dina 0.7.5.0 → 0.8.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 65fbba40026990fd8cfaa90803e8c909dc3431eea4585800093d9c433801bb25
+  metadata.gz: 0c6ae5abbf48a7b17f398ef9b7847f4e2a971f1819669c0202147a085cd20268
+  data.tar.gz: e59a3c1ab3548dba76c6294dcc7536b9c8644be776123b367c1484b7a5981122
 SHA512:
-  metadata.gz: 0a13c0b80dea86b275fa961cb0f6c17d7645c5a0ed99fc09b6dbbe087923aa6dc95dcc746bc3ebbdfe26f4200f7486fb94355295ea1ead24a632bcebebf5a233
-  data.tar.gz: 1b4fc2d14a4766fbd598cec301c4e39c002e044e34c70b6a6c48fe4852539e00775def68611a1197807e932de23802a9a568abceb76a04f2907d7405dcf09d74
+  metadata.gz: c4693d5abe72117aa16129a3f436ea7548537371446e6bc2ed335ddf03f4e2890816ffcf7093c02a481ec436b50c1d13203a1794d7ea119d59014488b33871c2
+  data.tar.gz: bfea8c578a6afdf3f30ea7857f1ebaafff6168a0952a47c0d6a8ab8c4c316eb1e05ce821a1cc66d6728016e85c99811b91c420817a34ec43996e9214506ff290

data/lib/dina/components/address.rb

@@ -0,0 +1,22 @@
+module Dina
+  class Address
+    attr_accessor :receiverName
+    attr_accessor :companyName
+    attr_accessor :addressLine1
+    attr_accessor :addressLine2
+    attr_accessor :city
+    attr_accessor :provinceState
+    attr_accessor :zipCode
+    attr_accessor :country
+
+    def initialize
+    end
+
+    def to_hash
+      hash = {}
+      instance_variables.each { |var| hash[var.to_s.delete('@')] = instance_variable_get(var) }
+      hash.deep_symbolize_keys
+    end
+
+  end
+end

data/lib/dina/components/geographic_source.rb

@@ -0,0 +1,21 @@
+module Dina
+  class GeographicSource
+    attr_accessor :sourceUrl
+    attr_accessor :customGeographicPlace
+    attr_accessor :selectedGeographicPlace
+    attr_accessor :higherGeographicPlaces
+    attr_accessor :stateProvince
+    attr_accessor :country
+    attr_accessor :recordedOn
+
+    def initialize
+    end
+
+    def to_hash
+      hash = {}
+      instance_variables.each { |var| hash[var.to_s.delete('@')] = instance_variable_get(var) }
+      hash.deep_symbolize_keys
+    end
+
+  end
+end

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

@@ -35,6 +35,10 @@ module Dina
       where("email": email).all
     end
 
+    # Searches for a Person by name using the search module
+    #
+    # @param name [String] any portion of a person's name
+    # @return array [Array] an array of Person objects, ordered by relevance
     def self.search_by_name(name)
       payload = {
         query: {
@@ -51,7 +55,7 @@ module Dina
           }
         }
       }
-      hits = Dina::Search.execute(index: "agent", payload: payload)[:hits]
+      hits = Search.execute(index: "agent", payload: payload)[:hits]
       hits.map{|a| self.find(a[:_source][:data][:id]).first }
     end
 

data/lib/dina/models/base_model.rb

@@ -2,6 +2,7 @@ module Dina
   class BaseModel < JsonApiClient::Resource
     include JsonApiClient::Helpers::Callbacks
 
+    self.raise_on_blank_find_param = true
     self.json_key_format = :camelized_key
     self.paginator = JsonApiClient::Paginating::NestedParamPaginator
 

data/lib/dina/models/managed_attribute.rb

@@ -6,7 +6,7 @@ module Dina
     property :group, type: :string
     property :name, type: :string
     property :key, type: :string
-    property :managedAttributeType, type: :string
+    property :vocabularyElementType, type: :string
     property :managedAttributeComponent, type: :string
     property :acceptedValues, type: :array
     property :multilingualDescription, type: :multilingual_description
@@ -15,7 +15,7 @@ module Dina
 
     validates_presence_of :group, message: "group is required"
     validates_presence_of :name, message: "name is required"
-    validates_presence_of :managedAttributeType, message: "managedAttributeType is required"
+    validates_presence_of :vocabularyElementType, message: "vocabularyElementType is required"
 
     attr_accessor :accepted_components, :accepted_types
 
@@ -52,8 +52,8 @@ module Dina
       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(", ")}"
+      if !self.vocabularyElementType.nil? && !self.class.accepted_types.include?(self.vocabularyElementType)
+        raise PropertyValueInvalid, "#{self.class} is invalid. Accepted value for vocabularyElementType is one of #{self.class.accepted_types.join(", ")}"
       end
       super
     end

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

@@ -35,7 +35,7 @@ module Dina
     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 :geographicPlaceNameSourceDetail, type: :object, default: {}
     property :managedAttributes, type: :array, default: []
     property :geoReferenceAssertions, type: :array, default: []
     property :eventGeom, type: :string

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

@@ -5,7 +5,7 @@ module Dina
     property :id, type: :string, default: SecureRandom.uuid
     property :name, type: :string
     property :key, type: :string
-    property :managedAttributeType, type: :string
+    property :vocabularyElementType, type: :string
     property :acceptedValues, type: :array
     property :multilingualDescription, type: :multilingual_description
     property :createdBy, type: :string
@@ -22,8 +22,8 @@ module Dina
     private
 
     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(", ")}"
+      if !self.vocabularyElementType.nil? && !ManagedAttribute.accepted_types.include?(self.vocabularyElementType)
+        raise PropertyValueInvalid, "#{self.class} is invalid. Accepted value for vocabularyElementType is one of #{ManagedAttribute.accepted_types.join(", ")}"
       end
       super
     end

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

@@ -4,8 +4,14 @@ module Dina
   class IndexSet < BaseModel
     property :id, type: :string, default: SecureRandom.uuid
     property :group, type: :string
+    property :name, type: :string
+    property :forwardAdapter, type: :string
+    property :reverseAdapter, type: :string
+    property :createdBy, type: :string
+    property :createdOn, type: :time
 
     validates_presence_of :group, message: "group is required"
+    validates_presence_of :name, message: "name is required"
 
     def self.endpoint_path
       "seqdb-api/"

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

@@ -4,8 +4,15 @@ module Dina
   class MolecularSample < BaseModel
     property :id, type: :string, default: SecureRandom.uuid
     property :group, type: :string
+    property :name, type: :string
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    has_one :kit, class_name: "Product"
+    has_one :materialSample, class_name: "MaterialSample"
 
     validates_presence_of :group, message: "group is required"
+    validates_presence_of :name, message: "name is required"
 
     def self.endpoint_path
       "seqdb-api/"
@@ -15,5 +22,20 @@ module Dina
       "molecular-sample"
     end
 
+    def self.sample_type
+      [
+        "DNA"
+      ]
+    end
+
+    private
+
+    def on_before_save
+      if !self.sampleType.nil? && !self.class.sample_type.include?(self.type)
+        raise PropertyValueInvalid, "#{self.class} is invalid. Accepted value for sampleType is one of #{self.class.sample_type.join(", ")}"
+      end
+      super
+    end
+
   end
 end

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

@@ -4,8 +4,10 @@ module Dina
   class PcrBatch < BaseModel
     property :id, type: :string, default: SecureRandom.uuid
     property :group, type: :string
+    property :name, type: :string
 
     validates_presence_of :group, message: "group is required"
+    validates_presence_of :name, message: "name is required"
 
     def self.endpoint_path
       "seqdb-api/"

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

@@ -4,8 +4,36 @@ module Dina
   class PcrPrimer < BaseModel
     property :id, type: :string, default: SecureRandom.uuid
     property :group, type: :string
+    property :type, type: :string
+    property :name, type: :string
+    property :version, type: :integer
+    property :seq, type: :string
+    property :position, type: :string
+    property :tmCalculated, type: :string
+    property :tmPe, type: :integer
+    property :application, type: :string
+    property :direction, type: :string
+    property :reference, type: :string
+    property :pooledPrimer, type: :string
+    property :lotNumber, type: :string
+    property :sequenceLength, type: :integer
+    property :targetSpecies, type: :string
+    property :supplier, type: :string
+    property :dateOrdered, type: :time
+    property :dateDestroyed, type: :time
+    property :purification, type: :string
+    property :designedBy, type: :string
+    property :stockConcentration, type: :string
+    property :lotNumber, type: :integer
+    property :region, type: :string
+    property :note, type: :string
+    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 :type, message: "type is required"
+    validates_presence_of :lotNumber, message: "lotNumber is required"
 
     def self.endpoint_path
       "seqdb-api/"
@@ -15,5 +43,24 @@ module Dina
       "pcr-primer"
     end
 
+    def self.accepted_types
+      [
+        "PRIMER",
+        "MID",
+        "FUSION_PRIMER",
+        "ILLUMINA_INDEX",
+        "ITRU_PRIMER"
+      ]
+    end
+
+    private
+
+    def on_before_save
+      if !self.type.nil? && !self.class.accepted_types.include?(self.type)
+        raise PropertyValueInvalid, "#{self.class} is invalid. Accepted value for type is one of #{self.class.accepted_types.join(", ")}"
+      end
+      super
+    end
+
   end
 end

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

@@ -4,8 +4,15 @@ module Dina
   class Product < BaseModel
     property :id, type: :string, default: SecureRandom.uuid
     property :group, type: :string
+    property :name, type: :string
+    property :upc, type: :string
+    property :type, type: :string
+    property :description, type: :string
+    property :createdBy, type: :string
+    property :createdOn, type: :time
 
     validates_presence_of :group, message: "group is required"
+    validates_presence_of :name, message: "name is required"
 
     def self.endpoint_path
       "seqdb-api/"

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

@@ -4,8 +4,16 @@ module Dina
   class Region < BaseModel
     property :id, type: :string, default: SecureRandom.uuid
     property :group, type: :string
+    property :name, type: :string
+    property :symbol, type: :string
+    property :description, type: :string
+    property :aliases, type: :string
+    property :applicableOrganisms, type: :string
+    property :createdBy, type: :string
+    property :createdOn, type: :time
 
     validates_presence_of :group, message: "group is required"
+    validates_presence_of :symbol, message: "symbol is required"
 
     def self.endpoint_path
       "seqdb-api/"

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

@@ -4,8 +4,17 @@ module Dina
   class ThermocyclerProfile < BaseModel
     property :id, type: :string, default: SecureRandom.uuid
     property :group, type: :string
+    property :name, type: :string
+    property :application, type: :string
+    property :cycles, type: :string
+    property :steps, type: :array
+    property :createdBy, type: :string
+    property :createdOn, type: :time
+
+    has_one :region, class_name: "Region"
 
     validates_presence_of :group, message: "group is required"
+    validates_presence_of :name, message: "name is required"
 
     def self.endpoint_path
       "seqdb-api/"

data/lib/dina/version.rb

@@ -2,8 +2,8 @@ module Dina
   class Version
 
     MAJOR = 0
-    MINOR = 7
-    PATCH = 5
+    MINOR = 8
+    PATCH = 1
     BUILD = 0
 
     def self.version

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: dina
 version: !ruby/object:Gem::Version
-  version: 0.7.5.0
+  version: 0.8.1.0
 platform: ruby
 authors:
 - David P. Shorthouse
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-01-12 00:00:00.000000000 Z
+date: 2023-01-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_api_client
@@ -150,8 +150,10 @@ files:
 - lib/dina/casters/multilingual_title.rb
 - lib/dina/casters/multilingual_title_caster.rb
 - lib/dina/casters/object_caster.rb
+- lib/dina/components/address.rb
 - lib/dina/components/agent_role.rb
 - lib/dina/components/determination.rb
+- lib/dina/components/geographic_source.rb
 - lib/dina/components/georeference_assertion.rb
 - lib/dina/components/shipment.rb
 - lib/dina/exceptions.rb