rbbt-util 5.32.7 → 5.32.13

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: d6e8f5a7e8cb2d2f0e9a99f36a7594e4fc3655dd1d4f9b571f73f0f947b19fd3
+  metadata.gz: 4c61ee9aa98e617b2cd43ea3c57b71439cbb5c2c65282ed7695fafd5c46ccbf3
+  data.tar.gz: e30e12b162f86ee74b4a4c33e44c7e976612a11e8219b2afd9c6cc0ea520fe24
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+  metadata.gz: abee1a9322982a9da1cca62f7c36e47a7517a6c8066177f5155f8bfc17e6bc19054bfc1b8068c67e58fb0bf4a1c7585c3d493c2ca70d600391348e03f61ebab6
+  data.tar.gz: 80e3f811802c5e33cefd1c7c9561a9bdfcc2cfbfa97f300babd3c095de1d5bfb14a88e2e52918c4be9e869f9bf2722df68a493895077101e42b2f4ee57e9427c

data/bin/rbbt

@@ -102,6 +102,7 @@ end
 
 if options[:config_keys]
   options[:config_keys].split(",").each do |config|
+    config = config.strip
     Rbbt::Config.process_config config
   end
 end

data/lib/rbbt/hpc/batch.rb

@@ -95,14 +95,15 @@ module HPC
 
       task = Symbol === job.overriden ? job.overriden : job.task_name
 
-      if job.overriden
-        override_deps = job.rec_dependencies.
-          select{|dep| Symbol === dep.overriden }.
+      if job.overriden?
+        #override_deps = job.rec_dependencies.
+        #  select{|dep| Symbol === dep.overriden }.
+        
+        override_deps = job.overriden_deps.
           collect do |dep| 
-
           name = [dep.workflow.to_s, dep.task_name] * "#"
           [name, dep.path] * "="  
-        end * ","
+        end.uniq * ","
 
         options[:override_deps] = override_deps unless override_deps.empty?
       end
@@ -156,10 +157,15 @@ EOF
         :singularity_ruby_inline,
         :sync,
         :task_cpus,
+        :mem,
+        :mem_per_cpu,
+        :licenses,
+        :contraints,
         :time,
         :user_group,
         :wipe_container,
         :workdir,
+        :purge_deps
       ]
 
       keys.each do |key|
@@ -378,9 +384,9 @@ echo "user_scratch: #{scratch_group_dir}/#{user}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}"
     end
 
     def execute(options)
-      exec_cmd, job_cmd = options.values_at :exec_cmd, :rbbt_cmd
+      exec_cmd, job_cmd, task_cpus = options.values_at :exec_cmd, :rbbt_cmd, :task_cpus
 
-      <<-EOF
+      script=<<-EOF
 step_path=$( 
       #{exec_cmd} #{job_cmd} --printpath
 )
@@ -388,7 +394,10 @@ exit_status=$?
 
 [[ -z $BATCH_JOB_ID ]] || #{exec_cmd} workflow write_info --recursive --force=false --check_pid "$step_path" batch_job $BATCH_JOB_ID
 [[ -z $BATCH_SYSTEM ]] || #{exec_cmd} workflow write_info --recursive --force=false --check_pid "$step_path" batch_system $BATCH_SYSTEM
+#{exec_cmd} workflow write_info --recursive --force=false --check_pid "$step_path" batch_cpus #{task_cpus}
       EOF
+
+      script
     end
 
     def sync_environment(options = {})
@@ -409,6 +418,13 @@ fi
 
     def cleanup_environment(options = {})
       cleanup_environment = ""
+
+      cleanup_environment +=<<-EOF if options[:purge_deps]
+if [ $exit_status == '0' ]; then 
+  #{options[:exec_cmd]} workflow forget_deps --purge --recursive_purge "$step_path" 2>1 >> '#{options[:fsync]}' 
+fi
+      EOF
+
       if options[:sync]
         if options[:wipe_container] == 'force'
           cleanup_environment +=<<-EOF

data/lib/rbbt/hpc/slurm.rb

@@ -28,6 +28,11 @@ export BATCH_SYSTEM=SLURM
       workdir        = Misc.process_options options, :workdir
       exclusive      = Misc.process_options options, :exclusive
       highmem        = Misc.process_options options, :highmem
+      licenses       = Misc.process_options options, :licenses
+      constraint     = Misc.process_options options, :constraint
+
+      mem            = Misc.process_options options, :mem
+      mem_per_cpu    = Misc.process_options options, :mem_per_cpu
 
       batch_dir  = Misc.process_options options, :batch_dir
       batch_name = Misc.process_options options, :batch_name
@@ -37,20 +42,34 @@ export BATCH_SYSTEM=SLURM
 
       time = Misc.format_seconds Misc.timespan(time) unless time.include? ":"
 
+      sbatch_params = {"job-name" => batch_name,
+                       "output" => fout,
+                       "error" => ferr,
+                       "cpus-per-task" => task_cpus,
+                       "nodes" => nodes,
+                       "time" => time,
+                       "exclusive" => exclusive,
+                       "licenses" => licenses,
+                       "mem" => mem,
+                       "mem-per-cpu" => mem_per_cpu,
+      }
+
       header =<<-EOF
 #!/bin/bash
-#SBATCH --job-name="#{batch_name}"
-#SBATCH --workdir="#{workdir}"
-#SBATCH --output="#{fout}"
-#SBATCH --error="#{ferr}"
-#SBATCH --qos="#{queue}"
-#SBATCH --cpus-per-task="#{task_cpus}"
-#SBATCH --time="#{time}"
-#SBATCH --nodes="#{nodes}"
       EOF
 
-      header << "#SBATCH --exclusive" << "\n" if exclusive
-      header << "#SBATCH --constraint=highmem" << "\n" if highmem
+      sbatch_params.each do |name,value|
+        next if value.nil? || value == ""
+        if TrueClass === value
+          header << "#SBATCH --#{name}" << "\n"
+        elsif Array === value
+          value.each do |v|
+            header << "#SBATCH --#{name}=\"#{v}\"" << "\n"
+          end
+        else
+          header << "#SBATCH --#{name}=\"#{value}\"" << "\n"
+        end
+      end
 
       header
     end

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

@@ -148,11 +148,7 @@ module Persist
     def write_lock
       write if closed?
       if write?
-        begin
-          return yield
-        ensure
-          close
-        end
+        return yield
       end
 
       lock do

data/lib/rbbt/resource.rb

@@ -4,10 +4,10 @@ require 'rbbt/resource/path'
 require 'net/http'
 require 'set'
 
- 
 module Resource
   class ResourceNotFound < RbbtException; end
 
+ 
   class << self
     attr_accessor :lock_dir
     
@@ -87,12 +87,21 @@ module Resource
       lock_filename = nil # it seems like this was locked already.
 
       Misc.lock lock_filename do
-        uri = URI(url)
+        begin
+          uri = URI(url)
+
+          http = Net::HTTP.new(uri.host, uri.port)
 
-        http = Net::HTTP.new(uri.host, uri.port)
-        request = Net::HTTP::Get.new(uri.request_uri)
-        timeout = 60 * 10
-        Net::HTTP.start(uri.host, uri.port, :timeout => timeout, :read_timeout => timeout, :open_timeout => timeout) do |http|
+          if uri.scheme == "https"
+            http.use_ssl = true
+            http.verify_mode = OpenSSL::SSL::VERIFY_NONE
+            http.instance_variable_set("@ssl_options", OpenSSL::SSL::OP_NO_SSLv2 + OpenSSL::SSL::OP_NO_SSLv3 + OpenSSL::SSL::OP_NO_COMPRESSION)
+          end
+
+          timeout = 60 * 10
+          http.read_timeout = timeout
+          http.open_timeout = timeout
+          request = Net::HTTP::Get.new(uri.request_uri)
           http.request request do |response|
             filename = if response["Content-Disposition"] 
                          response["Content-Disposition"].split(";").select{|f| f.include? "filename"}.collect{|f| f.split("=").last.gsub('"','')}.first
@@ -123,9 +132,11 @@ module Resource
                   FileUtils.mv tmp_dir, final_path
                 end
               else
-                Open.open(location, :nocache => true) do |s|
-                  Misc.sensiblewrite(final_path, s)
-                end
+                url = location
+                raise TryAgain
+                #Open.open(location, :nocache => true) do |s|
+                #  Misc.sensiblewrite(final_path, s)
+                #end
               end
             when Net::HTTPInternalServerError
               @server_missing_resource_cache << url
@@ -134,6 +145,8 @@ module Resource
               raise "Response not understood: #{response.inspect}"
             end
           end
+        rescue TryAgain
+          retry
         end
       end
     rescue

data/lib/rbbt/tsv/csv.rb

@@ -28,10 +28,10 @@ module TSV
             if Misc.is_filename?(obj)
               CSV.read obj, options
             else
-              CSV.new obj, options
+              CSV.new obj, **options
             end
           else
-            CSV.new obj, options
+            CSV.new obj, **options
           end
 
     tsv = if noheaders

data/lib/rbbt/tsv/manipulate.rb

@@ -174,6 +174,8 @@ module TSV
         if Hash === @monitor
           desc = @monitor[:desc] if @monitor.include? :desc 
           step = @monitor[:step] if @monitor.include? :step 
+        elsif String === @monitor
+          desc = @monitor
         end
         progress_monitor = Log::ProgressBar.new_bar(size, :desc => desc)
       end

data/lib/rbbt/util/R.rb

@@ -41,7 +41,7 @@ source('#{UTIL}');
 
     if monitor
       #io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
-      io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true, :xvfb => true))
+      io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true, :xvfb => options[:xvfb]))
       while line = io.gets
         case monitor
         when Proc
@@ -52,7 +52,7 @@ source('#{UTIL}');
       end
       nil
     else
-      CMD.cmd('R --no-save --slave --quiet', options.merge(:in => cmd, :xvfb => true))
+      CMD.cmd('R --no-save --slave --quiet', options.merge(:in => cmd, :xvfb => options[:xvfb]))
     end
   end
 

data/lib/rbbt/util/cmd.rb

@@ -192,25 +192,47 @@ module CMD
 
       ConcurrentStream.setup sout, :pids => pids, :autojoin => no_wait, :no_fail => no_fail 
 
-      err_thread = Thread.new do
-        while line = serr.gets
-          bar.process(line) if bar
-          sout.log = line
-          Log.log "STDERR [#{pid}]: " +  line, stderr 
-        end if Integer === stderr and log
-        serr.close
+      if (Integer === stderr and log) || bar
+        err_thread = Thread.new do
+          while line = serr.gets
+            bar.process(line) if bar
+            sout.log = line
+            Log.log "STDERR [#{pid}]: " +  line, stderr if log
+          end 
+          serr.close
+        end
+      else
+        err_thread = Misc.consume_stream(serr, true)
       end
 
       sout.threads = [in_thread, err_thread, wait_thr].compact
 
       sout
     else
-      err = ""
-      err_thread = Thread.new do
-        while not serr.eof?
-          err << serr.gets if Integer === stderr
+
+      if bar
+        err = ""
+        err_thread = Thread.new do
+          while not serr.eof?
+            line = serr.gets 
+            bar.process(line) 
+            err << line if Integer === stderr and log
+          end
+          serr.close
         end
-        serr.close
+      elsif log and Integer === stderr
+        err = ""
+        err_thread = Thread.new do
+          while not serr.eof?
+            err << serr.gets 
+          end
+          serr.close
+        end
+      else
+        Misc.consume_stream(serr, true)
+        #serr.close 
+        err_thread = nil
+        err = ""
       end
 
       ConcurrentStream.setup sout, :pids => pids, :threads => [in_thread, err_thread].compact, :autojoin => no_wait, :no_fail => no_fail 
@@ -220,7 +242,11 @@ module CMD
 
       status = wait_thr.value
       if not status.success? and not no_fail
-        raise ProcessFailed.new "Command [#{pid}] #{cmd} failed with error status #{status.exitstatus}.\n#{err}"
+        if !err.empty?
+          raise ProcessFailed.new "Command [#{pid}] #{cmd} failed with error status #{status.exitstatus}.\n#{err}"
+        else
+          raise ProcessFailed.new "Command [#{pid}] #{cmd} failed with error status #{status.exitstatus}"
+        end
       else
         Log.log err, stderr if Integer === stderr and log
       end
@@ -263,11 +289,6 @@ module CMD
       if c == "\n"
         bar.process(line) if bar
         starting = true
-        #if pid
-        #  Log.logn "STDOUT [#{pid}]: ", level
-        #else
-        #  Log.logn "STDOUT: ", level
-        #end
         line = "" if bar
       end
     end 

data/lib/rbbt/util/log/progress/report.rb

@@ -12,32 +12,35 @@ module Log
     attr_accessor :history, :mean_max, :max_history
     def thr_msg
       if @history.nil?
-        @history ||= [[@ticks, Time.now] ]
+        @history ||= [[0, @start], [@ticks, Time.now] ]
       elsif @last_ticks != @ticks
         @history << [@ticks, Time.now]
-        max_history ||= case 
-                      when @ticks > 20
-                        count = @ticks - @last_count
-                        count = 1 if count == 0
-                        if @max
-                          times = @max / count
-                          num = times / 20
-                          num = 2 if num < 2
-                        else
-                          num = 10
+        max_history ||= begin
+                          max_history = case 
+                                        when @ticks > 20
+                                          count = @ticks - @last_count
+                                          count = 1 if count == 0
+                                          if @max
+                                            times = @max / count
+                                            num = times / 20
+                                            num = 2 if num < 2
+                                          else
+                                            num = 10
+                                          end
+                                          count * num
+                                        else
+                                          20
+                                        end
+                          max_history = 30 if max_history > 30
+                          max_history
                         end
-                        count * num
-                      else
-                        20
-                      end
-        max_history = 30 if max_history > 30
         @history.shift if @history.length > max_history
       end
 
       @last_ticks = @ticks
 
       @mean_max ||= 0
-      if @history.length > 2
+      if @history.length > 3
 
         sticks, stime = @history.first
         ssticks, sstime = @history[-3]

data/lib/rbbt/util/python.rb

@@ -3,10 +3,17 @@ require 'pycall/import'
 
 module RbbtPython
   extend PyCall::Import
+
+  def self.exec(script)
+    PyCall.exec(script)
+  end
+
   def self.run(mod = nil, imports = nil, &block)
     if mod
-      if imports
+      if Array === imports
         pyfrom mod, :import => imports
+      elsif Hash === imports
+        pyimport mod, imports
       else
         pyimport mod 
       end
@@ -17,8 +24,10 @@ module RbbtPython
 
   def self.run_log(mod = nil, imports = nil, severity = 0, severity_err = nil, &block)
     if mod
-      if imports
+      if Array === imports
         pyfrom mod, :import => imports
+      elsif Hash === imports
+        pyimport mod, imports
       else
         pyimport mod 
       end
@@ -31,8 +40,10 @@ module RbbtPython
 
   def self.run_log_stderr(mod = nil, imports = nil, severity = 0, &block)
     if mod
-      if imports
+      if Array === imports
         pyfrom mod, :import => imports
+      elsif Hash === imports
+        pyimport mod, imports
       else
         pyimport mod 
       end
@@ -49,4 +60,14 @@ module RbbtPython
     end
   end
 
+  def self.add_paths(paths)
+    self.run 'sys' do
+      paths.each do |path|
+        sys.path.append path
+      end
+    end
+  end
+
+  RbbtPython.add_paths Rbbt.python.find_all
+  RbbtPython.pyimport "rbbt"
 end