rbbt-util 5.17.70 → 5.17.71

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: eb7786a8a1320ebdd5ba42434c814bc3cfeb758b
-  data.tar.gz: d6ea4ec9b859a9d5773c17c734547e313eddd99e
+  metadata.gz: 257d69c8b2bd1dd30b2140f0bf8a12da6d98cf05
+  data.tar.gz: 87ced61d3865d938fb316bef1cd99b0a2a842cb6
 SHA512:
-  metadata.gz: b57cd1832c8088500cc9d3717558709f66ac658795e5c1df10640d88769a24bf66d50a1de7de9525385f65ee24df9ddabf04031c168c115cd9b0e0aeb6f6e155
-  data.tar.gz: b3887676ccf5dee6600b87f831745fc6318860118f55bdb91e33d8d19a0bb1b702514b9378d57fdb7a4f62db4efcf52b1609a026255882818c8444c83711e12e
+  metadata.gz: be58086a415eed7d571d56c98bcdca03a8dc9c3c3222cbc8e6d36f0a827bef55e2a44a05431532bfa518a393e8031530207247aa0db8b38bfba1e58dc3625504
+  data.tar.gz: c9106df3f09c54d9443b4418e3b207c143540ea1c3191692f31f878a09ccc10435992c1f794fa1ee96e4c125a8277aaffd628ba276fa25b1a0be43f92f9f07ae

data/lib/rbbt/rest/client/step.rb

@@ -61,11 +61,11 @@ class WorkflowRESTClient
 
     #{{{ MANAGEMENT
     
-    def init_job(cache_type = nil)
+    def init_job(cache_type = nil, other_params = {})
       cache_type = :asynchronous if cache_type.nil? and not @is_exec
       cache_type = :exec if cache_type.nil?
       @name ||= Persist.memory("RemoteSteps", :workflow => self, :task => task, :jobname => @name, :inputs => inputs, :cache_type => cache_type) do
-        WorkflowRESTClient.post_jobname(File.join(base_url, task.to_s), inputs.merge(:jobname => @name||@base_name, :_cache_type => cache_type))
+        WorkflowRESTClient.post_jobname(File.join(base_url, task.to_s), inputs.merge(other_params).merge(:jobname => @name||@base_name, :_cache_type => cache_type))
       end
       @url = File.join(base_url, task.to_s, @name)
       nil
@@ -170,12 +170,10 @@ class WorkflowRESTClient
 
     def recursive_clean
       begin
-        inputs = Array === self.inputs ? Hash[*self.inputs.flatten] : self.inputs
-        params = inputs.merge(:_update => :recursive_clean)
-        init_job
+        params = {:_update => :recursive_clean}
+        init_job(nil, params)
         WorkflowRESTClient.get_raw(url, params)
         _restart
-        init_job
       rescue Exception
         Log.exception $!
       end
@@ -184,12 +182,10 @@ class WorkflowRESTClient
 
     def clean
       begin
-        inputs = Array === self.inputs ? Hash[*self.inputs.flatten] : self.inputs
-        params = inputs.merge(:_update => :clean)
-        init_job
+        params = {:_update => :clean}
+        init_job(nil, params)
         WorkflowRESTClient.get_raw(url, params)
         _restart
-        init_job
       rescue Exception
         Log.exception $!
       end

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -30,7 +30,7 @@ module TSV
         obj.size
       when File
         return nil if Open.gzip?(obj) or Open.bgzip?(obj)
-        CMD.cmd("wc -l '#{obj.filename}'").read.to_i
+        CMD.cmd("wc -l '#{obj.path}'").read.to_i
       when Path, String
         obj = obj.find if Path === obj
         if File.exists? obj

data/lib/rbbt/util/log/progress.rb

@@ -22,6 +22,7 @@ module Log
 
     def percent
       return 0 if @ticks == 0
+      return 100 if @max == 0
       (@ticks * 100) / @max
     end
 

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

@@ -140,8 +140,10 @@ class Step
     log :dependencies, "#{Log.color :magenta, "Dependencies"} #{Log.color :yellow, task.name.to_s || ""}"
     dupping = []
     @seen.each do |dependency|
-      next if (dependency.done? and not dependency.dirty?) or (dependency.streaming? and dependency.running?)
-      dependency.clean
+      next if (dependency.done? and not dependency.dirty?) or 
+              (dependency.streaming? and dependency.running?) or 
+              (defined? WorkflowRESTClient and WorkflowRESTClient::RemoteStep === dependency and not (dependency.error? or dependency.aborted?))
+      dependency.clean if dependency.started? and dependency
       dupping << dependency unless dependencies.include? dependency
     end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.70
+  version: 5.17.71
 platform: ruby
 authors:
 - Miguel Vazquez