rbbt-util 5.30.0 → 5.30.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 7c0e92d49399111157fae43149c7ec8e598aa64510591fc2f74314bbefc89b2d
+  metadata.gz: 0275d0f8a0922abe3e0abee0f02935fb6e393452a68c0cad86de075b153a8457
+  data.tar.gz: 8a182bd87be2e1b4c538d0faaf8a16848e8f077c9f61f96f6df67ca07dd222f6
 SHA512:
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+  metadata.gz: 02fd852c70355b89d187db04c52f27207012a2fe00f1fd7f414b95bea86bf47c3d19b0b766fa12d8520ee7c9270dfde369ce2a0c1dc60595e7a9b8062a176b92
+  data.tar.gz: 69591fffbf60d68a57dc319692adff4f4f28bb46d9b378fa23a0b01c55303b780d058f1e4ab1f41be52c43abb48ac8db7962e96f77fb2765f6f8f74587ee8825

data/lib/rbbt/hpc/orchestrate.rb

@@ -83,7 +83,7 @@ module HPC
 
         deps = seen[dep.path] ||= self.orchestrate_job(dep, options, skip_dep, seen)
         if job.canfail_paths.include? dep.path
-          [deps].flatten.collect{|id| ['canfail', id] * ":"}
+          [deps].flatten.compact.collect{|id| ['canfail', id] * ":"}
         else
           deps
         end

data/lib/rbbt/hpc/slurm.rb

@@ -525,7 +525,10 @@ EOF
       tail             = options.delete :tail
       dependencies     = options.delete :slurm_dependencies
       procpath         = options.delete :SLURM_procpath
+
       options[:jobname] = job.clean_name
+      log_level         = options.delete :log
+      log_level       ||= Log.severity
 
       workflow = job.workflow
 
@@ -550,16 +553,13 @@ EOF
         inputs_dir = File.join(tmp_directory, 'inputs_dir')
         saved = Step.save_job_inputs(job, inputs_dir)
 
-        if saved && saved.any?
-          options[:inputs_dir] = inputs_dir
-          cmd = ['workflow', 'task', workflow.to_s, task.to_s, '--printpath', '--load_inputs', inputs_dir, '--log', (options[:log] || Log.severity).to_s]
-        else
-          cmd = ['workflow', 'task', workflow.to_s, task.to_s, '--printpath', '--log', (options[:log] || Log.severity).to_s]
-        end
+        cmd = ['workflow', 'task', workflow.to_s, task.to_s, '--printpath', '--log', log_level.to_s]
+
+        cmd << "--procpath_performance='#{tmp_directory}/procpath##{procpath.gsub(',', '#')}'" if procpath
 
         cmd << "--override_deps='#{override_deps.gsub("'", '\'')}'" if override_deps and not override_deps.empty?
 
-        cmd << "--procpath_performance='#{tmp_directory}/procpath##{procpath.gsub(',', '#')}'" if procpath
+        cmd << "--load_inputs='#{inputs_dir}'" if saved && saved.any?
 
         template = self.template(cmd, options)
         jobid = self.issue_template(template, options.merge(:slurm_basedir => slurm_basedir, :dry_run => dry_run, :slurm_dependencies => dependencies))

data/lib/rbbt/persist/tsv/adapter.rb

@@ -133,11 +133,7 @@ module Persist
     def read_lock
       read if closed?
       if read?
-        begin
-          return yield
-        ensure
-          close
-        end
+        return yield
       end
 
       lock do

data/lib/rbbt/tsv.rb

@@ -113,8 +113,8 @@ module TSV
 
     data.entity_options = entity_options
 
-    if Path === source and data.identifiers
-      data.identifiers = Path.setup(data.identifiers, source.pkgdir, source.resource)
+    if Path === source && data.identifiers
+      Path.setup(data.identifiers, source.pkgdir, source.resource)
     end
 
     if data.respond_to? :persistence_path
@@ -124,6 +124,10 @@ module TSV
       data.clear
       data.annotate h
     end
+
+    data.read 
+
+    data
   end
 
   def self.parse_header(stream, options = {})

data/share/rbbt_commands/slurm/list

@@ -71,7 +71,7 @@ workdir.glob("**/command.slurm").sort_by{|f| File.mtime(f)}.each do |fcmd|
  end
 
  if m = Open.read(fcmd).match(/# Run command\n(.*?)\n/im)
-  exe = m[1]
+  exe = m[1].sub('step_path=$(','')
  else
   exe = nil
  end

data/share/rbbt_commands/workflow/task

@@ -410,10 +410,20 @@ begin
 
   if options[:procpath_performance]
     require 'rbbt/util/procpath'
+    current_pid = job.info[:pid]
     job.fork
     job.soft_grace
-    pid = job.info[:pid]
-    ProcPath.monitor(pid, options[:procpath_performance])
+    sleep 2 if job.info[:pid] == current_pid
+    if job.info[:pid] != current_pid
+      pid = job.info[:pid]
+      begin
+        ProcPath.monitor(pid, options[:procpath_performance])
+      rescue Errno::ECHILD
+        Log.warn "Procpath didn't find process #{pid} to monitor. Maybe it finished already"
+      rescue
+        Log.warn "Procpath failed: #{$!.message}"
+      end
+    end
   end
 
   if do_fork

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.30.0
+  version: 5.30.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-02-01 00:00:00.000000000 Z
+date: 2021-02-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake