dina 0.2.0.0 → 0.4.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ac8691de71d4edf3e8c55134a2eab3907db3330ab74e40d12779c960178d5d23
-  data.tar.gz: b3f6cb667ce6d648ff804ebec0d172b98801b877d38145d5e819e98f7e489f7d
+  metadata.gz: 4cae0ee74ed1a0967bb360af211c2ab37676dfdb39b54a377ec39b539e0f4301
+  data.tar.gz: 45ee9d1cda7f37da9fb5384690751dac5e5cc0fe30153cddf8306e11a20f7151
 SHA512:
-  metadata.gz: e9ba7de4e15555f92494770785e1ac42f97cea709a0542dfedce95fe19227536c36ef6bf5ee8cf009728c75ea4268a685f7bab88948ca277477c179ecfeb639b
-  data.tar.gz: 75d2b0e52d5399cca2ab1b9785338d5a3f51b58aa1d82452eb103e6bbecce9b4642aab3e1c309a9a1625587edecfd4a380715ed454a72bb53497e8d0737393ae
+  metadata.gz: 60a62ece7262ab086b88002497bd55f1ea04059b94468134b7c93d35a3349deff0c3ed58c45f634dd07a3149e4895da1525c215aef1895258beb62cf5af0aba5
+  data.tar.gz: dba63bace34688530c56cb56af702af39fe36bcb7ba86bf664b1192a7186ca51207ef9cef2deed311993671127772deb4f149f99fd90619ad56408dc379882a7

data/lib/dina/authentication/authentication.rb

@@ -81,11 +81,11 @@ module Dina
       end
 
       def access_token
-        read_token[:access_token] rescue nil
+        read_token[:access_token]
       end
 
       def refresh_token
-        read_token[:refresh_token] rescue nil
+        read_token[:refresh_token]
       end
 
       def auth_expiry

data/lib/dina/casters/array_caster.rb

@@ -1,4 +1,3 @@
-
 module Dina
   class ArrayCaster
     def self.cast(value, default)

data/lib/dina/exceptions.rb

@@ -2,4 +2,5 @@ module Dina
   class DinaException < StandardError; end
   class TokenStoreFileNotFound < DinaException; end
   class ObjectInvalid < DinaException; end
+  class PropertyValueInvalid < ObjectInvalid; end
 end

data/lib/dina/models/assemblage.rb

@@ -11,7 +11,7 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
-    has_many :attachment, class_name: "ObjectStore"
+    has_many :attachment, class_name: "Attachment"
 
     validates_presence_of :group, message: "group is required"
     validates_presence_of :name, message: "name is required"

data/lib/dina/models/attachment.rb

@@ -4,8 +4,10 @@ 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
+    belongs_to :material_sample, shallow_path: true, class_name: "MaterialSample"
+    belongs_to :collecting_event, shallow_path: true, class_name: "CollectingEvent"
+    belongs_to :project, shallow_path: true, class_name: "Project"
+    belongs_to :transaction, shallow_path: true, class_name: "Transaction"
 
     def self.endpoint_path
       "collection-api/"

data/lib/dina/models/collection.rb

@@ -15,7 +15,7 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
-    has_one :institution, class_name: "Institution"
+    belongs_to :institution, shallow_path: true, class_name: "Institution"
     has_one :parent_collection, class_name: "Collection"
 
     validates_presence_of :group, message: "group is required"

data/lib/dina/models/derivative.rb

@@ -3,16 +3,19 @@ require_rel 'base_model'
 module Dina
   class Derivative < BaseModel
     property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
     property :bucket, type: :string
     property :fileIdentifier, type: :string
     property :fileExtension, type: :string
     property :dcType, type: :string
-    property :cdFormat, type: :string
+    property :dcFormat, type: :string
     property :acHashFunction, type: :string, default: "SHA-1"
     property :acHashValue, type: :string
     property :derivativeType, type: :string
 
-    belongs_to :object_store, shallow_path: true
+    belongs_to :ac_derived_from, shallow_path: true, class_name: "ObjectStore"
+
+    validates_presence_of :group, message: "group is required"
 
     def self.endpoint_path
       "objectstore-api/"
@@ -22,5 +25,14 @@ module Dina
       "derivative"
     end
 
+    private
+
+    def on_before_save
+      if self.bucket.nil?
+        self.bucket = self.group
+      end
+      super
+    end
+
   end
 end

data/lib/dina/models/file.rb

@@ -1,40 +1,62 @@
-require_rel 'base_model'
-
 module Dina
-  class File < BaseModel
-    property :id, type: :string, default: SecureRandom.uuid
+  class File
+    attr_accessor :file_path, :group, :is_derivative, :id
+
+    def self.find(group:, id:)
+      obj = self.new
+      obj.group = group
+      RestClient::Request.execute(
+        method: :get,
+        headers: { authorization: Dina::Authentication.header },
+        url: obj.url + "/#{id}"
+      )
+    end
 
-    def self.endpoint_path
+    def initialize
+    end
+
+    def endpoint_path
       "objectstore-api/"
     end
 
-    def self.table_name
-      "file"
+    def table_name
+      "file/#{@group}"
     end
 
-    #TODO: a "bucket" as part of the path (=table_name) to permit POST with necessary permissions
-    #TODO: body not JSON but an asset
+    def url
+      Dina::Authentication.endpoint_url + endpoint_path + table_name
+    end
 
-=begin
+    def file
+      ::File.new(file_path)
+    end
 
-    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
+    def save
+      validate_params
+      response = RestClient::Request.execute(
+        method: :post,
+        headers: { authorization: Dina::Authentication.header },
+        url: (!is_derivative) ? url : url + "/derivative",
+        payload: {
+          multipart: true,
+          file: file
+        }
+      )
+      json = JSON.parse(response, symbolize_names: true)
+      self.id = json[:uuid]
+      json
     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)
+    def validate_params
+      if group.nil?
+        raise ObjectInvalid, "#{self.class} is invalid. group is required."
+      end
+      if file_path.nil? || !::File.exist?(file_path)
+        raise ObjectInvalid, "#{self.class} is invalid. file not found in file_path."
+      end
     end
-=end
 
   end
 end

data/lib/dina/models/identifier.rb

@@ -16,52 +16,5 @@ module Dina
       "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/managed_attribute.rb

@@ -6,14 +6,18 @@ module Dina
     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 :managedAttributeType, type: :string
+    property :managedAttributeComponent, type: :string
     property :acceptedValues, type: :array
     property :multilingualDescription, type: :multilingual_description
     property :createdBy, type: :string
     property :createdOn, type: :time
 
     validates_presence_of :group, message: "group is required"
+    validates_presence_of :name, message: "name is required"
+    validates_presence_of :managedAttributeType, message: "managedAttributeType is required"
+
+    attr_accessor :accepted_components, :accepted_types
 
     def self.endpoint_path
       "collection-api/"
@@ -23,6 +27,25 @@ module Dina
       "managed-attribute"
     end
 
+    def self.accepted_components
+      [
+        "COLLECTING_EVENT",
+        "MATERIAL_SAMPLE",
+        "DETERMINATION",
+        "ASSEMBLAGE"
+      ]
+    end
+
+    def self.accepted_types
+      [
+        "INTEGER",
+        "STRING",
+        "PICKLIST",
+        "DATE",
+        "BOOL"
+      ]
+    end
+
     def english_description=(desc)
       description[:en] = desc
     end
@@ -39,5 +62,17 @@ module Dina
       description[:fr]
     end
 
+    private
+
+    def on_before_save
+      if !self.managedAttributeComponent.nil? && !self.class.accepted_components.include?(self.managedAttributeComponent)
+        raise PropertyValueInvalid, "#{self.class} is invalid. Accepted value for managedAttributeComponent is one of #{self.class.accepted_components.join(", ")}"
+      end
+      if !self.managedAttributeType.nil? && !self.class.accepted_types.include?(self.managedAttributeType)
+        raise PropertyValueInvalid, "#{self.class} is invalid. Accepted value for managedAttributeType is one of #{self.class.accepted_types.join(", ")}"
+      end
+      super
+    end
+
   end
 end

data/lib/dina/models/material_sample.rb

@@ -12,7 +12,6 @@ module Dina
     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
@@ -24,6 +23,9 @@ module Dina
     property :stateChangedOn, type: :time
     property :stateChangeRemarks, type: :string
     property :materialSampleRemarks, type: :string
+    property :restrictionFieldsExtension, type: :array
+    property :restrictionRemarks, type: :string
+    property :isRestricted, type: :boolean
     property :materialSampleChildren, type: :array
     property :associations, type: :array, default: []
     property :tags, type: :array, default: []
@@ -34,22 +36,25 @@ module Dina
     property :hierarchy, type: :object
     property :allowDuplicateName, type: :boolean
 
-    has_one :collection
-    has_one :parent_material_sample, class_name: "MaterialSample"
+    has_one :collection, class_name: "Collection"
     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_one :preparation_type, class_name: "PreparationType"
+    has_one :preparation_method, class_name: "PreparationMethod"
+    has_one :parent_material_sample, class_name: "MaterialSample"
+    has_one :preparation_protocol, class_name: "Protocol"
+    has_one :acquisition_event, class_name: "AcquisitionEvent"
+    has_one :storage_unit, class_name: "StorageUnit"
+    has_many :prepared_by, class_name: "Person"
+    has_many :attachment, class_name: "Attachment"
     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 :assemblages, class_name: "Assemblage"
     has_many :organism, class_name: "Organism"
 
     validates_presence_of :group, message: "group is required"
     validates_presence_of :materialSampleName, message: "materialSampleName is required"
+    validates_presence_of :materialSampleType, message: "materialSampleType is required"
+
+    attr_accessor :accepted_types
 
     def self.endpoint_path
       "collection-api/"
@@ -59,5 +64,23 @@ module Dina
       "material-sample"
     end
 
+    def self.accepted_types
+      [
+        "WHOLE_ORGANISM",
+        "ORGANISM_PART",
+        "MIXED_ORGANISMS",
+        "MOLECULAR_SAMPLE"
+      ]
+    end
+
+    private
+
+    def on_before_save
+      if !self.materialSampleType.nil? && !self.class.accepted_types.include?(self.materialSampleType)
+        raise PropertyValueInvalid, "#{self.class} is invalid. Accepted value for materialSampleType is one of #{self.class.accepted_types.join(", ")}"
+      end
+      super
+    end
+
   end
 end

data/lib/dina/models/object_store.rb

@@ -3,34 +3,31 @@ require_rel 'base_model'
 module Dina
   class ObjectStore < BaseModel
     property :id, type: :string, default: SecureRandom.uuid
+    property :createdBy, type: :string
+    property :createdOn, type: :time
     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 :acSubtype, type: :string
+    property :fileIdentifier, type: :string
+    property :bucket, type: :string
     property :acCaption, type: :string
+    property :acDigitizationDate, type: :time
     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 :fileExtension, type: :string
     property :acHashFunction, type: :string, default: "SHA-1"
     property :acHashValue, type: :string
-    property :acSubtype, type: :string
+    property :xmpRightsUsageTerms, type: :string, default: "Government of Canada Usage Term"
+    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 :publiclyReleasable, type: :boolean, default: true
     property :notPubliclyReleasableReason, type: :string
+    property :managedAttributes, type: :object
     property :acTags, type: :string
+    property :orientation, type: :integer
     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"
@@ -38,6 +35,8 @@ module Dina
 
     validates_presence_of :group, message: "group is required"
 
+    attr_accessor :accepted_types
+
     def self.endpoint_path
       "objectstore-api/"
     end
@@ -46,5 +45,25 @@ module Dina
       "metadata"
     end
 
+    def self.accepted_types
+      [
+        "IMAGE",
+        "MOVING_IMAGE",
+        "SOUND",
+        "TEXT",
+        "DATASET",
+        "UNDETERMINED"
+      ]
+    end
+
+    private
+
+    def on_before_save
+      if !self.dcType.nil? && !self.class.accepted_types.include?(self.dcType)
+        raise PropertyValueInvalid, "#{self.class} is invalid. Accepted value for dcType is one of #{self.class.accepted_types.join(", ")}"
+      end
+      super
+    end
+
   end
 end

data/lib/dina/models/object_store_managed_attribute.rb

@@ -19,20 +19,13 @@ module Dina
       "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
+    private
 
-    def french_description
-      description[:fr]
+    def on_before_save
+      if !self.managedAttributeType.nil? && !ManagedAttribute.accepted_types.include?(self.managedAttributeType)
+        raise PropertyValueInvalid, "#{self.class} is invalid. Accepted value for managedAttributeType is one of #{ManagedAttribute.accepted_types.join(", ")}"
+      end
+      super
     end
 
   end

data/lib/dina/models/object_subtype.rb

@@ -3,6 +3,10 @@ require_rel 'base_model'
 module Dina
   class ObjectSubtype < BaseModel
     property :id, type: :string, default: SecureRandom.uuid
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+    property :dcType, type: :string
+    property :acSubtype, type: :string
 
