chemicalml 0.2.1 → 0.4.0

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

@@ -7,28 +7,54 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Bond
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :atom_refs2, :string
+            attribute :atom_refs, :string
             attribute :order, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :bond_stereo, :bondStereo
+            attribute :bond_type, :bondType
+            attribute :electrons, :electron, collection: true
 
             attribute :convention, :string
             attribute :ref, :string
             attribute :bond_refs, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "bond"
-              map_attribute "id", to: :id
-              map_attribute "atomRefs2", to: :atom_refs2
-              map_attribute "order", to: :order
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_element "bondStereo", to: :bond_stereo
-              map_attribute "convention", to: :convention
-              map_attribute "ref", to: :ref
-              map_attribute "bondRefs", to: :bond_refs
+              root 'bond'
+              map_attribute 'id', to: :id
+              map_attribute 'atomRefs2', to: :atom_refs2
+              map_attribute 'atomRefs', to: :atom_refs
+              map_attribute 'order', to: :order
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_element 'bondStereo', to: :bond_stereo
+              map_element 'bondType', to: :bond_type
+              map_element 'electron', to: :electrons
+              map_attribute 'convention', to: :convention
+              map_attribute 'ref', to: :ref
+              map_attribute 'bondRefs', to: :bond_refs
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'bondStereo', to: :bond_stereo
+              map 'bondType', to: :bond_type
+              map 'electron', to: :electrons
+              map 'id', to: :id
+              map 'atomRefs2', to: :atom_refs2
+              map 'atomRefs', to: :atom_refs
+              map 'order', to: :order
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'bondRefs', to: :bond_refs
             end
           end
         end

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

@@ -3,32 +3,55 @@
 module Chemicalml
   module Cml
     module Base
+      # Container for a list of bonds. Two equivalent serialisations:
+      #
+      #   <bondArray><bond atomRefs2="a1 a2" order="1"/></bondArray>
+      #
+      #   <bondArray atomRef1="a1 a2" atomRef2="a2 a3" order="1 2"/>
+      #
+      # The parallel-array form uses the wire attribute names
+      # `atomRef1`, `atomRef2`, `bondID`, `order` — the XSD attribute
+      # *group* is named `atomRef1Array` etc., but the wire attribute
+      # is `atomRef1`.
       module BondArray
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::BondArray
+
             attribute :bonds, :bond, collection: true
 
             attribute :title, :string
             attribute :id, :string
             attribute :convention, :string
             attribute :dict_ref, :string
-            attribute :bond_i_d_array, :string
+
+            attribute :bond_id_array, :string
             attribute :atom_ref1_array, :string
             attribute :atom_ref2_array, :string
             attribute :order_array, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "bondArray"
-              map_element "bond", to: :bonds
-              map_attribute "title", to: :title
-              map_attribute "id", to: :id
-              map_attribute "convention", to: :convention
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "bondIDArray", to: :bond_i_d_array
-              map_attribute "atomRef1Array", to: :atom_ref1_array
-              map_attribute "atomRef2Array", to: :atom_ref2_array
-              map_attribute "orderArray", to: :order_array
+              root 'bondArray'
+              map_element 'bond', to: :bonds
+              map_attribute 'title', to: :title
+              map_attribute 'id', to: :id
+              map_attribute 'convention', to: :convention
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'bondID', to: :bond_id_array
+              map_attribute 'atomRef1', to: :atom_ref1_array
+              map_attribute 'atomRef2', to: :atom_ref2_array
+              map_attribute 'order', to: :order_array
+            end
+            key_value do
+              map 'bond', to: :bonds
+              map 'title', to: :title
+              map 'id', to: :id
+              map 'convention', to: :convention
+              map 'dictRef', to: :dict_ref
+              map 'bondID', to: :bond_id_array
+              map 'atomRef1', to: :atom_ref1_array
+              map 'atomRef2', to: :atom_ref2_array
+              map 'order', to: :order_array
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::BondSet
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -15,12 +16,19 @@ module Chemicalml
             attribute :size, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "bondSet"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "size", to: :size
+              root 'bondSet'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'size', to: :size
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'size', to: :size
             end
           end
         end

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

@@ -7,30 +7,61 @@ 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
             attribute :property_lists, :propertyList, collection: true
             attribute :metadata_lists, :metadataList, collection: true
             attribute :lists, :list, collection: true
+            attribute :reaction_schemes, :reactionScheme, collection: true
+            attribute :spectra, :spectrum, collection: true
 
             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
+              map_element 'reactionScheme', to: :reaction_schemes
+              map_element 'spectrum', to: :spectra
+            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 '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
+              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

@@ -7,20 +7,29 @@ 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
             attribute :convention, :string
             attribute :content, :string
+            attribute :paragraphs, Chemicalml::Cml::Xhtml::P, collection: true
 
             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
+              map_element 'p', to: :paragraphs
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
             end
           end
         end