rbbt-util 5.26.162 → 5.26.163

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f2c2ede8d746f69d82b953d794c101536c975e7bafbd84d5c8265ea827f71fed
-  data.tar.gz: 70d9262d64a126c30bb987c251c1000bdc762d7a74180da148c2d550bfb3557a
+  metadata.gz: 7b14759cc0559ef2ae62b648dcf539b8ac974300da1c6a74d5cea2954dad71b8
+  data.tar.gz: 05acb42e2a10e975c94447d390db33415ae34a686260df43573e112f96134e26
 SHA512:
-  metadata.gz: 57ce06e0635fd13a5906e945df884c05e864aec59bd729ac191e80cd1f8628b68a780efe5b8e9e9a4964becc5b18be21ad1044b3f7e0df864d04284dbcd4555f
-  data.tar.gz: 6af68737fb7b4932f4f2d588806f786e62f49598824479374b4761ea9b27d93ea1b70f0b731bd9552c8f7b3a872b26c2aeb646dafd2afaacfa283b6b119b1d13
+  metadata.gz: c915e11233f1b92c5015399fd12b305d20997603b74f46e7031667f7d011686d4fc200fd2df919a2482134bfb6bbd2a610628a7d7e8e3bae7cd266b1883ebe06
+  data.tar.gz: cf3b872feeb95b37f25957014f21f6230af3f623bf4c7b59014fda4ff4d43e5a2fa2dcc8ec4d38305003a20013f03986ec53e976f3c6223e48660709f1459765

data/lib/rbbt/tsv/util.rb

@@ -107,7 +107,7 @@ module TSV
       end
       file
     when String
-      if Open.remote?(file) or Open.exist? file
+      if Open.remote?(file) || Open.ssh?(file) || Open.exist?(file) 
         Open.open(file, open_options)
       else
         StringIO.new file

data/lib/rbbt/workflow/definition.rb

@@ -52,10 +52,10 @@ module Workflow
       @dependencies << block
     else
       if Module === dependency.first or 
-        (defined? WorkflowRESTClient and WorkflowRESTClient === dependency.first) or
+        (defined? RemoteWorkflow and RemoteWorkflow === dependency.first) or
         Hash === dependency.last
 
-        dependency = ([self] + dependency) unless Module === dependency.first or (defined? WorkflowRESTClient and WorkflowRESTClient === dependency.first)
+        dependency = ([self] + dependency) unless Module === dependency.first || (defined?(RemoteWorkflow) && RemoteWorkflow === dependency.first)
         @dependencies << dependency
       else
         @dependencies.concat dependency

data/lib/rbbt/workflow/remote_workflow.rb

@@ -23,12 +23,13 @@ class RemoteWorkflow
     name
   end
 
-  def job(task, name = nil, inputs = {})
+  def __job(task, name = nil, inputs = {})
     task_info = task_info(task)
     fixed_inputs = {}
     input_types = IndiferentHash.setup(task_info[:input_types])
 
     inputs.each do |k,v| 
+      v = v.load if Step === v
       k = k.to_sym
       if TSV === v
         fixed_inputs[k] = v.to_s
@@ -44,7 +45,9 @@ class RemoteWorkflow
     end
 
     stream_input = @can_stream ? task_info(task)[:input_options].select{|k,o| o[:stream] }.collect{|k,o| k }.first : nil
-    RemoteStep.new(url, task, name, fixed_inputs, task_info[:input_types], task_info[:result_type], task_info[:result_description], @exec_exports.include?(task), @stream_exports.include?(task), stream_input)
+    step = RemoteStep.new(url, task, name, fixed_inputs, task_info[:input_types], task_info[:result_type], task_info[:result_description], @exec_exports.include?(task), @stream_exports.include?(task), stream_input)
+    step.workflow = self
+    step
   end
 
   def load_id(id)

data/lib/rbbt/workflow/remote_workflow/driver.rb

@@ -72,8 +72,12 @@ class RemoteWorkflow
     new_params
   end
 
+  def exported_tasks
+    @asynchronous_exports + @synchronous_exports + @exec_exports
+  end
+
   def load_tasks
-    (@asynchronous_exports + @synchronous_exports + @exec_exports).each{|name| tasks[name]}
+    exported_tasks.each{|name| tasks[name]}
   end
 
 end

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

@@ -126,6 +126,7 @@ class RemoteStep < Step
   end
 
   def info(check_lock=false)
+    return {:status => :waiting } unless started?
     @done = @info && @info[:status] && (@info[:status].to_sym == :done || @info[:status].to_sym == :error)
 
     if !@done && (@last_info_time.nil? || (Time.now - @last_info_time) > 0.5)
@@ -142,6 +143,7 @@ class RemoteStep < Step
       info[:status] = info[:status].to_sym if String === info[:status]
       info
     end
+
     @info
   end
 
@@ -302,6 +304,11 @@ class RemoteStep < Step
     end
   end
 
+
+  def input_checks
+    []
+  end
+
   def _restart
     @done = nil
     @name = nil
@@ -318,11 +325,6 @@ class RemoteStep < Step
     @inputs = new_inputs
     @info = nil
   end
-
-  def input_checks
-    []
-  end
-
 end
 
 require 'rbbt/workflow/remote_workflow/remote_step/rest'

data/lib/rbbt/workflow/remote_workflow/remote_step/rest.rb

@@ -89,7 +89,7 @@ class RemoteStep
 
     def stream_job(task_url, task_params, stream_input, cache_type = :exec)
       require 'rbbt/util/misc/multipart_payload'
-      WorkflowRESTClient.capture_exception do
+      RemoteWorkflow.capture_exception do
         @streaming = true
 
         Log.debug{ "RestClient stream #{Process.pid}: #{ task_url } #{stream_input} #{cache_type} - #{Misc.fingerprint task_params}" }
@@ -101,7 +101,7 @@ class RemoteStep
                 @url = res.gets
                 @url.sub!(/\?.*/,'')
                 join
-                WorkflowRESTClient.get_raw(@url)
+                RemoteWorkflow.get_raw(@url)
                 @done = true
                 @streaming = false
               when /STREAM: (.*)/

data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb

@@ -30,24 +30,32 @@ class RemoteStep
           RemoteWorkflow::SSH.post_job(File.join(base_url, task.to_s), @input_id, @base_name)
         end
       end
-      if Open.remote? @name
+
+      if Open.remote?(@name)
         @url = @name
         @name = File.basename(@name)
       else
         @url = File.join(base_url, task.to_s, @name)
       end
+
       self
     end
 
     def path
       @server, @server_path = RemoteWorkflow::SSH.parse_url @base_url
-      "ssh://" + @server + ":" + @remote_path
+      init_job unless @name
+      if info[:path]
+        "ssh://" + @server + ":" + info[:path]
+      else
+        "ssh://" + @server + ":" + ["var/jobs", self.workflow.to_s, task_name.to_s, @name] * "/"
+      end
     end
 
     def produce(*args)
       input_types = {}
       init_job
       @remote_path = RemoteWorkflow::SSH.run_job(File.join(base_url, task.to_s), @input_id, @base_name)
+      @started = true
       while ! done?
         sleep 1
       end

data/share/rbbt_commands/migrate

@@ -2,7 +2,7 @@
 
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
-require 'rbbt/workflow/remote/ssh/driver'
+require 'rbbt/workflow/remote_workflow'
 
 $0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
 
@@ -43,7 +43,7 @@ search_path = 'user' if search_path.nil?
 resource = Rbbt
 
 path, real_paths, lpath = if options[:source]
-          lpath, *paths = SSHDriver.run(options[:source], <<-EOF).split("\n")
+          lpath, *paths = Misc.ssh_run(options[:source], <<-EOF).split("\n")
 require 'rbbt-util'
 path = "#{path}"
 if Open.exists?(path)
@@ -66,13 +66,13 @@ puts path.glob_all.collect{|p| File.directory?(p) ? p + "/" : p } * "\n"
         end
 
 target = if options[:target] 
-          target = SSHDriver.run(options[:target], <<-EOF).split("\n").first
+           target = Misc.ssh_run(options[:target], <<-EOF).split("\n").first
 require 'rbbt-util'
 path = "#{path}"
 resource = #{resource.to_s}
 search_path = "#{search_path}"
 puts resource[path].find(search_path)
-          EOF
+           EOF
          else
            resource[lpath].find(search_path)
          end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.162
+  version: 5.26.163
 platform: ruby
 authors:
 - Miguel Vazquez