rbbt-util 5.23.19 → 5.23.20

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 4e8c74787a866cbfdf0bc0b45d18b89f043751a2
+  metadata.gz: d092d9923d01da9560a5e01b1da4d1d997acb866
+  data.tar.gz: 7d6ab5b9b06cfb2eb4ac7cdee01f6e40a3103e51
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+  data.tar.gz: 9e78df0466cb39d1329e44a26d4d0559c557ab3967b70b1c6565c9b45d17ccbab1ca740e44e42c18241ce3c293e8b1b075c87b68d92dbd197294fa6da39f1e62

data/lib/rbbt/util/log/progress/report.rb

@@ -117,6 +117,8 @@ module Log
                 1
               end
       end
+
+      thr = 0.0000001 if thr == 0
       
       if mean.nil? or mean.to_i > 1
         str = "#{ Log.color :blue, thr.to_i.to_s } per sec."

data/lib/rbbt/util/open.rb

@@ -565,6 +565,7 @@ module Open
   end
 
   def self.writable?(path)
+    path = path.find if Path === path
     if File.exists?(path)
       File.writable?(path)
     else

data/lib/rbbt/workflow.rb

@@ -470,7 +470,10 @@ module Workflow
   def  self.relocate(real, other)
     preal = real.split(/\/+/)
     pother = other.split(/\/+/)
-    (preal[0..-4] + pother[-3..-1]) * "/"
+    end_part = pother[-3..-1] * "/"
+    new_path = preal[0..-4] * "/" << end_part
+    return new_path if File.exists? new_path
+    Rbbt.var.jobs[end_part].find
   end
 
   def self.load_step(path)

data/lib/rbbt/workflow/accessor.rb

@@ -1038,7 +1038,8 @@ module Workflow
                        when :hash
                          clean_inputs = Annotated.purge(inputs)
                          clean_inputs = clean_inputs.collect{|i| Symbol === i ? i.to_s : i }
-                         key_obj = {:inputs => clean_inputs, :dependencies => dependencies}
+                         deps_str = dependencies.collect{|d| Step === d ? d.short_path : d }
+                         key_obj = {:inputs => clean_inputs, :dependencies => deps_str }
                          key_str = Misc.obj2str(key_obj)
                          hash_str = Misc.digest(key_str)
                          #Log.debug "Hash for '#{[taskname, jobname] * "/"}' #{hash_str} for #{key_str}"

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

@@ -85,6 +85,7 @@ class Step
       status = job.status.to_s
 
       if (status == 'error' && (job.recoverable_error? || job.dirty?)) ||
+          (job.noinfo? && Open.exists?(job.pid_file)) ||
           job.aborted? ||
           (job.done? && ! job.updated?)  || (job.error? && ! job.updated?) ||
           (job.done? && job.dirty?)  || (job.error? && job.dirty?) ||
@@ -118,6 +119,8 @@ class Step
 
   def execute_dependency(dependency, log = true)
     task_name = self.task_name
+    canfail_paths = self.canfail_paths
+    already_failed = []
     begin
 
       dependency.resolve_input_steps
@@ -132,17 +135,18 @@ class Step
       end
 
       dependency.status_lock.synchronize do
-        if dependency.aborted? or (dependency.error? and dependency.recoverable_error?) or (!Open.remote?(dependency.path) && dependency.missing?)
+        if dependency.aborted? || (dependency.error? && dependency.recoverable_error? && ! canfail_paths.include?(dependency.path) && ! already_failed << dependency.path) || (!Open.remote?(dependency.path) && dependency.missing?)
           Log.warn "Cleaning dep. on exec #{Log.color :blue, dependency.path} (missing: #{dependency.missing?}; error #{dependency.error?})"
           dependency.clean
+          already_failed << dependency.path
           raise TryAgain
         end
       end
 
-      if ! dependency.started? && ! dependency.error?
+      if ! (dependency.started? || dependency.error?)
         log_dependency_exec(dependency, :starting)
         dependency.run(true)
-          raise TryAgain
+        raise TryAgain
       end
 
       dependency.grace
@@ -302,7 +306,7 @@ class Step
       Set.new(info[:canfail_paths])
     else
       canfail_paths = Set.new
-      all_deps = rec_dependencies + [self]
+      all_deps = dependencies
       all_deps.each do |dep|
         next if canfail_paths.include? dep.path
         next unless ComputeDependency === dep && dep.canfail?

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.23.19
+  version: 5.23.20
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-24 00:00:00.000000000 Z
+date: 2018-08-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake