rbbt-util 5.30.4 → 5.30.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 9a9857c6b1565b9ed55f18f50fb1b242a1477dd6868111e10252ecc0c286ca44
+  metadata.gz: aa5b1545b1a92199d163bf398ca973c6aa3d78ab37cc724b988e007c87824b3b
+  data.tar.gz: 6cd3ce80ea589fb97a211ebe1d2973dd7c0d3f93b1ccefe10b9ecefbc77ff515
 SHA512:
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+  metadata.gz: d8246d2a2686cc38086800fb6c30949bba93c8e78b7feac220b710a4e80f66858f979c5ea41de0beb67aeefd29de045e2315c3b50128f448bfef521ce3d52e15
+  data.tar.gz: 26559322cae3bfb736565e8da0c7e63c3b006c793ab5cda8ec37a04fabfa460001bae6d7da8164ccd310730b81553d1d3b5a1d14cee9e6929793329ce508ec59

data/lib/rbbt/hpc/orchestrate.rb

@@ -5,7 +5,10 @@ module HPC
     def self.job_rules(rules, job)
       workflow = job.workflow.to_s
       task_name = job.task_name.to_s
+      task_name = job.overriden.to_s if Symbol === job.overriden
+
       defaults = rules["defaults"] || {}
+      defaults.merge(rules[workflow]["defaults"] || {}) if rules[workflow]
 
       job_rules = IndiferentHash.setup(defaults.dup)
 

data/lib/rbbt/hpc/slurm.rb

@@ -21,10 +21,10 @@ module HPC
       exclusive        = options.delete :exclusive
       highmem          = options.delete :highmem
 
-      queue            = options.delete(:queue) || 'bsc_ls'
+      queue            = options.delete(:queue) || Rbbt::Config.get('queue', :slurm_queue, :slurm, :SLURM, :default => 'bsc_ls')
       task_cpus        = options.delete(:task_cpus) || 1
       nodes            = options.delete(:nodes) || 1
-      time             = options.delete(:time) || "0:00:10"
+      time             = options.delete(:time) || "0:02:00"
 
       inputs_dir       = options.delete :inputs_dir
       config_keys      = options.delete :config_keys
@@ -301,11 +301,15 @@ EOF
         coda +=<<-EOF
 
 # Sync data to target location
-mkdir -p "$(dirname '#{target}')"
-rsync -avztAXHP --copy-unsafe-links "#{source}/" "#{target}/" &>> #{fsync} 
-sync_es="$?" 
-echo $sync_es > #{fsyncexit}
-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
+if [ $exit_status == '0' ]; then 
+  mkdir -p "$(dirname '#{target}')"
+  rsync -avztAXHP --copy-unsafe-links "#{source}/" "#{target}/" &>> #{fsync} 
+  sync_es="$?" 
+  echo $sync_es > #{fsyncexit}
+  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 $A; done
+else
+  sync_es="$exit_status" 
+fi
 EOF
 
         if  contain && (wipe_container == "post" || wipe_container == "both")
@@ -331,11 +335,11 @@ EOF
           else
             coda +=<<-EOF
 ##{exec_cmd} system clean
-if [ $exit_status == '0' -a $sync_es == '0' ]; then 
+#if [ $exit_status == '0' -a $sync_es == '0' ]; then 
     rm -Rfv #{contain} &>> #{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
 
           end

data/lib/rbbt/util/open.rb

@@ -748,7 +748,9 @@ module Open
     if (dir_sub_path = find_repo_dir(path))
       writable_repo?(*dir_sub_path)
     else
-      if File.exist?(path)
+      if File.symlink?(path)
+        File.writable?(File.dirname(path))
+      elsif File.exist?(path)
         File.writable?(path)
       else
         File.writable?(File.dirname(File.expand_path(path)))

data/lib/rbbt/workflow/examples.rb

@@ -53,7 +53,11 @@ module Workflow
           if file =~ /\.yaml/
             inputs[input.to_sym]  = YAML.load(Open.read(file))
           else
-            inputs[input.to_sym]  = Open.realpath(file)
+            if File.symlink?(file)
+              inputs[input.to_sym]  = File.readlink(file)
+            else
+              inputs[input.to_sym]  = Open.realpath(file)
+            end
           end
         when :text
           Log.debug "Reading #{ input } from #{file}"

data/share/rbbt_commands/slurm/list

@@ -133,7 +133,7 @@ workdir.glob("**/command.slurm").sort_by{|f| File.mtime(f)}.each do |fcmd|
    select = true if queued && deps && (running_jobs & deps).any? || queued && is_running && nodes.empty?
    select = true if running && nodes.any? && (exit_status.nil? && running_jobs.include?(id)) && (!deps || (running_jobs & deps).empty?)
    select = true if jobid && jobid.split(",").include?(id)
-   select &= search && cmd.match(/#{search}/) if search
+   select = select && cmd.match(/#{search}/) if search
    next unless select 
  elsif search
    select = false

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.30.4
+  version: 5.30.5
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-02-04 00:00:00.000000000 Z
+date: 2021-02-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake