rbbt-util 5.26.15 → 5.26.16

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 4ca1b6e54187f2a185a4808e193c8a7edf119c727ebd458a43de22c2ce459dbe
-  data.tar.gz: df37635156a96711ac3a17eb92ec342200d37561a24af7c159ef947f3b0b4520
+  metadata.gz: 0a5b6df0bdc2e42626606a7acb81daea7045d4b9084e55397e26bd43cf649bed
+  data.tar.gz: 0a02c5606b3ad0db3f49bb08253b3319086275f8c628c2058cfb947dad8589cc
 SHA512:
-  metadata.gz: d0f65a81a0bb09e76ed0dbb7460a3d3703d4bc4df4f1486ae40fec511b0fb931ea9d35b0db468a2ee8d266af367ca42ed61522c4b04c730b824695ecbf9bfb7c
-  data.tar.gz: 4265b0702cf71164fc828a8cc60c98c032be79734d0aa93f0b694d5698c82d89e599cab0456458aa778a649946e71da151c6a8888fa54ab85732b749b9844beb
+  metadata.gz: dbffbfb520c2ae55920a7bacbcb06fd9b329ccd4be1707b524661b39e0bf402d739687f010f85adc31dd2efdbbeb92108e05fc8fe69abcc1026719d7046359af
+  data.tar.gz: 5e9581b07924542606bc900acf1f808990f7527bb4082a054ac0fb3e2a42042f15ee14a2004a97734c9f9e379990b0c552972dc7b75393a60a3a7f56ec21fef2

data/lib/rbbt/workflow.rb

@@ -214,7 +214,17 @@ module Workflow
   end
 
   def import_task(workflow, orig, new)
-    new_task = workflow.tasks[orig].clone
+    orig_task = workflow.tasks[orig]
+    new_task = orig_task.dup
+    options = {}
+    orig_task.singleton_methods.
+      select{|method| method.to_s[-1] != "="[0]}.each{|method|
+      if orig_task.respond_to?(method.to_s + "=") 
+        options[method.to_s] = orig_task.send(method.to_s)
+      end
+    }
+
+    Task.setup(options, &new_task)
     new_task.workflow = self
     new_task.name = new
     tasks[new] = new_task

data/lib/rbbt/workflow/definition.rb

@@ -64,16 +64,18 @@ module Workflow
   end
 
   FORGET_DEP_TASKS = ENV["RBBT_FORGET_DEP_TASKS"] == "true"
-  def dep_task(name, *dependency, &block)
-    dep(*dependency, &block)
+  def dep_task(name, workflow, oname, *rest, &block)
+    dep(workflow, oname, *rest, &block) 
+    extension workflow.tasks[oname].extension if workflow.tasks.include?(oname) unless @extension
     task name do
       raise RbbtException, "dependency not found in dep_task" if dependencies.empty?
       dep = dependencies.last.join
       set_info :result_type, dep.info[:result_type]
       forget = config :forget_dep_tasks, :forget_dep_tasks, :default => FORGET_DEP_TASKS
       if forget
+        self.set_info :archived_info, archived_info
+        self.set_info :archived_dependencies, info[:dependencies]
         self.dependencies = self.dependencies - [dep]
-        self.set_info :dependency, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}
         Open.rm_rf self.files_dir if Open.exist? self.files_dir
         FileUtils.cp_r dep.files_dir, self.files_dir if Open.exist? dep.files_dir
         Open.ln_h dep.path, self.tmp_path

data/lib/rbbt/workflow/step.rb

@@ -67,6 +67,7 @@ class Step
     @workflow || info[:workflow]
   end
 
+
   def load_inputs_from_info
     if info[:inputs]
       info_inputs = info[:inputs]
@@ -92,6 +93,37 @@ class Step
     @inputs || []
   end
 
+  def archived_info
+    return info[:archived_info] if info[:archived_info]
+
+    archived_info = {}
+    dependencies.each do |dep|
+      archived_info[dep.path] = dep.info
+      archived_info.merge!(dep.archived_info)
+    end if dependencies
+
+    archived_info
+  end
+
+  def archived_inputs
+    return {} unless info[:archived_dependencies]
+    archived_info = self.archived_info
+
+    all_inputs = IndiferentHash.setup({})
+    deps = info[:archived_dependencies].collect{|p| p.last}
+    seen = []
+    while path = deps.pop
+      dep_info = archived_info[path]
+      dep_info[:inputs].each do |k,v|
+        all_inputs[k] = v unless all_inputs.include?(k)
+      end
+      deps.concat(dep_info[:dependencies].collect{|p| p.last } - seen)
+      seen << path
+    end
+
+    all_inputs
+  end
+
   def recursive_inputs
     if NamedArray === inputs
       i = {}
@@ -103,6 +135,7 @@ class Step
     end
     rec_dependencies.each do |dep|
       next unless NamedArray === dep.inputs
+
       dep.inputs.zip(dep.inputs.fields).each do |v,f|
         if i.include?(f) && i[f] != v
           Log.debug "Conflict in #{ f }: #{[i[f].inspect, v.inspect] * " <-> "}"
@@ -111,7 +144,16 @@ class Step
           i[f] = v
         end
       end
+
+      dep.archived_inputs.each do |k,v|
+        i[k] = v unless i.include? k
+      end
     end
+
+    self.archived_inputs.each do |k,v|
+      i[k] = v unless i.include? k
+    end
+
     #dependencies.each do |dep|
     #  di = dep.recursive_inputs
     #  next unless NamedArray === di
@@ -119,6 +161,7 @@ class Step
     #    i[k] = v unless i.include? k
     #  end
     #end
+    
     v = i.values
     NamedArray.setup v, i.keys 
     v

data/share/rbbt_commands/workflow/info

@@ -84,7 +84,7 @@ messages = info[:messages]
 backtrace = info[:backtrace]
 pid = info[:pid]
 exception = info[:exception]
-rest = info.keys - [:inputs, :dependencies, :status, :time_elapsed, :messages, :backtrace, :exception, :pid]
+rest = info.keys - [:inputs, :dependencies, :status, :time_elapsed, :messages, :backtrace, :exception, :pid, :archived_info]
 
 puts Log.color(:magenta, "File") << ": " << step.path
 puts Log.color(:magenta, "Status") << ": " << status_msg(status) << ((step.aborted? || step.error?) && step.recoverable_error? ? " (recoverable)" : "" ) << (step.dirty? ? " (dirty)" : "")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.15
+  version: 5.26.16
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-05-31 00:00:00.000000000 Z
+date: 2019-06-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake