rbbt-util 5.23.22 → 5.23.23

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f00bbaf07372fc3c72d60b438ce701b6336e21bb
-  data.tar.gz: f5e9cbffdc19992c1f2d606e7cef8963f84df2b0
+  metadata.gz: 9196b9af288157b75110a6bd4126f7a06caffee0
+  data.tar.gz: 666c7717915b6684ba727d70110a1ca5dd2cca1b
 SHA512:
-  metadata.gz: 8d087babf2c286d041e1585db266cd8abd1a39672eab0a965f772b00b9866eafb0ab27bb36242bb4fe4e344733d4f7a5a26033013a20d4f64524daeae0a493db
-  data.tar.gz: 28b6c11840f431d28c6e6bd32b75d72ce6eced2cf12d4f53661e5d316ff893c6c1e9e8d19d73cc78a235798ed9faf64dd389300e9be6e12decf743b335e31266
+  metadata.gz: 21fefbcb643e6ebde8896422b5003deb348c9a9fffbee2b0935aaafd766853bc234ffe37635eaec130718ba5862951206ffe8e8974b3bfc1498b324421ea355d
+  data.tar.gz: '0939898fa00d8b3120e8497abc688aae9832e32a1d276703eca93fd505ab441e2d4284c49658f3d43708d66262034bd479f2b1e7d55f64528c508c834d4d3cad'

data/lib/rbbt/util/misc.rb

@@ -72,6 +72,8 @@ module Misc
     tokens = {
       "s" => (1),
       "min" => (60),
+      "''" => (1),
+      "'" => (60),
       "h" => (60 * 60),
       "d" => (60 * 60 * 24),
       "w" => (60 * 60 * 24 * 7),

data/lib/rbbt/util/tar.rb

@@ -85,14 +85,21 @@ module Misc
 
   def self._untar_cmd(io, destination)
     FileUtils.mkdir_p destination unless File.exist? destination
-    CMD.cmd("tar xvf - -C '#{destination}'", :in => io)
+    CMD.cmd_log("tar xvf - -C '#{destination}'", :in => io)
     nil
   end
 
   # untars the given IO into the specified
   # directory
   def self.untar(io, destination)
-    return _untar_cmd(io, destination)
+    io = io.find if Path === io
+    if String === io and File.exists?(io)
+      Open.open(io) do |f|
+        untar(f, destination)
+      end
+    else
+      return _untar_cmd(io, destination)
+    end
   end
 end
 

data/lib/rbbt/workflow/accessor.rb

@@ -1028,6 +1028,7 @@ module Workflow
   end
 
   TAG = ENV["RBBT_INPUT_JOBNAME"] == "true" ? :inputs : :hash
+  DEBUG_JOB_HASH = ENV["RBBT_DEBUG_JOB_HASH"] == 'true'
   def step_path(taskname, jobname, inputs, dependencies, extension = nil)
     raise "Jobname makes an invalid path: #{ jobname }" if jobname.include? '..'
     if inputs.length > 0 or dependencies.any?
@@ -1039,7 +1040,7 @@ module Workflow
                          key_obj = {:inputs => clean_inputs, :dependencies => deps_str }
                          key_str = Misc.obj2str(key_obj)
                          hash_str = Misc.digest(key_str)
-                         #Log.debug "Hash for '#{[taskname, jobname] * "/"}' #{hash_str} for #{key_str}"
+                         Log.debug "Hash for '#{[taskname, jobname] * "/"}' #{hash_str} for #{key_str}" if DEBUG_JOB_HASH
                          jobname + '_' << hash_str
                        when :inputs
                          all_inputs = {}

data/lib/rbbt/workflow/examples.rb

@@ -27,26 +27,48 @@ module Workflow
 
   def self.load_inputs(dir, input_names, input_types)
     inputs = {}
-    dir = Path.setup(dir.dup)
-    input_names.each do |input|
-      file = dir[input].find
-      file = dir.glob(input.to_s + ".*").first if file.nil? or not file.exists?
-      Log.debug "Trying #{ input }: #{file}"
-      next unless file and file.exists?
-
-      case input_types[input]
-      when :tsv, :array, :text, :file
-        Log.debug "Pointing #{ input } to #{file}"
-        inputs[input.to_sym]  = file
-      when :boolean
-        inputs[input.to_sym]  = (file.read.strip == 'true')
-      else
-        Log.debug "Loading #{ input } from #{file}"
-        inputs[input.to_sym]  = file.read.strip
+    if File.exists?(dir) && ! File.directory?(dir)
+      Log.debug "Loading inputs from #{dir}, not a directory trying as tar.gz"
+      tarfile = dir
+      digest = CMD.cmd("md5sum '#{tarfile}'").read.split(" ").first
+      tmpdir = Rbbt.tmp.input_bundle[digest].find
+      Misc.untar(tarfile, tmpdir) unless File.exists? tmpdir
+      files = tmpdir.glob("*")
+      if files.length == 1 && File.directory?(files.first)
+        tmpdir = files.first
       end
+      load_inputs(tmpdir, input_names, input_types)
+    else
+      dir = Path.setup(dir.dup)
+      input_names.each do |input|
+        file = dir[input].find
+        file = dir.glob(input.to_s + ".*").first if file.nil? or not file.exists?
+        Log.debug "Trying #{ input }: #{file}"
+        next unless file and file.exists?
+
+        case input_types[input]
+        when :file
+          Log.debug "Pointing #{ input } to #{file}"
+          inputs[input.to_sym]  = file
+        when :text
+          Log.debug "Reading #{ input } from #{file}"
+          inputs[input.to_sym]  = Open.read(file)
+        when :array
+          Log.debug "Reading array #{ input } from #{file}"
+          inputs[input.to_sym]  = Open.read(file).split("\n")
+        when :tsv
+          Log.debug "Opening tsv #{ input } from #{file}"
+          inputs[input.to_sym]  = TSV.open(file)
+        when :boolean
+          inputs[input.to_sym]  = (file.read.strip == 'true')
+        else
+          Log.debug "Loading #{ input } from #{file}"
+          inputs[input.to_sym]  = file.read.strip
+        end
 
+      end
+      IndiferentHash.setup(inputs)
     end
-    IndiferentHash.setup(inputs)
   end
 
   def example_inputs(task_name, example)

data/test/rbbt/util/test_misc.rb

@@ -606,7 +606,7 @@ EOF
   def test_time_stamp
     assert_equal 10, Misc.timespan('10')
     assert_equal 10, Misc.timespan('10s')
-    assert_equal 60, Misc.timespan('1m')
+    assert_equal 60, Misc.timespan('1min')
     assert_equal 60*60*24, Misc.timespan('1d')
     assert_equal 60*60*24, Misc.timespan('1d')
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.23.22
+  version: 5.23.23
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-09-20 00:00:00.000000000 Z
+date: 2018-09-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake