dina 2.3.0.0 → 3.1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9ea5252ef054c209ba20f6838bb83a9ca4bd0316e4e6a6cf3f80b6376ebb584e
-  data.tar.gz: 1ee32a455976e479d30cc56fbdf87f570769cff606556ed18ade6d6bc896e277
+  metadata.gz: 5b5df9be26541369dc33ef722b3e1c3683bc1fc981585f15a5915dfe65d7621b
+  data.tar.gz: 292638ee427d55bfecd10af5a67f60cbba64ebabc3594438b803a54ab295261d
 SHA512:
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-  data.tar.gz: f21cd32cbcaad5ffca5ec8ae82cb63be9f6deba75eceddf2be5081b4c7132b0d7e5cb85ed74f4cc218121f86bc4d5137f9c98a1cdd30042831ec2d5da29faa1b
+  metadata.gz: 9b3dcde98ba46f4abd3ffb66750c9c7d90856da5b5f81d4d766bcac4e8028aa6287d4599ae0e3df9d3d7fa4c8edf647748cde129294476de46b96bb84f91c0fb
+  data.tar.gz: cd6f4bd3867f55ca17c7b8eed0d9024896d26ce3656e5c7b3a2d16f60fa635455469b1a7346756603bd524e7695230f3dc66a28755edfd03322f3dfb3eb3ab54

data/lib/dina/models/agent/identifier.rb

@@ -8,7 +8,7 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
-    belongs_to :person, shallow_path: true, class_name: "Person"
+    belongs_to :person, class_name: "Person", shallow_path: true
 
     validates_presence_of :namespace, message: "namespace is required"
     validates_presence_of :value, message: "value is required"

data/lib/dina/models/agent/organization.rb

@@ -8,8 +8,8 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
-    validates :english_name, presence: true, on: :create
-    validates :french_name, presence: true, on: :create
+    validates :englishName, presence: true, on: :create
+    validates :frenchName, presence: true, on: :create
 
     def self.endpoint_path
       "agent-api/"
@@ -19,21 +19,21 @@ module Dina
       "organization"
     end
 
-    def english_name=(name)
+    def englishName=(name)
       names.delete_if{|o| o[:languageCode] == "EN"}
       names << { languageCode: "EN", name: name }
     end
 
-    def english_name
+    def englishName
       names.select{|o| o[:languageCode] == "EN"}.first[:name]
     end
 
-    def french_name=(name)
+    def frenchName=(name)
       names.delete_if{|o| o[:languageCode] == "FR"}
       names << { languageCode: "FR", name: name }
     end
 
-    def french_name
+    def frenchName
       names.select{|o| o[:languageCode] == "FR"}.first[:name]
     end
 

data/lib/dina/models/attachment.rb

@@ -4,10 +4,10 @@ module Dina
   class Attachment < BaseModel
     property :id, type: :string, default: SecureRandom.uuid_v7
 
-    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"
+    belongs_to :materialSample, class_name: "MaterialSample", shallow_path: true 
+    belongs_to :collectingEvent, class_name: "CollectingEvent", shallow_path: true
+    belongs_to :project, class_name: "Project", shallow_path: true
+    belongs_to :transaction, class_name: "Transaction", shallow_path: true
 
     def self.endpoint_path
       "collection-api/"

data/lib/dina/models/base_model.rb

@@ -4,9 +4,15 @@ module Dina
 
     self.raise_on_blank_find_param = true
     self.add_defaults_to_changes = true
-    self.json_key_format = :camelized_key
     self.paginator = JsonApiClient::Paginating::NestedParamPaginator
 
+    resolve_custom_type "collection-method", "Dina::CollectionMethod"
+    resolve_custom_type "collecting-event", "Dina::CollectingEvent"
+    resolve_custom_type "preparation-type", "Dina::PreparationType"
+    resolve_custom_type "preparation-method", "Dina::PreparationMethod"
+    resolve_custom_type "material-sample", "Dina::MaterialSample"
+    resolve_custom_type "storage-unit", "Dina::StorageUnit"
+
     before_create :on_before_create
     before_save :on_before_save
 

data/lib/dina/models/material_sample/collecting_event.rb

@@ -43,11 +43,11 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
+    has_one :protocol, class_name: "Protocol" 
+    has_one :collectionMethod, class_name: "CollectionMethod"
     has_many :collectors, class_name: "Person"
     has_many :attachment, class_name: "Attachment"
 
-    has_one :collection_method, class_name: "CollectionMethod"
-
     validates_presence_of :group, message: "group is required"
 
     before_save :on_before_save

data/lib/dina/models/material_sample/collection.rb

@@ -15,8 +15,8 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
-    belongs_to :institution, shallow_path: true, class_name: "Institution"
-    has_one :parent_collection, class_name: "Collection"
+    belongs_to :institution, class_name: "Institution", shallow_path: true
+    has_one :parentCollection, class_name: "Collection"
 
     validates_presence_of :group, message: "group is required"
 

data/lib/dina/models/material_sample/collection_method.rb

@@ -9,8 +9,6 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
-    belongs_to :collecting_event, class: "CollectingEvent", shallow_path: true
-
     validates_presence_of :group, message: "group is required"
 
     def self.endpoint_path

data/lib/dina/models/material_sample/material_sample.rb

@@ -25,6 +25,7 @@ module Dina
     property :stateChangedOn, type: :date
     property :stateChangeRemarks, type: :string
     property :materialSampleRemarks, type: :string
+    property :sourceSet, type: :string
     property :extensionValues, type: :hash
     property :restrictionFieldsExtension, type: :hash
     property :restrictionRemarks, type: :string
@@ -40,14 +41,14 @@ module Dina
     property :targetOrganismPrimaryScientificName, type: :string
     property :allowDuplicateName, type: :boolean
 
+    has_one :collectingEvent, class_name: "CollectingEvent"
     has_one :collection, class_name: "Collection"
-    has_one :collecting_event, class_name: "CollectingEvent"
-    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 :storage_unit, class_name: "StorageUnit"
-    has_many :prepared_by, class_name: "Person"
+    has_one :preparationType, class_name: "PreparationType"
+    has_one :preparationMethod, class_name: "PreparationMethod"
+    has_one :parentMaterialSample, class_name: "MaterialSample"
+    has_one :preparationProtocol, class_name: "Protocol"
+    has_one :storageUnitUsage, class_name: "StorageUnitUsage"
+    has_many :preparedBy, class_name: "Person"
     has_many :attachment, class_name: "Attachment"
     has_many :projects, class_name: "Project"
     has_many :assemblages, class_name: "Assemblage"

data/lib/dina/models/object_store/derivative.rb

@@ -13,7 +13,7 @@ module Dina
     property :derivativeType, type: :string
     property :publiclyReleasable, type: :boolean, default: true
 
-    has_one :ac_derived_from, class_name: "ObjectStore"
+    has_one :acDerivedFrom, class_name: "ObjectStore"
 
     validates_presence_of :bucket, message: "bucket is required"
     validates_presence_of :dcFormat, message: "dcFormat is required"
@@ -33,7 +33,7 @@ module Dina
 
     def on_before_save
       if self.as_json_api["relationships"].nil? || !self.as_json_api["relationships"].has_key?("acDerivedFrom")
-        raise ObjectInvalid, "#{self.class} is invalid. ac_derived_from relationship is required"
+        raise ObjectInvalid, "#{self.class} is invalid. acDerivedFrom relationship is required"
       end
       super
     end

data/lib/dina/models/object_store/file.rb

@@ -4,14 +4,14 @@ require_rel 'file_connection'
 module Dina
 
   class File < BaseModel
+    self.connection_class = FileConnection
+
     property :id, type: :string, default: SecureRandom.uuid_v7
     property :group, type: :string
     property :filePath, type: :string
     property :fileName, type: :string
     property :dcFormat, type: :string
-    property :is_derivative, type: :boolean
-
-    self.connection_class = FileConnection
+    property :isDerivative, type: :boolean
 
     validates_presence_of :group, message: "group is required"
     validates_presence_of :filePath, message: "filePath is required"

data/lib/dina/models/object_store/file_connection.rb

@@ -10,6 +10,7 @@ module Dina
   
         @faraday = Faraday.new(site, connection_options) do |builder|
           builder.request :multipart
+          builder.response :json
           builder.adapter(*adapter_options)
         end
         yield(self) if block_given?
@@ -17,7 +18,7 @@ module Dina
   
       def run(request_method, path, params: nil, headers: {}, body: nil)
         path = path + "/#{body[:data]["attributes"]["group"].downcase}"
-        if body[:data]["attributes"].key?("is_derivative")
+        if body[:data]["attributes"].key?("isDerivative")
           path = path + "/derivative"
         end
         file_path = body[:data]["attributes"]["filePath"]
@@ -33,7 +34,7 @@ module Dina
         response = @faraday.run_request(request_method, path, body, headers) do |request|
           request.params.update(params) if params
         end
-        attributes = JSON.parse(response.body.dup)
+        attributes = response.body.dup
         response.body["meta"] = {}
         response.body["errors"] = []
         response.body["data"] = { 

data/lib/dina/models/object_store/object_store.rb

@@ -29,8 +29,8 @@ module Dina
     property :orientation, type: :integer
     property :resourceExternalURL, type: :string
 
-    has_one :ac_metadata_creator, class_name: "Person"
-    has_one :dc_creator, class_name: "Person"
+    has_one :acMetadataCreator, class_name: "Person"
+    has_one :dcCreator, class_name: "Person"
     has_many :derivatives, class_name: "Derivative"
 
     validates_presence_of :group, message: "group is required"

data/lib/dina/models/sequence/pcr_primer.rb

@@ -30,7 +30,7 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
-    has_one :region
+    has_one :region, class_name: "Region" 
 
     validates_presence_of :group, message: "group is required"
     validates_presence_of :name, message: "name is required"

data/lib/dina/models/storage/storage_unit.rb

@@ -5,13 +5,14 @@ module Dina
     property :id, type: :string, default: SecureRandom.uuid_v7
     property :group, type: :string
     property :name, type: :string
+    property :isGeneric, type: :boolean
     property :barcode, 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 :storage_unit_type, class_name: "StorageUnitType"
     has_one :parent_storage_unit, class_name: "StorageUnit"
 
     validates_presence_of :group, message: "group is required"

data/lib/dina/models/storage/storage_unit_usage.rb

@@ -0,0 +1,27 @@
+require_rel '../base_model'
+
+module Dina
+  class StorageUnitUsage < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid_v7
+    property :usageType, type: :string
+    property :wellRow, type: :string
+    property :wellColumn, type: :string
+    property :cellNumber, type: :string
+    property :storageUnitName, type: :string
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    has_one :storage_unit, class_name: "StorageUnit"
+    has_one :storage_unit_type, class_name: "StorageUnitType"
+
+    validates_presence_of :usageType, message: "usageType is required"
+
+    def self.endpoint_path
+      "collection-api/"
+    end
+
+    def self.table_name
+      "storage-unit-usage"
+    end
+  end
+end

data/lib/dina/search/search.rb

@@ -3,7 +3,6 @@ require_rel 'search_connection'
 
 module Dina
   class Search < BaseModel
-
     self.connection_class = SearchConnection
 
     custom_endpoint :execute, on: :collection, request_method: :post

data/lib/dina/search/search_autocomplete.rb

@@ -5,7 +5,6 @@ require_rel 'search_connection'
 
 module Dina
   class SearchAutoComplete < BaseModel
-
     self.connection_class = SearchConnection
 
     custom_endpoint :execute, on: :collection, request_method: :get

data/lib/dina/search/search_connection.rb

@@ -13,6 +13,7 @@ module Dina
 
       @faraday = Faraday.new(site, connection_options) do |builder|
         builder.request :json
+        builder.response :json
         builder.adapter(*adapter_options)
       end
       yield(self) if block_given?
@@ -47,7 +48,7 @@ module Dina
         request.body = payload
       end
 
-      attributes = JSON.parse(response.body.dup)
+      attributes = response.body.dup
       meta = {}
       if attributes.has_key?("hits")
         #TODO: does not work with SearchAutoComplete because response is different from Search
@@ -65,7 +66,6 @@ module Dina
 
     def use(middleware, *args, &block)
       return if faraday.builder.locked?
-      faraday.builder.insert_before(Middleware::ParseJson, middleware, *args, &block)
     end
 
   end

data/lib/dina/search/search_count.rb

@@ -3,7 +3,6 @@ require_rel 'search_connection'
 
 module Dina
   class SearchCount < BaseModel
-
     self.connection_class = SearchConnection
 
     custom_endpoint :execute, on: :collection, request_method: :post

data/lib/dina/search/search_mapping.rb

@@ -3,7 +3,6 @@ require_rel 'search_connection'
 
 module Dina
   class SearchMapping < BaseModel
-
     self.connection_class = SearchConnection
 
     custom_endpoint :execute, on: :collection, request_method: :get

data/lib/dina/version.rb

@@ -1,8 +1,8 @@
 module Dina
   class Version
 
-    MAJOR = 2
-    MINOR = 3
+    MAJOR = 3
+    MINOR = 1
     PATCH = 0
     BUILD = 0
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: dina
 version: !ruby/object:Gem::Version
-  version: 2.3.0.0
+  version: 3.1.0.0
 platform: ruby
 authors:
 - David P. Shorthouse
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-05-27 00:00:00.000000000 Z
+date: 2024-07-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_api_client
@@ -198,6 +198,7 @@ files:
 - lib/dina/models/sequence/thermocycler_profile.rb
 - lib/dina/models/storage/storage_unit.rb
 - lib/dina/models/storage/storage_unit_type.rb
+- lib/dina/models/storage/storage_unit_usage.rb
 - lib/dina/models/transaction/transaction.rb
 - lib/dina/models/user.rb
 - lib/dina/rest_client_request_patch.rb