rbbt-util 5.26.16 → 5.26.17

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 0a02c5606b3ad0db3f49bb08253b3319086275f8c628c2058cfb947dad8589cc
+  metadata.gz: 7cd4fb8b55aecafae6989ecaf79447dadbf5266f6adff7a7aac180f60486c12f
+  data.tar.gz: 74c2f293e4b913c78df2a7497bb7e99b750964a0c065b0f72cead6b544e5be99
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+  metadata.gz: 03dde3dd4ed5c7bf62d505e789928f6e259cbe1027ae3c3755d35626ff0d999b0a604599bcf2b0889622e608aec2bbe45f8bf2164a9aaf97924dd95da01a839c
+  data.tar.gz: f5ca51a17ab7f29f8f77e8de3a7b365199e07550b6408ca76949ccfc27b93a0a6618b8f5c24fdcbea7f1b4bb4a5ec587e9d686801fdafa534b1d065ba8b89263

data/lib/rbbt/resource/path.rb

@@ -378,9 +378,9 @@ module Path
 
   def replace_extension(new_extension = nil, multiple = false)
     if multiple
-      new_path = self.sub(/(\.[^\.\/]{2,4})+$/,'')
+      new_path = self.sub(/(\.[^\.\/]{2,5})+$/,'')
     else
-      new_path = self.sub(/\.[^\.\/]{2,4}$/,'')
+      new_path = self.sub(/\.[^\.\/]{2,5}$/,'')
     end
     new_path = new_path + "." + new_extension.to_s
     self.annotate(new_path)

data/lib/rbbt/util/docker.rb

@@ -1,5 +1,5 @@
 module Docker
-  def self.run(image, cmd, options)
+  def self.run(image, cmd, options = {})
     mounts, job_inputs, directory, pipe = Misc.process_options options, :mounts, :job_inputs, :directory, :pipe
 
     if mounts
@@ -18,7 +18,7 @@ module Docker
       job_inputs.each do |name,obj|
         case obj
         when File 
-          FileUtils.cp obj.filename, directory[name]
+          Open.ln_h Open.realpath(obj.filename), directory[name]
         when IO
           begin
             Open.write(directory[name], obj)
@@ -27,21 +27,27 @@ module Docker
           end
         when String
           if obj.length < 256 and File.exist?(obj)
-            FileUtils.cp obj, directory[name]
+            Open.ln_h Open.realpath(obj), directory[name]
           else
             Open.write(directory[name], obj)
           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
     else
       TmpFile.with_file do |tmpfile|
         Path.setup(tmpfile)
-        FileUtils.mkdir_p tmpfile
+        Open.mkdir tmpfile
         mount_cmd += " -v '#{tmpfile}':/job"
         job_inputs.each do |name,obj|
           case obj
           when File 
-            FileUtils.cp obj.filename, tmpfile[name]
+            Open.ln_h Open.realpath(obj.filename), tmpfile[name]
           when IO
             begin
               Open.write(tmpfile[name], obj)
@@ -50,21 +56,15 @@ module Docker
             end
           when String
             if obj.length < 256 and File.exist?(obj)
-              FileUtils.cp obj, tmpfile[name]
+              Open.ln_h Open.realpath(obj), tmpfile[name]
             else
               Open.write(tmpfile[name], obj)
             end
           end
         end if job_inputs
-        pipe = false
+        cmd = "docker run #{mount_cmd} #{image_cmd} #{cmd}"
+        CMD.cmd_log(cmd, :log => true)
       end
-
-    end
-    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
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.16
+  version: 5.26.17
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-06-05 00:00:00.000000000 Z
+date: 2019-06-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake