chemicalml 0.2.0 → 0.3.0

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

@@ -7,6 +7,8 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Lattice
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -14,18 +16,43 @@ module Chemicalml
             attribute :latticeType, :string
             attribute :units, :string
 
-                        attribute :lattice_vectors, :latticeVector, collection: true
+            attribute :lattice_vectors, :latticeVector, collection: true
+            attribute :matrices, :matrix, collection: true
+            attribute :scalars, :scalar, collection: true
+            attribute :symmetries, :symmetry, collection: true
 
+            attribute :space_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              map_element "latticeVector", to: :lattice_vectors
-              root "lattice"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "latticeType", to: :latticeType
-              map_attribute "units", to: :units
+              map_element 'latticeVector', to: :lattice_vectors
+              map_element 'matrix', to: :matrices
+              map_element 'scalar', to: :scalars
+              map_element 'symmetry', to: :symmetries
+              root 'lattice'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'latticeType', to: :latticeType
+              map_attribute 'units', to: :units
+              map_attribute 'spaceType', to: :space_type
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'latticeVector', to: :lattice_vectors
+              map 'matrix', to: :matrices
+              map 'scalar', to: :scalars
+              map 'symmetry', to: :symmetries
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'latticeType', to: :latticeType
+              map 'units', to: :units
+              map 'spaceType', to: :space_type
             end
           end
         end

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

@@ -7,20 +7,31 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::LatticeVector
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :units, :string
 
+            attribute :periodic, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "latticeVector"
-              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
+              root 'latticeVector'
+              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 'periodic', to: :periodic
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'units', to: :units
+              map 'periodic', to: :periodic
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Length
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -14,15 +15,38 @@ module Chemicalml
             attribute :atomRefs2, :string
             attribute :units, :string
 
+            attribute :error_value, :string
+            attribute :error_basis, :string
+            attribute :min, :string
+            attribute :max, :string
+            attribute :ref, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "length"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "atomRefs2", to: :atomRefs2
-              map_attribute "units", to: :units
+              root 'length'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'atomRefs2', to: :atomRefs2
+              map_attribute 'units', to: :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 'atomRefs2', to: :atomRefs2
+              map 'units', to: :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/line3.rb

@@ -7,20 +7,36 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Line3
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :content, :string
 
+            attribute :units, :string
+            attribute :point3, :string
+            attribute :vector3, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "line3"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'line3'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
               map_content to: :content
+              map_attribute 'units', to: :units
+              map_attribute 'point3', to: :point3
+              map_attribute 'vector3', to: :vector3
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'units', to: :units
+              map 'point3', to: :point3
+              map 'vector3', to: :vector3
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Link
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -17,18 +18,58 @@ module Chemicalml
             attribute :type, :string
             attribute :role, :string
 
+            attribute :from, :string
+            attribute :to, :string
+            attribute :ref, :string
+            attribute :from_type, :string
+            attribute :to_type, :string
+            attribute :from_set, :string
+            attribute :to_set, :string
+            attribute :from_context, :string
+            attribute :to_context, :string
+            attribute :link_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "link"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_attribute "href", to: :href
-              map_attribute "rel", to: :rel
-              map_attribute "title", to: :title
-              map_attribute "type", to: :type
-              map_attribute "role", to: :role
+              root 'link'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_attribute 'href', to: :href
+              map_attribute 'rel', to: :rel
+              map_attribute 'title', to: :title
+              map_attribute 'type', to: :type
+              map_attribute 'role', to: :role
+              map_attribute 'from', to: :from
+              map_attribute 'to', to: :to
+              map_attribute 'ref', to: :ref
+              map_attribute 'fromType', to: :from_type
+              map_attribute 'toType', to: :to_type
+              map_attribute 'fromSet', to: :from_set
+              map_attribute 'toSet', to: :to_set
+              map_attribute 'fromContext', to: :from_context
+              map_attribute 'toContext', to: :to_context
+              map_attribute 'linkType', to: :link_type
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'href', to: :href
+              map 'rel', to: :rel
+              map 'type', to: :type
+              map 'role', to: :role
+              map 'from', to: :from
+              map 'to', to: :to
+              map 'ref', to: :ref
+              map 'fromType', to: :from_type
+              map 'toType', to: :to_type
+              map 'fromSet', to: :from_set
+              map 'toSet', to: :to_set
+              map 'fromContext', to: :from_context
+              map 'toContext', to: :to_context
+              map 'linkType', to: :link_type
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::List
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -16,17 +17,30 @@ module Chemicalml
             attribute :matrices, :matrix, collection: true
             attribute :lists, :list, collection: true
 
+            attribute :type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "list"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
-              map_element "scalar", to: :scalars
-              map_element "array", to: :arrays
-              map_element "matrix", to: :matrices
-              map_element "list", to: :lists
+              root 'list'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'convention', to: :convention
+              map_element 'scalar', to: :scalars
+              map_element 'array', to: :arrays
+              map_element 'matrix', to: :matrices
+              map_element 'list', to: :lists
+              map_attribute 'type', to: :type
+            end
+            key_value do
+              map 'scalar', to: :scalars
+              map 'array', to: :arrays
+              map 'matrix', to: :matrices
+              map 'list', to: :lists
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'type', to: :type
             end
           end
         end

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

@@ -7,18 +7,51 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Map
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :convention, :string
 
+            attribute :ref, :string
+            attribute :from_type, :string
+            attribute :to_type, :string
+            attribute :from_context, :string
+            attribute :to_context, :string
+            attribute :role, :string
+            attribute :links, :link, collection: true
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "map"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "convention", to: :convention
+              root 'map'
+              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 'fromType', to: :from_type
+              map_attribute 'toType', to: :to_type
+              map_attribute 'fromContext', to: :from_context
+              map_attribute 'toContext', to: :to_context
+              map_attribute 'role', to: :role
+              map_element 'link', to: :links
+            end
+            key_value do
+              map 'metadataList', to: :metadata_lists
+              map 'label', to: :labels
+              map 'name', to: :names
+              map 'description', to: :descriptions
+              map 'link', to: :links
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'ref', to: :ref
+              map 'fromType', to: :from_type
+              map 'toType', to: :to_type
+              map 'fromContext', to: :from_context
+              map 'toContext', to: :to_context
+              map 'role', to: :role
             end
           end
         end

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

@@ -7,6 +7,7 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Matrix
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
@@ -17,18 +18,46 @@ module Chemicalml
             attribute :delimiter, :string
             attribute :content, :string
 
+            attribute :convention, :string
+            attribute :matrix_type, :string
+            attribute :error_value_array, :string
+            attribute :error_basis, :string
+            attribute :min_value_array, :string
+            attribute :max_value_array, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "matrix"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_attribute "dataType", to: :data_type
-              map_attribute "units", to: :units
-              map_attribute "rows", to: :rows
-              map_attribute "columns", to: :columns
-              map_attribute "delimiter", to: :delimiter
+              root 'matrix'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'dataType', to: :data_type
+              map_attribute 'units', to: :units
+              map_attribute 'rows', to: :rows
+              map_attribute 'columns', to: :columns
+              map_attribute 'delimiter', to: :delimiter
               map_content to: :content
+              map_attribute 'convention', to: :convention
+              map_attribute 'matrixType', to: :matrix_type
+              map_attribute 'errorValueArray', to: :error_value_array
+              map_attribute 'errorBasis', to: :error_basis
+              map_attribute 'minValueArray', to: :min_value_array
+              map_attribute 'maxValueArray', to: :max_value_array
+            end
+            key_value do
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'dataType', to: :data_type
+              map 'units', to: :units
+              map 'rows', to: :rows
+              map 'columns', to: :columns
+              map 'delimiter', to: :delimiter
+              map 'convention', to: :convention
+              map 'matrixType', to: :matrix_type
+              map 'errorValueArray', to: :error_value_array
+              map 'errorBasis', to: :error_basis
+              map 'minValueArray', to: :min_value_array
+              map 'maxValueArray', to: :max_value_array
             end
           end
         end

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

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

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

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

@@ -7,20 +7,34 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::Metadata
+
             attribute :id, :string
             attribute :name, :string
             attribute :content, :string
             attribute :convention, :string
             attribute :title, :string
 
+            attribute :dict_ref, :string
+            attribute :metadata_type, :string
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "metadata"
-              map_attribute "id", to: :id
-              map_attribute "name", to: :name
-              map_attribute "content", to: :content
-              map_attribute "convention", to: :convention
-              map_attribute "title", to: :title
+              root 'metadata'
+              map_attribute 'id', to: :id
+              map_attribute 'name', to: :name
+              map_attribute 'content', to: :content
+              map_attribute 'convention', to: :convention
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_attribute 'metadataType', to: :metadata_type
+            end
+            key_value do
+              map 'id', to: :id
+              map 'name', to: :name
+              map 'content', to: :content
+              map 'convention', to: :convention
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'metadataType', to: :metadata_type
             end
           end
         end

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

@@ -7,18 +7,43 @@ module Chemicalml
         def self.included(klass)
           klass.class_eval do
             include Chemicalml::Cml::Role::MetadataList
+            include Chemicalml::Cml::Base::CommonChildren
+
             attribute :id, :string
             attribute :title, :string
             attribute :dict_ref, :string
             attribute :metadata, :metadata, collection: true
 
+            attribute :convention, :string
+            attribute :name, :string
+            attribute :role, :string
+            attribute :metadata_lists_inner, :metadataList, collection: true
+
             xml do
               namespace Chemicalml::Cml::Namespace
-              root "metadataList"
-              map_attribute "id", to: :id
-              map_attribute "title", to: :title
-              map_attribute "dictRef", to: :dict_ref
-              map_element "metadata", to: :metadata
+              root 'metadataList'
+              map_attribute 'id', to: :id
+              map_attribute 'title', to: :title
+              map_attribute 'dictRef', to: :dict_ref
+              map_element 'metadata', to: :metadata
+              map_element 'metadataList', to: :metadata_lists_inner
+              map_attribute 'convention', to: :convention
+              map_attribute 'name', to: :name
+              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 'metadata', to: :metadata
+              map 'metadataList', to: :metadata_lists_inner
+              map 'id', to: :id
+              map 'title', to: :title
+              map 'dictRef', to: :dict_ref
+              map 'convention', to: :convention
+              map 'name', to: :name
+              map 'role', to: :role
             end
           end
         end