rbbt-util 5.32.1 → 5.32.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/rbbt/hpc/lsf.rb

@@ -8,7 +8,7 @@ module HPC
     def self.batch_system_variables
       <<-EOF
 let TOTAL_PROCESORS="$(cat /proc/cpuinfo|grep ^processor |wc -l)"
-let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $SLURM_CPUS_PER_TASK )"
+let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $LSB_MAX_NUM_PROCESSORS )"
 [ ! -z $LSB_MAX_MEM_RUSAGE ] && let MAX_MEMORY="$LSB_MAX_MEM_RUSAGE" || MAX_MEMORY="$MAX_MEMORY_DEFAULT"
 export MAX_MEMORY_DEFAULT
 export MAX_MEMORY

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

@@ -132,7 +132,7 @@ module Persist
 
     def read_lock
       read if closed?
-      if read?
+      if read? || write?
         return yield
       end
 

data/lib/rbbt/tsv/parser.rb

@@ -40,7 +40,7 @@ module TSV
       # Process fields line
 
       preamble << line if line
-      while line and (TrueClass === @header_hash or (String === @header_hash and Misc.fixutf8(line) =~ /^#{@header_hash}/ ))
+      while line && (TrueClass === @header_hash || (String === @header_hash && Misc.fixutf8(line) =~ /^#{@header_hash}/ ))
         @fields = line.split(@sep, -1)
         @key_field = @fields.shift
         @key_field = @key_field[(0 + header_hash.length)..-1] if String === @header_hash
@@ -49,7 +49,7 @@ module TSV
         line = (@header_hash != "" ?  stream.gets : nil)
         line = Misc.fixutf8 line.chomp if line
         preamble << line if line
-        @header_hash = false if TrueClass === @header_hash
+        @header_hash = false if TrueClass === @header_hash || @header_hash == ""
       end
 
       @preamble = preamble[0..-3] * "\n"

data/lib/rbbt/tsv/stream.rb

@@ -56,6 +56,7 @@ module TSV
       preambles     = []
 
       streams = streams.collect do |stream|
+
         parser = TSV::Parser.new stream, options.dup
         sfields = parser.fields
 

data/lib/rbbt/util/misc/pipes.rb

@@ -43,7 +43,7 @@ module Misc
       File.mkfifo path
       yield path
     ensure
-      FileUtils.rm path if erase
+      FileUtils.rm path if erase && File.exists?(path)
     end
   end
   

data/lib/rbbt/workflow.rb

@@ -187,17 +187,21 @@ module Workflow
       clean_name = wf_name.sub(/::.*/,'')  
       Log.info{"Looking for '#{wf_name}' in '#{clean_name}'"}
       require_workflow clean_name
-      return Misc.string2const Misc.camel_case(wf_name)
+      workflow = Misc.string2const Misc.camel_case(wf_name)
+      workflow.load_documentation
+      return workflow
     end
 
     Log.high{"Loading workflow #{wf_name}"}
     require_local_workflow(wf_name) or 
     (Workflow.autoinstall and `rbbt workflow install #{Misc.snake_case(wf_name)} || rbbt workflow install #{wf_name}` and require_local_workflow(wf_name)) or raise("Workflow not found or could not be loaded: #{ wf_name }")
-    begin
-      Misc.string2const Misc.camel_case(wf_name)
-    rescue
-      Workflow.workflows.last || true
-    end
+    workflow = begin
+                 Misc.string2const Misc.camel_case(wf_name)
+               rescue
+                 Workflow.workflows.last || true
+               end
+    workflow.load_documentation
+    workflow
   end
 
   attr_accessor :description

data/lib/rbbt/workflow/definition.rb

@@ -74,6 +74,7 @@ module Workflow
   def dep_task(name, workflow, oname, *rest, &block)
     dep(workflow, oname, *rest, &block) 
     extension workflow.tasks[oname].extension if workflow.tasks.include?(oname) unless @extension
+    returns workflow.tasks[oname].result_description if workflow.tasks.include?(oname) unless @result_description 
     task name do
       raise RbbtException, "dependency not found in dep_task" if dependencies.empty?
       dep = dependencies.last

data/lib/rbbt/workflow/doc.rb

@@ -45,10 +45,25 @@ module Workflow
   end
 
   def load_documentation
-    @documentation = Workflow.parse_workflow_doc documentation_markdown
+    return if @documentation
+    @documentation ||= Workflow.parse_workflow_doc documentation_markdown
     @documentation[:tasks].each do |task, description|
-      raise "Documentation for #{ task }, but not a #{ self.to_s } task" unless tasks.include? task.to_sym
-      tasks[task.to_sym].description = description
+      if task.include? "#"
+        workflow, task = task.split("#")
+        workflow = begin
+                     Kernel.const_get workflow
+                   rescue
+                     next
+                   end
+      else
+        workflow = self
+      end
+
+      if workflow.tasks.include? task.to_sym
+        workflow.tasks[task.to_sym].description = description
+      else
+        Log.low "Documentation for #{ task }, but not a #{ workflow.to_s } task" 
+      end
     end
   end
 

data/lib/rbbt/workflow/util/trace.rb

@@ -180,11 +180,17 @@ rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, poi
       jobs += step.rec_dependencies + [step]
       step.info[:archived_info].each do |path,ainfo|
         archived_step = Step.new path
-        class << archived_step
-          self
-        end.define_method :info do
+
+        archived_step.define_singleton_method :info do
           ainfo
         end
+
+        #class << archived_step
+        #  self
+        #end.define_method :info do
+        #  ainfo
+        #end
+
         jobs << archived_step
       end if step.info[:archived_info]
 

data/share/rbbt_commands/workflow/forget_deps

@@ -8,9 +8,11 @@ $0 = "rbbt #{$previous_commands*" "} #{ File.basename(__FILE__) }" if $previous_
 
 options = SOPT.setup <<EOF
 
-Make a job forget all its dependencies and archive their meta-data
+Make a job forget its dependencies and archive their meta-data
 
-$ #{$0} [options] <job_path>
+$ #{$0} [options] <job_path> [<task_name>|<workflow>#<task_name>] ...
+
+Specific dependencies can be specified as . Otherwise, all are forgoten.
 
 -h--help Print this help
 -p--purge Purge dependencies
@@ -26,7 +28,7 @@ if options[:help]
   exit 0
 end
 
-path = ARGV[0]
+path, *remove = ARGV
 
 raise ParameterException, "No path given" if path.nil?
 step = Workflow.load_step path
@@ -34,10 +36,20 @@ step = Workflow.load_step path
 step.archive_deps
 step.copy_files_dir
 dependencies = step.dependencies
-step.set_info :dependencies, []
 
-if options[:purge]
+if remove && remove.any?
+ remove_paths = dependencies.select do |dep|
+  remove.include?(dep.task_name) || remove.include?([dep.workflow.to_s, dep.task_name] * "#")
+ end.collect{|dep| dep.path } 
+else
+ remove_paths = dependencies.collect{|dep| dep.path }
+end
+
+step.set_info :dependencies, step.info[:dependencies].reject{|info| remove_paths.include? info.last}
+
+if options[:purge] || options[:recursive_purge]
   dependencies.each do |dependency|
+    next unless remove_paths.include? dependency.path
     Step.purge(dependency.path, options[:recursive_purge])
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.32.1
+  version: 5.32.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-21 00:00:00.000000000 Z
+date: 2021-04-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake