rfam 0.1.0-java

checksums.yaml

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+---
+SHA256:
+  metadata.gz: 7ef788d2bb36b1a69085a0353cb59d9e39527c1731e8691b11802ef8bda671be
+  data.tar.gz: 3cc54609a4e0ab9cc3fe9a3178568f7ad951750665465571b48e80fd6106b87a
+SHA512:
+  metadata.gz: c8480e079f6c7ad4f911daef96ce2ed5229ecd8b2a70343faba9e85d06cd9a444c6750377643594d1d37b7802ac116639799d687a6041fa0d856f7e874a19de5
+  data.tar.gz: 8a890f412ea7bb4cb3cdd6e412802e5419aa33100a8ae41d1490efdd79e49d0ee386467c85d7ee3c5fcbd4adb851dd590fa8aa8d80506542a500b755e7aaf09a

data/Dockerfile

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+FROM jruby:9.2.7.0
+
+RUN apt-get update -qq \
+	&& apt-get install -y \
+	vim less emacs-nox
+
+WORKDIR /usr/src/rfam
+
+COPY . .
+RUN gem install bundler -v '2.0.1' \
+	&& bundle install \
+	&& rake rfam:install
+
+CMD ["/bin/bash"]

data/Gemfile

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+source "https://rubygems.org"
+
+# Specify your gem's dependencies in rfam.gemspec
+gemspec

data/Rakefile

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+require "bundler/gem_tasks"
+
+require 'jars/installer'
+desc "Install JAR dependencies"
+task :install_jars do
+  Jars::Installer.vendor_jars!
+end
+
+desc "Install rfam gem and JAR dependencies"
+task "rfam:install" => [:install, :install_jars]

data/bin/rfam

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+#!/usr/bin/env jruby
+
+require 'rfam'
+require 'optparse'
+
+options = {}
+parser = OptionParser.new do |opts|
+  opts.banner = "Usage: rfam [options]"
+
+  opts.on("-p", "--path PATH", "Path to monitor") do |v|
+    options[:path] = v
+  end
+
+  opts.on("-i", "--interval [MILLISECONDS]", Integer, "Interval to check/notify") do |v|
+    options[:interval] = v
+  end
+end
+parser.parse! ARGV
+
+Rfam::Monitor.start(**options)

data/lib/rfam/listener.rb

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+module Rfam
+  class Listener
+    include Rfam::FileAlterationListener
+
+    def onDirectoryChange(path)
+      emit Alteration.new(path, :directory, :change, now)
+    end
+
+    def onDirectoryCreate(path)
+      emit Alteration.new(path, :directory, :create, now)
+    end
+
+    def onDirectoryDelete(path)
+      emit Alteration.new(path, :directory, :delete, now)
+    end
+
+    def onFileChange(path)
+      emit Alteration.new(path, :file, :change, now)
+    end
+
+    def onFileCreate(path)
+      emit Alteration.new(path, :file, :create, now)
+    end
+
+    def onFileDelete(path)
+      emit Alteration.new(path, :file, :delete, now)
+    end
+
+    def onStart(observer)
+      # no-op
+    end
+
+    def onStop(observer)
+      # no-op
+    end
+
+    private
+
+    def emit(alteration)
+      puts JSON.dump(alteration.to_h)
+    end
+
+    def now
+      Time.now
+    end
+  end
+end

data/lib/rfam/monitor.rb

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+require 'rfam/listener'
+
+module Rfam
+  class Monitor
+
+    DEFAULT_INTERVAL = 1000
+
+    def self.start(*args)
+      new(*args).start
+    end
+
+    def self.run(*args)
+      new(*args).run
+    end
+
+    attr_reader :path, :interval, :observer, :listener, :monitor
+
+    def initialize(path:, interval: nil)
+      @path = path
+      @interval = interval || DEFAULT_INTERVAL
+      @listener = Listener.new
+      @observer = Rfam::FileAlterationObserver.new(path)
+      @observer.addListener(@listener)
+      @monitor = Rfam::FileAlterationMonitor.new(@interval, @observer)
+    end
+
+    def start
+      monitor.start
+    end
+
+    def stop
+      monitor.stop(0)
+    end
+
+    def run
+      begin
+        start
+        sleep
+      ensure
+        stop
+      end
+    end
+
+  end
+end

data/lib/rfam/version.rb

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+module Rfam
+  VERSION = "0.1.0"
+end

data/lib/rfam.rb

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+require 'rfam/version'
+# require 'java'
+require 'rfam_jars'
+require 'json'
+
+module Rfam
+  include_package 'org.apache.commons.io.monitor'
+
+  Alteration = Struct.new(:path, :filetype, :alteration, :timestamp)
+end
+
+require 'rfam/monitor'

data/lib/rfam_jars.rb

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+# this is a generated file, to avoid over-writing it just delete this comment
+begin
+  require 'jar_dependencies'
+rescue LoadError
+  require 'commons-io/commons-io/2.6/commons-io-2.6.jar'
+end
+
+if defined? Jars
+  require_jar 'commons-io', 'commons-io', '2.6'
+end

data/rfam.gemspec

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+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "rfam/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "rfam"
+  spec.version       = Rfam::VERSION
+  spec.authors       = ["David Chandek-Stark"]
+  spec.email         = ["david.chandek.stark@duke.edu"]
+
+  spec.summary       = "JRuby library wrapping Apache Commons IO File Monitor."
+  spec.homepage      = "https://gitlab.oit.duke.edu/dc"
+  spec.license       = "MIT"
+  spec.platform      = "java"
+
+  # Specify which files should be added to the gem when it is released.
+  # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
+  # spec.files         = Dir.chdir(File.expand_path('..', __FILE__)) do
+  #   `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  # end
+
+  spec.files = Dir['lib/**/*.rb']
+  spec.files += Dir['lib/**/*.jar']
+  spec.files += Dir['*file']
+  spec.files += Dir['*.gemspec']
+
+  spec.executables = ["rfam"]
+  spec.require_paths = ["lib"]
+
+  spec.requirements << "jar commons-io, commons-io, 2.6"
+
+  spec.add_development_dependency "bundler", "~> 2.0"
+  spec.add_development_dependency "rake", "~> 12.0"
+  # spec.add_development_dependency "rspec", "~> 3.0"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: rfam
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: java
+authors:
+- David Chandek-Stark
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2019-07-23 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  name: bundler
+  prerelease: false
+  type: :development
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '12.0'
+  name: rake
+  prerelease: false
+  type: :development
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '12.0'
+description:
+email:
+- david.chandek.stark@duke.edu
+executables:
+- rfam
+extensions: []
+extra_rdoc_files: []
+files:
+- Dockerfile
+- Gemfile
+- Rakefile
+- bin/rfam
+- lib/commons-io/commons-io/2.6/commons-io-2.6.jar
+- lib/rfam.rb
+- lib/rfam/listener.rb
+- lib/rfam/monitor.rb
+- lib/rfam/version.rb
+- lib/rfam_jars.rb
+- rfam.gemspec
+homepage: https://gitlab.oit.duke.edu/dc
+licenses:
+- MIT
+metadata: {}
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements:
+- jar commons-io, commons-io, 2.6
+rubyforge_project:
+rubygems_version: 2.7.6
+signing_key:
+specification_version: 4
+summary: JRuby library wrapping Apache Commons IO File Monitor.
+test_files: []