biocgem 0.0.1

checksums.yaml

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data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2021 kojix2
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# BiocGem
+
+[![test](https://github.com/ruby-on-bioc/biocgem/actions/workflows/ci.yml/badge.svg)](https://github.com/ruby-on-bioc/biocgem/actions/workflows/ci.yml)
+
+Extract the database included in the Bioconductor annotation package and use it in the Ruby gem.
+
+## Installation
+
+```sh
+gem install biocgem
+```
+
+## Usage
+
+### 1.Generate your gem
+
+Short options
+
+```
+biocgem new \
+  -n org.Hs.eg.db \
+  -s org.Hs.eg.sqlite \
+  -v 3.14.0
+```
+
+Full options
+
+```sh
+biocgem new --bioc_package_name org.Mm.eg.db \
+            --bioc_sqlite_database_name org.Mm.eg.sqlite \
+            --gem_icon :mouse: \
+            --gem_constant_name OrgMmEgDb \
+            --gem_require_name org_mm_eg_db \
+            --bioc_package_sha256sum 56f228448b50f1cea0fc15d6f61b1e94359ef885336034bf346693315390ad45 \
+            --bioc_version 3.14 \
+            --bioc_package_version 3.14.0
+```
+
+### 2. Install your gem
+
+```
+cd org.Hs.eg.db
+rake extdata:download
+# rake test
+rake install
+```
+
+## Development
+
+With all due respect to the R language and Bioconductor maintainers...
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/ruby-on-bioc/biocgem.
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).

data/exe/biocgem

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+#!/usr/bin/env ruby
+
+require "bioc_gem"
+
+BiocGem::Command.new.run

data/lib/bioc_gem/command.rb

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+require "erb"
+require "fileutils"
+require "tmpdir"
+require_relative "parser"
+
+module BiocGem
+  class Command
+    attr_accessor :parser
+
+    def initialize(argv = ARGV)
+      @argv = argv
+      @parser = Parser.new
+    end
+
+    def run
+      parser.parse_options(@argv)
+
+      pp config = parser.options.to_h
+
+      target = config[:bioc_package_name]
+
+      base = File.expand_path("../../template/newgem", __dir__)
+
+      Dir.mktmpdir do |tmpdir|
+        Dir.glob("**/*", File::FNM_DOTMATCH, base: base) do |f|
+          src = File.expand_path(f, base)
+          next unless File.file?(src)
+
+          warn " - #{f}"
+
+          str = File.read(src)
+          erb = ERB.new(str)
+          str = erb.result(binding)
+
+          trg = File.expand_path(f, tmpdir)
+          fname = File.basename(trg, ".tt")
+          fname.gsub!("new_gem_entry", config[:gem_require_name])
+          dirname = File.dirname(trg)
+          FileUtils.mkdir_p(dirname)
+          File.write(File.join(dirname, fname), str)
+        end
+        FileUtils.cp_r(tmpdir, target)
+      end
+    end
+  end
+end

data/lib/bioc_gem/options.rb

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+module BiocGem
+  Options = Struct.new(
+    :bioc_package_name,
+    :bioc_sqlite_database_name,
+    :gem_icon,
+    :gem_constant_name,
+    :gem_require_name,
+    :bioc_package_sha256sum,
+    :bioc_version,
+    :bioc_package_version
+  )
+end

data/lib/bioc_gem/parser.rb

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+require "optparse"
+require_relative "options"
+
+module BiocGem
+  class Parser
+    attr_reader :command, :options
+
+    def initialize
+      @comand = nil
+
+      @options = Options.new
+    end
+
+    def parse_options(args = ARGV)
+      @command = args.shift&.to_sym
+
+      return if @command != :new
+
+      opt_parser = OptionParser.new do |parser|
+        parser.banner = "Usage: biocgem new [options]"
+
+        parser.on("-n", "--bioc_package_name VAL", "e.g. org.Hs.eg.db") do |v|
+          options[:bioc_package_name] = v
+        end
+        parser.on("-s", "--bioc_sqlite_database_name VAL", "e.g. org.Hs.eg.sqlite") do |v|
+          options[:bioc_sqlite_database_name] = v
+        end
+        parser.on("--gem_icon [VAL]", "e.g. :family:") do |v|
+          options[:gem_icon] = v
+        end
+        parser.on("--gem_constant_name [VAL]", "e.g. OrgHsEgDb") do |v|
+          options[:gem_constant_name] = v
+        end
+        parser.on("--gem_require_name [VAL]", "e.g. org_hs_eg_db") do |v|
+          options[:gem_require_name] = v
+        end
+        parser.on("--bioc_package_sha256sum [VAL]", "e.g. ") do |v|
+          options[:bioc_package_sha256sum] = v
+        end
+        parser.on("-v", "--bioc_version [VAL]", "e.g. 3.14") do |v|
+          options[:bioc_version] = v
+        end
+        parser.on("--bioc_package_version VAL", "e.g. 3.14.0") do |v|
+          options[:bioc_package_version] = v
+        end
+      end
+
+      opt_parser.parse!(args)
+
+      options.gem_icon = ":notes:" if options.gem_icon.nil?
+      if options.gem_constant_name.nil?
+        options.gem_constant_name = options.bioc_package_name.split(".").map(&:capitalize).join
+      end
+      if options.gem_require_name.nil?
+        options.gem_require_name = options.bioc_package_name.split(".").map(&:downcase).join("_")
+      end
+      options.bioc_version = "release" if options.bioc_version.nil?
+
+      options
+    end
+  end
+end

data/lib/bioc_gem/version.rb

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+# frozen_string_literal: true
+
+module BiocGem
+  VERSION = "0.0.1"
+end

data/lib/bioc_gem.rb

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+# frozen_string_literal: true
+
+require_relative "bioc_gem/version"
+require_relative "bioc_gem/command"
+
+module BiocGem
+end

data/template/newgem/.gitignore.tt

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+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+/extdata/
+*.lock
+*.sqlite

data/template/newgem/Gemfile.tt

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+# frozen_string_literal: true
+
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in <%= config[:gem_constant_name] %>.gemspec
+gemspec
+
+gem 'rake'
+
+gem 'test-unit'

data/template/newgem/LICENSE.txt.tt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2021 Ruby on Bioc
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/template/newgem/README.md.tt

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+# <%= config[:bioc_package_name] %>
+
+[![build](https://github.com/ruby-on-bioc/<%= config[:bioc_package_name] %>/actions/workflows/ci.yml/badge.svg)](https://github.com/ruby-on-bioc/<%= config[:bioc_package_name] %>/actions/workflows/ci.yml)
+
+<%= config[:gem_icon] %> [<%= config[:bioc_package_name] %>](https://bioconductor.org/packages/<%= config[:bioc_package_name] %>/) - for Ruby
+
+## Installation
+
+```
+git clone https://github.com/ruby-on-bioc/<%= config[:bioc_package_name] %>
+cd <%= config[:bioc_package_name] %>
+rake extdata:download
+rake install
+```
+
+## Usage
+
+```ruby
+require '<%= config[:gem_require_name] %>'
+
+<%= config[:gem_constant_name] %>.class # Sequel::SQLite::Database
+<%= config[:gem_constant_name] %>.tables
+```
+
+See [Sequel](https://github.com/jeremyevans/sequel) for more details.
+
+## Development
+
+With all due respect to the R language and Bioconductor maintainers...
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/ruby-on-bioc/<%= config[:gem_constant_name] %>.

data/template/newgem/Rakefile.tt

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+# frozen_string_literal: true
+
+require "bundler/gem_tasks"
+require "rake/testtask"
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList["test/**/*_test.rb"]
+end
+
+# ensure extdata files exist
+task :ensure_extdata do
+  [bioc_sqlite_database_name, "DESCRIPTION"].each do |file|
+    raise "Missing file: #{file}" unless File.exist?("extdata/#{file}")
+  end
+end
+
+Rake::Task["build"].enhance [:ensure_extdata]
+
+task default: :test
+
+def bioc_version
+  "<%= config[:bioc_version] %>"
+end
+
+def bioc_sqlite_database_name
+  "<%= config[:bioc_sqlite_database_name] %>"
+end
+
+def bioc_package_name
+  "<%= config[:bioc_package_name] %>"
+end
+
+def bioc_package_version
+  "<%= config[:bioc_package_version] %>"
+end
+
+def bioc_package_sha256sum
+  sha256 = "<%= config[:bioc_package_sha256sum] %>"
+  sha256 == "" ? nil : sha256
+end
+
+def bioc_package_file_name
+  "#{bioc_package_name}_#{bioc_package_version}.tar.gz"
+end
+
+def download_annotation(database, src, file, sha256)
+  require "fileutils"
+  require "open-uri"
+  require "tmpdir"
+
+  url = "https://bioconductor.org/packages/#{bioc_version}/data/annotation/src/contrib/#{file}"
+  puts "Downloading #{url}"
+  contents = URI.open(url).read
+
+  if sha256
+    computed_sha256 = Digest::SHA256.hexdigest(contents)
+    raise "Bad hash: #{computed_sha256}" if computed_sha256 != sha256
+  end
+
+  Dir.chdir(Dir.mktmpdir) do
+    File.binwrite(file, contents)
+    command = "tar xf"
+    system "#{command} #{file}"
+    dest = File.expand_path("extdata", __dir__)
+
+    FileUtils.mkdir_p(dest)
+
+    FileUtils.cp("#{src}/inst/extdata/#{database}", "#{dest}/#{database}")
+    puts "Saved extdata/#{database}"
+
+    FileUtils.cp("#{src}/DESCRIPTION", "#{dest}/DESCRIPTION")
+    puts "Saved extdata/DESCRIPTION"
+  end
+end
+
+namespace :extdata do
+  desc "download #{bioc_sqlite_database_name}"
+  task :download do
+    download_annotation(bioc_sqlite_database_name,
+                        bioc_package_name,
+                        bioc_package_file_name,
+                        bioc_package_sha256sum)
+  end
+end

data/template/newgem/lib/new_gem_entry.rb.tt

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+# frozen_string_literal: true
+
+require 'sequel'
+<%= config[:gem_constant_name] %> = Sequel.sqlite(
+  File.expand_path('../extdata/<%= config[:bioc_sqlite_database_name] %>', __dir__),
+  readonly: true
+)

data/template/newgem/new_gem_entry.gemspec.tt

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+# frozen_string_literal: true
+
+Gem::Specification.new do |spec|
+  spec.name = '<%= config[:gem_require_name] %>'
+  spec.version = '0.0.0'
+  spec.authors = ['kojix2']
+  spec.email = ['2xijok@gmail.com']
+
+  spec.summary = ''
+  spec.description = ''
+  spec.homepage = 'https://github.com/ruby-on-bioc/<%= config[:bioc_package_name] %>'
+  spec.required_ruby_version = '>= 2.6.0'
+
+  spec.files         = Dir['*.{md,txt}', 'lib/**/*', 'extdata/<%= config[:bioc_sqlite_database_name] %>']
+  spec.require_paths = ['lib']
+
+  spec.add_dependency 'sequel'
+  spec.add_dependency 'sqlite3'
+end

data/template/newgem/test/new_gem_entry_test.rb.tt

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+# frozen_string_literal: true
+
+require 'test_helper'
+
+class <%= config[:gem_constant_name] %>Test < Test::Unit::TestCase
+  test '<%= config[:gem_constant_name] %> is ready' do
+    assert_equal(Sequel::SQLite::Database, <%= config[:gem_constant_name] %>.class)
+  end
+end

data/template/newgem/test/test_helper.rb.tt

@@ -0,0 +1,6 @@
+# frozen_string_literal: true
+
+$LOAD_PATH.unshift File.expand_path('../lib', __dir__)
+require '<%= config[:gem_require_name] %>'
+
+require 'test-unit'

metadata

@@ -0,0 +1,61 @@
+--- !ruby/object:Gem::Specification
+name: biocgem
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- kojix2
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2021-12-05 00:00:00.000000000 Z
+dependencies: []
+description: biocgem command line tools
+email:
+- 2xijok@gmail.com
+executables:
+- biocgem
+extensions: []
+extra_rdoc_files: []
+files:
+- LICENSE.txt
+- README.md
+- exe/biocgem
+- lib/bioc_gem.rb
+- lib/bioc_gem/command.rb
+- lib/bioc_gem/options.rb
+- lib/bioc_gem/parser.rb
+- lib/bioc_gem/version.rb
+- template/newgem/.gitignore.tt
+- template/newgem/Gemfile.tt
+- template/newgem/LICENSE.txt.tt
+- template/newgem/README.md.tt
+- template/newgem/Rakefile.tt
+- template/newgem/lib/new_gem_entry.rb.tt
+- template/newgem/new_gem_entry.gemspec.tt
+- template/newgem/test/new_gem_entry_test.rb.tt
+- template/newgem/test/test_helper.rb.tt
+homepage: https://github.com/ruby-on-bioc/biocgem
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.6.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.2.22
+signing_key: 
+specification_version: 4
+summary: biocgem command line tools
+test_files: []