     def self.endpoint_path
       "objectstore-api/"
@@ -11,5 +15,15 @@ module Dina
     def self.table_name
       "object-subtype"
     end
+
+    private
+
+    def on_before_save
+      if !self.dcType.nil? && !ObjectStore.accepted_types.include?(self.dcType)
+        raise PropertyValueInvalid, "#{self.class} is invalid. Accepted value for dcType is one of #{ObjectStore.accepted_types.join(", ")}"
+      end
+      super
+    end
+
   end
 end

data/lib/dina/models/organization.rb

@@ -3,7 +3,6 @@ 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

data/lib/dina/models/person.rb

@@ -13,8 +13,8 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
-    has_many :organizations
-    has_many :identifiers
+    has_many :organizations, class_name: "Organization"
+    has_many :identifiers, class_name: "Identifier"
 
     validates_presence_of :familyNames, message: "familyNames is required"
     validates_presence_of :displayName
@@ -30,9 +30,9 @@ module Dina
     # Finds a Person object using an email address
     #
     # @param email [String] an email address
-    # @return Person [Object] a Person object
+    # @return array [Array] an array of Person objects
     def self.find_by_email(email)
-      where("email": email).all.first
+      where("email": email).all
     end
 
     private

data/lib/dina/models/preparation_method.rb

@@ -0,0 +1,23 @@
+require_rel 'base_model'
+
+module Dina
+  class PreparationMethod < 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, message: "group is required"
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "preparation-method"
+    end
+
+  end
+end

data/lib/dina/models/project.rb

@@ -12,7 +12,7 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
-    has_many :attachment, class_name: "ObjectStore"
+    has_many :attachment, class_name: "Attachment"
 
     validates_presence_of :group, message: "group is required"
 

data/lib/dina/models/protocol.rb

@@ -9,7 +9,7 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
-    has_many :attachment, class_name: "ObjectStore"
+    has_many :attachment, class_name: "Attachment"
 
     validates_presence_of :group, message: "group is required"
 

data/lib/dina/models/storage_unit_type.rb

@@ -6,6 +6,7 @@ module Dina
     property :group, type: :string
     property :name, type: :string
     property :isInseperable, type: :boolean
+    property :gridLayoutDefinition, type: :object
     property :createdBy, type: :string
     property :createdOn, type: :time
 

data/lib/dina/models/transaction.rb

@@ -22,11 +22,13 @@ module Dina
     property :createdOn, type: :time
 
     has_many :material_samples, class_name: "MaterialSample"
-    has_many :attachment
+    has_many :attachment, class_name: "Attachment"
     has_many :involved_agents, class_name: "Person"
 
     validates_presence_of :group, message: "group is required"
 
+    attr_accessor :accepted_directions
+
     def self.endpoint_path
       "loan-transaction/"
     end
@@ -35,5 +37,21 @@ module Dina
       "transaction"
     end
 
+    def self.accepted_directions
+      [
+        "IN",
+        "OUT"
+      ]
+    end
+
+    private
+
+    def on_before_save
+      if !self.materialDirection.nil? && !self.class.accepted_directions.include?(self.materialDirection)
+        raise PropertyValueInvalid, "#{self.class} is invalid. Accepted value for materialDirection is one of #{self.class.accepted_directions.join(", ")}"
+      end
+      super
+    end
+
   end
 end

data/lib/dina/version.rb

@@ -2,7 +2,7 @@ module Dina
   class Version
 
     MAJOR = 0
-    MINOR = 2
+    MINOR = 4
     PATCH = 0
     BUILD = 0
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: dina
 version: !ruby/object:Gem::Version
-  version: 0.2.0.0
+  version: 0.4.0.0
 platform: ruby
 authors:
 - David P. Shorthouse
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-11-28 00:00:00.000000000 Z
+date: 2022-11-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_api_client
@@ -145,7 +145,6 @@ files:
 - lib/dina/models/assemblage.rb
 - lib/dina/models/attachment.rb
 - lib/dina/models/base_model.rb
-- lib/dina/models/bucket.rb
 - lib/dina/models/collecting_event.rb
 - lib/dina/models/collecting_method.rb
 - lib/dina/models/collection.rb
@@ -162,6 +161,7 @@ files:
 - lib/dina/models/organism.rb
 - lib/dina/models/organization.rb
 - lib/dina/models/person.rb
+- lib/dina/models/preparation_method.rb
 - lib/dina/models/preparation_type.rb
 - lib/dina/models/project.rb
 - lib/dina/models/protocol.rb

data/lib/dina/models/bucket.rb

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