rbbt-util 5.5.52 → 5.5.53

checksums.yaml

@@ -1,15 +1,15 @@
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data/lib/rbbt/util/misc.rb

@@ -300,6 +300,10 @@ module Misc
     end
   end
 
+  def self.remove_long_items(obj)
+    return fingerprint(obj)
+  end
+
   def self.ensembl_server(organism)
     date = organism.split("/")[1]
     if date.nil?
@@ -800,12 +804,16 @@ end
     $__did_once = false
   end
 
-  def self.insist(times = 3, sleep = nil)
+  def self.insist(times = 3, sleep = nil, msg = nil)
     try = 0
     begin
       yield
     rescue
-      Log.warn("Insisting after exception: #{$!.message}")
+      if msg
+        Log.warn("Insisting after exception: #{$!.message} -- #{msg}")
+      else
+        Log.warn("Insisting after exception: #{$!.message}")
+      end
       sleep sleep if sleep
       try += 1
       retry if try < times

data/lib/rbbt/workflow/accessor.rb

@@ -28,8 +28,8 @@ class Step
   def info
     return {} if info_file.nil? or not Open.exists? info_file
     begin
-      Misc.insist(2, 2) do
-        Misc.insist(2, 0.5) do
+      Misc.insist(2, 2, info_file) do
+        Misc.insist(2, 0.5, info_file) do
           Open.open(info_file) do |file|
             INFO_SERIALIAZER.load(file) || {}
           end

data/share/rbbt_commands/workflow/task

@@ -92,9 +92,9 @@ def fix_options(workflow, task, job_options)
               when TSV
                 value
               when '-'
-                TSV.open(STDIN)
+                TSV.open(STDIN, :unnamed => true)
               else
-                TSV.open(value)
+                TSV.open(value, :unnamed => true)
               end
             else
               value

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.5.52
+  version: 5.5.53
 platform: ruby
 authors:
 - Miguel Vazquez