chemicalml 0.2.0 → 0.3.0

data/lib/chemicalml/cml/base/scalar.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Scalar
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -14,15 +15,49 @@ module Chemicalml
             attribute :units, :string
             attribute :content, :string
 
+            attribute :convention, :string
+            attribute :error_value, :string
+            attribute :error_basis, :string
+            attribute :min, :string
+            attribute :max, :string
+            attribute :ref, :string
+            attribute :constant_to_s_i, :string
+            attribute :multiplier_to_s_i, :string
+            attribute :unit_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "scalar"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "dataType", to: :data_type
-              map_attribute "units", to: :units
+              root 'scalar'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'dataType', to: :data_type
+              map_attribute 'units', to: :units
               map_content to: :content
+              map_attribute 'convention', to: :convention
+              map_attribute 'errorValue', to: :error_value
+              map_attribute 'errorBasis', to: :error_basis
+              map_attribute 'min', to: :min
+              map_attribute 'max', to: :max
+              map_attribute 'ref', to: :ref
+              map_attribute 'constantToSI', to: :constant_to_s_i
+              map_attribute 'multiplierToSI', to: :multiplier_to_s_i
+              map_attribute 'unitType', to: :unit_type
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'dataType', to: :data_type
+              map 'units', to: :units
+              map 'convention', to: :convention
+              map 'errorValue', to: :error_value
+              map 'errorBasis', to: :error_basis
+              map 'min', to: :min
+              map 'max', to: :max
+              map 'ref', to: :ref
+              map 'constantToSI', to: :constant_to_s_i
+              map 'multiplierToSI', to: :multiplier_to_s_i
+              map 'unitType', to: :unit_type
             end
           end
         end

data/lib/chemicalml/cml/base/spectator.rb

@@ -7,18 +7,39 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Spectator
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :role, :string
+            attribute :molecule, :molecule
+            attribute :objects, :object, collection: true
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "spectator"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'spectator'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'role', to: :role
+              map_element 'molecule', to: :molecule
+              map_element 'object', to: :objects
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'molecule', to: :molecule
+              map 'object', to: :objects
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'role', to: :role
             end
           end
         end

data/lib/chemicalml/cml/base/spectator_list.rb

@@ -7,21 +7,34 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::SpectatorList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :spectators, :spectator, collection: true
+            attribute :spectators, :spectator, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "spectator", to: :spectators
-              root "spectatorList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'spectator', to: :spectators
+              root 'spectatorList'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'spectator', to: :spectators
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
             end
           end
         end

data/lib/chemicalml/cml/base/spectrum.rb

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Spectrum
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -14,24 +16,73 @@ module Chemicalml
             attribute :format, :string
             attribute :condition, :string
 
-                        attribute :xaxis, :xaxis
+            attribute :xaxis, :xaxis
             attribute :yaxis, :yaxis
             attribute :peak_list, :peakList
             attribute :condition_list, :conditionList
+            attribute :sample, :sample
+            attribute :spectrum_data, :spectrumData
+            attribute :parameter_lists, :parameterList, collection: true
+            attribute :substance_lists, :substanceList, collection: true
 
+            attribute :ref, :string
+            attribute :molecule_ref, :string
+            attribute :spectrum_type, :string
+            attribute :type, :string
+            attribute :measurement, :string
+            attribute :ft, :string
+            attribute :state, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "xaxis", to: :xaxis
-              map_element "yaxis", to: :yaxis
-              map_element "peakList", to: :peak_list
-              map_element "conditionList", to: :condition_list
-              root "spectrum"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "format", to: :format
-              map_attribute "condition", to: :condition
+              map_element 'xaxis', to: :xaxis
+              map_element 'yaxis', to: :yaxis
+              map_element 'peakList', to: :peak_list
+              map_element 'conditionList', to: :condition_list
+              map_element 'sample', to: :sample
+              map_element 'spectrumData', to: :spectrum_data
+              map_element 'parameterList', to: :parameter_lists
+              map_element 'substanceList', to: :substance_lists
+              root 'spectrum'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'format', to: :format
+              map_attribute 'condition', to: :condition
+              map_attribute 'ref', to: :ref
+              map_attribute 'moleculeRef', to: :molecule_ref
+              map_attribute 'spectrumType', to: :spectrum_type
+              map_attribute 'type', to: :type
+              map_attribute 'measurement', to: :measurement
+              map_attribute 'ft', to: :ft
+              map_attribute 'state', to: :state
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'xaxis', to: :xaxis
+              map 'yaxis', to: :yaxis
+              map 'peakList', to: :peak_list
+              map 'conditionList', to: :condition_list
+              map 'sample', to: :sample
+              map 'spectrumData', to: :spectrum_data
+              map 'parameterList', to: :parameter_lists
+              map 'substanceList', to: :substance_lists
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'format', to: :format
+              map 'condition', to: :condition
+              map 'ref', to: :ref
+              map 'moleculeRef', to: :molecule_ref
+              map 'spectrumType', to: :spectrum_type
+              map 'type', to: :type
+              map 'measurement', to: :measurement
+              map 'ft', to: :ft
+              map 'state', to: :state
             end
           end
         end

data/lib/chemicalml/cml/base/spectrum_data.rb

@@ -7,23 +7,35 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::SpectrumData
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :xaxis, :xaxis
+            attribute :xaxis, :xaxis
             attribute :yaxis, :yaxis
 
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "xaxis", to: :xaxis
-              map_element "yaxis", to: :yaxis
-              root "spectrumData"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'xaxis', to: :xaxis
+              map_element 'yaxis', to: :yaxis
+              root 'spectrumData'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'ref', to: :ref
+            end
+            key_value do
+              map 'xaxis', to: :xaxis
+              map 'yaxis', to: :yaxis
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
             end
           end
         end

data/lib/chemicalml/cml/base/spectrum_list.rb

@@ -7,21 +7,44 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::SpectrumList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :spectra, :spectrum
+            attribute :spectra, :spectrum
+
+            attribute :ref, :string
+            attribute :molecule_ref, :string
+            attribute :spectrum_lists, :spectrumList, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "spectrum", to: :spectra
-              root "spectrumList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'spectrum', to: :spectra
+              map_element 'spectrumList', to: :spectrum_lists
+              root 'spectrumList'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'ref', to: :ref
+              map_attribute 'moleculeRef', to: :molecule_ref
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'spectrum', to: :spectra
+              map 'spectrumList', to: :spectrum_lists
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'moleculeRef', to: :molecule_ref
             end
           end
         end

data/lib/chemicalml/cml/base/sphere3.rb

@@ -7,20 +7,30 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Sphere3
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :content, :string
 
+            attribute :units, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "sphere3"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'sphere3'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
               map_content to: :content
+              map_attribute 'units', to: :units
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'units', to: :units
             end
           end
         end

data/lib/chemicalml/cml/base/stmml.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Stmml
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -14,11 +15,17 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "stmml"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'stmml'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
             end
           end
         end

data/lib/chemicalml/cml/base/string.rb

@@ -0,0 +1,40 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module String
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::String
+
+            attribute :builtin, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :id, :string
+            attribute :title, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root 'string'
+              map_attribute 'builtin', to: :builtin
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_content to: :content
+            end
+            key_value do
+              map 'builtin', to: :builtin
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'id', to: :id
+              map 'title', to: :title
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/base/string_array.rb

@@ -0,0 +1,52 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      module StringArray
+        def self.included(klass)
+          klass.class_eval do
+            include Chemicalml::Cml::Role::StringArray
+
+            attribute :builtin, :string
+            attribute :convention, :string
+            attribute :dict_ref, :string
+            attribute :id, :string
+            attribute :title, :string
+            attribute :min, :string
+            attribute :max, :string
+            attribute :size, :string
+            attribute :delimiter, :string
+            attribute :content, :string
+
+            xml do
+              namespace Chemicalml::Cml::Namespace
+              root 'stringArray'
+              map_attribute 'builtin', to: :builtin
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'min', to: :min
+              map_attribute 'max', to: :max
+              map_attribute 'size', to: :size
+              map_attribute 'delimiter', to: :delimiter
+              map_content to: :content
+            end
+            key_value do
+              map 'builtin', to: :builtin
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'min', to: :min
+              map 'max', to: :max
+              map 'size', to: :size
+              map 'delimiter', to: :delimiter
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/base/substance.rb

@@ -7,20 +7,54 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Substance
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :title, :string
             attribute :role, :string
+            attribute :id, :string
             attribute :molecule, :molecule
-            attribute :names, :name, collection: true
-            attribute :identifiers, :identifier, collection: true
+            attribute :amounts, :amount, collection: true
+            attribute :properties, :property, collection: true
 
+            attribute :dict_ref, :string
+            attribute :convention, :string
+            attribute :type, :string
+            attribute :ref, :string
+            attribute :count, :string
+            attribute :state, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "substance"
-              map_attribute "title", to: :title
-              map_attribute "role", to: :role
-              map_element "molecule", to: :molecule
-              map_element "name", to: :names
-              map_element "identifier", to: :identifiers
+              root 'substance'
+              map_attribute 'title', to: :title
+              map_attribute 'role', to: :role
+              map_attribute 'id', to: :id
+              map_element 'molecule', to: :molecule
+              map_element 'amount', to: :amounts
+              map_element 'property', to: :properties
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'type', to: :type
+              map_attribute 'ref', to: :ref
+              map_attribute 'count', to: :count
+              map_attribute 'state', to: :state
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'molecule', to: :molecule
+              map 'amount', to: :amounts
+              map 'property', to: :properties
+              map 'title', to: :title
+              map 'role', to: :role
+              map 'id', to: :id
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'type', to: :type
+              map 'ref', to: :ref
+              map 'count', to: :count
+              map 'state', to: :state
             end
           end
         end

data/lib/chemicalml/cml/base/substance_list.rb

@@ -7,21 +7,46 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::SubstanceList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :substances, :substance, collection: true
+            attribute :substances, :substance, collection: true
 
+            attribute :substance_list_type, :string
+            attribute :role, :string
+            attribute :ref, :string
+            attribute :type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "substance", to: :substances
-              root "substanceList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'substance', to: :substances
+              root 'substanceList'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'substanceListType', to: :substance_list_type
+              map_attribute 'type', to: :type
+              map_attribute 'role', to: :role
+              map_attribute 'ref', to: :ref
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'substance', to: :substances
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'substanceListType', to: :substance_list_type
+              map 'type', to: :type
+              map 'role', to: :role
+              map 'ref', to: :ref
             end
           end
         end