oddb2xml 2.9.9 → 3.0.1

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Files changed (14) hide show
  1. checksums.yaml +4 -4
  2. data/CLAUDE.md +69 -0
  3. data/Gemfile +3 -2
  4. data/Gemfile.lock +66 -64
  5. data/gemset.nix +103 -72
  6. data/lib/oddb2xml/cli.rb +23 -3
  7. data/lib/oddb2xml/compressor.rb +1 -3
  8. data/lib/oddb2xml/fhir_support.rb +752 -0
  9. data/lib/oddb2xml/options.rb +6 -0
  10. data/lib/oddb2xml/version.rb +1 -1
  11. data/lib/oddb2xml.rb +10 -0
  12. data/oddb2xml.gemspec +8 -8
  13. data/spec/downloader_spec.rb +1 -1
  14. metadata +28 -26
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data/CLAUDE.md ADDED
@@ -0,0 +1,69 @@
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+ # CLAUDE.md
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+
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+ This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
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+
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+ ## Project Overview
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+
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+ oddb2xml is a Ruby gem that downloads Swiss pharmaceutical data from 10+ sources (Swissmedic, BAG, Refdata, ZurRose, EPha, etc.), parses multiple formats (XML, XLSX, CSV, SOAP, fixed-width DAT), merges/deduplicates them, and generates standardized XML/DAT output files for healthcare systems. It also supports the Elexis EHR Artikelstamm format.
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+
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+ ## Common Commands
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+
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+ ```bash
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+ # Install dependencies
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+ bundle install
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+
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+ # Run full test suite
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+ bundle exec rake spec
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+
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+ # Run a single test file
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+ bundle exec rspec spec/builder_spec.rb
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+
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+ # Run a single test by line number
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+ bundle exec rspec spec/builder_spec.rb:42
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+
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+ # Lint with StandardRB
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+ bundle exec standardrb
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+
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+ # Auto-fix lint issues
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+ bundle exec standardrb --fix
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+
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+ # Build the gem
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+ bundle exec rake build
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+ ```
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+
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+ ## Architecture
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+
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+ The system follows a **download → extract → build → compress** pipeline:
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+ 1. **CLI** (`lib/oddb2xml/cli.rb`) — Entry point. Parses options via Optimist (`options.rb`), orchestrates the pipeline, manages multi-threaded downloads.
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+
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+ 2. **Downloaders** (`lib/oddb2xml/downloader.rb`) — 11 subclasses of `Downloader`, each fetching from a specific Swiss data source. Files cached in `./downloads/`.
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+ 3. **Extractors** (`lib/oddb2xml/extractor.rb`) — Matching extractor classes that parse downloaded files into Ruby hashes. Formats include XML (nokogiri/sax-machine), XLSX (rubyXL), SOAP (savon), CSV, and fixed-width text.
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+ 4. **Builder** (`lib/oddb2xml/builder.rb`) — The largest file (~1900 lines). Merges extracted data and generates output XML/DAT files. Methods follow `prepare_*` (data assembly) and `build_*` (output generation) naming.
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+
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+ 5. **Calc** (`lib/oddb2xml/calc.rb`) — Composition calculation logic, works with `parslet_compositions.rb` and `compositions_syntax.rb` (Parslet-based PEG parser for drug composition strings).
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+
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+ 6. **Compressor** (`lib/oddb2xml/compressor.rb`) — Optional ZIP/TAR.GZ output compression.
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+
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+ ### Key data identifiers
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+ - **GTIN/EAN13**: Primary article identifier (13-digit barcode)
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+ - **Pharmacode**: Swiss pharmacy code
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+ - **IKSNR**: Swissmedic registration number (5-digit)
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+ - **Swissmedic sequence/pack numbers**: Combined with IKSNR to form full identifiers
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+
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+ ### Static data overrides
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+ YAML files in `data/` provide manual overrides and mappings: `article_overrides.yaml`, `product_overrides.yaml`, `gtin2ignore.yaml`, `gal_forms.yaml`, `gal_groups.yaml`.
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+
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+ ## Testing
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+
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+ - Framework: RSpec with flexmock (mocking), webmock + VCR (HTTP recording/playback)
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+ - Test fixtures: `spec/data/` (sample files), `spec/fixtures/vcr_cassettes/` (recorded HTTP responses)
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+ - `spec/spec_helper.rb` defines test constants (GTINs) and configures VCR to avoid real HTTP calls during tests
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+ - CI runs on Ruby 3.0, 3.1, 3.2
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+
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+ ## Ruby Version
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+
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+ - Minimum: Ruby >= 2.5.0 (gemspec)
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+ - Current development: Ruby 3.2.0 (`.ruby-version`)
data/Gemfile CHANGED
@@ -7,5 +7,6 @@ group :debugger do
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  gem "pry-doc"
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  end
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- gem "nokogiri", "1.13.9"
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- gem "rack", "3.0.11"
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+ gem "nokogiri", ">= 1.19.1"
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+ gem "rack", ">= 3.1.20"
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+ gem "mutex_m"
data/Gemfile.lock CHANGED
@@ -1,54 +1,53 @@
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  PATH
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  remote: .
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  specs:
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- oddb2xml (2.9.2)
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+ oddb2xml (3.0.0)
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  htmlentities
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  httpi
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- mechanize
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+ mechanize (>= 2.8.5)
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  minitar
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  multi_json
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- nokogiri (>= 1.8.2)
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+ nokogiri (>= 1.19.1)
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  optimist
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  ox
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  parslet
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- rack (= 3.0.11)
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- rexml
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+ rack (>= 3.1.20)
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+ rexml (>= 3.3.9)
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  rubyXL (~> 3.4.0)
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- rubyntlm (= 0.5.1)
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- rubyzip
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+ rubyntlm (>= 0.6.3)
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+ rubyzip (~> 3.0.1)
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  savon (~> 2.12.0)
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  sax-machine
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  spreadsheet
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  standardrb
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- webrick
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+ webrick (>= 1.8.2)
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  xml-simple
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  GEM
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  remote: https://rubygems.org/
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  specs:
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- addressable (2.8.5)
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- public_suffix (>= 2.0.2, < 6.0)
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+ addressable (2.8.8)
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+ public_suffix (>= 2.0.2, < 8.0)
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  akami (1.3.1)
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  gyoku (>= 0.4.0)
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  nokogiri
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  ast (2.4.2)
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- base64 (0.1.1)
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+ base64 (0.3.0)
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  builder (3.2.4)
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  byebug (11.1.3)
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  coderay (1.1.3)
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- connection_pool (2.4.1)
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+ connection_pool (3.0.2)
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  crack (0.4.5)
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  rexml
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  diff-lcs (1.5.0)
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- domain_name (0.5.20190701)
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- unf (>= 0.0.5, < 1.0.0)
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+ domain_name (0.6.20240107)
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  flexmock (2.3.8)
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  gyoku (1.4.0)
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  builder (>= 2.1.2)
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  rexml (~> 3.0)
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  hashdiff (1.0.1)
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  htmlentities (4.3.4)
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- http-cookie (1.0.5)
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+ http-cookie (1.1.0)
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  domain_name (~> 0.5)
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  httpi (2.5.0)
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  rack
@@ -56,33 +55,39 @@ GEM
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  json (2.6.3)
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  language_server-protocol (3.17.0.3)
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  lint_roller (1.1.0)
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- mechanize (2.7.7)
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- domain_name (~> 0.5, >= 0.5.1)
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- http-cookie (~> 1.0)
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- mime-types (>= 1.17.2)
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- net-http-digest_auth (~> 1.1, >= 1.1.1)
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- net-http-persistent (>= 2.5.2)
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- nokogiri (~> 1.6)
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- ntlm-http (~> 0.1, >= 0.1.1)
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+ logger (1.7.0)
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+ mechanize (2.14.0)
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+ addressable (~> 2.8)
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+ base64
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+ domain_name (~> 0.5, >= 0.5.20190701)
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+ http-cookie (~> 1.0, >= 1.0.3)
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+ mime-types (~> 3.3)
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+ net-http-digest_auth (~> 1.4, >= 1.4.1)
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+ net-http-persistent (>= 2.5.2, < 5.0.dev)
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+ nkf
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+ nokogiri (~> 1.11, >= 1.11.2)
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+ rubyntlm (~> 0.6, >= 0.6.3)
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  webrick (~> 1.7)
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- webrobots (>= 0.0.9, < 0.2)
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+ webrobots (~> 0.1.2)
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  method_source (1.0.0)
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- mime-types (3.5.1)
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- mime-types-data (~> 3.2015)
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- mime-types-data (3.2023.0808)
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- mini_portile2 (2.8.4)
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+ mime-types (3.7.0)
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+ logger
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+ mime-types-data (~> 3.2025, >= 3.2025.0507)
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+ mime-types-data (3.2026.0203)
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+ mini_portile2 (2.8.9)
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  minitar (0.9)
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  multi_json (1.15.0)
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+ mutex_m (0.3.0)
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  net-http-digest_auth (1.4.1)
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- net-http-persistent (4.0.2)
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- connection_pool (~> 2.2)
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- nokogiri (1.13.9)
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- mini_portile2 (~> 2.8.0)
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+ net-http-persistent (4.0.8)
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+ connection_pool (>= 2.2.4, < 4)
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+ nkf (0.2.0)
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+ nokogiri (1.19.1)
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+ mini_portile2 (~> 2.8.2)
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  racc (~> 1.4)
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  nori (2.6.0)
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- ntlm-http (0.1.1)
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  optimist (3.1.0)
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- ox (2.14.17)
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+ ox (2.14.14)
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  parallel (1.23.0)
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  parser (3.2.2.3)
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  ast (~> 2.4.1)
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  pry (0.14.2)
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  coderay (~> 1.1)
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  method_source (~> 1.0)
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- pry-byebug (3.10.1)
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+ pry-byebug (3.8.0)
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  byebug (~> 11.0)
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- pry (>= 0.13, < 0.15)
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+ pry (~> 0.10)
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  pry-doc (1.4.0)
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  pry (~> 0.11)
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  yard (~> 0.9.11)
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  psych (3.3.4)
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- public_suffix (5.0.3)
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- racc (1.7.1)
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- rack (3.0.11)
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+ public_suffix (7.0.2)
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+ racc (1.8.1)
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+ rack (3.2.5)
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  rainbow (3.1.1)
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  rake (13.0.6)
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- rdoc (6.3.3)
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+ rdoc (6.3.4.1)
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  regexp_parser (2.8.1)
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- rexml (3.2.6)
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+ rexml (3.4.4)
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  rspec (3.12.0)
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  rspec-core (~> 3.12.0)
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  rspec-expectations (~> 3.12.0)
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  diff-lcs (>= 1.2.0, < 2.0)
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  rspec-support (~> 3.12.0)
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  rspec-support (3.12.1)
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- rubocop (1.56.4)
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- base64 (~> 0.1.1)
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+ rubocop (1.50.2)
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  json (~> 2.3)
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- language_server-protocol (>= 3.17.0)
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  parallel (~> 1.10)
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- parser (>= 3.2.2.3)
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+ parser (>= 3.2.0.0)
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  rainbow (>= 2.2.2, < 4.0)
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  regexp_parser (>= 1.8, < 3.0)
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  rexml (>= 3.2.5, < 4.0)
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- rubocop-ast (>= 1.28.1, < 2.0)
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+ rubocop-ast (>= 1.28.0, < 2.0)
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  ruby-progressbar (~> 1.7)
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  unicode-display_width (>= 2.4.0, < 3.0)
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  rubocop-ast (1.29.0)
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  parser (>= 3.2.1.0)
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- rubocop-performance (1.19.1)
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+ rubocop-performance (1.16.0)
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  rubocop (>= 1.7.0, < 2.0)
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  rubocop-ast (>= 0.4.0)
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  ruby-ole (1.2.12.2)
@@ -141,8 +144,9 @@ GEM
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  rubyXL (3.4.25)
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  nokogiri (>= 1.10.8)
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  rubyzip (>= 1.3.0)
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- rubyntlm (0.5.1)
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- rubyzip (2.3.2)
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+ rubyntlm (0.6.5)
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+ base64
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+ rubyzip (3.0.1)
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  savon (2.12.1)
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  akami (~> 1.2)
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  builder (>= 2.1.2)
@@ -155,26 +159,23 @@ GEM
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  socksify (1.7.1)
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  spreadsheet (1.3.0)
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  ruby-ole
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- standard (1.31.1)
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+ standard (1.28.5)
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  language_server-protocol (~> 3.17.0.2)
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  lint_roller (~> 1.0)
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- rubocop (~> 1.56.2)
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+ rubocop (~> 1.50.2)
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  standard-custom (~> 1.0.0)
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- standard-performance (~> 1.2)
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+ standard-performance (~> 1.0.1)
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  standard-custom (1.0.2)
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  lint_roller (~> 1.0)
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  rubocop (~> 1.50)
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- standard-performance (1.2.0)
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- lint_roller (~> 1.1)
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- rubocop-performance (~> 1.19.0)
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+ standard-performance (1.0.1)
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+ lint_roller (~> 1.0)
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+ rubocop-performance (~> 1.16.0)
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  standardrb (1.0.1)
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  standard
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  timecop (0.9.8)
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- unf (0.1.4)
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- unf_ext
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- unf_ext (0.0.8.2)
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  unicode-display_width (2.5.0)
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- vcr (6.2.0)
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+ vcr (6.1.0)
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  wasabi (3.7.0)
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  addressable
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  httpi (~> 2.0)
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  addressable (>= 2.8.0)
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  crack (>= 0.3.2)
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  hashdiff (>= 0.4.0, < 2.0.0)
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- webrick (1.8.1)
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+ webrick (1.9.2)
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  webrobots (0.1.2)
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  xml-simple (1.1.9)
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  rexml
@@ -195,18 +196,19 @@ PLATFORMS
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  DEPENDENCIES
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  bundler
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  flexmock
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- nokogiri (= 1.13.9)
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+ mutex_m
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+ nokogiri (>= 1.19.1)
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  oddb2xml!
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  pry-byebug
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  pry-doc
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  psych (< 4.0.0)
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- rack (= 3.0.11)
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+ rack (>= 3.1.20)
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  rake
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- rdoc (~> 6.3.3)
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+ rdoc (>= 6.3.4.1)
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  rspec
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  timecop
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  vcr
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  webmock
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  BUNDLED WITH
212
- 2.3.24
214
+ 2.4.19