rbbt-util 5.28.7 → 5.28.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 3568f646d3095448ac6c8d99f32a5513421c80fd9d8b1f9a049a7ce512f3139d
+  metadata.gz: 4d77757da0912cd41138ff33b99e19b7ffa1449be515fb7a8742f9d69c134ffd
+  data.tar.gz: 1edb139f92881591bbac18692dc6a0a739be9dfe0a820a4db2cffd30079fc328
 SHA512:
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-  data.tar.gz: da5fd395014feded588f223686bd032dd86e46cac0e48e4369e9d1ea2e1f0d021e0fab02539ab2be1f483efc5463b9487952783edf2e00f22d7158879b5fd32d
+  metadata.gz: 2219bd7152eda55f2c3c9b1e5d10d9593dd29232e7e77fe0707496031030455663983256930f35c2bcabd8b80e15c05d99f3bcdc9644135ee4a75d0267334c33
+  data.tar.gz: e4021aab6574fc10e960eec29f630075c8e95b27d6648ba47e1f76ecbf1a12b84a5859ad7b61ffde8591466ddcfec8ee5cfd27f6f82997648d712225ac099e1b

data/lib/rbbt/util/open.rb

@@ -397,7 +397,7 @@ module Open
     if dir_sub_path_source.nil? and dir_sub_path_target.nil?
       FileUtils.mkdir_p File.dirname(target) unless File.exist? File.dirname(target)
       tmp_target = File.join(File.dirname(target), '.tmp_mv.' + File.basename(target))
-      FileUtils.cp source, tmp_target
+      FileUtils.cp_r source, tmp_target
       FileUtils.mv tmp_target, target
       return
     end

data/lib/rbbt/workflow/definition.rb

@@ -81,6 +81,7 @@ module Workflow
       if forget
         remove = config :remove_dep_tasks, :remove_dep_tasks, :default => REMOVE_DEP_TASKS
         self.archive_deps
+        self.copy_files_dir
         self.dependencies = self.dependencies - [dep]
         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)

data/lib/rbbt/workflow/step.rb

@@ -109,6 +109,14 @@ class Step
     @inputs || []
   end
 
+  def copy_files_dir
+    if File.symlink?(self.files_dir)
+      realpath = Open.realpath(self.files_dir)
+      Open.rm self.files_dir
+      Open.cp realpath, self.files_dir
+    end
+  end
+
   def archive_deps
     self.set_info :archived_info, archived_info
     self.set_info :archived_dependencies, info[:dependencies]
@@ -455,12 +463,15 @@ class Step
     return [] if dependencies.nil? or dependencies.empty?
 
     new_dependencies = []
+    archived_deps = self.info[:archived_info] ? self.info[:archived_info].keys : []
+
     dependencies.each{|step| 
       #next if self.done? && Open.exists?(info_file) && info[:dependencies] && info[:dependencies].select{|task,name,path| path == step.path }.empty?
-      next if seen.include? step
+      next if archived_deps.include? step.path
+      next if seen.include? step.path
       next if self.done? && need_run && ! updatable?
 
-      r = step.rec_dependencies(need_run, new_dependencies)
+      r = step.rec_dependencies(need_run, new_dependencies.collect{|d| d.path})
       new_dependencies.concat r
       new_dependencies << step
     }

data/lib/rbbt/workflow/step/accessor.rb

@@ -439,7 +439,7 @@ class Step
     rec_dependencies = self.rec_dependencies
     return [] if rec_dependencies.empty?
     canfail_paths = self.canfail_paths
-    dep = rec_dependencies.select{|d| d.task_name.to_s == 'contamination'}.first
+
     dirty_files = rec_dependencies.reject{|dep|
       (defined?(WorkflowRemoteClient) && WorkflowRemoteClient::RemoteStep === dep) || 
         ! Open.exists?(dep.info_file) ||

data/share/rbbt_commands/workflow/forget_deps

@@ -29,8 +29,6 @@ path = ARGV[0]
 raise ParameterException, "No path given" if path.nil?
 step = Workflow.load_step path
 
-
-iif step.rec_dependencies
-
 step.archive_deps
+step.copy_files_dir
 step.set_info :dependencies, []

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.28.7
+  version: 5.28.8
 platform: ruby
 authors:
 - Miguel Vazquez