rbbt-util 5.32.28 → 5.32.30

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: a680ce3f6d91a1b0ff8060ee18b8e68efbd43df56f238869b30f6f88617d23d9
-  data.tar.gz: d6c8c724f15d4ce4c910ff9db6becbd0587c8dc04598abcc934884a8368dd93e
+  metadata.gz: e173c4373fc6358b63964247a0d81bab2bd632a2e6bce1b93ff9ac1bd6aa53ca
+  data.tar.gz: 26c3352b53615f1e1c057727ac6f129dedbb9fabb09742513b2368b0b2bd7327
 SHA512:
-  metadata.gz: 9b90c640f51de96d469af4b442d9ba66aa89a592c7776196058da3b20e13b07ef50f67e07018435b12bed13492c3bf9d9abf4de565902094a3d58be4ab628fd5
-  data.tar.gz: 523d7234c59bc1781d47827daebb07870913b8dec9851110d5c2e0c92441903601965f9a7bb4b494b0271d64e09ad0f3b80b254176ee3495744c2bbf1f34f714
+  metadata.gz: f8d84e234a76a38352786f869aaf5fee4f4b159a402b9241707c18f7cbe595d630a645e75bad7ae512652d664b98c61a13c24beb972e1c55db2b300a8c82744b
+  data.tar.gz: 0fdcfe8522907197eeacfffa0551dbde81db0fc859f0f85eb4281e87df44c9a0b90026423dfad79fd6c9cd8429be655eadc94e94c85cd79d0b971134ea6427ee

data/lib/rbbt/hpc/orchestrate/batches.rb

@@ -18,12 +18,24 @@ module HPC
 
     def self.job_workload(job)
       workload = []
+      path_jobs = {}
+
+      path_jobs[job.path] = job
+
       heap = []
-      heap << job
-      while job = heap.pop
+      heap << job.path
+      while job_path = heap.pop
+        job = path_jobs[job_path]
         next if job.done?
         workload << job
-        heap.concat job_dependencies(job)
+
+        deps =  job_dependencies(job)
+
+        deps.each do  |d|
+          path_jobs[d.path] ||= d
+        end
+
+        heap.concat deps.collect(&:path)
         heap.uniq!
       end
       workload.uniq
@@ -69,7 +81,7 @@ module HPC
         jobs = batch[:jobs]
         all_deps = jobs.collect{|d| job_dependencies(d) }.flatten.uniq
         deps = all_deps.collect do |d|
-          (batches - [batch]).select{|batch| batch[:jobs].include? d }
+          (batches - [batch]).select{|batch| batch[:jobs].collect(&:path).include? d.path }
         end.flatten.uniq
         batch[:deps] = deps
       end
@@ -130,7 +142,7 @@ module HPC
     def self.job_batches(rules, job)
       job_chains = self.job_chains(rules, job)
 
-      workload = job_workload(job)
+      workload = job_workload(job).uniq
 
       batches = chain_batches(rules, job_chains, workload)
       batches = add_batch_deps(batches)

data/lib/rbbt/util/migrate.rb

@@ -49,7 +49,7 @@ 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])}}"
+      Log.medium "Migrating #{source_path} #{options[:files].length} files to #{target} - #{Misc.fingerprint(options[:files])}}" if options[:files]
       if File.directory?(source_path) || source_path =~ /\/$/
         source_path += "/" unless source_path[-1] == "/"
         target += "/" unless target[-1] == "/"

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

@@ -24,7 +24,11 @@ module Workflow
 
         type = :io if file.split(".").last == 'as_io'
 
+        type = :path if file.split(".").last == 'as_path'
+
         case type
+        when :path
+          inputs[input.to_sym]  = Open.realpath(Open.read(file).strip)
         when :io
           inputs[input.to_sym] = Open.open(Open.realpath(file))
         when :file, :binary
@@ -96,12 +100,21 @@ class Step
         Open.write(path, value.to_s)
       when Step === value
         Open.ln_s(value.path, path)
+      when type.to_s == "binary"
+        if String === value && File.exists?(value)
+          value = File.expand_path(value)
+          Open.ln_s(value, path)
+        elsif String === value && Misc.is_filename?(value, false)
+          Open.write(path + '.as_path' , value)
+        else
+          Open.write(path, value, :mode => 'wb')
+        end
       when type.to_s == "file"
         if String === value && File.exists?(value)
           value = File.expand_path(value)
           Open.ln_s(value, path)
         else
-          value = value.collect{|v| v = "#{v}" if Path === v; v }if Array === value
+          value = value.collect{|v| v = "#{v}" if Path === v; v } if Array === value
           value = "#{value}" if Path === value
           Open.write(path + '.yaml', value.to_yaml)
         end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.32.28
+  version: 5.32.30
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-02-11 00:00:00.000000000 Z
+date: 2022-02-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake