rbbt-util 5.32.15 → 5.32.16

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 7a6c7290ff27c00ba5911a609897eb9104b357adec7a38b892ad5a8c01267e26
+  metadata.gz: c2898a052d60bd9d6c05e3d277482e2221d07c18067b592fe7b8fefd796e8a6a
+  data.tar.gz: 55bdd8b9a78d2d35a2c4c1574da11113c66b7621128076f29128941a5a0caf77
 SHA512:
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-  data.tar.gz: 35ff2212eccbb3fbb2141f7aa7ec1c6d6de4ae77f3e2289ce8d99b11ff5d657d967a25367e5710e0f1fa13f0e7cff2a6f525b13ce68b82b933a7113b16146b10
+  metadata.gz: 3dd350c68a0c931da771f789aa934e3a94cf52be343101743a14eb2e049b782665db8f941da1f28e7503386af3f17c6ef4e53afa0ef388aecb65c9571ea974a5
+  data.tar.gz: 110a0a0eed2343835e3c4598f9c91c0280e28c64911a4fa18662c423d4f3d1774893b2e0ed848676a60878cae608a9b3d2e50de7c1c724935894971320628f2e

data/lib/rbbt/tsv.rb

@@ -98,6 +98,11 @@ module TSV
         stream = get_stream source, options.merge(open_options)
         parse stream, data, options.merge(:tsv_grep => tsv_grep)
 
+        if ! open_options[:noclose]
+          stream.close unless stream.closed?
+          stream.join if stream.respond_to?(:join)
+        end
+
         data.filename = filename.to_s unless filename.nil?
 
         if data.identifiers.nil? and Path === filename and filename.identifier_file_path

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -389,7 +389,7 @@ module TSV
       when Set
         traverse_array(obj.to_a, options, &block)
       when String
-        if Open.remote? obj or Misc.is_filename? obj
+        if Open.remote?(obj) or Misc.is_filename?(obj)
           Open.open(obj) do |s|
             traverse_obj(s, options, &block)
           end

data/lib/rbbt/workflow.rb

@@ -411,12 +411,22 @@ module Workflow
 
     overriden = has_overriden_inputs || overriden_deps.any?
 
+    extension = task.extension
+
+    if extension == :dep_task
+      extension = nil
+      if dependencies.any?
+        dep_basename = File.basename(dependencies.last.path)
+        extension = dep_path.split(".").last if dep_basename.include?('.')
+      end
+    end
+
     if real_inputs.empty? && Workflow::TAG != :inputs && ! overriden 
-      step_path = step_path taskname, jobname, [], [], task.extension
+      step_path = step_path taskname, jobname, [], [], extension
       input_values = task.take_input_values(inputs)
     else
       input_values = task.take_input_values(inputs)
-      step_path = step_path taskname, jobname, input_values, dependencies, task.extension
+      step_path = step_path taskname, jobname, input_values, dependencies, extension
     end
 
     job = get_job_step step_path, task, input_values, dependencies

data/lib/rbbt/workflow/definition.rb

@@ -73,7 +73,7 @@ module Workflow
   REMOVE_DEP_TASKS = ENV["RBBT_REMOVE_DEP_TASKS"] == "true"
   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
+    extension :dep_task unless @extension
     returns workflow.tasks[oname].result_description if workflow.tasks.include?(oname) unless @result_description 
     task name do
       raise RbbtException, "dependency not found in dep_task" if dependencies.empty?

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

@@ -26,7 +26,7 @@ class Step
     Log.color(color, status.to_s)
   end
 
-  def self.prov_report_msg(status, name, path, info = nil)
+  def self.prov_report_msg(status, name, path, info, input = nil)
     parts = path.sub(/\{.*/,'').split "/"
 
     parts.pop
@@ -43,10 +43,17 @@ class Step
                  rescue Exception
                    nil
                  end
+
+    if input.nil? || input.empty?
+      input_str = nil
+    else
+      input_str = Log.color(:magenta, "-> ") + input.collect{|dep,name| Log.color(:yellow, dep.task_name.to_s) + ":" + Log.color(:yellow, name) }.uniq * " "
+    end
+
     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") })"
+            prov_status_msg(status.to_s) << " " << [workflow, task, path, input_str].compact * " " << " (#{Log.color(:red, "Mtime out of sync") })"
           else
-            prov_status_msg(status.to_s) << " " << [workflow, task, path].compact * " " 
+            prov_status_msg(status.to_s) << " " << [workflow, task, path, input_str].compact * " " 
           end
 
     if $inputs and $inputs.any? 
@@ -74,7 +81,7 @@ class Step
     str << "\n"
   end
 
-  def self.prov_report(step, offset = 0, task = nil, seen = [], expand_repeats = false)
+  def self.prov_report(step, offset = 0, task = nil, seen = [], expand_repeats = false, input = nil)
     info = step.info  || {}
     info[:task_name] = task
     path  = step.path
@@ -85,13 +92,25 @@ class Step
     status = :notfound if status == :noinfo and not Open.exist?(path)
 
     str = " " * offset
-    str << prov_report_msg(status, name, path, info)
+    str << prov_report_msg(status, name, path, info, input)
+
+    input_dependencies = {}
+    step.dependencies.each do |dep|
+      if dep.input_dependencies.any?
+        dep.input_dependencies.each do |id|
+          input_name = dep.inputs.fields.zip(dep.inputs).select{|f,d| d == id || String === d && d.start_with?(id.files_dir) }.first.first
+          input_dependencies[id] ||= []
+          input_dependencies[id] << [dep, input_name]
+        end
+      end
+    end
+
     step.dependencies.reverse.each do |dep|
       path = dep.path
       new = ! seen.include?(path)
       if new
         seen << path
-        str << prov_report(dep, offset + 1, task, seen, expand_repeats)
+        str << prov_report(dep, offset + 1, task, seen, expand_repeats, input_dependencies[dep])
       else
         if expand_repeats
           str << Log.color(Step.status_color(dep.status), Log.uncolor(prov_report(dep, offset+1, task)))
@@ -103,7 +122,7 @@ class Step
           status = :unsync if status == :done and not Open.exist?(path)
           status = :notfound if status == :noinfo and not Open.exist?(path)
 
-          str << Log.color(Step.status_color(status), " " * (offset + 1) + Log.uncolor(prov_report_msg(status, name, path, info)))
+          str << Log.color(Step.status_color(status), " " * (offset + 1) + Log.uncolor(prov_report_msg(status, name, path, info, input_dependencies[dep])))
         end
       end
     end if step.dependencies

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.32.15
+  version: 5.32.16
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-06-25 00:00:00.000000000 Z
+date: 2021-07-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake