lutaml 0.10.2 → 0.10.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/.rubocop.yml

@@ -16,4 +16,4 @@ plugins:
   - rubocop-rake
 
 AllCops:
-  TargetRubyVersion: 3.0
+  TargetRubyVersion: 3.2

data/.rubocop_todo.yml

@@ -1,47 +1,32 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config`
-# on 2026-04-20 02:27:04 UTC using RuboCop version 1.86.1.
+# on 2026-04-25 02:05:14 UTC using RuboCop version 1.86.1.
 # The point is for the user to remove these configuration records
 # one by one as the offenses are removed from the code base.
 # Note that changes in the inspected code, or installation of new
 # versions of RuboCop, may require this file to be generated again.
 
-# Offense count: 11
-# This cop supports safe autocorrection (--autocorrect).
-# Configuration parameters: TreatCommentsAsGroupSeparators, ConsiderPunctuation.
-Bundler/OrderedGems:
-  Exclude:
-    - 'Gemfile'
-
-# Offense count: 2
+# Offense count: 1
 # This cop supports safe autocorrection (--autocorrect).
-Layout/ClosingParenthesisIndentation:
+Layout/ElseAlignment:
   Exclude:
-    - 'lib/lutaml/qea/verification/document_verifier.rb'
+    - 'lib/lutaml/qea/factory/class_transformer.rb'
 
-# Offense count: 2
+# Offense count: 1
 # This cop supports safe autocorrection (--autocorrect).
-# Configuration parameters: EnforcedStyle, IndentationWidth.
-# SupportedStyles: consistent, consistent_relative_to_receiver, special_for_inner_method_call, special_for_inner_method_call_in_parentheses
-Layout/FirstArgumentIndentation:
+# Configuration parameters: Width, EnforcedStyleAlignWith, AllowedPatterns.
+# SupportedStylesAlignWith: start_of_line, relative_to_receiver
+Layout/IndentationWidth:
   Exclude:
-    - 'lib/lutaml/qea/verification/document_verifier.rb'
+    - 'lib/lutaml/qea/factory/class_transformer.rb'
 
-# Offense count: 63
+# Offense count: 80
 # This cop supports safe autocorrection (--autocorrect).
 # Configuration parameters: Max, AllowHeredoc, AllowURI, AllowQualifiedName, URISchemes, AllowRBSInlineAnnotation, AllowCopDirectives, AllowedPatterns, SplitStrings.
 # URISchemes: http, https
 Layout/LineLength:
   Enabled: false
 
-# Offense count: 2
-# This cop supports safe autocorrection (--autocorrect).
-# Configuration parameters: EnforcedStyle.
-# SupportedStyles: symmetrical, new_line, same_line
-Layout/MultilineMethodCallBraceLayout:
-  Exclude:
-    - 'lib/lutaml/qea/verification/document_verifier.rb'
-
 # Offense count: 1
 Lint/BinaryOperatorWithIdenticalOperands:
   Exclude:
@@ -58,6 +43,11 @@ Lint/ConstantDefinitionInBlock:
     - 'spec/lutaml/model_transformations_spec.rb'
     - 'spec/lutaml/uml_repository/presenters/presenter_factory_spec.rb'
 
+# Offense count: 1
+Lint/CopDirectiveSyntax:
+  Exclude:
+    - 'lib/lutaml/uml_repository/repository.rb'
+
 # Offense count: 8
 # Configuration parameters: IgnoreLiteralBranches, IgnoreConstantBranches, IgnoreDuplicateElseBranch.
 Lint/DuplicateBranch:
@@ -107,13 +97,17 @@ Lint/UnusedMethodArgument:
   Exclude:
     - 'lib/lutaml/cli/uml/export_command.rb'
 
-# Offense count: 3
+# Offense count: 8
 # Configuration parameters: AllowedMethods, AllowedPatterns, CountRepeatedAttributes, Max.
 Metrics/AbcSize:
   Exclude:
+    - 'lib/lutaml/converter/xmi_to_uml.rb'
     - 'lib/lutaml/model_transformations/parsers/base_parser.rb'
+    - 'lib/lutaml/qea/database.rb'
     - 'lib/lutaml/uml_repository/index_builder.rb'
+    - 'lib/lutaml/uml_repository/queries/class_query.rb'
     - 'lib/lutaml/uml_repository/queries/inheritance_query.rb'
+    - 'lib/lutaml/xmi/parsers/xmi_base.rb'
 
 # Offense count: 1
 # Configuration parameters: CountComments, CountAsOne, AllowedMethods, AllowedPatterns, inherit_mode.
@@ -121,26 +115,36 @@ Metrics/AbcSize:
 Metrics/BlockLength:
   Max: 28
 
-# Offense count: 4
+# Offense count: 11
 # Configuration parameters: AllowedMethods, AllowedPatterns, Max.
 Metrics/CyclomaticComplexity:
   Exclude:
     - 'lib/lutaml/cli/tree_view_formatter.rb'
     - 'lib/lutaml/converter/xmi_to_uml.rb'
+    - 'lib/lutaml/qea/database.rb'
+    - 'lib/lutaml/qea/factory/enum_transformer.rb'
+    - 'lib/lutaml/uml_repository/index_builder.rb'
+    - 'lib/lutaml/uml_repository/queries/class_query.rb'
     - 'lib/lutaml/uml_repository/queries/inheritance_query.rb'
     - 'lib/lutaml/uml_repository/queries/search_query.rb'
+    - 'lib/lutaml/xmi/parsers/xmi_base.rb'
 
-# Offense count: 5
+# Offense count: 11
 # Configuration parameters: CountComments, CountAsOne, AllowedMethods, AllowedPatterns.
 Metrics/MethodLength:
-  Max: 14
+  Max: 27
 
-# Offense count: 2
+# Offense count: 8
 # Configuration parameters: AllowedMethods, AllowedPatterns, Max.
 Metrics/PerceivedComplexity:
   Exclude:
+    - 'lib/lutaml/converter/xmi_to_uml.rb'
+    - 'lib/lutaml/qea/database.rb'
     - 'lib/lutaml/qea/factory/enum_transformer.rb'
+    - 'lib/lutaml/uml_repository/index_builder.rb'
+    - 'lib/lutaml/uml_repository/queries/class_query.rb'
     - 'lib/lutaml/uml_repository/queries/inheritance_query.rb'
+    - 'lib/lutaml/xmi/parsers/xmi_base.rb'
 
 # Offense count: 2
 # Configuration parameters: MinNameLength, AllowNamesEndingInNumbers, AllowedNames, ForbiddenNames.
@@ -158,10 +162,11 @@ Naming/PredicateMethod:
   Exclude:
     - 'lib/lutaml/qea/factory/document_builder.rb'
 
-# Offense count: 4
+# Offense count: 5
 # Configuration parameters: MinSize.
 Performance/CollectionLiteralInLoop:
   Exclude:
+    - 'lib/lutaml/xmi/parsers/xmi_base.rb'
     - 'spec/lutaml/qea/infrastructure/table_reader_spec.rb'
     - 'spec/lutaml/uml_repository/index_builder_spec.rb'
     - 'spec/lutaml/uml_repository/queries/inheritance_query_spec.rb'
@@ -206,7 +211,7 @@ RSpec/ContextWording:
 RSpec/DescribeClass:
   Enabled: false
 
-# Offense count: 651
+# Offense count: 657
 # Configuration parameters: CountAsOne.
 RSpec/ExampleLength:
   Max: 108
@@ -236,7 +241,7 @@ RSpec/IndexedLet:
     - 'spec/lutaml/qea/repositories/base_repository_spec.rb'
     - 'spec/lutaml/qea/repositories/object_repository_spec.rb'
 
-# Offense count: 26
+# Offense count: 48
 # Configuration parameters: AssignmentOnly.
 RSpec/InstanceVariable:
   Exclude:
@@ -274,11 +279,11 @@ RSpec/MessageSpies:
     - 'spec/lutaml/uml_repository/presenters/diagram_presenter_spec.rb'
     - 'spec/lutaml/uml_repository/repository_spec.rb'
 
-# Offense count: 943
+# Offense count: 946
 RSpec/MultipleExpectations:
   Max: 26
 
-# Offense count: 118
+# Offense count: 130
 # Configuration parameters: AllowSubject.
 RSpec/MultipleMemoizedHelpers:
   Max: 11

data/CHANGELOG.md

@@ -0,0 +1,108 @@
+# Changelog
+
+## v0.10.3 (2026-04-25)
+
+### Performance
+
+- Replace O(n) linear scans with O(1) hash lookups in QEA transformers
+  and XMI parsers (connector, diagram, element lookups)
+- Single-pass IndexBuilder replacing 9 separate tree traversals
+- Memoized inheritance depth in StatisticsCalculator
+- Set-based dedup in Repository associations_index
+
+### Bug fixes
+
+- Fix Windows EACCES: replace Tempfile.new with temp_lur_path helper
+  to avoid file handle conflicts with rubyzip
+- Fix xml_spec: use include matcher for platform-varying content nodes
+
+### Improvements
+
+- Consistent error hierarchy: all module error classes now inherit from
+  `Lutaml::Error` (single rescue point for consumers)
+- Fix gemspec email typo (mismatched quote)
+- Bump required_ruby_version from >= 2.7 to >= 3.2 (matching CI)
+- Rubocop: 0 offenses remaining
+
+## v0.10.2 (2026-04-24)
+
+### Bug fixes
+
+- Fix Windows Errno::EACCES in PackageExporter: retry on file lock race
+- Remove moxml git override (0.1.15 released)
+
+## v0.10.1 (2026-04-23)
+
+### Bug fixes
+
+- Fix flaky CI tests: benchmark speedup assertion and Windows Tempfile race
+- Fix xmi 0.5.6 compatibility: rename SparxRoot to Sparx::Root
+- Fix nil @xmi_index in liquid drops: auto-init via xmi_index method
+- Fix infinite loop in resolve_package_path with circular package hierarchy
+- Fix stereotype type bugs, diagram package_id overwrite, and
+  DataTypeTransformer crash
+- Fix 46 pending/failing spec tests across QEA, verification, and liquid specs
+
+## v0.10.0 (2026-04-21)
+
+### Breaking changes
+
+- Update to lutaml-model 0.8.0, expressir 2.3, and xmi 0.5.x
+- Migrate Lutaml::Uml models to lutaml-model serialization
+- Unify namespace of Sysml module
+
+### Features
+
+- Complete QEA to UML document migration
+- Add PackagePresenter for structured output
+- Add option to skip queries
+- Add function to get qualified name
+- Add Lutaml::Uml::Fidelity class
+- Add attributes type, weight and status to Lutaml::Uml::Constraint
+- Add generalization into Lutaml::Uml::Class
+- Transform option keys to symbol
+- Output find result based on format option
+- Implement default sorting for diff_with_score comparison
+- find_by_name returns single object instead of array
+
+### Bug fixes
+
+- Fix Windows EACCES file rename issues (Tempfile handle conflicts)
+- Fix YAML disallowed class loading error
+- Fix attribute parsing values
+- Fix association loading by QEA parser
+- Fix association_generalization parsed by xmi parser
+- Fix certificate CRL error
+
+## v0.9.43 (2025-11-20)
+
+- Refactor klass_hash to use KlassDrop object in upper_klass
+
+## v0.9.42 (2025-11-18)
+
+- Directly convert XMI into UML
+
+## v0.9.41 (2025-11-12)
+
+- Remove unneeded version files
+- Fix error when imports key is nil
+- Unify Sysml namespace
+
+## v0.9.40 (2025-11-10)
+
+- Convert DSL to UML
+- Change namespace of Formatter and HasAttributes
+- Update GraphViz and related specs
+- Add Lutaml::Uml::Fidelity class
+- Remove duplicated GraphViz code
+- Create Lutaml::Uml models by Xmi hash
+- Migrate Lutaml::Uml models to lutaml-model
+
+## v0.9.39 (2025-11-03)
+
+- Change selection criteria for dependencies
+
+## v0.9.38 (2025-10-31)
+
+- Add subtype_of to klass and enum drop models
+- Get stereotype by type idref in owned attribute

data/lib/lutaml/cli/uml_commands.rb

@@ -139,8 +139,8 @@ module Lutaml
 
       desc "diagram ACTION", "Diagram rendering commands"
       Uml::DiagramCommand.add_options_to(self, :diagram)
-      def diagram(action, *args)
-        Uml::DiagramCommand.new(options.to_h).run(action, *args)
+      def diagram(action, *)
+        Uml::DiagramCommand.new(options.to_h).run(action, *)
       end
 
       # ===================================================================

data/lib/lutaml/command_line.rb

@@ -10,7 +10,7 @@ require_relative "uml/parsers/yaml"
 
 module Lutaml
   class CommandLine
-    class Error < StandardError; end
+    class Error < Lutaml::Error; end
     class FileError < Error; end
     class NotSupportedInputFormat < Error; end
 

data/lib/lutaml/converter/xmi_to_uml.rb

@@ -126,9 +126,7 @@ module Lutaml
       def create_uml_diagrams(node_id) # rubocop:disable Metrics/AbcSize,Metrics/MethodLength,Metrics/CyclomaticComplexity,Metrics/PerceivedComplexity
         return [] if @xmi_root_model.extension&.diagrams&.diagram.nil?
 
-        diagrams = @xmi_root_model.extension.diagrams.diagram.select do |d|
-          d.model.package == node_id
-        end
+        diagrams = diagram_lookup[node_id]
 
         diagrams.map do |diagram|
           ::Lutaml::Uml::Diagram.new.tap do |dia|
@@ -145,6 +143,17 @@ module Lutaml
         end
       end
 
+      # Lazy-built hash index for O(1) diagram lookups by package
+      # @return [Hash] Mapping of package_id => [diagrams]
+      def diagram_lookup
+        @diagram_lookup ||= begin
+          idx = Hash.new { |h, k| h[k] = [] }
+          diagrams = @xmi_root_model.extension&.diagrams&.diagram || []
+          diagrams.each { |d| idx[d.model.package] << d if d.model&.package }
+          idx
+        end
+      end
+
       def create_uml_class_attributes(klass) # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/MethodLength
         return [] if klass.owned_attribute.nil?
 

data/lib/lutaml/model_transformations/parsers/base_parser.rb

@@ -421,7 +421,7 @@ module Lutaml
       end
 
       # Custom error class for parsing failures
-      class ParseError < StandardError
+      class ParseError < Lutaml::Error
         # @return [StandardError] Original error that caused parsing failure
         attr_reader :original_error
 

data/lib/lutaml/model_transformations/transformation_engine.rb

@@ -392,7 +392,7 @@ module Lutaml
     end
 
     # Error class for unsupported file formats
-    class UnsupportedFormatError < StandardError
+    class UnsupportedFormatError < Lutaml::Error
       # @return [String] Path to the unsupported file
       attr_reader :file_path
 

data/lib/lutaml/qea/database.rb

@@ -268,7 +268,9 @@ module Lutaml
       # @param id [Integer] Package ID
       # @return [Models::EaPackage, nil] The package or nil if not found
       def find_package(id)
-        packages.find { |pkg| pkg.package_id == id }
+        @packages_by_id ||= build_group_index(packages, :package_id,
+                                              single: true)
+        @packages_by_id[id]
       end
 
       # Find an attribute by ID
@@ -276,7 +278,8 @@ module Lutaml
       # @param id [Integer] Attribute ID
       # @return [Models::EaAttribute, nil] The attribute or nil if not found
       def find_attribute(id)
-        attributes.find { |attr| attr.id == id }
+        @attributes_by_id ||= build_group_index(attributes, :id, single: true)
+        @attributes_by_id[id]
       end
 
       # Find a connector by ID
@@ -284,7 +287,9 @@ module Lutaml
       # @param id [Integer] Connector ID
       # @return [Models::EaConnector, nil] The connector or nil if not found
       def find_connector(id)
-        connectors.find { |conn| conn.connector_id == id }
+        @connectors_by_id ||= build_group_index(connectors, :connector_id,
+                                                single: true)
+        @connectors_by_id[id]
       end
 
       # Find a diagram by ID
@@ -292,7 +297,9 @@ module Lutaml
       # @param id [Integer] Diagram ID
       # @return [Models::EaDiagram, nil] The diagram or nil if not found
       def find_diagram(id)
-        diagrams.find { |diag| diag.diagram_id == id }
+        @diagrams_by_id ||= build_group_index(diagrams, :diagram_id,
+                                              single: true)
+        @diagrams_by_id[id]
       end
 
       # Check if database is empty
@@ -309,6 +316,102 @@ module Lutaml
         @collections.keys
       end
 
+      # Find object by ea_guid
+      #
+      # @param ea_guid [String] Object GUID
+      # @return [Models::EaObject, nil] The object or nil if not found
+      def find_object_by_guid(ea_guid)
+        @objects_by_guid ||= build_group_index(objects, :ea_guid, single: true)
+        @objects_by_guid[ea_guid]
+      end
+
+      # Get attributes for a specific object
+      #
+      # @param object_id [Integer] Object ID
+      # @return [Array<Models::EaAttribute>] Attributes for the object
+      def attributes_for_object(object_id)
+        @attributes_by_object_id ||= build_group_index(attributes,
+                                                       :ea_object_id)
+        @attributes_by_object_id[object_id] || []
+      end
+
+      # Get operations for a specific object
+      #
+      # @param object_id [Integer] Object ID
+      # @return [Array<Models::EaOperation>] Operations for the object
+      def operations_for_object(object_id)
+        @operations_by_object_id ||= build_group_index(operations,
+                                                       :ea_object_id)
+        @operations_by_object_id[object_id] || []
+      end
+
+      # Get operation parameters for a specific operation
+      #
+      # @param operation_id [Integer] Operation ID
+      # @return [Array<Models::EaOperationParam>] Parameters for the operation
+      def operation_params_for(operation_id)
+        @operation_params_by_id ||= build_group_index(operation_params,
+                                                      :operationid)
+        @operation_params_by_id[operation_id] || []
+      end
+
+      # Get connectors involving a specific object (start or end)
+      #
+      # @param object_id [Integer] Object ID
+      # @return [Array<Models::EaConnector>] Connectors for the object
+      def connectors_for_object(object_id)
+        @connectors_by_start ||= build_group_index(connectors, :start_object_id)
+        @connectors_by_end ||= build_group_index(connectors, :end_object_id)
+        (@connectors_by_start[object_id] || []) +
+          (@connectors_by_end[object_id] || [])
+      end
+
+      # Get child packages for a parent
+      #
+      # @param parent_id [Integer] Parent package ID
+      # @return [Array<Models::EaPackage>] Child packages
+      def child_packages_for(parent_id)
+        @packages_by_parent ||= build_group_index(packages, :parent_id)
+        @packages_by_parent[parent_id] || []
+      end
+
+      # Get objects in a specific package
+      #
+      # @param package_id [Integer] Package ID
+      # @return [Array<Models::EaObject>] Objects in the package
+      def objects_in_package(package_id)
+        @objects_by_package_id ||= build_group_index(objects, :package_id)
+        @objects_by_package_id[package_id] || []
+      end
+
+      # Get diagrams in a specific package
+      #
+      # @param package_id [Integer] Package ID
+      # @return [Array<Models::EaDiagram>] Diagrams in the package
+      def diagrams_in_package(package_id)
+        @diagrams_by_package_id ||= build_group_index(diagrams, :package_id)
+        @diagrams_by_package_id[package_id] || []
+      end
+
+      # Get diagram objects for a specific diagram
+      #
+      # @param diagram_id [Integer] Diagram ID
+      # @return [Array<Models::EaDiagramObject>] Diagram objects
+      def diagram_objects_for(diagram_id)
+        @diagram_objects_by_id ||= build_group_index(diagram_objects,
+                                                     :diagram_id)
+        @diagram_objects_by_id[diagram_id] || []
+      end
+
+      # Get diagram links for a specific diagram
+      #
+      # @param diagram_id [Integer] Diagram ID
+      # @return [Array<Models::EaDiagramLink>] Diagram links
+      def diagram_links_for(diagram_id)
+        @diagram_links_by_id ||= build_group_index(diagram_links, :diagramid)
+        @diagram_links_by_id[diagram_id] || []
+      end
+
       # Freeze all collections to make database immutable
       #
       # @return [self]
@@ -316,9 +419,59 @@ module Lutaml
         # Memoize repositories before freezing
         objects
 
+        # Eagerly build all lookup indexes before freezing
+        build_lookup_indexes
+
         @collections.freeze
         super
       end
+
+      private
+
+      # Build a group index from a collection by a given attribute.
+      # BaseRepository overrides group_by to take a symbol (not a block),
+      # so we use each_with_object instead.
+      #
+      # @param collection [Array] Collection to index
+      # @param method [Symbol] Attribute method to group by
+      # @param single [Boolean] If true, return single object (last match)
+      #   instead of array
+      # @return [Hash] Group index
+      def build_group_index(collection, method, single: false)
+        if single
+          collection.each_with_object({}) do |item, hash|
+            key = item.send(method)
+            hash[key] = item if key
+          end
+        else
+          collection.each_with_object({}) do |item, hash|
+            key = item.send(method)
+            (hash[key] ||= []) << item if key
+          end
+        end
+      end
+
+      # Eagerly build all lazy lookup indexes before freezing
+      def build_lookup_indexes
+        @objects_by_guid = build_group_index(objects, :ea_guid, single: true)
+        @attributes_by_object_id = build_group_index(attributes, :ea_object_id)
+        @operations_by_object_id = build_group_index(operations, :ea_object_id)
+        @operation_params_by_id = build_group_index(operation_params,
+                                                    :operationid)
+        @connectors_by_start = build_group_index(connectors, :start_object_id)
+        @connectors_by_end = build_group_index(connectors, :end_object_id)
+        @packages_by_parent = build_group_index(packages, :parent_id)
+        @objects_by_package_id = build_group_index(objects, :package_id)
+        @diagrams_by_package_id = build_group_index(diagrams, :package_id)
+        @diagram_objects_by_id = build_group_index(diagram_objects, :diagram_id)
+        @diagram_links_by_id = build_group_index(diagram_links, :diagramid)
+        # Also build hash indexes for find_* methods
+        @packages_by_id = build_group_index(packages, :package_id, single: true)
+        @connectors_by_id = build_group_index(connectors, :connector_id,
+                                              single: true)
+        @diagrams_by_id = build_group_index(diagrams, :diagram_id, single: true)
+        @attributes_by_id = build_group_index(attributes, :id, single: true)
+      end
     end
   end
 end

data/lib/lutaml/qea/factory/association_transformer.rb

@@ -71,11 +71,7 @@ module Lutaml
         def find_object(object_id)
           return nil if object_id.nil?
 
-          query = "SELECT * FROM t_object WHERE Object_ID = ?"
-          rows = database.connection.execute(query, object_id)
-          return nil if rows.empty?
-
-          Models::EaObject.from_db_row(rows.first)
+          database.find_object(object_id)
         end
 
         # Build cardinality from string

data/lib/lutaml/qea/factory/attribute_transformer.rb

@@ -55,16 +55,10 @@ module Lutaml
         def lookup_type_xmi_id(classifier_id) # rubocop:disable Metrics/AbcSize
           return nil if classifier_id.nil? || classifier_id.to_i.zero?
 
-          query = "SELECT ea_guid FROM t_object WHERE Object_ID = ?"
-          rows = database.connection.execute(query, [classifier_id])
-          return nil if rows.empty?
-
-          ea_guid = if rows.first.is_a?(Hash)
-                      rows.first["ea_guid"] || rows.first[:ea_guid]
-                    else
-                      rows.first[0]
-                    end
-          normalize_guid_to_xmi_format(ea_guid, "EAID")
+          obj = database.find_object(classifier_id.to_i)
+          return nil unless obj
+
+          normalize_guid_to_xmi_format(obj.ea_guid, "EAID")
         end
 
         # Build cardinality from lower and upper bounds

data/lib/lutaml/qea/factory/base_transformer.rb

@@ -120,11 +120,7 @@ module Lutaml
         def find_object_by_id(object_id)
           return nil if object_id.nil?
 
-          query = "SELECT * FROM t_object WHERE Object_ID = ?"
-          rows = database.connection.execute(query, object_id)
-          return nil if rows.empty?
-
-          Models::EaObject.from_db_row(rows.first)
+          database.find_object(object_id)
         end
       end
     end