rbbt-util 5.26.145 → 5.26.146

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: '031648bb9feb9b389f8d79f1a0b9fbe2975417116a30449165f09edf34cb627d'
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+  data.tar.gz: 364b2612168f4223cd3752409c5dd8e6e678b6dc0d047c47c95579588f097ff8bc2b40f9caacc034bb2a0aceb52eacf5d174a88429ad4dd6c16014f128c5087c

data/lib/rbbt/hpc.rb

@@ -267,8 +267,6 @@ EOF
 # Save exit status
 exit_status=$?
 
-# Clean job.id, since we are done
-rm #{fjob}
 EOF
 
       # CODA
@@ -315,13 +313,13 @@ singularity exec -e -C -H "$CONTAINER_DIR" "$SINGULARITY_IMG" rm -v /dev/shm/sem
 
 
 # Clean container directory
-if [ $exit_status == '0' -a $sync_es == '0' ]; then 
+#if [ $exit_status == '0' -a $sync_es == '0' ]; then 
     singularity exec -e -C -H "$CONTAINER_DIR" "$SINGULARITY_IMG" rbbt system clean -f &>> #{fsync}
     singularity exec -e -C -H "$CONTAINER_DIR" "$SINGULARITY_IMG" rm -Rfv .rbbt/var/jobs &>> #{fsync}
     singularity exec -e -C -H "$CONTAINER_DIR" "$SINGULARITY_IMG" rm -Rfv tmp/ &>> #{fsync}
-else
-    echo "ERROR: Process failed or results could not sync correctly. Contain directory not purged" &>> #{fsync}
-fi
+#else
+#    echo "ERROR: Process failed or results could not sync correctly. Contain directory not purged" &>> #{fsync}
+#fi
 EOF
           else
             coda +=<<-EOF
@@ -531,7 +529,7 @@ EOF
     end
   end
 
-  def relay(job, options={})
+  def self.relay(job, options={})
     options = Misc.add_defaults options, :target => 'mn1', :search_path => 'user'
     done_deps = job.dependencies.select do |dep|
       dep.done? 

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

@@ -411,7 +411,8 @@ class Step
 
           set_info :dependencies, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}
 
-          set_info :config_keys, (Rbbt::Config::GOT_KEYS - config_keys_pre).uniq
+          config_keys = Rbbt::Config::GOT_KEYS[config_keys_pre.length..-1]
+          set_info :config_keys, config_keys
 
           if result.nil? && File.exists?(self.tmp_path) && ! File.exists?(self.path)
             Open.mv self.tmp_path, self.path

data/test/rbbt/test_hpc.rb

@@ -2,8 +2,10 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '..', 'test_helper.r
 require 'rbbt/hpc'
 require 'rbbt/workflow'
 
-class TestHPC < Test::Unit::TestSuite
+
+class TestHPC < Test::Unit::TestCase
   def test_relay
+
     Log.severity = 0
     Workflow.require_workflow "Translation"
     job = Translation.job(:translate, nil, :genes => %w(TP53 KRAS))

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.145
+  version: 5.26.146
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-02-17 00:00:00.000000000 Z
+date: 2020-02-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake