lutaml 0.10.18 → 0.11.2

data/Makefile

@@ -1,2 +0,0 @@
-fix-lint-staged:
-	git status --short | egrep '^(A|M)' | awk '{ print $$2}' | grep -v db/schema.rb | xargs bundle exec rubocop -a

data/TODO.cleanups/05-replace-marshal-load.md

@@ -1,37 +0,0 @@
-# 05 — Replace Marshal.load with safe deserialization (4 offenses)
-
-## Problem
-
-`Marshal.load` is flagged by `Security/MarshalLoad` because deserializing untrusted data can lead to remote code execution. The gem uses it in the `.lur` package format (a ZIP file containing serialized Ruby objects).
-
-## Affected files
-
-```ruby
-# lib/lutaml/uml_repository/package_loader.rb:194
-Marshal.load(entry.get_input_stream.read)
-
-# lib/lutaml/uml_repository/package_loader.rb:210
-Marshal.load(entry.get_input_stream.read)
-
-# spec/lutaml/uml_repository/package_exporter_spec.rb:141
-expect { Marshal.load(serialized) }.not_to raise_error
-
-# spec/lutaml/uml_repository/package_exporter_spec.rb:171
-expect { Marshal.load(serialized) }.not_to raise_error
-```
-
-## Approach
-
-**Option A: Switch to JSON serialization** — Replace `Marshal.dump`/`Marshal.load` with `JSON.generate`/`JSON.parse` in `PackageExporter` and `PackageLoader`. This is safe but requires models to be JSON-serializable.
-
-**Option B: Use YAML with permitted classes** — `YAML.safe_load` with an explicit allowlist of classes. More flexible but still requires maintaining the class list.
-
-**Option C: Keep Marshal but document the trust boundary** — If `.lur` files are only ever created by the gem itself (trusted), the risk is mitigated. Add a clear comment at the load site and suppress the cop with justification.
-
-**Recommended**: Option A if feasible (cleanest), Option C as a minimal fix.
-
-## Verification
-
-- `bundle exec rubocop --only Security/MarshalLoad` shows 0 offenses
-- `.lur` package round-trip (export → load) works correctly
-- `bundle exec rspec` passes

data/TODO.cleanups/06-replace-eval-in-tests.md

@@ -1,41 +0,0 @@
-# 06 — Replace eval in tests with StringIO redirection (3 Security/Eval + 2 Style/EvalWithLocation + 2 Style/DocumentDynamicEvalDefinition)
-
-## Problem
-
-`spec/lutaml/cli/uml/search_command_spec.rb` uses `eval` to redirect `$stdout`/`$stderr` for capturing output. This triggers 7 rubocop offenses across Security and Style cops.
-
-## Affected code
-
-```ruby
-# spec/lutaml/cli/uml/search_command_spec.rb:61-65
-old_stream = eval(stream_var.to_s)
-eval("#{stream_var} = StringIO.new")
-# ...
-eval("#{stream_var} = old_stream") if defined?(old_stream) && old_stream
-```
-
-## Fix
-
-Replace with a standard output capture pattern:
-
-```ruby
-# Use RSpec's built-in output matcher:
-expect { command.run }.to output(/expected text/).to_stdout
-
-# Or use a capture helper:
-def capture_output
-  old_stdout = $stdout
-  $stdout = StringIO.new
-  yield
-  $stdout.string
-ensure
-  $stdout = old_stdout
-end
-```
-
-No `eval` needed — just use `$stdout` directly instead of dynamically resolving the variable name.
-
-## Verification
-
-- `bundle exec rubocop --only Security/Eval,Style/EvalWithLocation,Style/DocumentDynamicEvalDefinition` shows 0 offenses
-- `bundle exec rspec spec/lutaml/cli/uml/search_command_spec.rb` passes

data/TODO.cleanups/10-split-large-files.md

@@ -1,47 +0,0 @@
-# 10 — Split large files into focused modules (Layout/LineLength + file organization)
-
-## Problem
-
-Several files have grown too large and do too much. The top offenders:
-
-| File | Lines | Role |
-|------|-------|------|
-| `lib/lutaml/xmi/parsers/xmi_base.rb` | 1047 | XMI parsing (13 Metrics offenses) |
-| `lib/lutaml/uml_repository/index_builder.rb` | 480 | Index building (8 Metrics offenses) |
-| `lib/lutaml/qea/database.rb` | 477 | QEA database (8 Metrics offenses) |
-| `lib/lutaml/converter/xmi_to_uml.rb` | 474 | XMI→UML conversion (8 Metrics offenses) |
-| `lib/lutaml/command_line.rb` | 272 | CLI option parsing |
-| `lib/lutaml/uml_repository/static_site/data_transformer.rb` | ~950 | Static site generation |
-
-Additionally, `Layout/LineLength` is globally disabled (80 offenses).
-
-## Approach
-
-### xmi_base.rb (1047 lines)
-Split into:
-- `xmi_base.rb` — shared module with common methods
-- `connector_parser.rb` — connector-related parsing
-- `diagram_parser.rb` — diagram-related parsing
-- `element_parser.rb` — element-related parsing
-
-### converter/xmi_to_uml.rb (474 lines)
-Split into:
-- `xmi_to_uml.rb` — main converter class
-- Per-element mapping methods extracted into separate modules or classes
-
-### database.rb (477 lines)
-Already well-organized with lazy accessors. Split:
-- `database.rb` — core + public API
-- `lookup_indexes.rb` — the `build_lookup_indexes` method and index logic
-
-### Layout/LineLength (80 offenses)
-Re-enable the cop with a reasonable Max (120) and fix the worst offenders. Long lines often indicate:
-- Deeply nested code → extract to methods
-- Complex string interpolation → use `format` or heredocs
-- Long method chains → use `tap` or break meaningfully
-
-## Verification
-
-- No file over ~300 lines in `lib/`
-- `bundle exec rubocop --only Layout/LineLength` with `Max: 120` shows 0 offenses
-- `bundle exec rspec` passes

data/config/diagram_styles.yml

@@ -1,200 +0,0 @@
-# diagram_styles.yml - Configurable EA Diagram Styling
-# This file defines the default styling for LutaML diagram generation
-
-# Global defaults - applied when no other configuration matches
-defaults:
-  colors:
-    background: "#FFFFFF"
-    default_fill: "#E0E0E0"
-    default_stroke: "#000000"
-    text: "#000000"
-
-  fonts:
-    default:
-      family: "Carlito, Arial, sans-serif"
-      size: 9
-      weight: 400
-      style: normal
-
-    class_name:
-      family: "Carlito, Arial, sans-serif"
-      size: 9
-      weight: 700  # bold
-      style: normal
-
-    stereotype:
-      family: "Carlito, Arial, sans-serif"
-      size: 9
-      weight: 400
-      style: normal
-
-    attribute:
-      family: "Carlito, Arial, sans-serif"
-      size: 9
-      weight: 400
-      style: normal
-
-    operation:
-      family: "Carlito, Arial, sans-serif"
-      size: 9
-      weight: 400
-      style: normal
-
-  box:
-    stroke_width: 2
-    stroke_linecap: round
-    stroke_linejoin: bevel
-    corner_radius: 0
-    padding: 5
-    fill_opacity: 1.0
-    stroke_opacity: 1.0
-
-  text:
-    visibility_public: "+"
-    visibility_private: "-"
-    visibility_protected: "#"
-    visibility_package: "~"
-    cardinality_format: "[%s]"
-    stereotype_format: "«%s»"
-
-# Stereotype-based styling
-# These apply when elements have specific stereotypes
-stereotypes:
-  DataType:
-    colors:
-      fill: "#FFCCFF"  # Pink for i-UR DataTypes
-      stroke: "#000000"
-    fonts:
-      class_name:
-        weight: 700
-        style: italic
-
-  FeatureType:
-    colors:
-      fill: "#FFFFCC"  # Yellow for CityGML FeatureTypes
-      stroke: "#000000"
-
-  GMLType:
-    colors:
-      fill: "#CCFFCC"  # Green for GML Types
-      stroke: "#000000"
-
-  Interface:
-    colors:
-      fill: "#FFFFEE"
-      stroke: "#000000"
-    fonts:
-      class_name:
-        style: italic
-
-  Enumeration:
-    colors:
-      fill: "#FFE6CC"
-      stroke: "#000000"
-
-  Abstract:
-    fonts:
-      class_name:
-        style: italic
-
-# Package-based styling (optional)
-# Supports wildcards: "CityGML::*" matches any package starting with "CityGML::"
-packages:
-  "CityGML::*":
-    colors:
-      fill: "#FFFFCC"
-
-  "i-UR::*":
-    colors:
-      fill: "#FFCCFF"
-
-  "gml::*":
-    colors:
-      fill: "#CCFFCC"
-
-# Class-specific overrides (highest priority after EA data)
-# These take precedence over package and stereotype styling
-classes: {}
-
-# Connector styling
-connectors:
-  generalization:
-    arrow:
-      type: hollow_triangle
-      size: 10
-    line:
-      stroke_width: 1
-      stroke: "#000000"
-      fill: none
-
-  association:
-    arrow:
-      type: open_arrow
-      size: 8
-    line:
-      stroke_width: 1
-      stroke: "#000000"
-    labels:
-      show_role_names: true
-      show_cardinality: true
-      font:
-        family: "Carlito, Arial, sans-serif"
-        size: 8
-
-  dependency:
-    arrow:
-      type: open_arrow
-      size: 8
-    line:
-      stroke_width: 1
-      stroke: "#000000"
-      stroke_dasharray: "5,5"
-
-  aggregation:
-    arrow:
-      type: diamond
-      size: 10
-      fill: white
-    line:
-      stroke_width: 1
-      stroke: "#000000"
-
-  composition:
-    arrow:
-      type: filled_diamond
-      size: 10
-      fill: black
-    line:
-      stroke_width: 1
-      stroke: "#000000"
-
-  realization:
-    arrow:
-      type: hollow_triangle
-      size: 10
-    line:
-      stroke_width: 1
-      stroke: "#000000"
-      stroke_dasharray: "5,5"
-
-# Legend configuration
-legend:
-  enabled: true
-  position: bottom_right
-  title: "Legend"
-  box:
-    fill: "#FFFFFF"
-    stroke: "#000000"
-    stroke_width: 1
-    padding: 10
-  font:
-    family: "Carlito, Arial, sans-serif"
-    size: 9
-    weight: 400
-  entries:
-    - label: "i-UR DataTypes"
-      color: "#FFCCFF"
-    - label: "CityGML FeatureTypes"
-      color: "#FFFFCC"
-    - label: "GML Types"
-      color: "#CCFFCC"

data/config/model_transformations.yml

@@ -1,266 +0,0 @@
-# Model Transformations Configuration
-# This file configures the unified model transformation system for LutaML
-#
-# Version: 1.0
-# Description: External configuration for model format parsers and transformation options
-
-version: "1.0"
-description: "LutaML Model Transformations Configuration"
-
-# Parser configurations define how different model formats are handled
-parsers:
-  # XML Metadata Interchange (XMI) Parser
-  - format: "xmi"
-    extension: ".xmi"
-    parser_class: "Lutaml::ModelTransformations::Parsers::XmiParser"
-    enabled: true
-    priority: 100
-    description: "XML Metadata Interchange parser for UML models"
-    options:
-      - "validate_xml"
-      - "resolve_references"
-      - "preserve_namespaces"
-      - "include_documentation"
-
-  # Enterprise Architect Database (QEA) Parser
-  - format: "qea"
-    extension: ".qea"
-    parser_class: "Lutaml::ModelTransformations::Parsers::QeaParser"
-    enabled: true
-    priority: 90
-    description: "Enterprise Architect database parser"
-    options:
-      - "include_diagrams"
-      - "validate_transformation"
-      - "load_progress_callback"
-      - "cache_database"
-
-  # Legacy XML support (lower priority than XMI)
-  - format: "xml"
-    extension: ".xml"
-    parser_class: "Lutaml::ModelTransformations::Parsers::XmiParser"
-    enabled: true
-    priority: 80
-    description: "Generic XML parser (delegates to XMI parser)"
-    options:
-      - "validate_xml"
-      - "resolve_references"
-
-  # Enterprise Architect Project files (legacy format)
-  - format: "eap"
-    extension: ".eap"
-    parser_class: "Lutaml::ModelTransformations::Parsers::QeaParser"
-    enabled: true
-    priority: 70
-    description: "Enterprise Architect project file parser"
-    options:
-      - "include_diagrams"
-      - "legacy_format_support"
-
-  # Enterprise Architect Exchange files
-  - format: "eapx"
-    extension: ".eapx"
-    parser_class: "Lutaml::ModelTransformations::Parsers::QeaParser"
-    enabled: true
-    priority: 75
-    description: "Enterprise Architect exchange file parser"
-    options:
-      - "include_diagrams"
-      - "compressed_format"
-
-# Global transformation options
-transformation_options:
-  # Validate output document structure after parsing
-  validate_output: false
-
-  # Include diagram information in transformed documents
-  include_diagrams: true
-
-  # Preserve original XMI/QEA IDs in transformed elements
-  preserve_ids: true
-
-  # Resolve cross-references between model elements
-  resolve_references: true
-
-  # Enable strict validation mode (fail on warnings)
-  strict_mode: false
-
-# Format detection configuration
-format_detection:
-  # Use file extensions for format detection
-  use_file_extension: true
-
-  # Use content analysis (magic bytes) for format detection
-  use_content_sniffing: true
-
-  # Fallback parser when format cannot be detected
-  fallback_parser: "Lutaml::ModelTransformations::Parsers::XmiParser"
-
-  # Magic byte signatures for content detection
-  magic_bytes:
-    - "SQLite format 3"  # QEA/SQLite files
-    - "<?xml"            # XML/XMI files
-
-# Error handling configuration
-error_handling:
-  # Error handling strategy: "continue", "fail_fast", "collect"
-  strategy: "continue"
-
-  # Log errors and warnings to console
-  log_errors: true
-
-  # Maximum number of errors before aborting (0 = unlimited)
-  max_errors: 10
-
-  # Fail immediately on first error
-  fail_fast: false
-
-# Format-specific configurations
-format_specific:
-  xmi:
-    # XMI-specific options
-    namespace_handling: "preserve"
-    reference_resolution: "eager"
-    xml_validation: "lenient"
-    encoding_detection: "auto"
-
-  qea:
-    # QEA-specific options
-    database_timeout: 30
-    load_strategy: "progressive"
-    diagram_processing: "full"
-    schema_validation: "basic"
-
-# Performance tuning
-performance:
-  # Enable parser instance caching
-  cache_parsers: true
-
-  # Maximum size for parser cache (number of instances)
-  max_parser_cache_size: 10
-
-  # Enable transformation history tracking
-  track_history: true
-
-  # Maximum number of history entries to keep
-  max_history_size: 1000
-
-# Logging configuration
-logging:
-  # Log level: "debug", "info", "warn", "error"
-  level: "info"
-
-  # Include timestamps in log messages
-  include_timestamps: true
-
-  # Include parser class names in log messages
-  include_parser_names: true
-
-  # Log transformation statistics
-  log_statistics: true
-
-# Plugin/extension support
-plugins:
-  # Enable plugin system
-  enabled: false
-
-  # Plugin discovery paths
-  discovery_paths:
-    - "lib/lutaml/model_transformations/plugins"
-    - "~/.lutaml/plugins"
-
-  # Auto-load plugins on startup
-  auto_load: false
-
-# Validation rules
-validation:
-  # Required elements validation
-  require_packages: false
-  require_classes: false
-
-  # Reference validation
-  check_broken_references: true
-  allow_external_references: true
-
-  # Naming validation
-  validate_naming_conventions: false
-  naming_patterns:
-    package: "^[A-Z][a-zA-Z0-9]*$"
-    class: "^[A-Z][a-zA-Z0-9]*$"
-    attribute: "^[a-z][a-zA-Z0-9]*$"
-
-# Transformation presets for common scenarios
-presets:
-  # Fast parsing preset (minimal validation, no diagrams)
-  fast:
-    transformation_options:
-      validate_output: false
-      include_diagrams: false
-      resolve_references: false
-    error_handling:
-      strategy: "fail_fast"
-      log_errors: false
-
-  # Comprehensive parsing preset (full validation and processing)
-  comprehensive:
-    transformation_options:
-      validate_output: true
-      include_diagrams: true
-      resolve_references: true
-      strict_mode: true
-    error_handling:
-      strategy: "collect"
-      log_errors: true
-      max_errors: 0
-
-  # Production preset (balanced performance and reliability)
-  production:
-    transformation_options:
-      validate_output: true
-      include_diagrams: true
-      resolve_references: true
-      strict_mode: false
-    error_handling:
-      strategy: "continue"
-      log_errors: true
-      max_errors: 5
-    performance:
-      cache_parsers: true
-      track_history: false
-
-# Compatibility settings
-compatibility:
-  # Support legacy LutaML API
-  legacy_api_support: true
-
-  # Automatic migration of old configuration formats
-  auto_migrate_config: true
-
-  # Deprecated feature warnings
-  warn_deprecated: true
-
-# Development/debugging options
-development:
-  # Enable debug mode
-  debug_mode: false
-
-  # Dump intermediate transformation results
-  dump_intermediate: false
-
-  # Benchmark transformation performance
-  benchmark_mode: false
-
-  # Verbose parser output
-  verbose_parsing: false
-
-# Integration settings
-integration:
-  # UML Repository integration
-  auto_build_repository: true
-  repository_lazy_loading: false
-
-  # CLI integration
-  register_cli_commands: true
-
-  # Web UI integration
-  enable_web_ui: false

data/config/package_metadata.example.yml

@@ -1,58 +0,0 @@
-# Package Metadata Configuration Example
-#
-# This file demonstrates how to configure package metadata for use with
-# LutaML's PackageMetadata system.
-#
-# Package metadata enables external configuration of:
-# - XSD generation: xmlns, targetNamespace, schemaLocation
-# - Documentation: Package descriptions
-# - Styling: Package-specific styling rules
-# - Validation: Package constraints
-#
-# Format: YAML with "packages" root key
-
-packages:
-  # Exact package path match
-  "ModelRoot::i-UR::Urban Planning ADE 3.2::uro":
-    xmlns: "http://www.kantei.go.jp/jp/singi/tiiki/toshisaisei/itoshisaisei/iur/uro/2.0"
-    targetNamespace: "http://www.kantei.go.jp/jp/singi/tiiki/toshisaisei/itoshisaisei/iur/uro/2.0"
-    schemaLocation: "../../schemas/uro/2.0/urbanObject.xsd"
-    prefix: "uro"
-    documentation: |
-      Urban Object package containing classes for urban planning and
-      infrastructure modeling in PLATEAU i-UR standard.
-    version: "2.0"
-
-  # Another exact match
-  "ModelRoot::CityGML2.0::Core":
-    xmlns: "http://www.opengis.net/citygml/2.0"
-    targetNamespace: "http://www.opengis.net/citygml/2.0/core"
-    schemaLocation: "http://schemas.opengis.net/citygml/2.0/cityGMLBase.xsd"
-    prefix: "core"
-    documentation: "CityGML 2.0 Core module - fundamental city model classes"
-
-  # Wildcard pattern: matches any direct child of ModelRoot::CityGML2.0
-  "ModelRoot::CityGML2.0::*":
-    xmlns: "http://www.opengis.net/citygml/2.0"
-    prefix: "citygml"
-    documentation: "Default CityGML 2.0 namespace"
-
-  # Multi-level wildcard: matches ModelRoot::<anything>::Common
-  "ModelRoot::*::Common":
-    documentation: "Common elements package"
-    category: "utilities"
-
-  # Package with custom metadata
-  "ModelRoot::CustomPackage":
-    xmlns: "http://example.com/custom/1.0"
-    prefix: "custom"
-    author: "Your Organization"
-    license: "Apache-2.0"
-    contact: "info@example.com"
-
-# Notes:
-# 1. Exact matches take precedence over wildcard patterns
-# 2. Multiple wildcards can match the same package path
-# 3. Metadata from all matches is merged (exact match wins)
-# 4. Any custom keys are supported beyond the standard ones
-# 5. Package paths use "::" as separator (UML qualified name format)