rbbt-util 6.0.4 → 6.0.5

data/lib/rbbt/knowledge_base.rb

@@ -1,35 +1,38 @@
-require 'rbbt/annotations'
-require 'rbbt/association'
-require 'rbbt/association/item'
-require 'rbbt/knowledge_base/entity'
-require 'rbbt/knowledge_base/query'
-require 'rbbt/knowledge_base/syndicate'
+require_relative 'refactor'
+Rbbt.require_instead 'scout/knowledge_base'
 
-class KnowledgeBase
-
-  attr_accessor :namespace, :dir, :databases, :indices, :registry, :format, :entity_options
-  def initialize(dir, namespace = nil)
-    @dir = Path.setup(dir.dup)
-
-    @namespace = namespace
-    @format = IndiferentHash.setup({})
-
-    @registry ||= IndiferentHash.setup({})
-    @entity_options = IndiferentHash.setup({})
-
-    @indices = IndiferentHash.setup({})
-    @databases = IndiferentHash.setup({})
-    @identifiers = IndiferentHash.setup({})
-    @fields = {}
-    @descriptions = {}
-    @databases = {}
-  end
-
-  def self.load(dir)
-    KnowledgeBase.new dir
-  end
-
-  def setup(name, matches, reverse = false)
-    AssociationItem.setup matches, self, name, reverse
-  end
-end
+#require 'rbbt/annotations'
+#require 'rbbt/association'
+#require 'rbbt/association/item'
+#require 'rbbt/knowledge_base/entity'
+#require 'rbbt/knowledge_base/query'
+#require 'rbbt/knowledge_base/syndicate'
+#
+#class KnowledgeBase
+#
+#  attr_accessor :namespace, :dir, :databases, :indices, :registry, :format, :entity_options
+#  def initialize(dir, namespace = nil)
+#    @dir = Path.setup(dir.dup)
+#
+#    @namespace = namespace
+#    @format = IndiferentHash.setup({})
+#
+#    @registry ||= IndiferentHash.setup({})
+#    @entity_options = IndiferentHash.setup({})
+#
+#    @indices = IndiferentHash.setup({})
+#    @databases = IndiferentHash.setup({})
+#    @identifiers = IndiferentHash.setup({})
+#    @fields = {}
+#    @descriptions = {}
+#    @databases = {}
+#  end
+#
+#  def self.load(dir)
+#    KnowledgeBase.new dir
+#  end
+#
+#  def setup(name, matches, reverse = false)
+#    AssociationItem.setup matches, self, name, reverse
+#  end
+#end

data/lib/rbbt/util/migrate.rb

@@ -2,7 +2,7 @@ module Rbbt
 
   def self.migrate_source_paths(path, resource = Rbbt, source = nil)
     if source
-      lpath, *paths = Misc.ssh_run(source, <<-EOF).split("\n")
+      lpath, *paths = SSHLine.ruby(source, <<-EOF).split("\n")
 require 'rbbt-util'
 path = "#{path}"
 if Open.exists?(path)
@@ -11,7 +11,7 @@ else
   path = Path.setup(path)
 end
 puts path
-puts path.glob_all.collect{|p| File.directory?(p) ? p + "/" : p } * "\n"
+puts path.find_all.collect{|p| File.directory?(p) ? p + "/" : p } * "\n"
       EOF
 
       [path, paths.collect{|p| [source, p] * ":"}, lpath]
@@ -36,7 +36,7 @@ puts path.glob_all.collect{|p| File.directory?(p) ? p + "/" : p } * "\n"
 
   def self.migrate_target_path(path, search_path = 'user', resource = Rbbt, target = nil)
     if target
-      Misc.ssh_run(target, <<-EOF).split("\n").first
+      SSHLine.ruby(target, <<-EOF).split("\n").first
 require 'rbbt-util'
 path = "#{path}"
 resource = #{resource.to_s}

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

@@ -94,7 +94,7 @@ job = wf.job(task, jobname, job_inputs)
 STDOUT.write res.to_json
       EOF
 
-      json = Misc.ssh_run(server, script)
+      json = SSHLine.ruby(server, script)
       Log.debug "JSON (#{ url }): #{json}" if RBBT_DEBUG_REMOTE_JSON
       JSON.parse(json)
     end
@@ -107,7 +107,7 @@ STDOUT.write res.to_json
 STDOUT.write res
       EOF
 
-      Misc.ssh_run(server, script)
+      SSHLine.ruby(server, script)
     end
 
     def self.post_job(url, inputs_id, jobname = nil)
@@ -119,7 +119,7 @@ STDOUT.write res
 job.init_info
 STDOUT.write job.path
       EOF
-      Misc.ssh_run(server, script)
+      SSHLine.ruby(server, script)
     end
 
     def self.run_job(url, input_id, jobname = nil)
@@ -133,7 +133,7 @@ job.clean if job.error? and job.recoverable_error?
 job.run unless job.done? || job.error?
 STDOUT.write job.path
       EOF
-      Misc.ssh_run(server, script)
+      SSHLine.ruby(server, script)
     end
 
     def self.run_batch_job(url, input_id, jobname = nil, batch_options = {})
@@ -149,7 +149,7 @@ job.clean if job.error? and job.recoverable_error?
 HPC::BATCH_MODULE.run_job(job, batch_options) unless job.done? || job.error?
 STDOUT.write job.path
       EOF
-      Misc.ssh_run(server, script)
+      SSHLine.ruby(server, script)
     end
 
     def self.orchestrate_batch_job(url, input_id, jobname = nil, batch_options = {})
@@ -165,7 +165,7 @@ job.clean if job.error? and job.recoverable_error?
 HPC::BATCH_MODULE.orchestrate_job(job, batch_options) unless job.done? || job.error?
 STDOUT.write job.path
       EOF
-      Misc.ssh_run(server, script)
+      SSHLine.ruby(server, script)
     end
 
     def self.clean(url, input_id, jobname = nil)
@@ -175,7 +175,7 @@ STDOUT.write job.path
       script +=<<-EOF
 job.clean
       EOF
-      Misc.ssh_run(server, script)
+      SSHLine.ruby(server, script)
     end
 
     def self.upload_inputs(server, inputs, input_types, input_id)
@@ -234,7 +234,7 @@ job.clean
       all_deps.each do |dep,jobs|
         next if dep.done?
         next if job_list.include?(dep)
-        Log.medium "Producing #{dep.workflow}:#{dep.short_path} dependency for #{Misc.fingerprint jobs}"
+        Log.medium "Producing #{dep.workflow}:#{dep.short_path} dependency for #{Log.fingerprint jobs}"
         dep.produce
         missing_deps << dep
       end if produce_dependencies
@@ -243,7 +243,7 @@ job.clean
 
       #migrate_dependencies = all_deps.keys.collect{|d| [d] + d.rec_dependencies + d.input_dependencies }.flatten.select{|d| d.done? }.collect{|d| d.path }
       migrate_dependencies = all_deps.keys.collect{|d| [d] + 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 }" 
+      Log.low "Migrating #{migrate_dependencies.length} dependencies from #{Log.fingerprint job_list} to #{ server }" 
       Step.migrate(migrate_dependencies, search_path, :target => server) if migrate_dependencies.any?
     end
 
@@ -287,7 +287,7 @@ job.clean
 
       if options[:migrate]
         rjob.produce
-        Step.migrate(Rbbt.identify(job.path), 'user', :source => server) 
+        Step.migrate(Path.identify(job.path), 'user', :source => server) 
       end
 
       rjob
@@ -337,7 +337,7 @@ job.clean
       if options[:migrate]
         rjobs_job.each do |rjob,job|
           rjob.produce
-          Step.migrate(Rbbt.identify(job.path), 'user', :source => server) 
+          Step.migrate(Path.identify(job.path), 'user', :source => server) 
         end
       end
 

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

@@ -289,7 +289,7 @@ class RemoteStep < Step
 
     stream = true if res.respond_to? :read
     join unless stream
-    result_type ||= self.result_type
+    result_type ||= self.type
 
     case result_type.to_sym
     when :string

data/lib/rbbt/workflow/remote_workflow.rb

@@ -5,7 +5,8 @@ class RemoteWorkflow
 
   attr_accessor :url, :name, :exec_exports, :synchronous_exports, :asynchronous_exports, :stream_exports
 
-  def initialize(url, name)
+  def initialize(url, name = nil)
+    name = File.basename(url) if name.nil?
     Log.debug{ "Loading remote workflow #{ name }: #{ url }" }
     @url, @name = url, name
 

data/lib/rbbt.rb

@@ -3,7 +3,7 @@ $LOAD_PATH.unshift File.join(__dir__, '../../lib')
 
 require 'scout/path'
 require 'scout/resource'
-Path.add_path :rbbt_util, File.join(Path.caller_lib_dir(__FILE__), "{TOPLEVEL}/{SUBPATH}")
+Path.add_path :rbbt_util_lib, File.join(Path.caller_lib_dir(__FILE__), "{TOPLEVEL}/{SUBPATH}")
 module Rbbt
   extend Resource
 

data/share/rbbt_commands/hpc/list

@@ -338,7 +338,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
       step_path = step_line.split(": ").last.strip
       step = Step.new step_path
       has_bar = false
-      (step.rec_dependencies + [step]).reverse.each do |j|
+      (step.rec_dependencies + [step]).to_a.reverse.each do |j|
         next if j.done? 
         if j.file(:progress).exists?
           bar = Log::ProgressBar.new 

data/share/rbbt_commands/lsf/list

@@ -338,7 +338,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
       step_path = step_line.split(": ").last.strip
       step = Step.new step_path
       has_bar = false
-      (step.rec_dependencies + [step]).reverse.each do |j|
+      (step.rec_dependencies + [step]).to_a.reverse.each do |j|
         next if j.done? 
         if j.file(:progress).exists?
           bar = Log::ProgressBar.new 

data/share/rbbt_commands/pbs/list

@@ -338,7 +338,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
       step_path = step_line.split(": ").last.strip
       step = Step.new step_path
       has_bar = false
-      (step.rec_dependencies + [step]).reverse.each do |j|
+      (step.rec_dependencies + [step]).to_a.reverse.each do |j|
         next if j.done? 
         if j.file(:progress).exists?
           bar = Log::ProgressBar.new 

data/share/rbbt_commands/resource/find

@@ -74,7 +74,7 @@ end if resource
 
 path = (resource || Rbbt)[path]
 
-if where.nil? || where == 'all' || path.search_paths.include?(where.to_sym)
+if where.nil? || where == 'all' || path.map_maps.include?(where.to_sym)
   location = path.find(where)
 
   if Array === location

data/share/rbbt_commands/slurm/list

@@ -338,7 +338,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
       step_path = step_line.split(": ").last.strip
       step = Step.new step_path
       has_bar = false
-      (step.rec_dependencies + [step]).reverse.each do |j|
+      (step.rec_dependencies + [step]).to_a.reverse.each do |j|
         next if j.done? 
         if j.file(:progress).exists?
           bar = Log::ProgressBar.new 

data/share/rbbt_commands/system/status

@@ -36,7 +36,7 @@ inputs = (options[:inputs] || "").split(",")
 info_fields = (options[:info_fields] || "").split(",")
 
 def pid_msg(pid)
-  color = if pid and Misc.pid_exists? pid
+  color = if pid and Misc.pid_alive? pid
             :green
           else
             :red
@@ -211,7 +211,7 @@ workflows.sort.each do |workflow,tasks|
         status = :missing if status == :done and not (Open.exist?(file) && ! Open.broken_link?(file))
         status = :broken if Open.broken_link?(file)
         status = status.to_s
-        if status != "done" and pid and not Misc.pid_exists?(pid)
+        if status != "done" and pid and not Misc.pid_alive?(pid)
           if File.exist? file
             status << Log.color(:red, " (out of sync)") 
           else

data/share/rbbt_commands/workflow/info

@@ -56,7 +56,7 @@ def status_msg(status)
 end
 
 def pid_msg(pid, done = false)
-  color = if pid and (done or Misc.pid_exists? pid)
+  color = if pid and (done or Misc.pid_alive? pid)
             :green
           else
             :red

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 6.0.4
+  version: 6.0.5
 platform: ruby
 authors:
 - Miguel Vazquez
 bindir: bin
 cert_chain: []
-date: 2025-03-31 00:00:00.000000000 Z
+date: 2025-06-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: scout-gear
@@ -374,6 +374,7 @@ files:
 - lib/rbbt/workflow/util/orchestrator.rb
 - lib/rbbt/workflow/util/provenance.rb
 - lib/rbbt/workflow/util/trace.rb
+- python/rbbt/'/Users/miki/config/tmp/undodir'/%Users%miki%git%rbbt-util%python%rbbt%__init__.py
 - python/rbbt/__init__.py
 - python/rbbt/workflow.py
 - python/rbbt/workflow/remote.py
@@ -517,7 +518,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.6.5
+rubygems_version: 3.6.6
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files: []