sample-template-generator-gem 0.2.1 → 0.3.0

data/lib/seek/sample_templates.rb

@@ -0,0 +1,22 @@
+require 'seek/sample_templates/column'
+require 'seek/sample_templates/generator'
+
+module Seek
+  # Main entry point for generating templates
+  module SampleTemplates
+    # generates a template at the specific path
+    def self.generate(sheet_name, sheet_index, columns, path)
+      Seek::SampleTemplates::Generator.new(
+        path, create_json(columns, sheet_index, sheet_name)
+      ).generate
+    end
+
+    def self.create_json(columns, sheet_index, sheet_name)
+      { sheet_name: sheet_name,
+        sheet_index: sheet_index,
+        columns: columns.collect(&:as_json) }.to_json
+    end
+
+    private_class_method :create_json
+  end
+end

data/lib/seek/sample_templates/column.rb

@@ -0,0 +1,19 @@
+module Seek
+  module SampleTemplates
+    # Describes a column in the template.
+    # The name is the text put in the top row,
+    # and contents will create a dropdown in the row below unless empty
+    class Column
+      attr_reader :name, :contents
+
+      def initialize(name, contents = [])
+        @name = name
+        @contents = contents
+      end
+
+      def as_json
+        { @name => @contents }
+      end
+    end
+  end
+end

data/lib/seek/sample_templates/generator.rb

@@ -1,44 +1,27 @@
-require 'open4'
+require 'cocaine'
 
 module Seek
   module SampleTemplates
-    def self.generate(sheet_name, sheet_index, columns, path)
-      Seek::SampleTemplates::Generator.new(path, create_json(columns, sheet_index, sheet_name)).generate
-    end
-
-    def self.create_json(columns, sheet_index, sheet_name)
-      { sheet_name: sheet_name, sheet_index: sheet_index, columns: columns.collect(&:as_json) }.to_json
-    end
-
-    class Column
-      attr_accessor :name, :contents
-      def initialize(name, contents = [])
-        @name = name
-        @contents = contents
-      end
-
-      def as_json
-        { @name => @contents }
-      end
-    end
-
+    # Generator class for creating templates.
+    # Generally this shouldn't be used directly, but instead should be used
+    # through Seek::SampleTemplates.generate(..)
     class Generator
-      JAR_VERSION = '0.2'.freeze
-      JAR_PATH = File.dirname(__FILE__) + "/../../../jars/sample-template-generator-#{JAR_VERSION}.jar"
+      JAR_VERSION = '0.3'.freeze
+      JAR_PATH = File.dirname(__FILE__) +
+                 "/../../../jars/sample-template-generator-#{JAR_VERSION}.jar"
       DEFAULT_MEMORY_ALLOCATION = '512M'.freeze
       BUFFER_SIZE = 250_000 # 1/4 a megabyte
 
-      attr_accessor :json, :path, :memory_allocation
+      attr_reader :json, :path, :memory_allocation
 
       def initialize(path, json, memory_allocation = DEFAULT_MEMORY_ALLOCATION)
         @path = path
         @json = json
         @memory_allocation = memory_allocation
-        raise Exception, 'Windows is not currently supported' if windows?
       end
 
       def generate
-        run_with_open4
+        run_with_cocaine
       end
 
       private
@@ -50,29 +33,11 @@ module Seek
         command
       end
 
-      def run_with_open4
-        output = ''
-        err_message = ''
-        command = command()
-        status = Open4.popen4(command) do |_pid, _stdin, stdout, stderr|
-          until (line = stdout.gets(BUFFER_SIZE)).nil?
-            output << line
-          end
-          stdout.close
-
-          until (line = stderr.gets(BUFFER_SIZE)).nil?
-            err_message << line
-          end
-          stderr.close
-        end
-
-        raise err_message if status.to_i.nonzero?
-
+      def run_with_cocaine
+        output = Cocaine::CommandLine.new(command).run
         output.strip
-      end
-
-      def windows?
-        !(RUBY_PLATFORM =~ /mswin32/ || RUBY_PLATFORM =~ /mingw32/).nil?
+      rescue Cocaine::ExitStatusError => exception
+        raise exception.message
       end
     end
   end

data/lib/seek/sample_templates/version.rb

@@ -1,5 +1,5 @@
 module Seek
   module SampleTemplates
-    VERSION = '0.2.1'.freeze
+    VERSION = '0.3.0'.freeze
   end
 end

data/sample-template-generator-gem.gemspec

@@ -9,29 +9,22 @@ Gem::Specification.new do |spec|
   spec.authors       = ['Stuart Owen']
   spec.email         = ['stuart.owen@manchester.ac.uk']
 
-  spec.summary       = 'Prototype for generating spreadsheet templates for use with SEEK.'
+  spec.summary       = 'Bespoke tool for generating spreadsheet templates from Sample Types for use with SEEK.'
   spec.homepage      = 'http://seek4science.org'
-  spec.license       = 'BSD-3-Clause' # https://spdx.org/licenses/BSD-3-Clause.html#licenseText
-
-  # Prevent pushing this gem to RubyGems.org. To allow pushes either set the 'allowed_push_host'
-  # to allow pushing to a single host or delete this section to allow pushing to any host.
-  # if spec.respond_to?(:metadata)
-  #   spec.metadata['allowed_push_host'] = "TODO: Set to 'http://mygemserver.com'"
-  # else
-  #   raise "RubyGems 2.0 or newer is required to protect against public gem pushes."
-  # end
+  spec.license       = 'BSD-3-Clause'
 
   spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
   spec.bindir        = 'exe'
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ['lib']
 
-  spec.add_dependency('open4', ['= 1.3.0'])
   spec.add_dependency('rdoc', ['>= 0'])
+  spec.add_dependency('cocaine', ['>= 0'])
 
   spec.add_development_dependency('rubocop', ['>= 0'])
   spec.add_development_dependency('rubycritic', ['>= 0'])
   spec.add_development_dependency 'bundler', '~> 1.12'
   spec.add_development_dependency 'rake', '~> 10.0'
   spec.add_development_dependency 'minitest', '~> 5.0'
+  spec.add_development_dependency('activesupport', ">= 3.0.0", "< 5.0")
 end

metadata

@@ -1,31 +1,31 @@
 --- !ruby/object:Gem::Specification
 name: sample-template-generator-gem
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.3.0
 platform: ruby
 authors:
 - Stuart Owen
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-09-12 00:00:00.000000000 Z
+date: 2016-09-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: open4
+  name: rdoc
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.3.0
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.3.0
+        version: '0'
 - !ruby/object:Gem::Dependency
-  name: rdoc
+  name: cocaine
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -108,6 +108,26 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '5.0'
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '5.0'
 description: 
 email:
 - stuart.owen@manchester.ac.uk
@@ -137,7 +157,9 @@ files:
 - jars/lib/poi-ooxml-schemas-3.14.jar
 - jars/lib/stax-api-1.0.1.jar
 - jars/lib/xmlbeans-2.6.0.jar
-- jars/sample-template-generator-0.2.jar
+- jars/sample-template-generator-0.3.jar
+- lib/seek/sample_templates.rb
+- lib/seek/sample_templates/column.rb
 - lib/seek/sample_templates/generator.rb
 - lib/seek/sample_templates/version.rb
 - sample-template-generator-gem.gemspec
@@ -164,5 +186,6 @@ rubyforge_project:
 rubygems_version: 2.4.8
 signing_key: 
 specification_version: 4
-summary: Prototype for generating spreadsheet templates for use with SEEK.
+summary: Bespoke tool for generating spreadsheet templates from Sample Types for use
+  with SEEK.
 test_files: []