rbbt-util 5.26.167 → 5.26.168

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 33b4251a885bb44b1ec45aab8e2aa2f96c4066c024e5133f3d28786c9b11aaa3
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data/lib/rbbt/util/open.rb

@@ -781,7 +781,6 @@ module Open
         return nil unless File.exists?(file)
         File.mtime(file)
       rescue
-        Log.exception $!
         nil
       end
     end

data/lib/rbbt/workflow.rb

@@ -540,12 +540,13 @@ module Workflow
 
   def self.__load_step(path)
     if Open.remote?(path) || Open.ssh?(path)
-      return RemoteStep.new path
+      require 'rbbt/workflow/remote_workflow'
+      return RemoteWorkflow.load_path path
     end
     step = Step.new path
     relocated = false
     step.dependencies = (step.info[:dependencies] || []).collect do |task,name,dep_path|
-      if Open.exists?(dep_path) || Open.exists?(dep_path + '.info')
+      if Open.exists?(dep_path) || Open.exists?(dep_path + '.info') || Open.remote?(dep_path) || Open.ssh?(dep_path)
         Workflow._load_step dep_path
       else
         new_path = relocate(path, dep_path)
@@ -559,6 +560,11 @@ module Workflow
   end
     
   def self.fast_load_step(path)
+    if Open.remote?(path) || Open.ssh?(path)
+      require 'rbbt/workflow/remote_workflow'
+      return RemoteWorkflow.load_path path
+    end
+
     step = Step.new path
     step.dependencies = nil
     class << step
@@ -618,7 +624,7 @@ module Workflow
              File.join(workdir, id)
            end
     task = task_for path
-    return remote_tasks[task].load_id(id) if remote_tasks and remote_tasks.include? task
+    return remote_tasks[task].load_id(id) if remote_tasks && remote_tasks.include?(task)
     return Workflow.load_step path
   end
 
@@ -630,7 +636,7 @@ module Workflow
              File.join(workdir, id)
            end
     task = task_for path
-    return remote_tasks[task].load_id(id) if remote_tasks and remote_tasks.include? task
+    return remote_tasks[task].load_id(id) if remote_tasks && remote_tasks.include?(task)
     return Workflow.fast_load_step path
   end
 

data/lib/rbbt/workflow/remote_workflow.rb

@@ -57,6 +57,23 @@ class RemoteWorkflow
     step.result_description = task_info(task)[:result_description]
     step
   end
+
+  def self.load_path(job_url)
+    parts = job_url.split("/")
+    name = parts.pop.split("?").first
+    task = parts.pop
+    workflow = parts.last
+    url = parts * "/"
+
+    step = RemoteStep.new url, task, nil
+    step.name = name
+    step.workflow = workflow
+    step.started = true
+    step.result_type = step.info[:result_type]
+    step.result_description = step.info[:result_description]
+
+    step
+  end
 end
 
 require 'rbbt/workflow/remote_workflow/driver'

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

@@ -2,7 +2,7 @@ require 'rbbt/workflow'
 
 class RemoteStep < Step
 
-  attr_accessor :url, :base_url, :task, :base_name, :inputs, :input_types, :result_type, :result_description, :is_exec, :is_stream, :stream_input
+  attr_accessor :url, :base_url, :task, :base_name, :inputs, :input_types, :result_type, :result_description, :is_exec, :is_stream, :stream_input, :started
 
   def initialize(base_url, task = nil, base_name = nil, inputs = nil, input_types = nil, result_type = nil, result_description = nil, is_exec = false, is_stream = false, stream_input = nil)
     @base_url, @task, @base_name, @inputs, @input_types, @result_type, @result_description, @is_exec, @is_stream, @stream_input = base_url, task, base_name, inputs, input_types, result_type, result_description, is_exec, is_stream, stream_input
@@ -179,7 +179,7 @@ class RemoteStep < Step
   end
 
   def file(file)
-    @adaptor.get_raw(File.join(url, 'file', file))
+    @adaptor.get_raw(File.join(url, 'file', file.to_s))
   end
 
   def get_stream

data/lib/rbbt/workflow/util/provenance.rb

@@ -32,10 +32,10 @@ class Step
 
     path_mtime = begin
                    Open.mtime(path)
-                 rescue
+                 rescue Exception
                    nil
                  end
-    str = if not Open.remote?(path) and (Open.exists?(path) and $main_mtime and path_mtime and ($main_mtime - path_mtime) < -2)
+    str = if ! (Open.remote?(path) || Open.ssh?(path)) && (Open.exists?(path) && $main_mtime && path_mtime && ($main_mtime - path_mtime) < -2)
             prov_status_msg(status.to_s) << " " << [workflow, task, path].compact * " " << " (#{Log.color(:red, "Mtime out of sync") })"
           else
             prov_status_msg(status.to_s) << " " << [workflow, task, path].compact * " " 
@@ -71,7 +71,7 @@ class Step
     info[:task_name] = task
     path  = step.path
     status = info[:status] || :missing
-    status = "remote" if Open.remote?(path)
+    status = "remote" if Open.remote?(path) || Open.ssh?(path)
     name = info[:name] || File.basename(path)
     status = :unsync if status == :done and not Open.exist?(path)
     status = :notfound if status == :noinfo and not Open.exist?(path)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.167
+  version: 5.26.168
 platform: ruby
 authors:
 - Miguel Vazquez