ruby-igv 0.0.8 → 0.0.9

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data/README.md

@@ -1,16 +1,17 @@
 # ruby-igv
 
 [![Gem Version](https://badge.fury.io/rb/ruby-igv.svg)](https://badge.fury.io/rb/ruby-igv)
-[![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://rubydoc.info/gems/ruby-igv)
+[![Docs Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/ruby-igv)
+[![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://kojix2.github.io/ruby-igv)
 [![The MIT License](https://img.shields.io/badge/license-MIT-orange.svg)](LICENSE.txt)
 [![DOI](https://zenodo.org/badge/281373245.svg)](https://zenodo.org/badge/latestdoi/281373245)
 
 Ruby-IGV is a simple tool for controlling the Integrated Genomics Viewer (IGV) from the Ruby language. It provides an automated way to load files, specify genome locations, and take and save screenshots using IGV.
 
-<img src="https://user-images.githubusercontent.com/5798442/182540876-c3ca2906-7d05-4c93-9107-ce4135ae9765.png" align="right">
-
 ## Installation
 
+<img src="https://user-images.githubusercontent.com/5798442/182540876-c3ca2906-7d05-4c93-9107-ce4135ae9765.png" width="300" align="right">
+
 Requirement : 
 
 * [Ruby](https://github.com/ruby/ruby)
@@ -24,7 +25,7 @@ gem install ruby-igv
 
 ## Quickstart
 
-<img src="https://user-images.githubusercontent.com/5798442/182623864-a9fa59aa-abb9-4cb1-8311-2b3479b7414e.png" width="300" align="left">
+<img src="https://user-images.githubusercontent.com/5798442/182623864-a9fa59aa-abb9-4cb1-8311-2b3479b7414e.png" width="300" align="right">
 
 ```ruby
 require 'igv'
@@ -42,9 +43,9 @@ igv.snapshot 'region.png'
 
 ## Usage
 
-### commands
+### IGV batch commands
 
-The commonly used commands in IGV are summarized in the official [list of Batch commands](https://github.com/igvteam/igv/wiki/Batch-commands). (but even this does not seem to be all of them). You can also call the `commands` method from Ruby to open a browser and view the list.
+The commonly used commands in IGV are summarized in the official [list of batch commands](https://github.com/igvteam/igv/wiki/Batch-commands). (but even this does not seem to be all of them). You can also call the `commands` method from Ruby to open a browser and view the list.
 
 ```ruby
 igv.commands # Show the IGV command reference in your browser
@@ -52,7 +53,7 @@ igv.commands # Show the IGV command reference in your browser
 
 ### docs
 
-See [docs](https://rubydoc.info/gems/ruby-igv/IGV). Not all commands are implemented in Ruby.
+See [yard docs](https://rubydoc.info/gems/ruby-igv/IGV). Commonly used IGV batch commands can be called from Ruby methods of the same name. However, not all IGV batch commands are implemented in Ruby. Use the `send` method described below.
 
 ### send
 
@@ -62,6 +63,8 @@ Commands that are not implemented can be sent using the send method.
 igv.send("maxPanelHeight", 10)
 ```
 
+To avoid unexpected behavior, ruby-igv does not use the `method_missing` mechanism.
+
 ### Launch IGV
 
 Launch IGV from Ruby script.
@@ -70,11 +73,39 @@ Launch IGV from Ruby script.
 igv = IGV.start # launch IGV app using spawn
 ```
 
+You can specify the port.
+
+```ruby
+igv = IGV.start(port: 60152)
+```
+
+If you start IGV in this way, you can force IGV to terminate by calling the kill method.
+
+```ruby
+igv.kill
+```
+
 ### Open socket connection to IGV
 
+If IGV is already running, use `new` or `open`.
+
+new
+
 ```ruby
 igv = IGV.new   # create an IGV object. Then you will type `igv.connect`
+igv = IGV.new(host: "127.0.0.1", port: 60151, snapshot_dir: "~/igv_snapshot")
+igv.connect # To start a connection, call connect explicitly.
+igv.close
+```
+
+open
+
+```ruby
 igv = IGV.open  # create an IGV object and connect it to an already activated IGV.
+igv.close
+IGV.open(host: "127.0.0.1", port: 60151, snapshot_dir: "~/igv_snapshot") do |igv|
+  # do something
+end # The socket is automatically closed.
 ```
 
 ### Close IGV
@@ -96,7 +127,7 @@ igv.kill        # kill group pid created with IGV.start
 * Suggest or add new features
 
 ```
-Do you need commit rights to my repository?
+Do you need commit rights to this repository?
 Do you want to get admin rights and take over the project?
 If so, please feel free to contact me @kojix2.
 ```

data/lib/igv/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 class IGV
-  VERSION = '0.0.8'
+  VERSION = '0.0.9'
 end

data/lib/igv.rb

@@ -1,6 +1,7 @@
 # frozen_string_literal: true
 
 require 'igv/version'
+require 'uri'
 require 'socket'
 require 'fileutils'
 
@@ -19,7 +20,7 @@ class IGV
   # @return [IGV] IGV client object
 
   def initialize(host: '127.0.0.1', port: 60_151, snapshot_dir: Dir.pwd)
-    raise ArgumentError, 'new dose not take a block' if block_given?
+    raise ArgumentError, 'IGV#initialize does not accept a block.' if block_given?
 
     @host = host
     @port = port
@@ -50,7 +51,7 @@ class IGV
   end
 
   def self.port_open?(port)
-    !system("lsof -i:#{port}", out: '/dev/null')
+    system("lsof -i:#{port}", out: '/dev/null')
   end
   private_class_method :port_open?
 
@@ -64,8 +65,9 @@ class IGV
   def self.start(port: 60_151, command: 'igv', snapshot_dir: Dir.pwd)
     case port_open?(port)
     when nil   then warn "Cannot tell if port #{port} is open"
-    when false then raise("Port #{port} is already in use")
-    when true  then warn "Port #{port} is available"
+    when true  then raise("Port #{port} is already in use")
+    when false then warn "Port #{port} is available"
+    else raise "Unexpected return value from port_open?(#{port})"
     end
     r, w = IO.pipe
     pid_igv = spawn(command, '-p', port.to_s, pgroup: true, out: w, err: w)
@@ -77,7 +79,7 @@ class IGV
       break if line.include? "Listening on port #{port}"
     end
     puts "\e[0m"
-    igv = open(port: port, snapshot_dir: snapshot_dir)
+    igv = self.open(port: port, snapshot_dir: snapshot_dir)
     igv.instance_variable_set(:@pgid_igv, pgid_igv)
     igv
   end
@@ -129,11 +131,11 @@ class IGV
     cmd = \
       cmds
       .compact
-      .map do |cmd|
-        case cmd
-        when String, Symbol, Numeric          then cmd.to_s
-        when ->(c) { c.respond_to?(:to_str) } then cmd.to_str
-        else raise ArgumentError, "#{cmd.inspect} is not a string"
+      .map do |cm|
+        case cm
+        when String, Symbol, Numeric          then cm.to_s
+        when ->(c) { c.respond_to?(:to_str) } then cm.to_str
+        else raise ArgumentError, "#{cm.inspect} is not a string"
         end.strip.encode(Encoding::UTF_8)
       end
       .join(' ')
@@ -201,6 +203,8 @@ class IGV
                   end
     index = "index=#{index}" if index
     send :load, path_or_url, index
+  rescue URI::InvalidURIError
+    raise ArgumentError, "Invalid URI or file path: #{path_or_url}"
   end
 
   # Go to the specified location
@@ -208,8 +212,8 @@ class IGV
   #
   # @param location [String] The location to go to.
 
-  def goto(position)
-    send :goto, position
+  def goto(*position)
+    send :goto, *position
   end
   alias go goto
 
@@ -272,12 +276,18 @@ class IGV
 
   # @note IGV Batch command
 
+  def new
+    send :new
+  end
+
+  # @note IGV Batch command
+
   def clear
     send :clear
   end
 
   # Exit (close) the IGV application and close the socket.
-  # @note IGV Batch command (modifyed)
+  # @note IGV Batch command (modified)
 
   def exit
     send :exit
@@ -286,7 +296,7 @@ class IGV
   alias quit exit
 
   #	Sets the directory in which to write images.
-  # Retruns the current snapshot directory if no argument is given.
+  # Returns the current snapshot directory if no argument is given.
   # @note IGV Batch command (modified)
   #
   # @param path [String] The path to the directory.
@@ -360,4 +370,80 @@ class IGV
     file_path = File.expand_path(file_path)
     send :saveSession, file_path
   end
+
+  # @note IGV Batch command
+
+  def set_alt_color(color, track)
+    send :setAltColor, color, track
+  end
+
+  # @note IGV Batch command
+
+  def set_color(color, track)
+    send :setColor, color, track
+  end
+
+  # @note IGV Batch command
+
+  def set_data_range(range, track)
+    send :setDataRange, range, track
+  end
+
+  # @note IGV Batch command
+
+  def set_log_scale(bool, track)
+    bool = 'true' if bool == true
+    bool = 'false' if bool == false
+    send :setLogScale, bool, track
+  end
+
+  # @note IGV Batch command
+
+  def set_sequence_strand(strand)
+    send :setSequenceStrand, strand
+  end
+
+  # @note IGV Batch command
+
+  def set_sequence_show_translation(bool)
+    bool = 'true' if bool == true
+    bool = 'false' if bool == false
+    send :setSequenceShowTranslation, bool
+  end
+
+  # @note IGV Batch command
+
+  def set_sleep_interval(ms)
+    send :setSleepInterval, ms
+  end
+
+  # @note IGV Batch command
+
+  def set_track_height(height, track)
+    send :setTrackHeight, height, track
+  end
+
+  # @note IGV Batch command
+
+  def max_panel_height(height)
+    send :maxPanelHeight, height
+  end
+
+  # @note IGV Batch command
+
+  def color_by(option, tag)
+    send :colorBy, option, tag
+  end
+
+  # @note IGV Batch command
+
+  def group(option, tag)
+    send :group, option, tag
+  end
+
+  # @note IGV Batch command
+
+  def overlay(overlaid_track, *tracks)
+    send :overlay, overlaid_track, *tracks
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ruby-igv
 version: !ruby/object:Gem::Version
-  version: 0.0.8
+  version: 0.0.9
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-08-03 00:00:00.000000000 Z
+date: 2024-04-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: launchy
@@ -95,7 +95,7 @@ homepage: https://github.com/kojix2/ruby-igv
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -103,15 +103,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '2.4'
+      version: '2.6'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.7
-signing_key: 
+rubygems_version: 3.5.5
+signing_key:
 specification_version: 4
 summary: Control IGV (Integrative Genomics Viewer) with Ruby.
 test_files: []