rbbt-util 5.38.0 → 5.39.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: 12c5401cf3ecb8495ba5c21d0f3d3f35c741c1c335ffa0d3a7d3ee498f6daae8
+  data.tar.gz: 344f30b6651a272f5e9665d3ec6383b4a1d62ba7c64c7889af5cfc573b2285ac
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+  data.tar.gz: 511c72833b4a8ef747e574376d44a3b4799f96f6a922301d3f405df1cd7aac79a2d2de388075aaab4fc3ef6962ee66ded3de8684227912399f41f7ad00006148

data/lib/rbbt/annotations.rb

@@ -154,6 +154,8 @@ module Annotated
 
   def self.purge(object)
     case object
+    when Path
+      object
     when String
       object.respond_to?(:clean_annotations) ?
         object.clean_annotations : 

data/lib/rbbt/persist.rb

@@ -115,7 +115,7 @@ module Persist
     begin
       case (type || :marshal).to_sym
       when :path
-        path
+        Path.setup(Open.read(path).strip)
       when :nil
         nil
       when :boolean
@@ -172,7 +172,7 @@ module Persist
 
     case (type || :marshal).to_sym
     when :path
-      nil
+      Open.write(path, content)
     when :nil
       nil
     when :boolean

data/lib/rbbt/resource.rb

@@ -350,13 +350,15 @@ url='#{url}'
   end
 
   def identify(path)
+    return path unless path.start_with?("/")
     path = File.expand_path(path)
     path += "/" if File.directory?(path)
     resource ||= Rbbt
-    locations = (Path::STANDARD_SEARCH + resource.search_order + resource.search_paths.keys)
+    locations = (Path::STANDARD_SEARCH + resource.search_order + resource.search_paths.keys).uniq
     locations -= [:current, "current"]
     locations << :current
     search_paths = IndiferentHash.setup(resource.search_paths)
+    choices = []
     locations.uniq.each do |name|
       pattern = search_paths[name]
       pattern = resource.search_paths[pattern] while Symbol === pattern
@@ -370,12 +372,19 @@ url='#{url}'
         "(?:/(?<REST>.*))?/?$"
         if m = path.match(regexp) 
           if ! m.named_captures.include?("PKGDIR") || m["PKGDIR"] == resource.pkgdir
-            return self[m["TOPLEVEL"]][m["SUBPATH"]][m["REST"]]
+            unlocated = ([m["TOPLEVEL"],m["SUBPATH"],m["REST"]] * "/")
+            unlocated.gsub!(/\/+/,'/')
+            if self.subdir && ! self.subdir.empty?
+              subdir = self.subdir
+              subdir += "/" unless subdir.end_with?("/")
+              unlocated[subdir] = ""
+            end
+            choices << self.annotate(unlocated)
           end
         end
       end
     end
-    nil
+    choices.sort_by{|s| s.length }.first
   end
 end
 

data/lib/rbbt/tsv/excel.rb

@@ -154,7 +154,11 @@ module TSV
       sheet1 = book.create_worksheet 
       sheet1.name = sheet if sheet
 
-      sheet1.row(0).concat fields
+      if fields
+        sheet1.row(0).concat fields if fields
+      else
+        sheet1.row(0).concat ["No field info"]
+      end
 
       rows.each_with_index do |cells,i|
         sheet1.row(i+1).concat cells

data/lib/rbbt/tsv/parser.rb

@@ -130,12 +130,12 @@ module TSV
       keys = parts[key_position].split(@sep2, -1)
       values = case
                when field_positions.nil?
-                parts.tap{|o| o.delete_at key_position}
+                 parts.tap{|o| o.delete_at key_position}
                when field_positions.empty?
                  []
                else
                  parts.values_at *field_positions
-               end.collect{|value| (value.nil? || value.empty?) ? [] : value.split(@sep2, -1) }
+               end.collect{|value| (value.nil? || value.empty?) ? [""] : value.split(@sep2, -1) }
       [keys, values]
     end
 

data/lib/rbbt/tsv/util.rb

@@ -400,5 +400,9 @@ module TSV
     end
     index
   end
+
+  def merge(other)
+    self.annotate(super(other))
+  end
 end
 

data/lib/rbbt/util/cmd.rb

@@ -22,13 +22,17 @@ module CMD
     return tool.to_s unless TOOLS[tool]
 
     @@init_cmd_tool ||= IndiferentHash.setup({})
+
+    claim, test, block, cmd = TOOLS[tool]
+    cmd = tool.to_s if cmd.nil?
+
     if !@@init_cmd_tool[tool]
-      claim, test, block, cmd = TOOLS[tool]
+
       begin
         if test
           CMD.cmd(test + " ")
         else
-          CMD.cmd("#{tool} --help")
+          CMD.cmd("#{cmd} --help")
         end
       rescue
         if claim
@@ -41,7 +45,7 @@ module CMD
       version = nil
       ["--version", "-version", "--help", ""].each do |f|
         begin
-          version_txt += CMD.cmd("#{tool} #{f} 2>&1", :nofail => true).read
+          version_txt += CMD.cmd("#{cmd} #{f} 2>&1", :nofail => true).read
           version = Misc.scan_version_text(version_txt, tool)
           break if version
         rescue
@@ -54,7 +58,7 @@ module CMD
       return cmd if cmd
     end
 
-    tool.to_s
+    cmd
   end
 
   def self.versions

data/lib/rbbt/util/concurrency/processes.rb

@@ -245,7 +245,7 @@ class RbbtProcessQueue
         end
       end if @callback_queue
 
-      @callback_thread.report_on_exception = false
+      @callback_thread.report_on_exception = false if @callback_thread
       
     end
 

data/lib/rbbt/util/migrate.rb

@@ -1,6 +1,5 @@
 module Rbbt 
 
-  prepare_for_execution(job)
   def self.migrate_source_paths(path, resource = Rbbt, source = nil)
     if source
       lpath, *paths = Misc.ssh_run(source, <<-EOF).split("\n")
@@ -60,7 +59,7 @@ puts resource[path].find(search_path)
     test_str = options[:test] ? '-nv' : ''
 
     real_paths.each do |source_path|
-      Log.medium "Migrating #{source_path} #{options[:files].length} files to #{target} - #{Misc.fingerprint(options[:files])}}" if options[:files]
+      Log.low "Migrating #{source_path} #{options[:files].length} files to #{target} - #{Misc.fingerprint(options[:files])}}" if options[:files]
       if File.directory?(source_path) || source_path.end_with?("/")
         source_path += "/" unless source_path.end_with? '/'
         target += "/" unless target.end_with? '/'

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

@@ -432,8 +432,6 @@ def self.add_libdir(dir=nil)
 
   def self.ssh_run(server, script = nil)
     require 'rbbt/util/ssh'
-    Log.debug "Run ssh script in #{server}:\n#{script}"
-
     SSHLine.ruby(server, script)
   end
 

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

@@ -27,6 +27,9 @@ module Misc
 
   def self.format_paragraph(text, size = 80, indent = 0, offset = 0)
     i = 0
+    offset = 0 if offset.nil?
+    indent = 0 if indent.nil?
+    size = 80 if size.nil?
     size = size + offset + indent
     re = /((?:\n\s*\n\s*)|(?:\n\s*(?=\*)))/
       text.split(re).collect do |paragraph|

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

@@ -22,18 +22,21 @@ module IndiferentHash
     @_default ||= self.default or self.default_proc
   end
 
-  def [](key)
-    res = super(key) 
+  def [](key, *args)
+    res = super(key, *args) 
+    res = IndiferentHash.setup(res) if Hash === res
     return res unless res.nil? or (_default? and not keys.include? key)
 
     case key
     when Symbol, Module
-      super(key.to_s)
+      res = super(key.to_s, *args)
     when String
-      super(key.to_sym)
-    else
-      res
+      res = super(key.to_sym, *args)
     end
+
+    res = IndiferentHash.setup(res) if Hash === res
+
+    res
   end
 
   def values_at(*key_list)

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

@@ -275,7 +275,6 @@ module Misc
 
 
   def self.step_file?(path)
-    return true if defined?(Step) && Step === path.resource
     return false unless path =~ /\.files(?:\/|$)/
     parts = path.split("/")
     job = parts.select{|p| p =~ /\.files$/}.first
@@ -283,9 +282,19 @@ module Misc
       i = parts.index job
       begin
         workflow, task = parts.values_at i - 2, i - 1
-        Workflow.require_workflow workflow
+        _loaded = false
+        begin
+          Kernel.const_get(workflow)
+        rescue 
+          if ! _loaded
+            Workflow.require_workflow workflow 
+            _loaded = true
+            retry
+          end
+          raise $!
+        end
         #return Kernel.const_get(workflow).tasks.include? task.to_sym
-        return true
+        return parts[i-2..-1] * "/"
       rescue
         Log.exception $!
       end
@@ -293,6 +302,8 @@ module Misc
     false
   end
 
+  RBBT_IDENTIFY_PATH = ENV["RBBT_IDENTIFY_PATH"] != 'false'
+
   def self.obj2str(obj)
     _obj = obj
     obj = Annotated.purge(obj) if Annotated === obj
@@ -310,18 +321,21 @@ module Misc
             'false'
           when Hash
             "{"<< obj.collect{|k,v| obj2str(k) + '=>' << obj2str(v)}*"," << "}"
-          when (defined?(Path) and Path)
+          when (defined?(Path) && Path)
             if defined?(Step) && Open.exists?(Step.info_file(obj))
               obj2str(Workflow.load_step(obj))
-            elsif step_file?(obj)
-              "Step file: " + obj
+            elsif step_file_path = step_file?(obj)
+              "Step file: " + step_file_path
             else
               if obj.exists?
+                obj = (obj.resource || Rbbt).identify obj if RBBT_IDENTIFY_PATH
                 if obj.directory?
                   files = obj.glob("**/*")
-                  "directory: #{Misc.fingerprint(files)}"
-                else
+                  "directory: #{Misc.fingerprint(files.collect{|f| Misc.path_relative_to(obj.find, f)}.sort)}"
+                elsif obj.located?
                   "file: " << Open.realpath(obj) << "--" << mtime_str(obj)
+                else
+                  "path: " << obj 
                 end
               else
                 obj + " (file missing)"
@@ -441,6 +455,7 @@ module Misc
   end
 
   def self.scan_version_text(text, cmd = nil)
+    text = Misc.fixutf8 text
     cmd = "NOCMDGIVE" if cmd.nil? || cmd.empty?
     text.split("\n").each do |line|
       next unless line =~ /\W#{cmd}\W/i

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

@@ -111,7 +111,7 @@ module Misc
     html = if content.nil?
       "<#{ tag }#{attr_str}/>"
     else
-      "<#{ tag }#{attr_str}>#{ content }</#{ tag }>"
+      "<#{ tag }#{attr_str}>#{ content.to_s }</#{ tag }>"
     end
 
     html

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

@@ -318,9 +318,9 @@ module Misc
           Open.mkdir dir unless Open.exists?(dir)
           into_path, into = into, Open.open(into, :mode => 'w') 
         end
-        into.sync = true if IO === into
+        #into.sync = true if IO === into
         into_close = false unless into.respond_to? :close
-        io.sync = true
+        #io.sync = true
 
         begin
           while c = io.readpartial(BLOCK_SIZE)
@@ -402,7 +402,7 @@ module Misc
           when (IO === content or StringIO === content or File === content)
 
             Open.write(tmp_path) do |f|
-              f.sync = true
+              #f.sync = true
               while block = content.read(BLOCK_SIZE)
                 f.write block
               end 

data/lib/rbbt/util/open.rb

@@ -240,7 +240,6 @@ module Open
   end
 
   def self.find_repo_dir(file)
-    return nil
     self.repository_dirs.each do |dir|
       dir = dir + '/' unless dir.chars[-1] == "/"
 
@@ -531,16 +530,22 @@ module Open
 
   def self.gzip?(file)
     file = file.find if Path === file
+    file = file.filename if File === file
+    return false unless String === file
     !! (file =~ /\.gz$/)
   end
 
   def self.bgzip?(file)
     file = file.find if Path === file
+    file = file.filename if File === file
+    return false unless String === file
     !! (file =~ /\.bgz$/)
   end
 
   def self.zip?(file)
     file = file.find if Path === file
+    file = file.filename if File === file
+    return false unless String === file
     !! (file =~ /\.zip$/)
   end
 

data/lib/rbbt/util/ssh.rb

@@ -9,7 +9,7 @@ class SSHLine
     @ssh = Net::SSH.start(@host, @user)
 
     @ch = @ssh.open_channel do |ch|
-      ch.exec 'bash'
+      ch.exec 'bash -l'
     end
 
     @ch.on_data do |_,data|
@@ -37,7 +37,7 @@ class SSHLine
     @complete_output = true
   end
 
-  def cmd(command)
+  def run(command)
     send_cmd(command)
     @ssh.loop{ ! @complete_output}
     if @exit_status.to_i == 0
@@ -51,6 +51,7 @@ class SSHLine
     @output = ""
     @complete_output = false
     cmd = "ruby -e \"#{script.gsub('"','\\"')}\"\n"
+    Log.debug "Running ruby on #{@host}:\n#{ script }"
     @ch.send_data(cmd)
     @ch.send_data("echo DONECMD: $?\n")
     @ssh.loop{ !@complete_output }
@@ -61,16 +62,57 @@ class SSHLine
     end
   end
 
+  def rbbt(script)
+    rbbt_script =<<-EOF
+require 'rbbt-util'
+require 'rbbt/workflow'
+
+  res = begin
+      old_stdout = STDOUT.dup; STDOUT.reopen(STDERR)
+#{script}
+      ensure
+        STDOUT.reopen(old_stdout)
+      end
+
+  puts Marshal.dump(res)
+    EOF
+
+    m = ruby(rbbt_script)
+    Marshal.load m
+  end
+
+  def workflow(workflow, script)
+    preamble =<<-EOF
+wf = Workflow.require_workflow('#{workflow}')
+    EOF
+
+    rbbt(preamble + "\n" + script)
+  end
+
   @connections = {}
   def self.open(host, user = nil)
     @connections[[host, user]] ||= SSHLine.new host, user
   end
 
-  def self.run(server, cmd)
-    open(server).cmd(cmd)
+  def self.run(server, cmd, options = nil)
+    cmd = cmd * " " if Array === cmd
+    cmd += " " + CMD.process_cmd_options(options) if options
+    open(server).run(cmd)
   end
 
   def self.ruby(server, script)
     open(server).ruby(script)
   end
+
+  def self.rbbt(server, script)
+    open(server).rbbt(script)
+  end
+
+  def self.workflow(server, workflow, script)
+    open(server).workflow(workflow, script)
+  end
+
+  def self.command(server, command, argv = [], options = nil)
+    run(server, [command] + argv, options)
+  end
 end

data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb

@@ -99,7 +99,7 @@ STDOUT.write res.to_json
       JSON.parse(json)
     end
 
-    def self.get_raw(url, params)
+    def self.get_raw(url, params = {})
       server, path = parse_url(url)
       script = path_script(path)
 
@@ -224,7 +224,7 @@ job.clean
     def self.upload_dependencies(job_list, server, search_path = 'user', produce_dependencies = false)
       server, path = parse_url(server) if server =~ /^ssh:\/\//
 
-      job_list = [job] unless Array === job_list
+      job_list = [job_list] unless Array === job_list
 
       all_deps = {}
       if produce_dependencies
@@ -242,7 +242,6 @@ job.clean
           all_deps[dep] << job
         end
       end
-      iif all_deps
 
       missing_deps = []
       all_deps.each do |dep,jobs|
@@ -250,11 +249,11 @@ job.clean
         Log.medium "Producing #{dep.workflow}:#{dep.short_path} dependency for #{Misc.fingerprint jobs}"
         dep.run(true)
         missing_deps << dep
-      end 
+      end if produce_dependencies
       Step.wait_for_jobs missing_deps
 
-      migrate_dependencies = all_deps.keys.select{|d| d.done? }.collect{|d| d.path }
-      Log.medium "Migrating #{migrate_dependencies.length} dependencies from #{Misc.fingerprint job_list} to #{ server }" 
+      migrate_dependencies = all_deps.keys.collect{|d| [d] + d.rec_dependencies + d.input_dependencies }.flatten.select{|d| d.done? }.collect{|d| d.path }
+      Log.low "Migrating #{migrate_dependencies.length} dependencies from #{Misc.fingerprint job_list} to #{ server }" 
       Step.migrate(migrate_dependencies, search_path, :target => server) if migrate_dependencies.any?
     end
 
@@ -312,7 +311,7 @@ job.clean
         
         workflow_name = job.workflow.to_s
         remote_workflow = RemoteWorkflow.new("ssh://#{server}:#{workflow_name}", "#{workflow_name}")
-        inputs = job.recursive_inputs.to_hash.slice(*job.real_inputs.map{|i| i.to_s})
+        inputs = IndiferentHash.setup(job.recursive_inputs.to_hash).slice(*job.real_inputs.map{|i| i.to_s})
         Log.medium "Relaying dependency #{job.workflow}:#{job.short_path} to #{server} (#{inputs.keys * ", "})"
 
         rjob = remote_workflow.job(job.task_name.to_s, job.clean_name, inputs)
@@ -331,6 +330,7 @@ job.clean
       if options[:migrate]
         rjobs_job.each do |rjob,job|
           rjob.produce
+          iif [:migrate, job]
           Step.migrate(Rbbt.identify(job.path), 'user', :source => server) 
         end
       end

data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb

@@ -1,6 +1,6 @@
 class RemoteStep
   module SSH
-    attr_accessor :override_dependencies, :run_type, :slurm_options
+    attr_accessor :override_dependencies, :run_type, :slurm_options, :produce_dependencies
 
     def init_job(cache_type = nil, other_params = {})
       return self if @url
@@ -52,11 +52,12 @@ class RemoteStep
     end
     
     def _run
-      RemoteWorkflow::SSH.upload_dependencies(self, @server)
+      RemoteWorkflow::SSH.upload_dependencies(self, @server, 'user', @produce_dependencies)
       RemoteWorkflow::SSH.run_job(File.join(base_url, task.to_s), @input_id, @base_name)
     end
 
     def _run_slurm
+      RemoteWorkflow::SSH.upload_dependencies(self, @server, 'user', @produce_dependencies)
       RemoteWorkflow::SSH.run_slurm_job(File.join(base_url, task.to_s), @input_id, @base_name, @slurm_options || {})
     end
 
@@ -115,7 +116,7 @@ class RemoteStep
         select{|i| Step === i || (defined?(RemoteStep) && RemoteStep === i) } + 
         inputs.values.flatten.
         select{|dep| Path === dep && Step === dep.resource }.
-        select{|dep| ! dep.resource.started? }. # Ignore input_deps already started
+        #select{|dep| ! dep.resource.started? }. # Ignore input_deps already started
         collect{|dep| dep.resource }
     end
   end

data/lib/rbbt/workflow/remote_workflow/remote_step.rb

@@ -188,6 +188,7 @@ class RemoteStep < Step
   end
 
   def file(file)
+    init_job
     @adaptor.get_raw(File.join(url, 'file', file.to_s))
   end
 

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

@@ -107,7 +107,7 @@ class Step
       canfail = ComputeDependency === job && job.canfail?
     end
 
-    raise_dependency_error(job) if job.error? and not canfail
+    Step.raise_dependency_error(job) if job.error? and not canfail
   end
 
   def self.raise_dependency_error(job)
@@ -145,11 +145,11 @@ class Step
   end
 
   def input_dependencies
-    @input_dependencies ||= recursive_inputs.flatten.
+    @input_dependencies ||= recursive_inputs(true).flatten.
       select{|i| Step === i || (defined?(RemoteStep) && RemoteStep === i) } + 
-      recursive_inputs.flatten.
+      recursive_inputs(true).flatten.
       select{|dep| Path === dep && Step === dep.resource }.
-      select{|dep| ! dep.resource.started? }. # Ignore input_deps already started
+      #select{|dep| ! dep.resource.started? }. # Ignore input_deps already started
       collect{|dep| dep.resource }
   end
 
@@ -193,7 +193,7 @@ class Step
 
       if dependency.error?
         log_dependency_exec(dependency, :error)
-        raise_dependency_error dependency 
+        Step.raise_dependency_error dependency 
       end
 
       if dependency.streaming?
@@ -382,7 +382,7 @@ class Step
 
   def run_dependencies
 
-    rec_dependencies = self.rec_dependencies(true) + input_dependencies
+    rec_dependencies = self.rec_dependencies(true) + input_dependencies.reject{|d| d.started? }
 
     return if rec_dependencies.empty?
 
@@ -402,7 +402,7 @@ class Step
       seen_paths << step.path
 
       begin
-        Step.prepare_for_execution(step) unless step == self
+        Step.prepare_for_execution(step) unless step == self 
       rescue DependencyError, DependencyRbbtException
         raise $! unless canfail_paths.include? step.path
       end
@@ -423,6 +423,7 @@ class Step
 
     produced = []
     (dependencies + input_dependencies).each do |dep|
+      next if dep.started?
       next unless ComputeDependency === dep
       if dep.compute == :produce
         dep.produce 
@@ -580,7 +581,6 @@ class Step
   #but dependencies are absent, meanining that the file could have been dropped
   #in
   def rec_dependencies(connected = false, seen = [])
-
     # A step result with no info_file means that it was manually
     # placed. In that case, do not consider its dependencies
     return [] if ! (defined? WorkflowRemoteClient && WorkflowRemoteClient::RemoteStep === self) && ! Open.exists?(self.info_file) && Open.exists?(self.path.to_s) 
@@ -598,7 +598,7 @@ class Step
       #next if self.done? && Open.exists?(info_file) && info[:dependencies] && info[:dependencies].select{|task,name,path| path == step.path }.empty?
       next if archived_deps.include? step.path
       next if seen.include? step
-      next if self.done? && connected && ! updatable?
+      next if step.done? && connected && ! step.updatable?
 
       r = step.rec_dependencies(connected, new_dependencies)
       new_dependencies.concat r

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

@@ -132,7 +132,7 @@ class Step
       messages
     else
       set_info(:messages, []) if self.respond_to?(:set_info)
-    end
+    end || []
   end
 
   def message(message)

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

@@ -49,9 +49,9 @@ module Workflow
         when :nofile
           inputs[input.to_sym]  = Open.realpath(file)
         when :path_array
-          inputs[input.to_sym]  = Open.read(file).strip.split("\n")
+          inputs[input.to_sym]  = Open.read(file).strip.split("\n").collect{|p| Path.setup(p) }
         when :path
-          inputs[input.to_sym]  = Open.read(file).strip.split("\n").first
+          inputs[input.to_sym]  = Path.setup(Open.read(file).strip.split("\n").first)
         when :io
           inputs[input.to_sym] = Open.open(Open.realpath(file))
         when :io_array
@@ -156,7 +156,7 @@ class Step
         path = path + '.as_path'
       end
     when String
-      if Misc.is_filename?(value, false)
+      if Misc.is_filename?(value, true)
         value = value.dup
         value.extend Path
         return save_input(name, value, type, dir)
@@ -175,7 +175,7 @@ class Step
           path = path + '.as_path_array'
         end
       when String
-        if Misc.is_filename?(value.first, false)
+        if Misc.is_filename?(value.first, true)
           path = path + '.as_path_array'
         end
       when IO
@@ -251,5 +251,4 @@ class Step
 
     inputs.keys
   end
-
 end