rbbt-util 5.23.32 → 5.23.34

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 74066e9c626e51bd9c625ed741cff14a177a9ea2
+  metadata.gz: bb30046034803f9f8fa05cc114a25b41fbff60bb
+  data.tar.gz: 27fdf9b8cee90400d5929d3282fbcb4d7bf3d638
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+  data.tar.gz: 3d56953e218a3c0bcd256d35e053d27fe0f3ce2bdc410462a47ec93815c88d125107e85603c29824e2897f6f15639ef3ed088736dd13dac61254e3ad0650828f

data/lib/rbbt/util/log.rb

@@ -114,7 +114,7 @@ module Log
   HIGHLIGHT = "\033[1m"
 
   def self.uncolor(str)
-    Term::ANSIColor.uncolor(str)
+    "" << Term::ANSIColor.uncolor(str)
   end
 
   def self.reset_color

data/lib/rbbt/workflow.rb

@@ -487,13 +487,12 @@ module Workflow
     Rbbt.var.jobs[end_part].find
   end
 
-
   def self.__load_step(path)
     step = Step.new path
     relocated = false
     step.dependencies = (step.info[:dependencies] || []).collect do |task,name,dep_path|
       if Open.exists?(dep_path)
-        Workflow.load_step dep_path
+        Workflow._load_step dep_path
       else
         new_path = relocate(path, dep_path)
         relocated = true if Open.exists?(new_path)
@@ -502,7 +501,42 @@ module Workflow
     end
     step.relocated = relocated
     step.load_inputs_from_info
+    step
+  end
+    
+  def self.fast_load_step(path)
+    return load_step(path)
+    step = Step.new path
+    step.dependencies = nil
+    class << step
+      def dependencies
+        @dependencies ||= (self.info[:dependencies] || []).collect do |task,name,dep_path|
+          dep = if Open.exists?(dep_path)
+                  relocate = false
+                  Workflow.fast_load_step dep_path
+                else
+                  new_path = Workflow.relocate(path, dep_path)
+                  relocated = true if Open.exists?(new_path)
+                  Workflow.fast_load_step new_path
+                end
+          dep.relocated = relocated
+          dep
+        end
+        @dependencies
+      end
+
+      def inputs
+        self.load_inputs_from_info unless @inputs
+        @inputs
+      end
 
+      def dirty?
+        false
+      end
+      def updated?
+        true
+      end
+    end
     step
   end
 
@@ -529,13 +563,20 @@ module Workflow
     task = task_for path
     return remote_tasks[task].load_id(id) if remote_tasks and remote_tasks.include? task
     return Workflow.load_step path
-    #step = Step.new path, tasks[task.to_sym]
-    #step.load_inputs_from_info
-    #set_step_dependencies(step)
-    #step
   end
 
 
+  def fast_load_id(id)
+    path = if Path === workdir
+             workdir[id].find
+           else
+             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 Workflow.fast_load_step path
+  end
+
   def load_name(task, name)
     return remote_tasks[task].load_step(path) if remote_tasks and remote_tasks.include? task
     task = tasks[task.to_sym] if String === task or Symbol === task

data/lib/rbbt/workflow/accessor.rb

@@ -222,6 +222,7 @@ class Step
   end
 
   def message(message)
+    message = Log.uncolor(message)
     set_info(:messages, (messages || []) << message)
   end
 
@@ -456,12 +457,13 @@ class Step
   end
 
   def nopid?
-    pid = info[:pid]
-    pid.nil? && ! (status.nil? || status.nil? || status == :aborted || status == :done || status == :error)
+    pid = info[:pid] || Open.exists?(pid_file)
+    ! pid && ! (status.nil? || status == :aborted || status == :done || status == :error)
   end
 
   def aborted?
-    status == :aborted || (status != :noinfo && nopid?)
+    status = self.status
+    status == :aborted || ((status != :noinfo && status != :setup && status != :noinfo) && nopid?)
   end
 
   # {{{ INFO

data/lib/rbbt/workflow/step.rb

@@ -58,6 +58,9 @@ class Step
     @info_mutex = Mutex.new
     @inputs = inputs 
     NamedArray.setup @inputs, task.inputs.collect{|s| s.to_s} if task and task.respond_to? :inputs and task.inputs
+    if Open.exists?(info_file) and (info[:path] != path)
+      @relocated = true
+    end
   end
 
   def workflow

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

@@ -315,7 +315,6 @@ class Step
                              canfail_paths += dep.canfail_paths
                              next unless ComputeDependency === dep && dep.canfail?
                              canfail_paths << dep.path
-                             iii dep.path
                              canfail_paths += dep.rec_dependencies.collect{|d| d.path }
                            end
                            canfail_paths

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

@@ -218,6 +218,7 @@ class Step
           merge_info({
             :issued => (issue_time = Time.now),
             :name => name,
+            :pid => Process.pid.to_s,
             :clean_name => clean_name,
             :workflow => (@workflow || @task.workflow).to_s,
             :task_name => @task.name,
@@ -636,7 +637,7 @@ class Step
   end
 
   def soft_grace
-    until done? or Open.exist?(info_file)
+    until done? or (Open.exist?(info_file) && info[:status] != :noinfo)
       sleep 1 
     end
     self

data/share/Rlib/util.R

@@ -711,6 +711,13 @@ rbbt.plot.venn <- function(data, a, ...) {
     return(out)
 }
 
+rbbt.plot.pca <- function(data, center = TRUE, scale. = TRUE, ...) {
+  rbbt.require('vqv/ggbiplot')
+  data <- rbbt.impute(data)
+  pca <- prcomp(data, center=center, scale.=scale.)
+  ggbiplot(pca, ...)
+}
+
 
 rbbt.plot.text_scatter <- function(formula, data) {
     plot(formula, data=data, cex = 0)

data/share/rbbt_commands/system/clean

@@ -94,14 +94,15 @@ TSV.traverse jobs, :_bar => "Checking job status" do |file,i|
              {:status => :noinfo}
            end
 
-    pid = info[:pid]
+    done = Open.exists?(file)
+    pid = info[:pid] || (Open.exists?(file + '.pid') && Open.read(file + '.pid')) unless done
 
     status = info[:status].to_s
     if status != "noinfo"
-      status = :missing if status == "done" and not File.exist? file
+      status = :missing if status == "done" and not done
       status = :nopid if status != "done" and pid.nil?
       status = :dead if status != "done" and pid and not Misc.pid_exists?(pid)
-      status = :sync if status != "done" and File.exist? file
+      status = :sync if status != "done" and done
     end
 
     status = :dirty if info[:status].to_s == "done" and dirty and Workflow.load_step(file).dirty?
@@ -126,6 +127,7 @@ TSV.traverse jobs, :_bar => "Checking job status" do |file,i|
 
   if (force and status !~ /done/) or 
     status =~ /\b(old|dirty|nopid|error|missing|aborted|dead|sync)$/ or
+    (status == "noinfo" and not done) or
     status == "" 
 
     puts "  Removing #{ file } - #{status}" 

data/share/rbbt_commands/workflow/task

@@ -399,7 +399,7 @@ begin
 
   if options.delete(:printpath)
     job.join
-    raise job.messages.last if job.error? or job.aborted?
+    raise job.messages.last if job.error? or job.aborted? and job.messages
     if Open.remote? job.path
       puts job.url + Log.color(:blue, "?_format=raw")
     else

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.23.32
+  version: 5.23.34
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-23 00:00:00.000000000 Z
+date: 2018-11-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake