rbbt-util 5.26.136 → 5.26.137

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 29491b581677ed091db2132d41a0be22817ae907888050200453d05cdaf7394d
+  metadata.gz: 5517c44e5438fffb2c8e3fddbb99fef53084bbda02f74f7866fd51f8b7eadef9
+  data.tar.gz: 4aeba437356614ef827b9224169dfe7c84e543bf6ea5e87426bb545b71afe8ad
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+  metadata.gz: 4d0474e8b079996176dc6f9947ec190c5b0b80cc8d0d4770f886556d69cb05fc943e04766c8679933efde4554811a0be225c5646823d31e2bd9e208a96a7dcb4
+  data.tar.gz: 47c703e6745fc998bef9d1304a55177a9d3607adff270061981d4c19adab11b8b8bf3ed2d7308a5e9504878bef0aad46105a47857b418b37674d924d9434c5ed

data/lib/rbbt/workflow/remote/remote_step.rb

@@ -23,31 +23,33 @@ class WorkflowRemoteClient
     end
 
     def cache_file
-      digest = Misc.obj2digest([url, task, base_name, inputs])
-      Rbbt.var.cache.REST[digest].find
+      digest = Misc.obj2digest([base_url, task, base_name, inputs])
+      Rbbt.var.cache.REST[[task, clean_name, digest] * "."].find
+    end
+
+    def cache_files
+      Dir.glob(cache_file + '.*')
     end
 
     def run(no_load = false)
       no_load = @is_stream ? :stream : true if no_load
 
       @mutex.synchronize do
-        @result ||= Persist.persist("REST persist", result_type, :file => cache_file) do
-          begin
-            if @is_exec
-              exec(no_load)
-            elsif no_load == :stream
-              _run_job(:stream)
-            elsif no_load
-              init_job 
-              nil
-            else
-              init_job 
-              join
-              self.load
-            end
-          ensure
-            @started = true
+        begin
+          if @is_exec
+            exec(no_load)
+          elsif no_load == :stream
+            _run_job(:stream)
+          elsif no_load
+            init_job 
+            nil
+          else
+            init_job 
+            join
+            self.load
           end
+        ensure
+          @started = true
         end
       end
 
@@ -159,6 +161,7 @@ class WorkflowRemoteClient
     end
 
     def done?
+      return true if cache_files.any?
       init_job unless @url
       @done || status.to_s == 'done' || status.to_s == 'noinfo'
     end

data/lib/rbbt/workflow/remote/rest/adaptor.rb

@@ -25,22 +25,25 @@ module WorkflowRESTClient
     @documention ||= IndiferentHash.setup(WorkflowRESTClient.get_json(File.join(url, "documentation"),{}))
   end
 
+  def self.task_info(url, task)
+    @@task_info ||= {}
+
+    key = [url, task] * "#"
+    @@task_info[key] ||= begin
+                           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[key] = task_info
+                         end
+  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]
+    WorkflowRESTClient.task_info(url, task)
   end
 
   def exported_tasks

data/lib/rbbt/workflow/remote/rest/get.rb

@@ -165,14 +165,16 @@ module WorkflowRESTClient
 
   def get
     params ||= {}
-    params = params.merge(:_format => [:string, :boolean, :tsv, :annotations,:array].include?(result_type.to_sym) ? :raw : :json )
-    Misc.insist 3, rand(2) + 1 do
-      begin
-        init_job if url.nil?
-        @adaptor.get_raw(url, params)
-      rescue
-        Log.exception $!
-        raise $!
+    params = params.merge(:_format => [:string, :boolean, :tsv, :annotations, :array].include?(result_type.to_sym) ? :raw : :json )
+    @cache_result ||= Persist.persist("REST persist", :binary, :file => cache_file + "." + Misc.obj2digest(params)) do
+      Misc.insist 3, rand(2) + 1 do
+        begin
+          init_job if url.nil?
+          @adaptor.get_raw(url, params)
+        rescue
+          Log.exception $!
+          raise $!
+        end
       end
     end
   end
@@ -231,7 +233,9 @@ module WorkflowRESTClient
   def _clean
     begin
       _restart
-      Open.rm cache_file
+      cache_files.each do |cache_file|
+        Open.rm cache_file
+      end
       params = {:_update => :clean}
       @adaptor.clean_url(url, params) if @url
     rescue Exception

data/share/rbbt_commands/app/start

@@ -18,6 +18,7 @@ $ rbbt app start [options] <app_name>
 -s--server* Server type:  thin, webrick, unicorn, etc
 -f--finder Start server with finder functionality
 -fs--file_server Activate file serving for resources
+-mj--monitor_jobs Monitor jobs (UNSAFE)
 -R--Rserve_session* Rserve session to use, otherwise start new one
 -wd--workdir* Change the working directory of the workflow
 --views* Directory with view templates
@@ -62,6 +63,7 @@ Misc.in_dir(app_dir) do
   ENV["RACK_ENV"] = options[:environment] if options.include?(:environment)
   ENV["RBBT_VIEWS_DIR"] = options[:views] if options.include?(:views)
   ENV["RBBT_REST_FILE_SERVER"] = "true" if  options[:file_server]
+  ENV["RBBT_MONITOR_REST_JOBS"] = "true" if  options[:monitor_jobs]
 
 
   if options[:stream]

data/share/rbbt_commands/workflow/server

@@ -24,6 +24,7 @@ $ rbbt workflow server [options] <Workflow>
 --views* Directory with view templates
 --stream Activate streaming of workflow tasks
 -fs--file_server Activate file serving for resources
+-mj--monitor_jobs Monitor jobs (UNSAFE)
 --export_all Export all workflow tasks (use with caution!)
 --export* Export workflow tasks (asynchronous)
 --export_asynchronous* Export workflow tasks as asynchronous
@@ -86,6 +87,7 @@ TmpFile.with_file do |app_dir|
     ENV["RACK_ENV"] = options[:environment] if options.include?(:environment)
     ENV["RBBT_VIEWS_DIR"] = options[:views] if options.include?(:views)
     ENV["RBBT_REST_FILE_SERVER"] = "true" if  options[:file_server]
+    ENV["RBBT_MONITOR_REST_JOBS"] = "true" if  options[:monitor_jobs]
 
     if options[:export_all]
       ENV["RBBT_WORKFLOW_EXPORT_ALL"] = 'true'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.136
+  version: 5.26.137
 platform: ruby
 authors:
 - Miguel Vazquez