rbbt-util 5.26.30 → 5.26.31

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: cb2336c9d10c8c90f466b98d533accfa60cd2d7485ef3172df146891d5d35c62
+  data.tar.gz: 4033671c874b9aaf6b9313291010aea9979110b9075377f6018b18495be08516
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+  data.tar.gz: e870e508f1923b918538f1ddf390cbbfac08b0daf926758937e3fd5e0553749c2222d8f54d1953f934a90ebe7253ea5711b12b9adf07aebb6b248f74551408e0

data/lib/rbbt/hpc.rb

@@ -259,12 +259,12 @@ EOF
         target = File.expand_path(sync)
         coda +=<<-EOF
 rsync -avt "#{source}/" "#{target}/" &>> #{fsync} 
+sync_es="$?" 
 find '#{target}' -type l -ls | awk '$13 ~ /^#{target.gsub('/','\/')}/ { sub("#{source}", "#{target}", $13); print $11, $13 }' | while read A B; do rm $A; ln -s $B $A; done
 EOF
 
         if  contain && (wipe_container == "post" || wipe_container == "both")
           coda +=<<-EOF
-sync_es="$?" 
 singularity exec -e -C -H "$CONTAINER_DIR" "$SINGULARITY_IMG" rbbt system clean -f &>> #{fsync}
 singularity exec -e -C -H "$CONTAINER_DIR" "$SINGULARITY_IMG" rm -v /dev/shm/sem.*.{in,out,process} /dev/shm/sem.Session-PID.*.sem 2> /dev/null >> #{fsync}
 if [ $sync_es == '0' ]; then 

data/lib/rbbt/workflow.rb

@@ -511,6 +511,18 @@ module Workflow
     Rbbt.var.jobs[end_part].find
   end
 
+  def self.relocate_dependency(main, dep)
+    dep_path = dep.path
+    path = main.path
+    if Open.exists?(dep_path) || Open.exists?(dep_path + '.info')
+      dep
+    else
+      new_path = relocate(path, dep_path)
+      relocated = true if Open.exists?(new_path) || Open.exists?(new_path + '.info')
+      Workflow._load_step new_path
+    end
+  end
+
   def self.__load_step(path)
     step = Step.new path
     relocated = false
@@ -519,7 +531,7 @@ module Workflow
         Workflow._load_step dep_path
       else
         new_path = relocate(path, dep_path)
-        relocated = true if Open.exists?(new_path)
+        relocated = true if Open.exists?(new_path) || Open.exists?(new_path + '.info')
         Workflow._load_step new_path
       end
     end
@@ -534,12 +546,12 @@ module Workflow
     class << step
       def dependencies
         @dependencies ||= (self.info[:dependencies] || []).collect do |task,name,dep_path|
-          dep = if Open.exists?(dep_path)
+          dep = if Open.exists?(dep_path) || Open.exists?(dep_path + '.info')
                   relocate = false
                   Workflow.fast_load_step dep_path
                 else
                   new_path = Workflow.relocate(path, dep_path)
-                  relocated = true if Open.exists?(new_path)
+                  relocated = true if Open.exists?(new_path) || Open.exists?(new_path + '.info')
                   Workflow.fast_load_step new_path
                 end
           dep.relocated = relocated

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

@@ -112,13 +112,14 @@ class Step
   end
 
   def updatable?
-    (ENV["RBBT_UPDATE_ALL_JOBS"] == 'true' || Open.exists?(info_file)) && ! relocated?
+    (ENV["RBBT_UPDATE_ALL_JOBS"] == 'true' || Open.exists?(info_file)) && ! (relocated? && done?)
   end
 
   def dependency_checks
     rec_dependencies.
       select{|dependency| ! (defined? WorkflowRESTClient and WorkflowRESTClient::RemoteStep === dependency) }.
-      select{|dependency| ! Open.exists?(dependency.path) }.
+      collect{|dependency| Workflow.relocate_dependency self, dependency}.
+      select{|dependency| Open.exists?(dependency.path) || Open.exists?(dependency.info_file) }.
       select{|dependency| ! Open.remote?(dependency.path) }.
       select{|dependency| dependency.updatable? }.
       select{|dependency| ! dependency.error? }

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.30
+  version: 5.26.31
 platform: ruby
 authors:
 - Miguel Vazquez