ndr_import 10.2.0 → 10.3.0

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data/CHANGELOG.md

@@ -1,6 +1,12 @@
 ## [Unreleased]
+=======
 *no unreleased changes*
 
+## 10.3.0 / 2023-09-07
+### Added
+* VCF file support
+* Support Ruby 3.2. Drop support for Ruby 2.7, Rails 6.0
+
 ## 10.2.0 / 2023-05-16
 * avro file support
 * allow storage of `significant_mapped_fields` in `Table`

data/README.md

@@ -1,7 +1,7 @@
 # NdrImport [![Build Status](https://github.com/NHSDigital/ndr_import/workflows/Test/badge.svg)](https://github.com/NHSDigital/ndr_import/actions?query=workflow%3Atest) [![Gem Version](https://badge.fury.io/rb/ndr_import.svg)](https://rubygems.org/gems/ndr_import) [![Documentation](https://img.shields.io/badge/ndr_import-docs-blue.svg)](https://www.rubydoc.info/gems/ndr_import)
 This is the NHS Digital (NHSD) National Disease Registers (NDR) Import ETL ruby gem, providing:
 
-1. file import handlers for *extracting* data from delimited files (csv, pipe, tab, thorn), JSON Lines, .xls(x) spreadsheets, .doc(x) word documents, PDF, PDF AcroForms, XML, 7-Zip, Zip and avro files.
+1. file import handlers for *extracting* data from delimited files (csv, pipe, tab, thorn), JSON Lines, .xls(x) spreadsheets, .doc(x) word documents, PDF, PDF AcroForms, XML, 7-Zip, Zip, avro and VCF files.
 2. table mappers for *transforming* tabular and non-tabular data into key value pairs grouped by a common "klass".
 
 ## Installation

data/lib/ndr_import/file/all.rb

@@ -8,6 +8,7 @@ require_relative 'pdf'
 require_relative 'seven_zip'
 require_relative 'text'
 require_relative 'unregistered_filetype'
+require_relative 'vcf'
 require_relative 'word'
 require_relative 'xml'
 require_relative 'zip'

data/lib/ndr_import/file/vcf.rb

@@ -0,0 +1,25 @@
+require 'bio-vcf/vcfline'
+require 'ndr_support/safe_file'
+require_relative 'registry'
+
+module NdrImport
+  # This is one of a collection of file handlers that deal with individual formats of data.
+  # They can be instantiated directly or via the factory method Registry.tables
+  module File
+    # This class is a vcf file handler that returns a single table.
+    class Vcf < Base
+      private
+
+      def rows(&block)
+        return enum_for(:rows) unless block
+
+        ::File.read(@filename).each_line do |line|
+          next if line =~ /^##/
+
+          yield BioVcf::VcfLine.parse(line)
+        end
+      end
+    end
+    Registry.register(Vcf, 'vcf')
+  end
+end

data/lib/ndr_import/vcf/table.rb

@@ -0,0 +1,21 @@
+require 'ndr_import/table'
+
+module NdrImport
+  module Vcf
+    # Syntatic sugar to ensure `header_lines` and `footer_lines` are 1 and 0 respectively.
+    # All other Table logic is inherited from `NdrImport::Table`
+    class Table < ::NdrImport::Table
+      def self.all_valid_options
+        super - %w[delimiter header_lines footer_lines xml_record_xpath]
+      end
+
+      def header_lines
+        1
+      end
+
+      def footer_lines
+        0
+      end
+    end
+  end
+end

data/lib/ndr_import/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 # This stores the current version of the NdrImport gem
 module NdrImport
-  VERSION = '10.2.0'
+  VERSION = '10.3.0'
 end

data/lib/ndr_import.rb

@@ -10,6 +10,7 @@ require 'ndr_import/fixed_width/table'
 require 'ndr_import/xml/table'
 require 'ndr_import/pdf_form/table'
 require 'ndr_import/avro/table'
+require 'ndr_import/vcf/table'
 require 'ndr_import/unmapped_data_error'
 require 'ndr_import/acroform_reader'
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ndr_import
 version: !ruby/object:Gem::Version
-  version: 10.2.0
+  version: 10.3.0
 platform: ruby
 authors:
 - NCRS Development Team
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2023-05-18 00:00:00.000000000 Z
+date: 2023-09-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activemodel
@@ -30,7 +30,7 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '6.0'
+        version: '6.1'
     - - "<"
       - !ruby/object:Gem::Version
         version: '7.1'
@@ -40,7 +40,7 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '6.0'
+        version: '6.1'
     - - "<"
       - !ruby/object:Gem::Version
         version: '7.1'
@@ -106,6 +106,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.11.0
+- !ruby/object:Gem::Dependency
+  name: bio-vcf
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.5
 - !ruby/object:Gem::Dependency
   name: docx
   requirement: !ruby/object:Gem::Requirement
@@ -399,6 +413,7 @@ files:
 - lib/ndr_import/file/seven_zip.rb
 - lib/ndr_import/file/text.rb
 - lib/ndr_import/file/unregistered_filetype.rb
+- lib/ndr_import/file/vcf.rb
 - lib/ndr_import/file/word.rb
 - lib/ndr_import/file/xml.rb
 - lib/ndr_import/file/zip.rb
@@ -424,6 +439,7 @@ files:
 - lib/ndr_import/table.rb
 - lib/ndr_import/universal_importer_helper.rb
 - lib/ndr_import/unmapped_data_error.rb
+- lib/ndr_import/vcf/table.rb
 - lib/ndr_import/version.rb
 - lib/ndr_import/xml/control_char_escaper.rb
 - lib/ndr_import/xml/table.rb
@@ -439,14 +455,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '2.7'
+      version: '3.0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.33
+rubygems_version: 3.4.10
 signing_key:
 specification_version: 4
 summary: NDR Import