cloudalign-cli 0.1.1

data/README.md

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+# Introduction
+This is a Command Line Interface (CLI) to be used for accessing a remote CloudAlign system and interacting with it. This
+tool is useful for creating scripts or other automated processes that one would need to interface with CloudAlign.
+
+Also included with this tool is a simple Ruby library for talking to CloudAlign directly.
+
+## Installation
+
+### Dependencies
+- Ruby 1.9.3 or greater
+- RubyGems (http://www.rubygems.org ships with 1.9.x)
+- A Unix like OS (Tested with Ubuntu 12 and Mac OSX)
+
+### Setup
+Simply install the CloudAlign CLI using GEM
+<pre>
+$ gem install cloudalign-cli
+</pre>
+
+### Configuration
+Create a config file
+<pre>
+$ mkdir -p ~/cloudalign
+$ vi ~/cloudalign/config.yml
+</pre>
+
+Finally, populate the config file with your credentials
+<pre>
+# File ~/cloudalign/config.yml
+api_url: http://web1.dev.cloudalign.accetia.com
+api_user: jmccaffrey
+api_password: shhhitssecret
+</pre>
+
+## Usage
+
+### Supported Commands
+Here are the supported operations with the current version of the CloudAlign Command Line Interface (CLI).  Also listed
+with each operation is a sample of how to use it.
+
+#### Access Help Documentation
+<pre>
+$ cloudalign
+Tasks:
+  cloudalign artifact <command>  # Manipulate artifacts in the CloudAlign system
+  cloudalign help [TASK]         # Describe available tasks or one specific task
+  cloudalign project <command>   # Manipulate projects in the CloudAlign system
+
+$ cloudalign artifact
+  cloudalign artifact align ARTIFACT              # ...
+  cloudalign artifact compare ARTIFACT REFERENCE  # ...
+  cloudalign artifact download ARTIFACT FILE      # Downloads file FILE ...
+  cloudalign artifact help [COMMAND]              # Describe subcommands...
+  cloudalign artifact list_files ARTIFACT         # Lists all files in ...
+
+$ cloudalign project
+  cloudalign project help [COMMAND]            # Describe subcommands or...
+  cloudalign project list                      # Lists all viewable proj...
+  cloudalign project list_artifacts PROJECT    # Lists all viewable arti...
+  cloudalign project upload_file PROJECT PATH  # Uploads a file located ...
+
+$ cloudalign project help list
+Usage:
+  cloudalign list
+
+Lists all viewable projects for your user
+</pre>
+
+#### List Projects
+<pre>
+$ cloudalign project list
+  +----+-----------------+
+  | id | name            |
+  +----+-----------------+
+  | 1  | My Test Project |
+  +----+-----------------+
+  | 2  | asdf            |
+  +----+-----------------+
+
+</pre>
+
+#### List Artifacts in a Project
+<pre>
+$ cloudalign project list_artifacts 2
+  +----+-----------+
+  | id | name      |
+  +----+-----------+
+  | 20 | 40mb_file |
+  +----+-----------+
+</pre>
+
+#### List Files within an Artifact
+<pre>
+$ cloudalign artifact list_files 20
+  +-----+---------------+----------+--------+
+  | id  | name          | size     | status |
+  +-----+---------------+----------+--------+
+  | 137 | 40mb_file.bin | 41943040 | READY  |
+  +-----+---------------+----------+--------+
+</pre>
+
+#### Download a File
+<pre>
+$ cloudalign file download 20 137
+Downloading file 40mb_file.bin from Artifact 20 to ./
+...
+Done
+</pre>
+
+#### Upload a File and Create Artifact
+<pre>
+$ cloudalign project upload 2 test.fastq
+Uploading file test.fastq to project 'asdf'
+...
+Done
+</pre>
+
+#### Run BWA Alignment
+<pre>
+$ cloudalign artifact 20 align
+Running alignment on artifact 'Test Artifact 123', use artifact list_files to see the status.
+</pre>

data/bin/cloudalign

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+#!/usr/bin/env ruby
+$LOAD_PATH.unshift 'lib'
+require "cloudalign"
+require "thor"
+require "thor/group"
+require "pp"
+require "formatador"
+
+class ProjectTask < Thor
+  desc "list", "Lists all viewable projects for your user"
+  def list
+    projects = CloudAlign::Project.find_all.map do |p|
+      {
+        :id => p.id,
+        :name => p.name
+      }
+    end
+
+    Formatador.display_table(projects)
+  end
+
+  desc "list_artifacts PROJECT", "Lists all viewable artifacts in <PROJECT>"
+  def list_artifacts(project_id)
+    artifacts = CloudAlign::Artifact.find_by_project(project_id).map do |a|
+      {
+        :id => a.id,
+        :name => a.name,
+      }
+    end
+
+    Formatador.display_table(artifacts)
+  end
+
+  desc "upload_file PROJECT PATH", "Uploads a file located at PATH to the PROJECT in CloudAlign"
+  def upload_file(project_id, path)
+    project = CloudAlign::Project.find(project_id)
+    puts "Uploading file #{File.basename(path)} to project '#{project.name}'"
+    puts "..."
+    project.upload_file(path)
+    puts "Done"
+  end
+
+end
+
+class ArtifactTask < Thor
+  desc "list_files ARTIFACT", "Lists all files in <ARTIFACT>"
+  def list_files(artifact_id)
+    files = CloudAlign::File.find_by_artifact(artifact_id).map do |f|
+      {
+        :id => f.id,
+        :name => f.name,
+        :size => f.size,
+        :status => f.status
+      }
+    end
+
+    Formatador.display_table(files)
+  end
+
+  desc "download ARTIFACT FILE", "Downloads file FILE from the ARTIFACT in CloudAlign"
+  def download(artifact_id, file_id)
+    file = CloudAlign::File.find(artifact_id, file_id)
+    puts "Downloading file #{file.file_name} from Artifact #{file.artifact_id} to ./"
+    puts "..."
+    file.download
+    puts "Done"
+  end
+
+  desc "align ARTIFACT", "..."
+  def align(artifact_id)
+    artifact = CloudAlign::Artifact.find(artifact_id)
+    artifact.analyze(:bwa_alignment)
+  end
+
+  desc "compare ARTIFACT REFERENCE", "..."
+  def compare(artifact_id, reference)
+    puts "Not Implemented!"
+  end
+end
+
+class CLI < Thor
+  register(ProjectTask, 'project', 'project <command>', 'Manipulate projects in the CloudAlign system')
+  register(ArtifactTask, 'artifact', 'artifact <command>', 'Manipulate artifacts in the CloudAlign system')
+end
+
+CLI.start

data/lib/cloudalign/artifact.rb

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+module CloudAlign
+  class Artifact < BaseEntity
+    attr_accessor :name, :description
+
+    class << self
+
+      def find_by_project(project_id)
+        Client.get_json("/projects/#{project_id}/artifacts").map do |row|
+          Artifact.new(row)
+        end
+      end
+
+    end
+
+    def analyze(analyzer, options = {})
+      options[:analyzer] = analyzer
+      Client.post("/artifacts/#{@id}/analyze", options)
+    end
+
+    def destroy
+      Client.delete("/artifacts/#{@id}")
+    end
+  end
+end

data/lib/cloudalign/base_entity.rb

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+module CloudAlign
+  class BaseEntity
+    attr_accessor :id, :created_at, :updated_at
+
+    def initialize(args = {})
+      args.each do |k,v|
+        instance_variable_set("@#{k}", v) unless v.nil?
+      end
+    end
+
+  end
+end

data/lib/cloudalign/client.rb

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+require 'rest-client'
+require 'cgi'
+
+class String
+  def starts_with?(prefix)
+    prefix = prefix.to_s
+    self[0, prefix.length] == prefix
+  end
+end
+
+module CloudAlign
+  class Client
+
+    class << self
+      def get(path)
+        RestClient.get(authorized_url(path))
+      end
+
+      def get_json(path)
+        uri = URI.parse(path)
+        uri.path += '.json' unless uri.path.match(/\.json$|\/$/)
+        JSON.parse(get(uri.to_s))
+      end
+
+      def delete(path)
+        RestClient.delete(authorized_url(path))
+      end
+
+      def get_file(path, output_path)
+        ::File.open(output_path, 'w') do |out|
+          process_response = lambda do |response|
+            response.read_body do |chunk|
+              print "."
+              out.write chunk
+            end
+          end
+
+          RestClient::Request.execute(:method => :get, :url => authorized_url(path), :block_response => process_response)
+        end
+      end
+
+      def post(path, data)
+        RestClient.post(authorized_url(path), data)
+      end
+
+      def post_for_upload(path, data)
+        pp data
+        RestClient.post(authorized_url(path), data) do |response, request, result, &block|
+          if [301, 302, 303, 307].include? response.code
+            return get_json(response.headers[:location])
+          end
+        end
+      end
+
+      def authorized_url(path)
+        url = CloudAlign.config.get("api_url", "http://api.cloudalign.com").sub(/\/$/, '')
+
+        if path.starts_with?(url)
+          uri = URI.parse(path)
+        elsif path.starts_with?('/')
+          uri = URI.parse(url)
+          uri.path = path
+        else
+          return path
+        end
+
+        uri.user = CGI.escape(CloudAlign.config.get("api_user"))
+        uri.password = CGI.escape(CloudAlign.config.get("api_password"))
+
+        uri.to_s
+      end
+    end
+  end
+end

data/lib/cloudalign/config.rb

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+require 'yaml'
+require 'pathname'
+
+module CloudAlign
+  class Config
+    def initialize(path = nil)
+      @config = {}
+      load path
+    end
+
+    def set(key, value)
+      set_recursive(key, value, @config)
+    end
+
+    def get(key, default = nil)
+      p = @config
+      key.split('.').each do |part|
+        return default unless p.has_key? part
+        p = p[part]
+      end
+
+      p
+    end
+
+    def load(path = nil)
+      if path.nil?
+        config_paths = [Pathname.new(Dir.home).join('.cloudalign', 'config.yml').to_s]
+        path = config_paths.detect{|p| ::File.exists?(p)}
+      end
+
+      @config = YAML.load_file(path)
+    end
+
+    private
+
+    def set_recursive(key, value, array)
+      if key.include? '.'
+        (part, key) = key.split('.', 2)
+        array[part] = {} unless array.has_key? part
+        return set_recursive(key, value, array[part])
+      end
+
+      array[key] = value
+    end
+  end
+end

data/lib/cloudalign/file.rb

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+module CloudAlign
+  class File < BaseEntity
+    attr_accessor :name, :storage_path, :size, :ready
+
+    def download(output_path = nil)
+      output_path = self.file_name if output_path.nil?
+      download_info = Client.get_json("/artifacts/#{@artifact_id}/files/#{@id}/download")
+      Client.get_file(download_info["download_url"], output_path)
+    end
+
+    def file_name
+      ::File.basename(@storage_path)
+    end
+
+    def status
+      statuses = %w(READY BUILDING UPLOADING)
+      (@status >= 0 && @status < statuses.length) ? statuses[@status] : @status
+    end
+
+    class << self
+
+      def find(artifact_id, id)
+        File.new(Client.get_json("/artifacts/#{artifact_id}/files/#{id}"))
+      end
+
+      def find_by_artifact(artifact_id)
+        Client.get_json("/artifacts/#{artifact_id}/files").map do |row|
+          File.new(row)
+        end
+      end
+
+    end
+  end
+end

data/lib/cloudalign/project.rb

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+module CloudAlign
+  class Project < BaseEntity
+    attr_accessor :name, :description
+
+    def self.find(id)
+      Project.new(Client.get_json("/projects/#{id}"))
+    end
+
+    def self.find_all
+      Client.get_json("/projects").map do |row|
+        Project.new(row)
+      end
+    end
+
+    def upload_file(path)
+      post_data = Client.get_json("/projects/#{@id}/upload_file")
+      upload_url = post_data.delete("url")
+      post_data[:file] = ::File.new(path, 'rb')
+
+      Client.post_for_upload(upload_url, post_data)
+    end
+
+  end
+end

data/lib/cloudalign.rb

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+require 'json'
+require 'logger'
+require 'pathname'
+
+module CloudAlign
+  autoload :BaseEntity, 'cloudalign/base_entity'
+  autoload :Client, 'cloudalign/client'
+  autoload :Project, 'cloudalign/project'
+  autoload :Artifact, 'cloudalign/artifact'
+  autoload :File, 'cloudalign/file'
+  autoload :Config, 'cloudalign/config'
+
+  API_VERSION = 1
+
+  class Error < StandardError; end
+
+  def self.logger
+    @logger ||= Logger.new(STDOUT)
+  end
+
+  def self.logger=(logger)
+    @logger = logger
+  end
+
+  def self.config
+    @config ||= Config.new
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: cloudalign-cli
+version: !ruby/object:Gem::Version
+  version: 0.1.1
+  prerelease: 
+platform: ruby
+authors:
+- Jonathan McCaffrey
+- Jeffrey Biles
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-08-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: thor
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: formatador
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Cloudalign brings the power of the cloud straight to your lab
+email: 
+executables:
+- cloudalign
+extensions: []
+extra_rdoc_files: []
+files:
+- bin/cloudalign
+- lib/cloudalign/artifact.rb
+- lib/cloudalign/base_entity.rb
+- lib/cloudalign/client.rb
+- lib/cloudalign/config.rb
+- lib/cloudalign/file.rb
+- lib/cloudalign/project.rb
+- lib/cloudalign.rb
+- README.md
+homepage: http://rubygems.org/gems/cloudalign-cli
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: cloudalign-cli
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: Access cloudalign from your command line
+test_files: []