rbbt-util 6.0.3 → 6.0.5

data/share/rbbt_commands/workflow/retry

@@ -0,0 +1,43 @@
+#!/usr/bin/env ruby
+
+require 'rbbt/workflow'
+
+require 'rbbt-util'
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+Retry a failed job
+
+$ rbbt workflow retry <job-path>
+
+Does not retry if job is done unless clean is specified
+
+-h--help Help
+-cl--clean Clean the job
+-rcl--recursive_clean Recursively clean the job
+EOF
+
+SOPT.usage if options[:help]
+
+file = ARGV.shift
+def get_step(file)
+  file = file.sub(/\.(info|files)/,'')
+  step = Workflow.load_step file
+  step
+end
+
+step = get_step(file)
+inputs = step.recursive_inputs
+
+step.clean if options[:clean]
+step.recursive_clean if options[:recursive_clean]
+
+if ! step.done?
+  wf = Workflow.require_workflow step.workflow
+  job = wf.job(step.task_name, step.clean_name, inputs.to_hash)
+  job.run
+end
+

data/share/rbbt_commands/workflow/server

@@ -140,7 +140,7 @@ TmpFile.with_file do |app_dir|
 
       begin
         Rack::Server.start(options)
-      rescue LoadError
+      rescue LoadError, Exception
         require 'rackup'
 
         begin

data/share/rbbt_commands/workflow/task

@@ -535,12 +535,14 @@ begin
     end
   end
 
-  if do_fork
+  if do_fork || detach
     ENV["SCOUT_NO_PROGRESS"] = "true"
     if detach
       job.fork
       Process.detach job.pid if job.pid
-      puts Log.color(:magenta, "Issued: ") + Log.color(:magenta, job.pid ? job.pid.to_s : 'no pid') + ' -- ' + job.path
+      Log.info(Log.color(:magenta, "Issued: ") + Log.color(:magenta, job.pid ? job.pid.to_s : 'no pid') + ' -- ' + job.path)
+      puts job.path
+
       exit 0
     end
 

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 6.0.3
+  version: 6.0.5
 platform: ruby
 authors:
 - Miguel Vazquez
-autorequire: 
 bindir: bin
 cert_chain: []
-date: 2025-02-13 00:00:00.000000000 Z
+date: 2025-06-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: scout-gear
@@ -375,7 +374,11 @@ 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
+- python/test.py
 - share/Rlib/plot.R
 - share/Rlib/svg.R
 - share/Rlib/util.R
@@ -488,6 +491,7 @@ files:
 - share/rbbt_commands/workflow/remote/add
 - share/rbbt_commands/workflow/remote/list
 - share/rbbt_commands/workflow/remote/remove
+- share/rbbt_commands/workflow/retry
 - share/rbbt_commands/workflow/server
 - share/rbbt_commands/workflow/task
 - share/rbbt_commands/workflow/trace
@@ -500,7 +504,6 @@ homepage: http://github.com/mikisvaz/rbbt-util
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -515,8 +518,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.23
-signing_key: 
+rubygems_version: 3.6.6
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files: []