dina 0.4.0.0 → 0.4.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 4cae0ee74ed1a0967bb360af211c2ab37676dfdb39b54a377ec39b539e0f4301
-  data.tar.gz: 45ee9d1cda7f37da9fb5384690751dac5e5cc0fe30153cddf8306e11a20f7151
+  metadata.gz: 868b096ec196f62ae6cf4507cadf08c277b26f462957873140abc93ecf88a1a6
+  data.tar.gz: 26c127ec2bf4e6e9c990b4361aff69d1ce9f6a5e578ae01065472e8ede524bf5
 SHA512:
-  metadata.gz: 60a62ece7262ab086b88002497bd55f1ea04059b94468134b7c93d35a3349deff0c3ed58c45f634dd07a3149e4895da1525c215aef1895258beb62cf5af0aba5
-  data.tar.gz: dba63bace34688530c56cb56af702af39fe36bcb7ba86bf664b1192a7186ca51207ef9cef2deed311993671127772deb4f149f99fd90619ad56408dc379882a7
+  metadata.gz: 9fcd3ceca0594b95caaea14870a0ff6ebc9284fab58eac5e98bd236c04e8235b4fb542c720cba9c394b63b719a4883642f82e0871b347a9a18c5225c8e42e5b6
+  data.tar.gz: 95d262c72d8955a9eb944886efcd0784af500f4f8235846bc062a69d5128652e0af0260d85f7243bd608e8d2bd3f895a309cc752baac6b742282f84db658f88e

data/lib/dina/json_api_client_patch.rb

@@ -0,0 +1,11 @@
+# Monkeypatch the data method because the relations urls in the DINA JSON:API spec are incorrectly formed through its frontend proxy
+module JsonApiClient
+  module Associations
+    class BaseAssociation
+      def data(url)
+        url.sub!("/api/v1/", "/api/#{association_class.requestor.instance_variable_get(:@klass).endpoint_path}")
+        from_result_set(association_class.requestor.linked(url))
+      end
+    end
+  end
+end

data/lib/dina/models/{identifier.rb → agent/identifier.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class Identifier < BaseModel
@@ -8,6 +8,8 @@ module Dina
     property :createdBy, type: :string
     property :createdOn, type: :time
 
+    belongs_to :person, shallow_path: true, class_name: "Person"
+
     def self.endpoint_path
       "agent-api/"
     end

data/lib/dina/models/{organization.rb → agent/organization.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class Organization < BaseModel

data/lib/dina/models/{person.rb → agent/person.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class Person < BaseModel
@@ -35,6 +35,26 @@ module Dina
       where("email": email).all
     end
 
+    def self.search_by_name(name)
+      payload = {
+        query: {
+          multi_match: {
+            query: name,
+            type: :cross_fields,
+            fields: [
+              "data.attributes.familyNames^3",
+              "data.attributes.givenNames",
+              "data.attributes.displayName^5",
+              "data.attributes.aliases",
+              "data.attributes.displayName.autocomplete"
+            ]
+          }
+        }
+      }
+      hits = Dina::Search.execute(index: "agent", payload: payload)[:hits]
+      hits.map{|a| self.find(a[:_source][:data][:id]).first }
+    end
+
     private
 
     def on_before_save

data/lib/dina/models/{collecting_event.rb → material_sample/collecting_event.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class CollectingEvent < BaseModel

data/lib/dina/models/{collecting_method.rb → material_sample/collecting_method.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class CollectingMethod < BaseModel

data/lib/dina/models/{collection.rb → material_sample/collection.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class Collection < BaseModel

data/lib/dina/models/{collection_sequence_generator.rb → material_sample/collection_sequence_generator.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class CollectionSequenceGenerator < BaseModel

data/lib/dina/models/{material_sample.rb → material_sample/material_sample.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class MaterialSample < BaseModel

data/lib/dina/models/{organism.rb → material_sample/organism.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class Organism < BaseModel

data/lib/dina/models/{preparation_method.rb → material_sample/preparation_method.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class PreparationMethod < BaseModel

data/lib/dina/models/{preparation_type.rb → material_sample/preparation_type.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class PreparationType < BaseModel

data/lib/dina/models/{project.rb → material_sample/project.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class Project < BaseModel

data/lib/dina/models/{protocol.rb → material_sample/protocol.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class Protocol < BaseModel

data/lib/dina/models/{derivative.rb → object_store/derivative.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class Derivative < BaseModel

data/lib/dina/models/{object_store.rb → object_store/object_store.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class ObjectStore < BaseModel

data/lib/dina/models/{object_store_managed_attribute.rb → object_store/object_store_managed_attribute.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class ObjectStoreManagedAttribute < BaseModel

data/lib/dina/models/{object_subtype.rb → object_store/object_subtype.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class ObjectSubtype < BaseModel

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

@@ -0,0 +1,19 @@
+require_rel '../base_model'
+
+module Dina
+  class IndexSet < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+
+    validates_presence_of :group, message: "group is required"
+
+    def self.endpoint_path
+      "seqdb-api/"
+    end
+
+    def self.table_name
+      "index-set"
+    end
+
+  end
+end

