biocgem 0.0.2 → 0.0.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b8bfbcb8142aae417fe036d452d5aaeb97e36741bf368a656ff363914277cc01
-  data.tar.gz: 96cf48a41ea9874da8e6f35623a63218247ecbca355d07056ab3d0c7433fe9ca
+  metadata.gz: 42cd5ff623873b8031d52cb669f1e5c8f5893a4d6c4744c49012bc570d145871
+  data.tar.gz: ad395c534ceb64ad0dc6493120ce7870a02ad09dab4a804cc88599dc71363184
 SHA512:
-  metadata.gz: da47849575cacbd3225292dd6796e58721ec27235f658221cdcc82fd884b7a014823cf11941ef7aee42aadc3f95f0668637990d9271e157619f08a7ae47446b2
-  data.tar.gz: b434fc243049e98310a7d18ee798b7e0b165275fe065591cc371fd44fa3296b2d370e385e96a573c23f0e369c424e0e86d293857d43ea8508105c9d612f70d34
+  metadata.gz: cc5968031537f5057914f724500dbe9a162d95f3da4bc488edfb1df59f4412ae733a4a434c2e2a1ea75bfb32b1f6ef9f26797bc295a65ac268501b8c8cfa0645
+  data.tar.gz: 9db05fb3944a0cecc5985f6a794ae678329241b2989db2a14d7386583eb63f673bee4b6a887f92f25d0a62b305755f44f4f538be3a20bf4b894950131dd98f5a

data/lib/bioc_gem/command.rb

@@ -8,16 +8,26 @@ module BiocGem
     attr_accessor :parser
 
     def initialize(argv = ARGV)
-      @argv = argv
+      @argv = argv.clone
       @parser = Parser.new
     end
 
     def run
-      parser.parse_options(@argv)
+      parser.parse!(@argv)
 
-      pp config = parser.options.to_h
+      command = parser.command
+      options = parser.options
 
-      target = config[:bioc_package_name]
+      public_send("run_#{command}", options) if [:new].include?(command)
+    end
+
+    def run_new(options)
+      config = parser.options
+      require_name     = config.gem_require_name
+      package_name     = config.bioc_package_name
+      output_directory = config.output_directory
+
+      target = File.join(output_directory, package_name)
 
       base = File.expand_path("../../template/newgem", __dir__)
 
@@ -26,21 +36,21 @@ module BiocGem
           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])
+          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
+
+      warn "Created #{target}"
     end
   end
 end

data/lib/bioc_gem/options.rb

@@ -1,10 +1,12 @@
 module BiocGem
   Options = Struct.new(
+    :output_directory,
     :bioc_package_name,
     :bioc_sqlite_database_name,
     :gem_icon,
     :gem_constant_name,
     :gem_require_name,
+    :bioc_package_md5sum,
     :bioc_package_sha256sum,
     :bioc_version,
     :bioc_package_version

data/lib/bioc_gem/parser.rb

@@ -5,56 +5,70 @@ module BiocGem
   class Parser
     attr_reader :command, :options
 
-    def initialize
+    def initialize(args = nil)
       @comand = nil
 
       @options = Options.new
+      parse_options(args) if args
     end
 
-    def parse_options(args = ARGV)
+    def parse!(args = ARGV)
       @command = args.shift&.to_sym
+      if [:new].include?(command)
+        public_send("parse_options_#{command}", args)
+      else
+        warn "Unknown command #{command}"
+        nil
+      end
+    end
 
-      return if @command != :new
-
+    def parse_options_new(args)
       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
+        parser.on("-o", "--output [DIR]", "Output directory") do |dir|
+          options.output_directory = dir
+        end
+        parser.on("-n", "--bioc_package_name VAL", "e.g. org.Hs.eg.db") do |n|
+          options.bioc_package_name = n
         end
-        parser.on("-s", "--bioc_sqlite_database_name VAL", "e.g. org.Hs.eg.sqlite") do |v|
-          options[:bioc_sqlite_database_name] = v
+        parser.on("-s", "--bioc_sqlite_database_name VAL", "e.g. org.Hs.eg.sqlite") do |db|
+          options.bioc_sqlite_database_name = db
         end
-        parser.on("--gem_icon [VAL]", "e.g. :family:") do |v|
-          options[:gem_icon] = v
+        parser.on("--gem_icon [VAL]", "e.g. :family:") do |icon|
+          options.gem_icon = icon
         end
-        parser.on("--gem_constant_name [VAL]", "e.g. OrgHsEgDb") do |v|
-          options[:gem_constant_name] = v
+        parser.on("--gem_constant_name [VAL]", "e.g. OrgHsEgDb") do |c|
+          options.gem_constant_name = c
         end
-        parser.on("--gem_require_name [VAL]", "e.g. org_hs_eg_db") do |v|
-          options[:gem_require_name] = v
+        parser.on("--gem_require_name [VAL]", "e.g. org_hs_eg_db") do |rname|
+          options.gem_require_name = rname
         end
-        parser.on("--bioc_package_sha256sum [VAL]", "e.g. ") do |v|
-          options[:bioc_package_sha256sum] = v
+        parser.on("-m", "--bioc_package_md5sum [VAL]", "check md5sum") do |md5|
+          options.bioc_package_md5sum = md5
         end
-        parser.on("--bioc_version [VAL]", "e.g. 3.14") do |v|
-          options[:bioc_version] = v
+        parser.on("--bioc_package_sha256sum [VAL]", "check sha256sum") do |sha256|
+          options.bioc_package_sha256sum = sha256
+        end
+        parser.on("--bioc_version [VAL]", "e.g. 3.14") do |bv|
+          options.bioc_version = bv
         end
         parser.on("-v", "--bioc_package_version VAL", "e.g. 3.14.0") do |v|
-          options[:bioc_package_version] = 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.gem_icon ||= ":notes:"
+      options.gem_constant_name ||= \
+        options.bioc_package_name
+               .split(".").map(&:capitalize).join
+      options.gem_require_name.nil?
+      options.gem_require_name ||= \
+        options.bioc_package_name
+               .split(".").map(&:downcase).join("_")
+      options.bioc_version ||= "release"
 
       options
     end

data/lib/bioc_gem/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module BiocGem
-  VERSION = "0.0.2"
+  VERSION = "0.0.3"
 end

data/template/newgem/Rakefile.tt

@@ -36,16 +36,23 @@ def bioc_package_version
   "<%= config[:bioc_package_version] %>"
 end
 
+def bioc_package_md5sum
+  "<%= config[:bioc_package_md5sum] %>"
+end
+
 def bioc_package_sha256sum
-  sha256 = "<%= config[:bioc_package_sha256sum] %>"
-  sha256 == "" ? nil : sha256
+  "<%= config[:bioc_package_sha256sum] %>"
 end
 
 def bioc_package_file_name
   "#{bioc_package_name}_#{bioc_package_version}.tar.gz"
 end
 
-def download_annotation(database, src, file, sha256)
+def gem_require_name
+  "<%= config[:gem_require_name] %>"
+end
+
+def download_annotation(src, database, file, md5sum, sha256)
   require "fileutils"
   require "open-uri"
   require "tmpdir"
@@ -54,11 +61,17 @@ def download_annotation(database, src, file, sha256)
   puts "Downloading #{url}"
   contents = URI.open(url).read
 
-  if sha256
+  unless md5sum == ""
+    computed_md5sum = Digest::MD5.hexdigest(contents)
+    raise "MD5 checksum mismatch for #{url}" unless md5sum == computed_md5sum
+  end
+
+  unless sha256 == ""
     computed_sha256 = Digest::SHA256.hexdigest(contents)
-    raise "Bad hash: #{computed_sha256}" if computed_sha256 != sha256
+    raise "SHA256 checksum mismatch for #{url}" unless sha256 == computed_sha256
   end
 
+
   Dir.chdir(Dir.mktmpdir) do
     File.binwrite(file, contents)
     command = "tar xf"
@@ -67,6 +80,18 @@ def download_annotation(database, src, file, sha256)
 
     FileUtils.mkdir_p(dest)
 
+    if database == ""
+      databases = Dir.glob("#{src}/inst/extdata/*.sqlite")
+      raise "No database found in #{src}/inst/extdata" if databases.empty?
+      raise "Multiple databases found in #{src}/inst/extdata" if databases.size > 1
+
+      database = File.basename(databases.first)
+      require_path = File.expand_path("lib/#{gem_require_name}.rb", __dir__)
+      str = File.read(require_path)
+                .sub!("*", File.basename(database, ".sqlite"))
+      File.write(require_path, str)
+    end
+
     FileUtils.cp("#{src}/inst/extdata/#{database}", "#{dest}/#{database}")
     puts "Saved extdata/#{database}"
 
@@ -78,9 +103,10 @@ end
 namespace :extdata do
   desc "download #{bioc_sqlite_database_name}"
   task :download do
-    download_annotation(bioc_sqlite_database_name,
-                        bioc_package_name,
+    download_annotation(bioc_package_name,
+                        bioc_sqlite_database_name,
                         bioc_package_file_name,
+                        bioc_package_md5sum,
                         bioc_package_sha256sum)
   end
 end

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

@@ -2,6 +2,6 @@
 
 require 'sequel'
 <%= config[:gem_constant_name] %> = Sequel.sqlite(
-  File.expand_path('../extdata/<%= config[:bioc_sqlite_database_name] %>', __dir__),
+  File.expand_path('../extdata/<%= config[:bioc_sqlite_database_name] || "*.sqlite" %>', __dir__),
   readonly: true
 )

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: biocgem
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors:
 - kojix2
-autorequire:
+autorequire: 
 bindir: exe
 cert_chain: []
-date: 2021-12-06 00:00:00.000000000 Z
+date: 2021-12-08 00:00:00.000000000 Z
 dependencies: []
 description: biocgem command line tools
 email:
@@ -39,7 +39,7 @@ homepage: https://github.com/ruby-on-bioc/biocgem
 licenses:
 - MIT
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -54,8 +54,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
-signing_key:
+rubygems_version: 3.2.22
+signing_key: 
 specification_version: 4
 summary: biocgem command line tools
 test_files: []