rbbt-util 5.17.76 → 5.17.77

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 38e3e52b6284fd289652ab74e0ce40c72af08744
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data/lib/rbbt/annotations.rb

@@ -241,7 +241,7 @@ module Annotation
         next
       end
 
-      value = value.split("|") if String === value and value.index "|"
+      value = value.split("|") if String === value and value.include? "|"
 
       annotation_values[key] = value
     end

data/lib/rbbt/util/docker.rb

@@ -0,0 +1,57 @@
+module Docker
+  def self.run(image,cmd, options)
+    mounts, job_inputs, directory, pipe = Misc.process_options options, :mounts, :job_inputs, :directory, :pipe
+
+    if mounts
+      mount_cmd = mounts.sort.collect{|t,s| "-v " + ["'" + s + "'", "'" + t + "'"] * ":" } * " "
+    else
+      mount_cmd = ""
+    end
+
+    image_cmd = "-t #{image}"
+
+    if directory
+      Path.setup(directory) unless Path === directory
+      FileUtils.mkdir_p directory unless File.directory? directory
+      mount_cmd += " -v '#{directory}':/job"
+      job_inputs.each do |name,obj|
+        case obj
+        when File 
+          FileUtils.cp obj.filename, directory[name]
+        when IO
+          Open.write(tmpfile[name], obj)
+        when String
+          if obj.length < 256 and File.exists?(obj)
+            FileUtils.cp obj, directory[name]
+          else
+            Open.write(directory[name], obj)
+          end
+        end
+      end
+    else
+      TmpFile.with_file do |tmpfile|
+        Path.setup(tmpfile)
+        FileUtils.mkdir_p tmpfile
+        mount_cmd += " -v '#{tmpfile}':/job"
+        job_inputs.each do |name,obj|
+          case obj
+          when File 
+            FileUtils.cp obj.filename, tmpfile[name]
+          when IO
+            Open.write(tmpfile[name], obj)
+          when String
+            if obj.length < 256 and File.exists?(obj)
+              FileUtils.cp obj, tmpfile[name]
+            else
+              Open.write(tmpfile[name], obj)
+            end
+          end
+        end
+        pipe = false
+      end
+
+    end
+    cmd = "docker run #{mount_cmd} #{image_cmd} #{cmd}"
+    CMD.cmd(cmd, :log => true, :pipe => pipe)
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.76
+  version: 5.17.77
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-09-23 00:00:00.000000000 Z
+date: 2015-09-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -227,6 +227,7 @@ files:
 - lib/rbbt/util/concurrency/processes/socket_old.rb
 - lib/rbbt/util/concurrency/processes/worker.rb
 - lib/rbbt/util/concurrency/threads.rb
+- lib/rbbt/util/docker.rb
 - lib/rbbt/util/excel2tsv.rb
 - lib/rbbt/util/filecache.rb
 - lib/rbbt/util/log.rb