agri-Food | © Sa Majesté la Reine du chef du Canada, représentée par le ministre de l’Agriculture et de l’Agroalimentaire"
+    property :xmpRightsOwner, type: :string, default: "Government of Canada"
+    property :xmpRightsUsageTerms, type: :string, default: "Government of Canada Usage Term"
+    property :orientation, type: :integer
+    property :originalFilename, type: :string
+    property :acHashFunction, type: :string, default: "SHA-1"
+    property :acHashValue, type: :string
+    property :acSubtype, type: :string
+    property :publiclyReleasable, type: :boolean, default: true
+    property :notPubliclyReleasableReason, type: :string
+    property :acTags, type: :string
+    property :resourceExternalURL, type: :string
+    property :managedAttributes, type: :object
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    has_one :ac_metadata_creator, class_name: "Person"
+    has_one :dc_creator, class_name: "Person"
+    has_many :derivatives, class_name: "Derivative"
+
+    validates_presence_of :group
+
+    def self.endpoint_path
+      "objectstore-api/"
+    end
+
+    def self.table_name
+      "metadata"
+    end
+
+  end
+end

data/lib/dina/models/object_store_managed_attribute.rb

@@ -0,0 +1,39 @@
+require_rel 'base_model'
+
+module Dina
+  class ObjectStoreManagedAttribute < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :name, type: :string
+    property :key, type: :string
+    property :managedAttributeType, type: :string
+    property :acceptedValues, type: :array
+    property :multilingualDescription, type: :multilingual_description
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    def self.endpoint_path
+      "objectstore-api/"
+    end
+
+    def self.table_name
+      "managed-attribute"
+    end
+
+    def english_description=(desc)
+      description[:en] = desc
+    end
+
+    def english_description
+      description[:en]
+    end
+
+    def french_description=(desc)
+      description[:fr] = desc
+    end
+
+    def french_description
+      description[:fr]
+    end
+
+  end
+end

data/lib/dina/models/object_subtype.rb

@@ -0,0 +1,15 @@
+require_rel 'base_model'
+
+module Dina
+  class ObjectSubtype < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+
+    def self.endpoint_path
+      "objectstore-api/"
+    end
+
+    def self.table_name
+      "object-subtype"
+    end
+  end
+end

data/lib/dina/models/organism.rb

@@ -0,0 +1,26 @@
+require_rel 'base_model'
+
+module Dina
+  class Organism < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+    property :lifeStage, type: :string
+    property :sex, type: :string
+    property :remarks, type: :string
+    property :isTarget, type: :boolean
+    property :determination, type: :array, default: []
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    validates_presence_of :group
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "organism"
+    end
+
+  end
+end

data/lib/dina/models/organization.rb

@@ -0,0 +1,42 @@
+require_rel 'base_model'
+
+module Dina
+  class Organization < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    #NOTE: should be type: :multilingual_description but API not adjusted
+    property :names, type: :array, default: [{languageCode: "EN", name: nil}, {languageCode: "FR", name: nil}]
+    property :aliases, type: :array, default: []
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    validates :english_name, presence: true, on: :create
+    validates :french_name, presence: true, on: :create
+
+    def self.endpoint_path
+      "agent-api/"
+    end
+
+    def self.table_name
+      "organization"
+    end
+
+    def english_name=(name)
+      names.delete_if{|o| o[:languageCode] == "EN"}
+      names << { languageCode: "EN", name: name }
+    end
+
+    def english_name
+      names.select{|o| o[:languageCode] == "EN"}.first[:name]
+    end
+
+    def french_name=(name)
+      names.delete_if{|o| o[:languageCode] == "FR"}
+      names << { languageCode: "FR", name: name }
+    end
+
+    def french_name
+      names.select{|o| o[:languageCode] == "FR"}.first[:name]
+    end
+
+  end
+end

data/lib/dina/models/person.rb

@@ -0,0 +1,43 @@
+require_rel 'base_model'
+
+module Dina
+  class Person < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :displayName, type: :string, default: nil
+    property :givenNames, type: :string
+    property :familyNames, type: :string
+    property :email, type: :string
+    property :webpage, type: :string
+    property :remarks, type: :string
+    property :aliases, type: :array, default: []
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    has_many :organizations
+    has_many :identifiers
+
+    validates_presence_of :familyNames
+
+    def self.endpoint_path
+      "agent-api/"
+    end
+
+    def self.table_name
+      "person"
+    end
+
+    def self.find_by_email(email)
+      where("email": email).all.first
+    end
+
+    private
+
+    def set_defaults
+      if self.displayName.nil? || self.displayName == ""
+        self.displayName = [familyNames, givenNames].compact.join(", ")
+      end
+      super
+    end
+
+  end
+end

data/lib/dina/models/preparation_type.rb

@@ -0,0 +1,23 @@
+require_rel 'base_model'
+
+module Dina
+  class PreparationType < 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
+      "preparation-type"
+    end
+
+  end
+end

data/lib/dina/models/project.rb

@@ -0,0 +1,28 @@
+require_rel 'base_model'
+
+module Dina
+  class Project < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+    property :name, type: :string
+    property :multilingualDescription, type: :multilingual_description
+    property :startDate, type: :string
+    property :endDate, type: :string
+    property :status, type: :string
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    has_many :attachment, class_name: "ObjectStore"
+
+    validates_presence_of :group
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "project"
+    end
+
+  end
+end

data/lib/dina/models/protocol.rb

@@ -0,0 +1,25 @@
+require_rel 'base_model'
+
+module Dina
+  class Protocol < 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
+
+    has_many :attachment, class_name: "ObjectStore"
+
+    validates_presence_of :group
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "protocol"
+    end
+
+  end
+end

data/lib/dina/models/storage_unit.rb

@@ -0,0 +1,26 @@
+require_rel 'base_model'
+
+module Dina
+  class StorageUnit < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+    property :name, type: :string
+    property :storageUnitChildren, type: :array
+    property :hierarchy, type: :string
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    has_one :storage_unit_type
+    has_one :parent_storage_unit, class_name: "StorageUnit"
+
+    validates_presence_of :group
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "storage-unit"
+    end
+  end
+end

data/lib/dina/models/storage_unit_type.rb

@@ -0,0 +1,22 @@
+require_rel 'base_model'
+
+module Dina
+  class StorageUnitType < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+    property :name, type: :string
+    property :isInseperable, type: :boolean
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    validates_presence_of :group
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "storage-unit-type"
+    end
+  end
+end

data/lib/dina/models/user.rb

@@ -0,0 +1,26 @@
+require_rel 'base_model'
+
+module Dina
+  class User < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :username, type: :string
+    property :firstName, type: :string
+    property :lastName, type: :string
+    property :agentId, type: :string
+    property :emailAddress, type: :string
+    property :rolesPerGroup, type: :object
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    validates_presence_of :username
+
+    def self.endpoint_path
+      "user-api/"
+    end
+
+    def self.table_name
+      "user"
+    end
+
+  end
+end

data/lib/dina/search/base_search.rb

@@ -0,0 +1,32 @@
+module Dina
+  class BaseSearch
+
+    def self.endpoint
+      Settings.server.endpoint
+    end
+
+    def self.endpoint_path
+      "search-api/search-ws/"
+    end
+
+    def self.index_name(index:)
+      return nil if !index
+      "dina_#{index}_index"
+    end
+
+    def self.execute(params, method: :get, payload: {})
+      begin
+        response = RestClient::Request.execute(
+            method: method,
+            url: endpoint + endpoint_path + "?" + params.to_query,
+            payload: payload.to_json,
+            headers: { accept: 'application/json', content_type: 'application/json' }
+          )
+        JSON.parse(response, symbolize_names: true)
+      rescue RestClient::ExceptionWithResponse => e
+        e.response
+      end
+    end
+
+  end
+end

data/lib/dina/search/search.rb

@@ -0,0 +1,20 @@
+require_rel 'base_search'
+
+module Dina
+  class Search < BaseSearch
+
+    def self.endpoint_path
+      "search-api/search-ws/search"
+    end
+
+    # index values: "agent", "material_sample", "object_store"
+    # payload is a hash in the form of an Elasticsearch body
+    def self.execute(index:, payload: { query: { match_all: {} } })
+      params = {
+        indexName: index_name(index: index)
+      }
+      super(params.compact, method: :post, payload: payload)[:hits]
+    end
+
+  end
+end

data/lib/dina/search/search_autocomplete.rb

@@ -0,0 +1,26 @@
+require_rel 'base_search'
+
+module Dina
+  class SearchAutocomplete < BaseSearch
+
+    def self.endpoint_path
+      "search-api/search-ws/auto-complete"
+    end
+
+    # index values: "agent", "material_sample", "object_store"
+    # known autocomplete fields:
+    #   agent: data.attributes.displayName
+    #   material_sample: included.attributes.dwcRecordedBy, included.attributes.verbatimDeterminer
+    #   object_store: none
+    def self.execute(term:, index:, field: nil, group: nil)
+      params = {
+        prefix: term,
+        indexName: index_name(index: index),
+        autoCompleteField: field,
+        group: group
+      }
+      super(params.compact)[:hits]
+    end
+
+  end
+end

data/lib/dina/search/search_count.rb

@@ -0,0 +1,20 @@
+require_rel 'base_search'
+
+module Dina
+  class SearchCount < BaseSearch
+
+    def self.endpoint_path
+      "search-api/search-ws/count"
+    end
+
+    # index values: "agent", "material_sample", "object_store"
+    # Payload is a has like: {query: {bool: {filter: {term: {"data.attributes.group": "dao"}}}}}
+    def self.execute(index:, payload: {})
+      params = {
+        indexName: index_name(index: index)
+      }
+      super(params.compact, method: :post, payload: payload)[:count]
+    end
+
+  end
+end