rbbt-rest 1.3.2 → 1.3.3

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: b556674b8552bf64d8680def41f2316821743b64
+  data.tar.gz: 3f1fb6faa193e793870d65706e3ca828b7de897f
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data/lib/rbbt/rest/client.rb

@@ -4,174 +4,12 @@ require 'rbbt/workflow'
 require 'rbbt/workflow/step'
 require 'rbbt/util/misc'
 
-class WorkflowRESTClient
+require 'rbbt/rest/client/get'
+require 'rbbt/rest/client/adaptor'
+require 'rbbt/rest/client/step'
 
-  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 = {})
-    Log.debug{ "RestClient get_raw: #{ url } - #{Misc.fingerprint params}" }
-    params = params.merge({ :_format => 'raw' })
-    Misc.insist(2, 0.5) do
-      RestClient.get(URI.encode(url), :params => params)
-    end
-  end
- 
-  def self.post_jobname(url, params = {})
-    Log.debug{ "RestClient post_jobname: #{ url } - #{Misc.fingerprint params}" }
-    params = params.merge({ :_format => 'jobname' })
-    RestClient.post(URI.encode(url), params)
-  end
-  
-  def self.get_json(url, params = {})
-    Log.debug{ "RestClient get_json: #{ url } - #{Misc.fingerprint params }" }
-    params = params.merge({ :_format => 'json' })
-    begin
-      res = RestClient.get(URI.encode(url), :params => params)
-    rescue => e
-      raise JSON.parse(e.response)["message"]
-    end
-    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(URI.encode(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 done?
-      status.to_s == 'done'
-    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(noload = false)
-      if Array === @url
-        url, params = @url
-      else
-        url, params = @url, {:_cache_type => :synchronous}
-      end
-
-      params[:jobname] = @name if @name
-
-      if noload and %w(boolean string tsv).include? result_type
-        WorkflowRESTClient.get_raw(url, params) 
-      else
-        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
-    end
-
-    def exec
-      res = _exec
-      prepare_result(res, result_type)
-    end
-
-    def run(noload = false)
-      if noload
-        _exec(noload)
-      else
-        exec
-      end
-    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
+class WorkflowRESTClient 
+  include Workflow
 
   attr_accessor :url, :name, :exec_exports, :asynchronous_exports, :synchronous_exports
 
@@ -185,103 +23,6 @@ class WorkflowRESTClient
     name
   end
 
-  def workflow_description
-    WorkflowRESTClient.get_raw(File.join(url, 'description'))
-  end
-
-  def documentation
-    @documention ||= IndiferentHash.setup(WorkflowRESTClient.get_json(File.join(url, "documentation"),{}))
-  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
-    @tasks ||= Hash.new do |hash,task_name| 
-      info = task_info(task_name)
-      task = Task.setup info do |*args|
-        raise "This is a remote task" 
-      end
-      task.name = task_name.to_sym
-      hash[task_name] = task
-    end
-  end
-
-  def load_tasks
-    exported_tasks.each{|name| tasks[name]}
-    nil
-  end
-
-  def task_dependencies
-    @task_dependencies ||= Hash.new do |hash,task| 
-      hash[task] = if exported_tasks.include? task
-        WorkflowRESTClient.get_json(File.join(url, task.to_s, 'dependencies'))
-      else
-        []
-      end
-    end
-  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}.
-      tap{|h| IndiferentHash.setup(h) }
-  end
-
-  def rec_input_types(taskname)
-    [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_types}.
-      tap{|h| IndiferentHash.setup(h) }
-  end
-
-  def rec_input_descriptions(taskname)
-    [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_descriptions}.
-      tap{|h| IndiferentHash.setup(h) }
-  end
-
-  def rec_input_options(taskname)
-    [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_options}.
-      tap{|h| IndiferentHash.setup(h) }
-  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)
     fixed_inputs = {}
@@ -293,78 +34,16 @@ class WorkflowRESTClient
                           v
                         end
     end
+
     RemoteStep.new(url, task, name, fixed_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 = RemoteStep.new url, task, nil
+    step.name = name
     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
-
-  def doc(task = nil)
-
-    if task.nil?
-      puts Log.color :magenta, self.to_s 
-      puts Log.color :magenta, "=" * self.to_s.length
-      if self.documentation[:description] and not self.documentation[:description].empty?
-        puts
-        puts Misc.format_paragraph self.documentation[:description] 
-      end
-      puts
-
-      puts Log.color :magenta, "## TASKS"
-      if self.documentation[:task_description] and not self.documentation[:task_description].empty?
-        puts
-        puts Misc.format_paragraph self.documentation[:task_description] 
-      end
-      puts
-
-      tasks.each do |name,task|
-        puts Misc.format_definition_list_item(name.to_s, task.description || "", 80, 30, :yellow)
-      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

data/lib/rbbt/rest/client/adaptor.rb

@@ -0,0 +1,66 @@
+class WorkflowRESTClient
+
+  def workflow_description
+    WorkflowRESTClient.get_raw(File.join(url, 'description'))
+  end
+
+  def documentation
+    @documention ||= IndiferentHash.setup(WorkflowRESTClient.get_json(File.join(url, "documentation"),{}))
+  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
+    @tasks ||= Hash.new do |hash,task_name| 
+      info = task_info(task_name)
+      task = Task.setup info do |*args|
+        raise "This is a remote task" 
+      end
+      task.name = task_name.to_sym
+      hash[task_name] = task
+    end
+  end
+
+  def load_tasks
+    exported_tasks.each{|name| tasks[name]}
+    nil
+  end
+
+  def task_dependencies
+    @task_dependencies ||= Hash.new do |hash,task| 
+      hash[task] = if exported_tasks.include? task
+        WorkflowRESTClient.get_json(File.join(url, task.to_s, 'dependencies'))
+      else
+        []
+      end
+    end
+  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 }
+    nil
+  end
+end

data/lib/rbbt/rest/client/get.rb

@@ -0,0 +1,83 @@
+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.capture_exception
+    begin
+      yield
+    rescue Exception => e
+      klass, message = e.response.split " => "
+      begin
+        klass = Kernel.const_get klass
+      rescue
+        raise message
+      end
+      raise klass.new message
+    end
+  end
+
+  def self.get_raw(url, params = {})
+    Log.debug{ "RestClient get_raw: #{ url } - #{Misc.fingerprint params}" }
+    params = params.merge({ :_format => 'raw' })
+    capture_exception do
+      Misc.insist(2, 0.5) do
+        RestClient.get(URI.encode(url), :params => params)
+      end
+    end
+  end
+ 
+  def self.post_jobname(url, params = {})
+    Log.debug{ "RestClient post_jobname: #{ url } - #{Misc.fingerprint params}" }
+    params = params.merge({ :_format => 'jobname' })
+
+    capture_exception do
+      RestClient.post(URI.encode(url), params)
+    end
+  end
+  
+  def self.get_json(url, params = {})
+    Log.debug{ "RestClient get_json: #{ url } - #{Misc.fingerprint params }" }
+    params = params.merge({ :_format => 'json' })
+
+    res = capture_exception do
+      RestClient.get(URI.encode(url), :params => params)
+    end
+
+    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 = capture_exception do
+        RestClient.post(URI.encode(url), params)
+      end
+
+      begin
+        JSON.parse(res)
+      rescue
+        res
+      end
+    end
+  end
+
+end

data/lib/rbbt/rest/client/step.rb

@@ -0,0 +1,123 @@
+class WorkflowRESTClient
+  class RemoteStep < Step
+
+    attr_accessor :url, :base_url, :task, :base_name, :inputs, :result_type, :result_description, :exec
+
+    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 initialize(base_url, task = nil, base_name = nil, inputs = nil, result_type = nil, result_description = nil, exec = false)
+      @base_url, @task, @base_name, @inputs, @result_type, @result_description, @exec = base_url, task, base_name, inputs, result_type, result_description, exec
+    end
+
+    def name
+      return nil if exec
+      (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 status
+      info[:status]
+    end
+
+    def done?
+      status.to_s == 'done'
+    end
+
+    def files
+      WorkflowRESTClient.get_json(File.join(url, 'files'))
+    end
+
+    def file(file)
+      WorkflowRESTClient.get_raw(File.join(url, 'file', file))
+    end
+
+    #{{{ MANAGEMENT
+    
+    def init_job(cache_type = :asynchronous)
+      @name = WorkflowRESTClient.post_jobname(File.join(base_url, task.to_s), inputs.merge(:jobname => @name, :_cache_type => cache_type))
+      @url = File.join(base_url, task.to_s, @name)
+      nil
+    end
+
+    def load_res(res)
+      case result_type
+      when :string
+        res
+      when :boolean
+        res == "true"
+      when :tsv
+        TSV.open(StringIO.new(res))
+      when :annotations
+        Annotated.load_tsv(TSV.open(StringIO.new(res)))
+      else
+        JSON.parse res
+      end
+    end
+
+    def get
+      params = params.merge(:_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json )
+      begin
+        WorkflowRESTClient.get_raw(url, params) 
+      rescue => e
+        raise e.response
+      end
+    end
+
+    def load
+      params = {}
+      load_res get
+    end
+    
+    def exec_job
+      res = WorkflowRESTClient.capture_exception do
+        RestClient.post(URI.encode(File.join(base_url, task.to_s)), inputs.merge(:_cache_type => :exec, :_format => [:string, :boolean, :tsv, :annotations].include?(result_type) ? :raw : :json))
+      end
+      load_res res
+    end
+
+    def fork
+      init_job
+    end
+
+    def run(noload = false)
+      return exec_job if exec
+      init_job(:synchronous)
+      noload ? name : self.load
+    end
+
+    def exec
+      exec_job
+    end
+
+    def join
+      self.load
+      self
+    end
+
+    def clean
+      WorkflowRESTClient.get_raw(url, :_update => :clean) unless exec
+      self
+    end
+  end
+end

data/lib/rbbt/rest/common/misc.rb

@@ -18,7 +18,7 @@ module RbbtRESTHelpers
   end
 
   def production?
-    ENV["RACK_ENV"] == "production"
+    settings.environment && settings.environment.to_s == 'production'
   end
 
   def process_common_parameters

data/lib/rbbt/rest/main.rb

@@ -26,6 +26,8 @@ module Sinatra
 
         set :public_folder, Rbbt.share.views.public.find 
 
+        set :environment, ENV["RACK_ENV"].to_sym if ENV["RACK_ENV"]
+
         attr_accessor :ajax, :layout, :format, :size, :update, :cache_type, :_, :profile
 
         if production?
@@ -135,10 +137,8 @@ module Sinatra
           halt 404, e.message
         end
 
-        if production?
-          error Exception do |e|
-            halt 404, e.message
-          end
+        error Exception do |e|
+          halt 500, [e.class.to_s, e.message] * " => "
         end
       end
     end

data/lib/rbbt/rest/workflow.rb

@@ -69,6 +69,8 @@ module Sinatra
       get "/#{workflow.to_s}/:task/info" do
         task     = consume_parameter(:task)
 
+        raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
+
         case format
         when :html
           workflow_render('task_info', workflow)
@@ -83,6 +85,8 @@ module Sinatra
       get "/#{workflow.to_s}/:task/dependencies" do
         task     = consume_parameter(:task)
 
+        raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
+
         case format
         when :html
           workflow_render('task_dependencies', workflow)
@@ -103,6 +107,8 @@ module Sinatra
         task     = consume_parameter(:task)
         jobname  = consume_parameter(:jobname)
 
+        raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
+
         task_parameters = consume_task_parameters(workflow, task, params)
 
         if complete_input_set(workflow, task, task_parameters) or format != :html 
@@ -116,6 +122,8 @@ module Sinatra
         task = consume_parameter(:task)
         jobname  = consume_parameter(:jobname)
 
+        raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
+
         task_parameters = consume_task_parameters(workflow, task, params)
 
         issue_job(workflow, task, jobname, task_parameters)
@@ -125,6 +133,8 @@ module Sinatra
         task = consume_parameter(:task)
         job  = consume_parameter(:job)
 
+        raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
+
         job = workflow.load_id(File.join(task, job))
 
         clean_job(workflow, job) if update == :clean
@@ -160,6 +170,8 @@ module Sinatra
         task = consume_parameter(:task)
         job  = consume_parameter(:job)
 
+        raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
+
         job = workflow.load_id(File.join(task, job))
 
         case format
@@ -177,6 +189,8 @@ module Sinatra
         task = consume_parameter(:task)
         job  = consume_parameter(:job)
 
+        raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
+
         job = workflow.load_id(File.join(task, job))
 
         case format
@@ -195,6 +209,8 @@ module Sinatra
         job  = consume_parameter(:job)
         filename = params[:splat].first
 
+        raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
+
         job = workflow.load_id(File.join(task, job))
 
         send_file job.file(filename)
@@ -205,6 +221,8 @@ module Sinatra
         job  = consume_parameter(:job)
         job  = workflow.load_id(File.join(task, job))
 
+        raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
+
         clean_job(workflow, job)
       end
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.3.2
+  version: 1.3.3
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -175,6 +175,9 @@ files:
 - Rakefile
 - config.ru
 - lib/rbbt/rest/client.rb
+- lib/rbbt/rest/client/adaptor.rb
+- lib/rbbt/rest/client/get.rb
+- lib/rbbt/rest/client/step.rb
 - lib/rbbt/rest/common/cache.rb
 - lib/rbbt/rest/common/forms.rb
 - lib/rbbt/rest/common/locate.rb