chemicalml 0.2.1 → 0.3.0

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

@@ -7,13 +7,17 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Table
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :table_content, :tableContent
+            attribute :table_content, :tableContent
             attribute :table_header, :tableHeader
+            attribute :array_lists, :arrayList, collection: true
+            attribute :table_row_lists, :tableRowList, collection: true
 
             attribute :rows, :string
             attribute :columns, :string
@@ -22,18 +26,39 @@ module Chemicalml
             attribute :data_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "tableContent", to: :table_content
-              map_element "tableHeader", to: :table_header
-              root "table"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "rows", to: :rows
-              map_attribute "columns", to: :columns
-              map_attribute "units", to: :units
-              map_attribute "tableType", to: :table_type
-              map_attribute "dataType", to: :data_type
+              map_element 'tableContent', to: :table_content
+              map_element 'tableHeader', to: :table_header
+              map_element 'arrayList', to: :array_lists
+              map_element 'tableRowList', to: :table_row_lists
+              root 'table'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'rows', to: :rows
+              map_attribute 'columns', to: :columns
+              map_attribute 'units', to: :units
+              map_attribute 'tableType', to: :table_type
+              map_attribute 'dataType', to: :data_type
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'tableContent', to: :table_content
+              map 'tableHeader', to: :table_header
+              map 'arrayList', to: :array_lists
+              map 'tableRowList', to: :table_row_lists
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'rows', to: :rows
+              map 'columns', to: :columns
+              map 'units', to: :units
+              map 'tableType', to: :table_type
+              map 'dataType', to: :data_type
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableCell
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,13 +16,19 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "tableCell"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'tableCell'
+              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
             end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+            end
           end
         end
       end

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

@@ -7,25 +7,35 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableContent
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :table_rows, :tableRow, collection: true
+            attribute :table_rows, :tableRow, collection: true
             attribute :table_row_lists, :tableRowList, collection: true
 
             attribute :delimiter, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "tableRow", to: :table_rows
-              map_element "tableRowList", to: :table_row_lists
-              root "tableContent"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "delimiter", to: :delimiter
+              map_element 'tableRow', to: :table_rows
+              map_element 'tableRowList', to: :table_row_lists
+              root 'tableContent'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'delimiter', to: :delimiter
+            end
+            key_value do
+              map 'tableRow', to: :table_rows
+              map 'tableRowList', to: :table_row_lists
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'delimiter', to: :delimiter
             end
           end
         end

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

@@ -7,21 +7,29 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableHeader
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :table_header_cells, :tableHeaderCell, collection: true
+            attribute :table_header_cells, :tableHeaderCell, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "tableHeaderCell", to: :table_header_cells
-              root "tableHeader"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'tableHeaderCell', to: :table_header_cells
+              root 'tableHeader'
+              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 'tableHeaderCell', to: :table_header_cells
+              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/table_header_cell.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableHeaderCell
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -20,17 +21,28 @@ module Chemicalml
             attribute :unit_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "tableHeaderCell"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'tableHeaderCell'
+              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 "dataType", to: :data_type
-              map_attribute "units", to: :units
-              map_attribute "constantToSI", to: :constant_to_s_i
-              map_attribute "multiplierToSI", to: :multiplier_to_s_i
-              map_attribute "unitType", to: :unit_type
+              map_attribute 'dataType', to: :data_type
+              map_attribute 'units', to: :units
+              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 'convention', to: :convention
+              map 'dataType', to: :data_type
+              map 'units', to: :units
+              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/table_row.rb

@@ -7,21 +7,29 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableRow
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :table_cells, :tableCell, collection: true
+            attribute :table_cells, :tableCell, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "tableCell", to: :table_cells
-              root "tableRow"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'tableCell', to: :table_cells
+              root 'tableRow'
+              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 'tableCell', to: :table_cells
+              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/table_row_list.rb

