chemicalml 0.2.1 → 0.4.0

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

@@ -7,22 +7,32 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Description
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :content, :string
+            attribute :paragraphs, Chemicalml::Cml::Xhtml::P, collection: true
 
             attribute :object_class, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "description"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'description'
+              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 "objectClass", to: :object_class
+              map_element 'p', to: :paragraphs
+              map_attribute 'objectClass', to: :object_class
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'objectClass', to: :object_class
             end
           end
         end

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

@@ -7,28 +7,45 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Dictionary
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :title, :string
             attribute :namespace, :string
             attribute :dictionary_prefix, :string
             attribute :convention, :string
-            attribute :description, :string
             attribute :entries, :entry, collection: true
+            attribute :definitions, :definition, collection: true
 
             attribute :id, :string
             attribute :dict_ref, :string
             attribute :href, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "dictionary"
-              map_attribute "title", to: :title
-              map_attribute "namespace", to: :namespace
-              map_attribute "dictionaryPrefix", to: :dictionary_prefix
-              map_attribute "convention", to: :convention
-              map_element "description", to: :description
-              map_element "entry", to: :entries
-              map_attribute "id", to: :id
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "href", to: :href
+              root 'dictionary'
+              map_attribute 'title', to: :title
+              map_attribute 'namespace', to: :namespace
+              map_attribute 'dictionaryPrefix', to: :dictionary_prefix
+              map_attribute 'convention', to: :convention
+              map_element 'definition', to: :definitions
+              map_element 'entry', to: :entries
+              map_attribute 'id', to: :id
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'href', to: :href
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'definition', to: :definitions
+              map 'entry', to: :entries
+              map 'title', to: :title
+              map 'namespace', to: :namespace
+              map 'dictionaryPrefix', to: :dictionary_prefix
+              map 'convention', to: :convention
+              map 'id', to: :id
+              map 'dictRef', to: :dict_ref
+              map 'href', to: :href
             end
           end
         end

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

@@ -7,24 +7,83 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::DictionaryEntry
+
             attribute :id, :string
             attribute :term, :string
             attribute :data_type, :string
             attribute :unit_type, :string
             attribute :units, :string
-            attribute :definition, :string
-            attribute :description, :string
+            attribute :definition, :definition
+            attribute :description, :description
+            attribute :title, :string
+            attribute :convention, :string
+
+            # XSD facet attributes — describe the data type the entry
+            # represents. Emitted by upstream CML dictionaries to
+            # constrain the value space of the term.
+            attribute :columns, :string
+            attribute :rows, :string
+            attribute :length, :string
+            attribute :min_length, :string
+            attribute :max_length, :string
+            attribute :pattern, :string
+            attribute :min_exclusive, :string
+            attribute :min_inclusive, :string
+            attribute :max_exclusive, :string
+            attribute :max_inclusive, :string
+            attribute :fraction_digits, :string
+            attribute :total_digits, :string
+            attribute :white_space, :string
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "entry"
-              map_attribute "id", to: :id
-              map_attribute "term", to: :term
-              map_attribute "dataType", to: :data_type
-              map_attribute "unitType", to: :unit_type
-              map_attribute "units", to: :units
-              map_element "definition", to: :definition
-              map_element "description", to: :description
+              root 'entry'
+              map_attribute 'id', to: :id
+              map_attribute 'term', to: :term
+              map_attribute 'dataType', to: :data_type
+              map_attribute 'unitType', to: :unit_type
+              map_attribute 'units', to: :units
+              map_attribute 'title', to: :title
+              map_attribute 'convention', to: :convention
+              map_attribute 'columns', to: :columns
+              map_attribute 'rows', to: :rows
+              map_attribute 'length', to: :length
+              map_attribute 'minLength', to: :min_length
+              map_attribute 'maxLength', to: :max_length
+              map_attribute 'pattern', to: :pattern
+              map_attribute 'minExclusive', to: :min_exclusive
+              map_attribute 'minInclusive', to: :min_inclusive
+              map_attribute 'maxExclusive', to: :max_exclusive
+              map_attribute 'maxInclusive', to: :max_inclusive
+              map_attribute 'fractionDigits', to: :fraction_digits
+              map_attribute 'totalDigits', to: :total_digits
+              map_attribute 'whiteSpace', to: :white_space
+              map_element 'definition', to: :definition
+              map_element 'description', to: :description
+            end
+            key_value do
+              map 'definition', to: :definition
+              map 'description', to: :description
+              map 'id', to: :id
+              map 'term', to: :term
+              map 'dataType', to: :data_type
+              map 'unitType', to: :unit_type
+              map 'units', to: :units
+              map 'title', to: :title
+              map 'convention', to: :convention
+              map 'columns', to: :columns
+              map 'rows', to: :rows
+              map 'length', to: :length
+              map 'minLength', to: :min_length
+              map 'maxLength', to: :max_length
+              map 'pattern', to: :pattern
+              map 'minExclusive', to: :min_exclusive
+              map 'minInclusive', to: :min_inclusive
+              map 'maxExclusive', to: :max_exclusive
+              map 'maxInclusive', to: :max_inclusive
+              map 'fractionDigits', to: :fraction_digits
+              map 'totalDigits', to: :total_digits
+              map 'whiteSpace', to: :white_space
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Dimension
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -21,18 +22,31 @@ module Chemicalml
             attribute :unit_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "dimension"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "dataType", to: :dataType
-              map_attribute "units", to: :units
-              map_attribute "dimensionBasis", to: :dimension_basis
-              map_attribute "name", to: :name
-              map_attribute "power", to: :power
-              map_attribute "preserve", to: :preserve
-              map_attribute "unitType", to: :unit_type
+              root 'dimension'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'dataType', to: :dataType
+              map_attribute 'units', to: :units
+              map_attribute 'dimensionBasis', to: :dimension_basis
+              map_attribute 'name', to: :name
+              map_attribute 'power', to: :power
+              map_attribute 'preserve', to: :preserve
+              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: :dataType
+              map 'units', to: :units
+              map 'dimensionBasis', to: :dimension_basis
+              map 'name', to: :name
+              map 'power', to: :power
+              map 'preserve', to: :preserve
+              map 'unitType', to: :unit_type
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Document
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -14,17 +15,32 @@ module Chemicalml
             attribute :molecules, :molecule, collection: true
             attribute :reaction_lists, :reactionList, collection: true
             attribute :reactions, :reaction, collection: true
+            attribute :reaction_schemes, :reactionScheme, collection: true
+            attribute :spectra, :spectrum, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "cml"
-              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: :molecules
-              map_element "reactionList", to: :reaction_lists
-              map_element "reaction", to: :reactions
+              root 'cml'
+              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: :molecules
+              map_element 'reactionList', to: :reaction_lists
+              map_element 'reaction', to: :reactions
+              map_element 'reactionScheme', to: :reaction_schemes
+              map_element 'spectrum', to: :spectra
+            end
+            key_value do
+              map 'molecule', to: :molecules
+              map 'reactionList', to: :reaction_lists
+              map 'reaction', to: :reactions
+              map 'reactionScheme', to: :reaction_schemes
+              map 'spectrum', to: :spectra
+              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/documentation.rb

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Eigen
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -16,17 +18,39 @@ module Chemicalml
             attribute :content, :string
 
             attribute :eigen_orientation, :string
+            attribute :orientation, :string
+            attribute :arrays, :array, collection: true
+            attribute :matrices, :matrix, collection: true
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "eigen"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "units", to: :units
-              map_attribute "type", to: :type
+              root 'eigen'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'units', to: :units
+              map_attribute 'type', to: :type
               map_content to: :content
-              map_attribute "eigenOrientation", to: :eigen_orientation
+              map_attribute 'eigenOrientation', to: :eigen_orientation
+              map_attribute 'orientation', to: :orientation
+              map_element 'array', to: :arrays
+              map_element 'matrix', to: :matrices
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'array', to: :arrays
+              map 'matrix', to: :matrices
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'units', to: :units
+              map 'type', to: :type
+              map 'eigenOrientation', to: :eigen_orientation
+              map 'orientation', to: :orientation
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Electron
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -21,18 +22,31 @@ module Chemicalml
             attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "electron"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "atomRef", to: :atomRef
-              map_attribute "bondRef", to: :bondRef
-              map_attribute "count", to: :count
-              map_attribute "spinMultiplicity", to: :spinMultiplicity
-              map_attribute "atomRefs", to: :atom_refs
-              map_attribute "bondRefs", to: :bond_refs
-              map_attribute "ref", to: :ref
+              root 'electron'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'atomRef', to: :atomRef
+              map_attribute 'bondRef', to: :bondRef
+              map_attribute 'count', to: :count
+              map_attribute 'spinMultiplicity', to: :spinMultiplicity
+              map_attribute 'atomRefs', to: :atom_refs
+              map_attribute 'bondRefs', to: :bond_refs
+              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 'atomRef', to: :atomRef
+              map 'bondRef', to: :bondRef
+              map 'count', to: :count
+              map 'spinMultiplicity', to: :spinMultiplicity
+              map 'atomRefs', to: :atom_refs
+              map 'bondRefs', to: :bond_refs
+              map 'ref', to: :ref
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Enumeration
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -16,13 +17,21 @@ module Chemicalml
             attribute :default, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "enumeration"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "value", to: :value
-              map_attribute "default", to: :default
+              root 'enumeration'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'value', to: :value
+              map_attribute 'default', to: :default
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'value', to: :value
+              map 'default', to: :default
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Expression
+
             attribute :title, :string
             attribute :id, :string
             attribute :convention, :string
@@ -14,15 +15,29 @@ module Chemicalml
             attribute :data_type, :string
             attribute :content, :string
 
+            attribute :operators, :operator, collection: true
+            attribute :parameters, :parameter, collection: true
+
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "expression"
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "dataType", to: :data_type
+              root 'expression'
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'dataType', to: :data_type
               map_content to: :content
+              map_element 'operator', to: :operators
+              map_element 'parameter', to: :parameters
+            end
+            key_value do
+              map 'operator', to: :operators
+              map 'parameter', to: :parameters
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'dataType', to: :data_type
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Float
+
             attribute :builtin, :string
             attribute :convention, :string
             attribute :dict_ref, :string
@@ -20,18 +21,29 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "float"
-              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 "units", to: :units
-              map_attribute "unitsRef", to: :units_ref
+              root 'float'
+              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 'units', to: :units
+              map_attribute 'unitsRef', to: :units_ref
               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 'units', to: :units
+              map 'unitsRef', to: :units_ref
+            end
           end
         end
       end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::FloatArray
+
             attribute :builtin, :string
             attribute :convention, :string
             attribute :dict_ref, :string
@@ -21,19 +22,31 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "floatArray"
-              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 "units", to: :units
-              map_attribute "unitsRef", to: :units_ref
+              root 'floatArray'
+              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 'units', to: :units
+              map_attribute 'unitsRef', to: :units_ref
               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 'units', to: :units
+              map 'unitsRef', to: :units_ref
+            end
           end
         end
       end