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

@@ -0,0 +1,19 @@
+require_rel '../base_model'
+
+module Dina
+  class MolecularSample < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+
+    validates_presence_of :group, message: "group is required"
+
+    def self.endpoint_path
+      "seqdb-api/"
+    end
+
+    def self.table_name
+      "molecular-sample"
+    end
+
+  end
+end

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

@@ -0,0 +1,19 @@
+require_rel '../base_model'
+
+module Dina
+  class NgsWorkflow < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+
+    validates_presence_of :group, message: "group is required"
+
+    def self.endpoint_path
+      "seqdb-api/"
+    end
+
+    def self.table_name
+      "chain"
+    end
+
+  end
+end

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

@@ -0,0 +1,19 @@
+require_rel '../base_model'
+
+module Dina
+  class PcrBatch < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+
+    validates_presence_of :group, message: "group is required"
+
+    def self.endpoint_path
+      "seqdb-api/"
+    end
+
+    def self.table_name
+      "pcr-batch"
+    end
+
+  end
+end

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

@@ -0,0 +1,19 @@
+require_rel '../base_model'
+
+module Dina
+  class PcrPrimer < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+
+    validates_presence_of :group, message: "group is required"
+
+    def self.endpoint_path
+      "seqdb-api/"
+    end
+
+    def self.table_name
+      "pcr-primer"
+    end
+
+  end
+end

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

@@ -0,0 +1,19 @@
+require_rel '../base_model'
+
+module Dina
+  class Product < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+
+    validates_presence_of :group, message: "group is required"
+
+    def self.endpoint_path
+      "seqdb-api/"
+    end
+
+    def self.table_name
+      "product"
+    end
+
+  end
+end

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

@@ -0,0 +1,19 @@
+require_rel '../base_model'
+
+module Dina
+  class Region < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+
+    validates_presence_of :group, message: "group is required"
+
+    def self.endpoint_path
+      "seqdb-api/"
+    end
+
+    def self.table_name
+      "region"
+    end
+
+  end
+end

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

@@ -0,0 +1,19 @@
+require_rel '../base_model'
+
+module Dina
+  class ThermocyclerProfile < BaseModel
+    property :id, type: :string, default: SecureRandom.uuid
+    property :group, type: :string
+
+    validates_presence_of :group, message: "group is required"
+
+    def self.endpoint_path
+      "seqdb-api/"
+    end
+
+    def self.table_name
+      "thermocycler-profile"
+    end
+
+  end
+end

data/lib/dina/models/{storage_unit.rb → storage/storage_unit.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class StorageUnit < BaseModel

data/lib/dina/models/{storage_unit_type.rb → storage/storage_unit_type.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class StorageUnitType < BaseModel

data/lib/dina/models/{transaction.rb → transaction/transaction.rb}

@@ -1,4 +1,4 @@
-require_rel 'base_model'
+require_rel '../base_model'
 
 module Dina
   class Transaction < BaseModel

data/lib/dina/search/base_search.rb

@@ -2,26 +2,42 @@ module Dina
   class BaseSearch
 
     def self.endpoint
-      Settings.server.endpoint
+      Dina::Authentication.endpoint_url
     end
 
     def self.endpoint_path
       "search-api/search-ws/"
     end
 
+    # Sets the search index name
+    #
+    # @param index [String] the search index; options are "agent", "material_sample", "object_store"
+    #
+    # @return [String] the internally-recognized search index name
     def self.index_name(index:)
       return nil if !index
       "dina_#{index}_index"
     end
 
+    # Executes a search
+    #
+    # @param params [Hash] the parameters to be included in the endpoint URL
+    # @param method [Symbol] the request type as :get or :post
+    # @param payload [Hash] the elasticsearch query
+    #
+    # @return [Hash] the search response with symbolized keys
     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' }
-          )
+          method: method,
+          url: endpoint + endpoint_path + "?" + params.to_query,
+          payload: payload.to_json,
+          headers: {
+            accept: 'application/json',
+            content_type: 'application/json',
+            authorization: Dina::Authentication.header
+          }
+        )
         JSON.parse(response, symbolize_names: true)
       rescue RestClient::ExceptionWithResponse => e
         e.response

data/lib/dina/search/search.rb

@@ -7,8 +7,13 @@ module Dina
       "search-api/search-ws/search"
     end
 
-    # index values: "agent", "material_sample", "object_store"
-    # payload is a hash in the form of an Elasticsearch body
+    # Executes a search
+    #
+    # @param index [String] the index, accepted value is one of "agent", "material_sample", "object_store"
+    # @param payload [Hash] the payload hash as an Elasticsearch-formatted body
+    # => { query: { match_all: {} }
+    #
+    # @return [Hash] the search result with symbolized keys
     def self.execute(index:, payload: { query: { match_all: {} } })
       params = {
         indexName: index_name(index: index)

data/lib/dina/search/search_autocomplete.rb

@@ -7,11 +7,19 @@ module Dina
       "search-api/search-ws/auto-complete"
     end
 
-    # index values: "agent", "material_sample", "object_store"
-    # known autocomplete fields:
+    # Executes an autocomplete search
+    #
+    # Known field values (dependent on chosen index):
     #   agent: data.attributes.displayName
     #   material_sample: included.attributes.dwcRecordedBy, included.attributes.verbatimDeterminer
     #   object_store: none
+    #
+    # @param term [String] the search term
+    # @param index [String] the index, accepted value is one of "agent", "material_sample", "object_store"
+    # @param field [String]
+    # @param group [String] the DINA group name
+    #
+    # @return [Hash] the search result with symbolized keys
     def self.execute(term:, index:, field: nil, group: nil)
       params = {
         prefix: term,

data/lib/dina/search/search_count.rb

@@ -7,9 +7,14 @@ module Dina
       "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: {})
+    # Executes an count search
+    #
+    # @param index [String] the index, accepted value is one of "agent", "material_sample", "object_store"
+    # @param payload [Hash] the Elasticsearch query hash
+    # => Example: {query: {bool: {filter: {term: {"data.attributes.group": "dao"}}}}}
+    #
+    # @return [Integer] the count of items in the index according to the query/filter
+    def self.execute(index:, payload: { query: { match_all: {} }})
       params = {
         indexName: index_name(index: index)
       }

data/lib/dina/search/search_mapping.rb

@@ -7,7 +7,11 @@ module Dina
       "search-api/search-ws/mapping"
     end
 
-    # index values: "agent", "material_sample", "object_store"
+    # Return the search mapping document
+    #
+    # @param index [String] the index, accepted value is one of "agent", "material_sample", "object_store"
+    #
+    # @return [Hash] the mapping document as a hash with symbolized keys
     def self.execute(index:)
       params = {
         indexName: index_name(index: index)

data/lib/dina/version.rb

@@ -3,7 +3,7 @@ module Dina
 
     MAJOR = 0
     MINOR = 4
-    PATCH = 0
+    PATCH = 2
     BUILD = 0
 
     def self.version

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: dina
 version: !ruby/object:Gem::Version
-  version: 0.4.0.0
+  version: 0.4.2.0
 platform: ruby
 authors:
 - David P. Shorthouse
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-11-30 00:00:00.000000000 Z
+date: 2022-12-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_api_client
@@ -66,6 +66,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 3.0.0
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.1.0
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -141,33 +155,42 @@ files:
 - lib/dina/components/georeference_assertion.rb
 - lib/dina/components/shipment.rb
 - lib/dina/exceptions.rb
+- lib/dina/json_api_client_patch.rb
 - lib/dina/models/acquisition_event.rb
+- lib/dina/models/agent/identifier.rb
+- lib/dina/models/agent/organization.rb
+- lib/dina/models/agent/person.rb
 - lib/dina/models/assemblage.rb
 - lib/dina/models/attachment.rb
 - lib/dina/models/base_model.rb
-- lib/dina/models/collecting_event.rb
-- lib/dina/models/collecting_method.rb
-- lib/dina/models/collection.rb
-- lib/dina/models/collection_sequence_generator.rb
-- lib/dina/models/derivative.rb
-- lib/dina/models/file.rb
-- lib/dina/models/identifier.rb
 - lib/dina/models/institution.rb
 - lib/dina/models/managed_attribute.rb
-- lib/dina/models/material_sample.rb
-- lib/dina/models/object_store.rb
-- lib/dina/models/object_store_managed_attribute.rb
-- lib/dina/models/object_subtype.rb
-- 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
-- lib/dina/models/storage_unit.rb
-- lib/dina/models/storage_unit_type.rb
-- lib/dina/models/transaction.rb
+- lib/dina/models/material_sample/collecting_event.rb
+- lib/dina/models/material_sample/collecting_method.rb
+- lib/dina/models/material_sample/collection.rb
+- lib/dina/models/material_sample/collection_sequence_generator.rb
+- lib/dina/models/material_sample/material_sample.rb
+- lib/dina/models/material_sample/organism.rb
+- lib/dina/models/material_sample/preparation_method.rb
+- lib/dina/models/material_sample/preparation_type.rb
+- lib/dina/models/material_sample/project.rb
+- lib/dina/models/material_sample/protocol.rb
+- lib/dina/models/object_store/derivative.rb
+- lib/dina/models/object_store/file.rb
+- lib/dina/models/object_store/object_store.rb
+- lib/dina/models/object_store/object_store_managed_attribute.rb
+- lib/dina/models/object_store/object_subtype.rb
+- lib/dina/models/sequence/index_set.rb
+- lib/dina/models/sequence/molecular_sample.rb
+- lib/dina/models/sequence/ngs_workflow.rb
+- lib/dina/models/sequence/pcr_batch.rb
+- lib/dina/models/sequence/pcr_primer.rb
+- lib/dina/models/sequence/product.rb
+- lib/dina/models/sequence/region.rb
+- 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/transaction/transaction.rb
 - lib/dina/models/user.rb
 - lib/dina/search/base_search.rb
 - lib/dina/search/search.rb