@@ -7,21 +7,29 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TableRowList
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :table_rows, :tableRow, collection: true
+            attribute :table_rows, :tableRow, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "tableRow", to: :table_rows
-              root "tableRowList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              map_element 'tableRow', to: :table_rows
+              root 'tableRowList'
+              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 'tableRow', to: :table_rows
+              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/tcell.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Tcell
+
             attribute :units, :string
             attribute :data_type, :string
             attribute :title, :string
@@ -17,15 +18,23 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "tcell"
-              map_attribute "units", to: :units
-              map_attribute "dataType", to: :data_type
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
+              root 'tcell'
+              map_attribute 'units', to: :units
+              map_attribute 'dataType', to: :data_type
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
               map_content to: :content
             end
+            key_value do
+              map 'units', to: :units
+              map 'dataType', to: :data_type
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+            end
           end
         end
       end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Torsion
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -22,19 +23,33 @@ module Chemicalml
             attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "torsion"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "atomRefs4", to: :atomRefs4
-              map_attribute "units", to: :units
-              map_attribute "angleUnits", to: :angle_units
-              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
+              root 'torsion'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'atomRefs4', to: :atomRefs4
+              map_attribute 'units', to: :units
+              map_attribute 'angleUnits', to: :angle_units
+              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
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'atomRefs4', to: :atomRefs4
+              map 'units', to: :units
+              map 'angleUnits', to: :angle_units
+              map 'errorValue', to: :error_value
+              map 'errorBasis', to: :error_basis
+              map 'min', to: :min
+              map 'max', to: :max
+              map 'ref', to: :ref
             end
           end
         end

data/lib/chemicalml/cml/base/transform3.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Transform3
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,13 +16,19 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "transform3"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'transform3'
+              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
             end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+            end
           end
         end
       end

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

@@ -7,18 +7,36 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::TransitionState
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
+            attribute :molecule, :molecule
+            attribute :property_lists, :propertyList, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "transitionState"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'transitionState'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_element 'molecule', to: :molecule
+              map_element 'propertyList', to: :property_lists
+            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 'propertyList', to: :property_lists
+              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/trow.rb

@@ -7,22 +7,38 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Trow
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :data_type, :string
             attribute :title, :string
             attribute :id, :string
             attribute :convention, :string
             attribute :dict_ref, :string
             attribute :content, :string
+            attribute :tcells, :tcell, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "trow"
-              map_attribute "dataType", to: :data_type
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
+              root 'trow'
+              map_attribute 'dataType', to: :data_type
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
               map_content to: :content
+              map_element 'tcell', to: :tcells
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'tcell', to: :tcells
+              map 'dataType', to: :data_type
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
             end
           end
         end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Unit
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :symbol, :string
@@ -25,22 +27,43 @@ module Chemicalml
             attribute :abbreviation, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "unit"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "symbol", to: :symbol
-              map_attribute "parentSI", to: :parent_si
-              map_attribute "multiplierToSI", to: :multiplier_to_si
-              map_attribute "constantToSI", to: :constant_to_si
-              map_attribute "unitType", to: :unit_type
-              map_element "definition", to: :definition
-              map_element "description", to: :description
-              map_attribute "units", to: :units
-              map_attribute "name", to: :name
-              map_attribute "isSI", to: :is_s_i
-              map_attribute "multiplierToData", to: :multiplier_to_data
-              map_attribute "power", to: :power
-              map_attribute "abbreviation", to: :abbreviation
+              root 'unit'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'symbol', to: :symbol
+              map_attribute 'parentSI', to: :parent_si
+              map_attribute 'multiplierToSI', to: :multiplier_to_si
+              map_attribute 'constantToSI', to: :constant_to_si
+              map_attribute 'unitType', to: :unit_type
+              map_element 'definition', to: :definition
+              map_element 'description', to: :description
+              map_attribute 'units', to: :units
+              map_attribute 'name', to: :name
+              map_attribute 'isSI', to: :is_s_i
+              map_attribute 'multiplierToData', to: :multiplier_to_data
+              map_attribute 'power', to: :power
+              map_attribute 'abbreviation', to: :abbreviation
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'definition', to: :definition
+              map 'description', to: :description
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'symbol', to: :symbol
+              map 'parentSI', to: :parent_si
+              map 'multiplierToSI', to: :multiplier_to_si
+              map 'constantToSI', to: :constant_to_si
+              map 'unitType', to: :unit_type
+              map 'units', to: :units
+              map 'name', to: :name
+              map 'isSI', to: :is_s_i
+              map 'multiplierToData', to: :multiplier_to_data
+              map 'power', to: :power
+              map 'abbreviation', to: :abbreviation
             end
           end
         end