chemicalml 0.2.1 → 0.3.0

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::BondStereo
+
             attribute :atom_refs2, :string
             attribute :atom_refs4, :string
             attribute :dict_ref, :string
@@ -19,16 +20,26 @@ module Chemicalml
             attribute :convention_value, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "bondStereo"
-              map_attribute "atomRefs2", to: :atom_refs2
-              map_attribute "atomRefs4", to: :atom_refs4
-              map_attribute "dictRef", to: :dict_ref
+              root 'bondStereo'
+              map_attribute 'atomRefs2', to: :atom_refs2
+              map_attribute 'atomRefs4', to: :atom_refs4
+              map_attribute 'dictRef', to: :dict_ref
               map_content to: :content
-              map_attribute "atomRefArray", to: :atom_ref_array
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "conventionValue", to: :convention_value
+              map_attribute 'atomRefArray', to: :atom_ref_array
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'conventionValue', to: :convention_value
+            end
+            key_value do
+              map 'atomRefs2', to: :atom_refs2
+              map 'atomRefs4', to: :atom_refs4
+              map 'dictRef', to: :dict_ref
+              map 'atomRefArray', to: :atom_ref_array
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'conventionValue', to: :convention_value
             end
           end
         end

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::BondType
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -17,14 +19,27 @@ module Chemicalml
             attribute :name, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "bondType"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "order", to: :order
-              map_attribute "ref", to: :ref
-              map_attribute "name", to: :name
+              root 'bondType'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'order', to: :order
+              map_attribute 'ref', to: :ref
+              map_attribute 'name', to: :name
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'order', to: :order
+              map 'ref', to: :ref
+              map 'name', to: :name
             end
           end
         end

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

@@ -7,23 +7,37 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::BondTypeList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :bond_types, :bondType, collection: true
+            attribute :bond_types, :bondType, collection: true
 
             attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "bondType", to: :bond_types
-              root "bondTypeList"
-              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_element 'bondType', to: :bond_types
+              root 'bondTypeList'
+              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 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'bondType', to: :bond_types
+              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/cell_parameter.rb

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::CellParameter
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -17,18 +18,35 @@ module Chemicalml
 
             attribute :cell_parameter_type, :string
             attribute :cell_parameter_error, :string
+            attribute :type, :string
+            attribute :error, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "cellParameter"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "cellType", to: :cellType
-              map_attribute "parameterType", to: :parameterType
-              map_attribute "units", to: :units
-              map_attribute "cellParameterType", to: :cell_parameter_type
-              map_attribute "cellParameterError", to: :cell_parameter_error
+              root 'cellParameter'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'cellType', to: :cellType
+              map_attribute 'parameterType', to: :parameterType
+              map_attribute 'units', to: :units
+              map_attribute 'cellParameterType', to: :cell_parameter_type
+              map_attribute 'cellParameterError', to: :cell_parameter_error
+              map_attribute 'type', to: :type
+              map_attribute 'error', to: :error
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'cellType', to: :cellType
+              map 'parameterType', to: :parameterType
+              map 'units', to: :units
+              map 'cellParameterType', to: :cell_parameter_type
+              map 'cellParameterError', to: :cell_parameter_error
+              map 'type', to: :type
+              map 'error', to: :error
             end
           end
         end

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

@@ -7,10 +7,15 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Module
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
+            attribute :file_id, :string
+            attribute :version, :string
+            attribute :role, :string
+            attribute :serial, :string
             attribute :molecules, :molecule, collection: true
             attribute :modules, :module, collection: true
             attribute :parameter_lists, :parameterList, collection: true
@@ -20,17 +25,37 @@ module Chemicalml
 
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "module"
-              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 "module", to: :modules
-              map_element "parameterList", to: :parameter_lists
-              map_element "propertyList", to: :property_lists
-              map_element "metadataList", to: :metadata_lists
-              map_element "list", to: :lists
+              root 'module'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'fileId', to: :file_id
+              map_attribute 'version', to: :version
+              map_attribute 'role', to: :role
+              map_attribute 'serial', to: :serial
+              map_element 'molecule', to: :molecules
+              map_element 'module', to: :modules
+              map_element 'parameterList', to: :parameter_lists
+              map_element 'propertyList', to: :property_lists
+              map_element 'metadataList', to: :metadata_lists
+              map_element 'list', to: :lists
+            end
+            key_value do
+              map 'molecule', to: :molecules
+              map 'module', to: :modules
+              map 'parameterList', to: :parameter_lists
+              map 'propertyList', to: :property_lists
+              map 'metadataList', to: :metadata_lists
+              map 'list', to: :lists
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'fileId', to: :file_id
+              map 'version', to: :version
+              map 'role', to: :role
+              map 'serial', to: :serial
             end
           end
         end

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

@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Base
+      # Universal CML child elements. The XSD grants metadataList,
+      # label, name, and description as children to most CML elements.
+      # Mixing this module into a Base::* module adds the four child
+      # declarations in one place — keeping DRY discipline.
+      #
+      # Opt-in: only Base modules whose XSD declares these children
+      # include this mixin. This respects MECE ownership — each child
+      # declaration lives in exactly one place (here, for the universal
+      # set; in the specific Base module for element-specific
+      # children).
+      module CommonChildren
+        def self.included(klass)
+          klass.class_eval do
+            attribute :metadata_lists, :metadataList, collection: true
+            attribute :labels, :label, collection: true
+            attribute :names, :name, collection: true
+            attribute :descriptions, :description, collection: true
+
+            xml do
+              map_element 'metadataList', to: :metadata_lists
+              map_element 'label', to: :labels
+              map_element 'name', to: :names
+              map_element 'description', to: :descriptions
+            end
+          end
+        end
+      end
+    end
+  end
+end

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

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

@@ -7,27 +7,43 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::ConditionList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :scalars, :scalar, collection: true
+            attribute :scalars, :scalar, collection: true
             attribute :metadata, :metadata
 
             attribute :ref, :string
             attribute :role, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "scalar", to: :scalars
-              map_element "metadata", to: :metadata
-              root "conditionList"
-              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 "role", to: :role
+              map_element 'scalar', to: :scalars
+              map_element 'metadata', to: :metadata
+              root 'conditionList'
+              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 'role', to: :role
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'scalar', to: :scalars
+              map 'metadata', to: :metadata
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'role', to: :role
             end
           end
         end

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

@@ -7,27 +7,43 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Crystal
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
-                        attribute :scalars, :scalar, collection: true
+            attribute :scalars, :scalar, collection: true
             attribute :lattice, :lattice
             attribute :symmetry, :symmetry
 
             attribute :z, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "scalar", to: :scalars
-              map_element "lattice", to: :lattice
-              map_element "symmetry", to: :symmetry
-              root "crystal"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "z", to: :z
+              map_element 'scalar', to: :scalars
+              map_element 'lattice', to: :lattice
+              map_element 'symmetry', to: :symmetry
+              root 'crystal'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'z', to: :z
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'scalar', to: :scalars
+              map 'lattice', to: :lattice
+              map 'symmetry', to: :symmetry
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'z', to: :z
             end
           end
         end

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

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

@@ -7,6 +7,7 @@ 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
@@ -16,13 +17,20 @@ module Chemicalml
             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_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

@@ -7,6 +7,8 @@ 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
@@ -19,16 +21,31 @@ module Chemicalml
             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 'description', to: :description
+              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 'description', to: :description
+              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

@@ -7,6 +7,7 @@ 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
@@ -14,17 +15,75 @@ module Chemicalml
             attribute :units, :string
             attribute :definition, :string
             attribute :description, :string
+            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