rbbt-util 5.34.0 → 5.34.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: d612eb753e090f1221cd4d3b2c17e13e0e87f4cea7bc76c920717ba8055cbe8b
-  data.tar.gz: 9bea5062d3d73982ef5a35526c39ca3208fae9b817233344045144cbd0619920
+  metadata.gz: dce81f37830228a43c702909b856ebf661002d17b49614d67b6c04e16d339d4b
+  data.tar.gz: d7cb5ef82e50da2287c4bf9cf3912d66e36c27bb72a1c1c702d86cf7d1e8df78
 SHA512:
-  metadata.gz: 2d1e5c3fe701bb42049ab34bbe74fddb3e9a0a29d292cc8c8fbfc93049b0004be5b449aa83939de8924f2cdf19a720c044ea7491aacc96037e1acd549bd1201f
-  data.tar.gz: 54abc57de1a43b04337d8f9ad27668af2d07db21dbac7ee925728d6058dee280624385ef5b40280c0ec2439b6d80ed350bc136c9bef15116ba56292532d5e210
+  metadata.gz: fd9ad6b40180ef8cdc5a8e8335f291e557543f14cdd0cbc6760e7dd6f1327a5a73b5be92b1c037ccd46bca8596c86e7bf6eb7221989e9edac52ad34e81ad4e45
+  data.tar.gz: 72798bb53863c93aa768edc6c523d34e682dc374ebf4fe0307590faddb9022237a49f0556de364e7139345b35504b6d19b9c134abf8d0ae751a38c1d2c0331f7

data/lib/rbbt/hpc/orchestrate.rb

@@ -31,6 +31,7 @@ module HPC
       options.delete "detach"
       options.delete "jobname"
       options.delete "load_inputs"
+      options.delete "provenance"
 
       Log.high "Prepare for exec"
       prepare_for_execution(job)

data/lib/rbbt/util/open.rb

@@ -678,7 +678,7 @@ module Open
       if Open.exists? notification_file
         key = Open.read(notification_file).strip
         key = nil if key.empty?
-        if key.include?("@")
+        if key && key.include?("@")
           to = from = key
           subject = "Wrote " << file
           message = "Content attached"

data/lib/rbbt/workflow.rb

@@ -542,8 +542,17 @@ module Workflow
     step_path = step_path.call if Proc === step_path
     persist = input_values.nil? ? false : true
     persist = false
+
+    if ! (Path === step_path ? step_path.find : File.exists?(step_path)) && step_path.split("/").length == 3 && File.exists?(new_path = Rbbt.var.jobs[step_path].find)
+      step_path = new_path
+    end
+    
     key = Path === step_path ? step_path.find : step_path
 
+    if ! File.exists?(step_path) && step_path.split("/").length == 3 && File.exists?(new_path = Rbbt.var.jobs[step_path].find)
+      step_path = new_path
+    end
+
     step = Step.new step_path, task, input_values, dependencies
 
     set_step_dependencies(step) unless dependencies
@@ -703,7 +712,15 @@ module Workflow
 
   def self.load_step(path)
     path = Path.setup(path.dup) unless Path === path
-    path = path.find
+
+    if ! (Path === path ? path.exists? : File.exists?(path)) && path.split("/").length == 3 
+      new_path = Rbbt.var.jobs[path]
+      if new_path.exists? || new_path.set_extension('info').exists?
+        path = new_path
+      end
+    end
+
+    path = path.find if Path === path
 
     begin
       _load_step(path)

data/share/rbbt_commands/workflow/prov

@@ -36,7 +36,7 @@ file = ARGV.shift
 
 $seen = []
 def get_step(file)
-  file = File.expand_path(file)
+  file = File.expand_path(file) if File.exists?(file)
   file = file.sub(/\.(info|files)$/,'')
   $seen << file
   Workflow.load_step file

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.34.0
+  version: 5.34.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-06-03 00:00:00.000000000 Z
+date: 2022-06-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake