rbbt-rest 1.1.0

data/LICENSE

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+Copyright (c) 2010-2013 Miguel Vázquez García
+
+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/Rakefile

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+require 'rubygems'
+require 'rake'
+
+begin
+  require 'jeweler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "rbbt-rest"
+    gem.summary = %Q{Rbbt Web and REST interfaces}
+    gem.description = %Q{Basic web app controllers and templates}
+    gem.email = "miguel.vazquez@cnio.es"
+    gem.homepage = "http://github.com/mikisvaz/rbbt-rest"
+    gem.authors = ["Miguel Vazquez"]
+    gem.files = Dir['lib/**/*.rb', 'share/R/*', 'share/views/**/*', 'config.ru', "Rakefile", 'LICENCE']
+
+    gem.add_dependency('rake')
+    gem.add_dependency('sinatra')
+    gem.add_dependency('zurb-foundation')
+    gem.add_dependency('compass')
+    gem.add_dependency('json')
+    gem.add_dependency('haml')
+    gem.add_dependency('rest-client')
+    gem.add_dependency('sinatra-authorization')
+    gem.add_dependency('sinatra-cross_origin')
+
+
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+  Jeweler::GemcutterTasks.new  
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: sudo gem install jeweler"
+end
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+begin
+  require 'rcov/rcovtask'
+  Rcov::RcovTask.new do |test|
+    test.libs << 'test'
+    test.pattern = 'test/**/test_*.rb'
+    test.verbose = true
+  end
+rescue LoadError
+  task :rcov do
+    abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
+  end
+end
+
+task :test => :check_dependencies
+
+task :default => :test

data/config.ru

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+require 'zurb-foundation'
+require 'modular-scale'
+
+require 'rbbt'
+require 'rbbt/rest/main'
+require 'rbbt/rest/entity'
+require 'rbbt/rest/workflow'
+require 'rbbt/rest/file_server'
+require 'rbbt/rest/helpers'
+
+YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler
+
+class RbbtRest < Sinatra::Base
+  
+  #{{{ MODULES AND HELPERS
+  register Sinatra::RbbtRESTMain
+  register Sinatra::RbbtRESTEntity
+  register Sinatra::RbbtRESTWorkflow
+  register Sinatra::RbbtRESTFileServer
+  helpers Sinatra::RbbtMiscHelpers
+
+  #{{{ DIRECTORIES
+  local_var = Rbbt.var.find(:lib)
+  set :cache_dir           , local_var.sinatra.cache.find
+  set :file_dir            , local_var.sinatra.files.find
+  set :favourites_dir      , local_var.sinatra.favourites.find
+  set :favourite_lists_dir , local_var.sinatra.favourite_lists
+
+  #{{{ SESSIONS
+  use Rack::Session::Cookie, :key => 'rack.session',
+    :path => '/',
+    :expire_after => 2592000,
+    :secret => 'StudyExplorer secret!!'
+
+  #{{{ FOUNDATION RESOURCES
+  add_sass_load_path "#{Gem.loaded_specs['compass'].full_gem_path}/frameworks/compass/stylesheets"
+  add_sass_load_path "#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/scss/" 
+  add_sass_load_path "#{Gem.loaded_specs['modular-scale'].full_gem_path}/stylesheets/" 
+  RbbtRESTHelpers.javascript_resources << Path.setup("#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/js/foundation")
+  RbbtRESTHelpers.javascript_resources << Path.setup("#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/js/vendor")
+end
+
+#{{{ WORKFLOWS
+
+if Rbbt.etc.workflows.find(:lib).exists?
+  class RbbtRest
+    Rbbt.etc.workflows.find(:lib).read.split("\n").each do |workflow|
+      Workflow.require_workflow workflow
+      add_workflow Kernel.const_get(workflow), true
+    end
+  end
+end
+
+#{{{ ENTITIES
+
+require 'rbbt/entity'
+require 'rbbt/entity/genomic_mutation'
+require 'rbbt/entity/snp'
+require 'rbbt/entity/mutated_isoform'
+require 'rbbt/entity/chromosome_range'
+require 'rbbt/entity/study'
+require 'rbbt/entity/study/genotypes'
+require 'rbbt/entity/study/cnv'
+require 'rbbt/entity/study/methylation'
+
+require 'rbbt/sources/string'
+require 'rbbt/sources/pina'
+require 'rbbt/sources/go'
+require 'rbbt/sources/kegg'
+require 'rbbt/sources/InterPro'
+require 'rbbt/sources/pfam'
+require 'rbbt/sources/tfacts'
+
+$annotation_repo = Rbbt.var.find(:lib).cache.annotation_repo.find
+
+Entity.entity_list_cache = Rbbt.var.find(:lib).sinatra.entity_lists
+
+[Study, Sample, MutatedIsoform, GenomicMutation, SNP, ChromosomeRange, CNV, Gene, Protein, PMID, InterProDomain, KeggPathway, GOTerm, PfamDomain, NCINaturePathway, NCIReactomePathway, NCIReactomePathway].each do |mod|
+  mod.module_eval do
+    include Entity::REST
+  end
+end
+
+#{{{ FINDER
+class RbbtRest
+  finder = Finder.new
+  if production?
+   Thread.new do
+    #finder.add_instance(KEGG.pathways, :grep => "^hsa", :fields => ["Pathway Name"], :namespace => "Hsa/jun2011")
+    #finder.add_instance(Organism.lexicon("Hsa/jun2011"), :persist => true, :namespace => "Hsa/jun2011", :grep => "^LRG_", :invert_grep => true)
+   end
+  end
+  set :finder, finder
+end
+
+#{{{ RUN
+$title = "RbbtRest"
+use Rack::Deflater
+run RbbtRest

data/lib/rbbt/rest/client.rb

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+require 'rest_client'
+require 'json'
+require 'rbbt/workflow'
+require 'rbbt/workflow/step'
+require 'rbbt/util/misc'
+
+class WorkflowRESTClient
+
+  def self.fix_hash(hash, fix_values = false)
+    fixed = {}
+    hash.each do |key, value|
+      fixed[key.to_sym] = case
+                          when Hash === value 
+                            fix_hash(value)  
+                          when (fix_values and String === value)
+                            value.to_sym
+                          else
+                            value
+                          end
+    end
+    fixed
+  end
+
+  def self.get_raw(url, params = {})
+    params = params.merge({ :_format => 'raw' })
+    RestClient.get(url, :params => params)
+  end
+ 
+  def self.post_jobname(url, params = {})
+    params = params.merge({ :_format => 'jobname' })
+    RestClient.post(url, params)
+  end
+  
+  def self.get_json(url, params = {})
+    params = params.merge({ :_format => 'json' })
+    res = RestClient.get(url, :params => params)
+    begin
+      JSON.parse(res)
+    rescue
+      res
+    end
+  end
+  
+  def self.post_json(url, params = {})
+    if url =~ /_cache_type=:exec/
+      JSON.parse(Open.open(url, :nocache => true))
+    else
+      params = params.merge({ :_format => 'json' })
+      res = RestClient.post(url, params)
+      begin
+        JSON.parse(res)
+      rescue
+        res
+      end
+    end
+  end
+
+  class RemoteStep < Step
+
+    attr_accessor :url, :base_url, :task, :name, :inputs, :result_type, :result_description
+
+    def name
+      (Array === @url ? @url.first : @url).split("/").last
+    end
+
+    def task_name
+      (Array === @url ? @url.first : @url).split("/")[-2]
+    end
+
+    def info
+      info = WorkflowRESTClient.get_json(File.join(url, 'info'))
+      info = WorkflowRESTClient.fix_hash(info)
+      info[:status] = info[:status].to_sym if String === info[:status]
+      info
+    end
+
+    def fork
+      @name = WorkflowRESTClient.post_jobname(File.join(base_url, task.to_s), inputs.merge(:jobname => @name, :_cache_type => :asynchronous))
+      @url = File.join(base_url, task.to_s, @name)
+      self
+    end
+
+    def initialize(base_url, task = nil, name = nil, inputs = nil, result_type = nil, result_description = nil, exec = false)
+      if task.nil?
+        @url = base_url
+      else
+        @base_url, @task, @name, @inputs, @result_type, @result_description = base_url, task, name, inputs, result_type, result_description
+        if exec
+          @url = [File.join(base_url, task.to_s), inputs]
+        else
+          self.fork 
+        end
+      end
+    end
+
+    def _exec
+      if Array === @url
+        url, params = @url
+      else
+        url, params = @url, {:_cache_type => :synchronous}
+      end
+      case result_type
+      when :string
+        WorkflowRESTClient.get_raw(url, params) 
+      when :boolean
+        WorkflowRESTClient.get_raw(url, params) == "true"
+      when :tsv
+        TSV.open(StringIO.new(WorkflowRESTClient.get_raw(url, params)))
+      when :annotations
+        Annotated.load_tsv(TSV.open(StringIO.new(WorkflowRESTClient.get_raw(url, params))))
+      else
+        WorkflowRESTClient.get_json(url, params)
+      end
+    end
+
+    def exec
+      res = _exec
+      prepare_result(res, result_type)
+    end
+
+    def run
+      exec
+    end
+
+    def load
+      exec
+    end
+
+    def join
+      exec
+      self
+    end
+
+    def status
+      info[:status]
+    end
+
+    def clean
+      WorkflowRESTClient.get_raw(url, :_update => :clean)
+      self
+    end
+
+    def files
+      WorkflowRESTClient.get_json(File.join(url, 'files'))
+    end
+
+    def file(file)
+      WorkflowRESTClient.get_json(File.join(url, 'file', file))
+    end
+  end
+
+  attr_accessor :url, :name, :exec_exports, :asynchronous_exports, :synchronous_exports
+
+  def initialize(url, name)
+    Log.debug("Loading remote workflow #{ name }: #{ url }")
+    @url, @name = url, name
+    init_remote_tasks
+  end
+  
+  def to_s
+    name
+  end
+
+  def task_info(task)
+    @task_info ||= {}
+    @task_info[task]
+    
+    if @task_info[task].nil?
+      task_info = WorkflowRESTClient.get_json(File.join(url, task.to_s, 'info'))
+      task_info = WorkflowRESTClient.fix_hash(task_info)
+
+      task_info[:result_type] = task_info[:result_type].to_sym
+      task_info[:export] = task_info[:export].to_sym
+      task_info[:input_types] = WorkflowRESTClient.fix_hash(task_info[:input_types], true)
+      task_info[:inputs] = task_info[:inputs].collect{|input| input.to_sym }
+
+      @task_info[task] = task_info
+    end
+    @task_info[task]
+  end
+
+  def exported_tasks
+    (@asynchronous_exports  + @synchronous_exports + @exec_exports).compact.flatten
+  end
+
+  def tasks
+    if @tasks.nil?
+      @tasks = {}
+      exported_tasks.each do |task_name|
+        info = task_info(task_name)
+        tasks[task_name.to_sym] = Task.setup info do |*args|
+          raise "This is a remote task" 
+        end
+        tasks[task_name.to_sym].name = task_name.to_sym
+      end
+      @tasks
+    end
+    @tasks
+  end
+
+  def task_dependencies
+    if @task_dependencies.nil?
+      @task_dependencies = {}
+      exported_tasks.each do |task|
+        task_dependencies[task] = WorkflowRESTClient.get_json(File.join(url, task.to_s, 'dependencies'))
+      end
+      @task_dependencies
+    end
+    @task_dependencies
+  end
+
+  def rec_dependencies(taskname)
+    if task_dependencies.include? taskname
+      deps = task_dependencies[taskname].select{|dep| String === dep or Symbol === dep}
+      deps.concat deps.collect{|dep| rec_dependencies(dep)}.compact.flatten
+      deps.uniq
+    else
+      []
+    end
+  end
+
+  def rec_inputs(taskname)
+    [taskname].concat(rec_dependencies(taskname)).inject([]){|acc, tn| acc.concat tasks[tn.to_sym].inputs}
+  end
+
+  def rec_input_defaults(taskname)
+    [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_defaults}
+  end
+
+  def rec_input_types(taskname)
+    [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_types}
+  end
+
+  def rec_input_descriptions(taskname)
+    [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_descriptions}
+  end
+
+  def rec_input_options(taskname)
+    [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_options}
+  end
+
+  def init_remote_tasks
+    task_exports = WorkflowRESTClient.get_json(url)
+    @asynchronous_exports = task_exports["asynchronous"].collect{|task| task.to_sym }
+    @synchronous_exports = task_exports["synchronous"].collect{|task| task.to_sym }
+    @exec_exports = task_exports["exec"].collect{|task| task.to_sym }
+  end
+
+  def job(task, name, inputs)
+    task_info = task_info(task)
+    RemoteStep.new(url, task, name, inputs, task_info[:result_type], task_info[:result_description], @exec_exports.include?(task))
+  end
+
+  def load_id(id)
+    task, name = id.split("/")
+    step = RemoteStep.new File.join(url, id)
+    step.result_type = task_info(task)[:result_type]
+    step.result_description = task_info(task)[:result_description]
+    step
+  end
+
+  def doc(task = nil)
+
+    if task.nil?
+      puts self.to_s 
+      puts "=" * self.to_s.length
+      puts
+
+      puts "## TASKS"
+      puts
+      tasks.each do |name,task|
+        puts "  * #{ name }:"
+        puts "    " << task.description if task.description and not task.description.empty?
+        puts
+      end
+    else
+
+      if Task === task
+        task_name = task.name
+      else
+        task_name = task
+        task = self.tasks[task_name]
+      end
+      dependencies = self.rec_dependencies(task_name).collect{|dep_name| self.tasks[dep_name.to_sym]}
+
+      task.doc(dependencies)
+    end
+  end
+end
+
+if __FILE__ == $0
+  client = WorkflowRESTClient.new("http://darthcaedus:9292/Sequence", "Sequence")
+
+  job = client.job(:genes_at_genomic_positions, "1", :organism => "Hsa", :positions => ["2:198266834:R"]).clean.fork
+  puts job.join.load.to_s
+  
+end
+