rbbt-util 5.28.4 → 5.28.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 1eb8b404c84b1c6d07f3d13ffeaeb97a4b9fd59bf237241b98e184cbfdb98a43
-  data.tar.gz: f2a0e7c55aa053a7d559143b1ae235558355fd1f4f61f2845864e47b621e37fc
+  metadata.gz: 2dc2c06d6d3e5f783f24a671c0150d6cb2da641d003770ee5315c10118a0ea34
+  data.tar.gz: 0e5cf607bd69452be51bf21d36ceeef49ab3d0cb2821728900547e7db60a03af
 SHA512:
-  metadata.gz: fd8348766af38ef48c379966ae2766e59fcb14714d78a5130856cdfef2d5a87eeabb4ae519a2fa6a2fa862d6b71cfff711eefe293b3f0954af6b0f70bbf58bdd
-  data.tar.gz: a8187db527df84d7db46e1cc049ed8e3a850188da16d0834408af102bf7f02977524786ab1267e6d047744d3e8cca3cc02c1382ede7b8766a61468867e2f8464
+  metadata.gz: 6d949e77540e01389eb90a757dbf7a499e6aadf237b998b533ffb964fee46bf2ff9c7145c00fa355ce4ff30a1710caab9169bebbf5be22a998c74cc84610c11e
+  data.tar.gz: c2d18ea2d6b45db2878c4a8ae07ac433d1ed365813bf7fe5635c325b743415575998ed6ae3db64d6429719c369ab8be5f263149d9fee8d3ca6edba15b0da1265

data/lib/rbbt/hpc.rb

@@ -451,12 +451,15 @@ EOF
           out = CMD.cmd("tail -f '#{fout}'", :pipe => true) if File.exists?(fout) and not tail == :STDERR
           err = CMD.cmd("tail -f '#{ferr}'", :pipe => true) if File.exists?(ferr)
 
-          Misc.consume_stream(err, true, STDERR) if err
-          Misc.consume_stream(out, true, STDOUT) if out
+          terr = Misc.consume_stream(err, true, STDERR) if err
+          tout = Misc.consume_stream(out, true, STDOUT) if out
 
           sleep 3 while CMD.cmd("squeue --job #{job}").read.include? job.to_s
+        rescue Aborted
         ensure
           begin
+            terr.exit if terr
+            tout.exit if tout
             err.close if err
             err.join if err
           rescue Exception

data/lib/rbbt/workflow/integration/cromwell.rb

@@ -1,9 +1,9 @@
-module Workflow
+module Cromwell
 
   Rbbt.claim Rbbt.software.opt.jar["cromwell.jar"], :url, "https://github.com/broadinstitute/cromwell/releases/download/48/cromwell-48.jar"
   Rbbt.claim Rbbt.software.opt.jar["wdltool.jar"], :url, "https://github.com/broadinstitute/wdltool/releases/download/0.14/wdltool-0.14.jar"
 
-  def run_cromwell(file, work_dir, options = {})
+  def self.run_cromwell(file, work_dir, options = {})
     cromwell_inputs_file = Misc.process_options options, :cromwell_inputs_file
     jar = Rbbt.software.opt.jar["cromwell.jar"].produce.find
     if cromwell_inputs_file
@@ -12,7 +12,9 @@ module Workflow
       CMD.cmd_log("java -jar '#{jar}' run '#{file}' --workflow-root='#{work_dir}'", options.merge("add_option_dashes" => true))
     end
   end
+end
 
+module Workflow
   def load_cromwell(file)
     jar = Rbbt.software.opt.jar["wdltool.jar"].produce.find
     inputs = JSON.load(CMD.cmd("java -jar '#{jar}' inputs '#{file}'"))

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

@@ -437,11 +437,12 @@ class Step
     rec_dependencies = self.rec_dependencies
     return [] if rec_dependencies.empty?
     canfail_paths = self.canfail_paths
+    dep = rec_dependencies.select{|d| d.task_name.to_s == 'contamination'}.first
     dirty_files = rec_dependencies.reject{|dep|
       (defined?(WorkflowRemoteClient) && WorkflowRemoteClient::RemoteStep === dep) || 
         ! Open.exists?(dep.info_file) ||
         (dep.path && (Open.exists?(dep.path) || Open.remote?(dep.path))) || 
-        ((dep.error? || dep.aborted? || dep.waiting?) && (! dep.recoverable_error? || canfail_paths.include?(dep.path)))
+        ((dep.error? || dep.aborted?) && (! dep.recoverable_error? || canfail_paths.include?(dep.path)))
     }
   end
 
@@ -508,12 +509,12 @@ class Step
 
   def nopid?
     pid = info[:pid] || Open.exists?(pid_file)
-    ! pid && ! (status.nil? || status == :aborted || status == :done || status == :error)
+    ! pid && ! (status.nil? || status == :aborted || status == :done || status == :error || status == :cleaned)
   end
 
   def aborted?
     status = self.status
-    status == :aborted || ((status != :noinfo && status != :setup && status != :noinfo) && nopid?)
+    status == :aborted || ((status != :cleaned && status != :noinfo && status != :setup && status != :noinfo) && nopid?)
   end
 
   # {{{ INFO

data/share/rbbt_commands/app/start

@@ -54,9 +54,9 @@ app = ARGV.shift
 
 ENV["RServe-session"] = options[:RServe_session] || app
 
-app_dir = Rbbt.etc.app_dir.exists? ? Path.setup(Rbbt.etc.app_dir.read.strip) : Rbbt.apps.find
+app_dir = Rbbt.etc.app_dir.exists? ? Path.setup(Rbbt.etc.app_dir.read.strip) : Rbbt.apps
 
-app_dir = app_dir[app]
+app_dir = app_dir[app].find
 
 server = options[:server] || 'puma'
 Misc.in_dir(app_dir) do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.28.4
+  version: 5.28.5
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-09-21 00:00:00.000000000 Z
+date: 2020-09-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake