rbbt-util 5.26.17 → 5.26.18

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: deb3c88c74d37ca13e19b72130fd4e1d48db2d226f17bd53ce0542b3ad3bdb38
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+  data.tar.gz: 8766644b5b4b22c3c66fb6f9f9e63c777ef8bf9c115f89dbd12450ea8ef146a5d8485bbd9a0b102d39169be605581c4955f246db01996b20c6f32fbfa20eba1e

data/lib/rbbt/util/docker.rb

@@ -1,6 +1,7 @@
 module Docker
   def self.run(image, cmd, options = {})
-    mounts, job_inputs, directory, pipe = Misc.process_options options, :mounts, :job_inputs, :directory, :pipe
+    mounts, job_inputs, directory, pipe, host_user = Misc.process_options options, :mounts, :job_inputs, :directory, :pipe, :host_user
+    pipe = false if pipe.nil?
 
     if mounts
       mounts.each{|t,s| FileUtils.mkdir_p s unless File.exist? s}
@@ -10,6 +11,8 @@ module Docker
     end
 
     image_cmd = "-t #{image}"
+    
+    user_cmd = host_user ? "-u $(id -u ${USER}):$(id -g ${USER})" : "" 
 
     if directory
       Path.setup(directory) unless Path === directory
@@ -33,12 +36,9 @@ module Docker
           end
         end
       end if job_inputs
-      cmd = "docker run #{mount_cmd} #{image_cmd} #{cmd}"
-      if pipe
-        CMD.cmd(cmd, :log => true, :pipe => true)
-      else
-        CMD.cmd_log(cmd, :log => true)
-      end
+
+      cmd = "docker run #{mount_cmd} #{user_cmd} #{image_cmd} #{cmd}"
+      CMD.cmd_log(cmd, :log => true, :pipe => pipe)
     else
       TmpFile.with_file do |tmpfile|
         Path.setup(tmpfile)
@@ -62,7 +62,8 @@ module Docker
             end
           end
         end if job_inputs
-        cmd = "docker run #{mount_cmd} #{image_cmd} #{cmd}"
+
+        cmd = "docker run #{mount_cmd} #{user_cmd} #{image_cmd} #{cmd}"
         CMD.cmd_log(cmd, :log => true)
       end
     end

data/lib/rbbt/util/misc/pipes.rb

@@ -194,8 +194,11 @@ module Misc
               begin 
                 sin.write block
               rescue IOError
-                Log.error("Tee stream #{i} #{Misc.fingerprint stream} IOError: #{$!.message}");
+                Log.error("Tee stream #{i} #{Misc.fingerprint stream} IOError: #{$!.message} (#{Misc.fingerprint sin})");
                 skip[i] = true
+              rescue
+                Log.error("Tee stream #{i} #{Misc.fingerprint stream} Exception: #{$!.message} (#{Misc.fingerprint sin})");
+                raise $!
               end unless skip[i] 
             end
           end

data/lib/rbbt/util/open.rb

@@ -272,7 +272,6 @@ module Open
   def self.file_open(file, grep, mode = 'r', invert_grep = false)
     if (dir_sub_path = find_repo_dir(file))
       if mode.include? 'w'
-
         stream = StringIO.new
         class << stream
           attr_accessor :dir_sub_path
@@ -287,6 +286,8 @@ module Open
         stream = get_stream_from_repo(*dir_sub_path)
       end
     else
+      Open.mkdir File.dirname(file) if mode.include? 'w'
+
       file = file.find if Path === file
       stream =  File.open(file, mode)
     end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.17
+  version: 5.26.18
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-06-06 00:00:00.000000000 Z
+date: 2019-06-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake