bio-commandeer 0.3.0 → 0.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 28b5b0e5f6813c5d61adba3ad0a4b1cda7dac555
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+  data.tar.gz: 443e5ea43b398f5a916bf84fb43225d0ecc7b694
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+  data.tar.gz: 48e2c1049ed3848e92e37f0c1516eac923774635a27f087245bc0a7451b4e3c1e4aa260a6c9efb534b7df42707a86ef297ff84c3162b09e95992dfa526ca9976

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.4.0

data/lib/bio-commandeer/commandeer.rb

@@ -1,4 +1,5 @@
 require 'systemu'
+require 'timeout'
 
 module Bio
   # See #run
@@ -9,6 +10,8 @@ module Bio
     # * options is a hash, with keys:
     # :stdin: a string that is the stdin
     # :log: if true, turn on logging. If given an object use it as the logger
+    # :timeout: number of seconds to allow the process to run for. If nil (the default),
+    #           no timeout.
     def self.run(command, options={})
       obj = run_to_finish(command, options)
       obj.raise_if_failed
@@ -34,7 +37,13 @@ module Bio
       end
       res = CommandResult.new
       res.command = command
-      res.status, res.stdout, res.stderr = systemu command, :stdin => options[:stdin]
+      begin
+        Timeout::timeout(options[:timeout]) do
+          res.status, res.stdout, res.stderr = systemu command, :stdin => options[:stdin]
+        end
+      rescue Timeout::Error => e
+        res.timed_out = true
+      end
 
       if @log
         @log.info "Command finished with exitstatus #{res.status.exitstatus}"
@@ -44,10 +53,12 @@ module Bio
   end
 
   class CommandResult
-    attr_accessor :stdout, :stderr, :command, :status
+    attr_accessor :stdout, :stderr, :command, :status, :timed_out
 
     def raise_if_failed
-      if @status.exitstatus != 0
+      if @timed_out
+        raise Bio::CommandFailedException, "Command timed out. Command run was #{command}."
+      elsif @status.exitstatus != 0
         raise Bio::CommandFailedException, "Command returned non-zero exit status (#{@status.exitstatus}), likely indicating failure. Command run was #{@command} and the STDERR was:\n#{@stderr}\nSTDOUT was: #{@stdout}"
       end
     end

data/spec/bio-commandeer_spec.rb

@@ -64,4 +64,10 @@ describe "BioCommandeer" do
     obj = Bio::Commandeer.run_to_finish("cat /definitelyNotAFile")
     expect{obj.raise_if_failed}.to raise_error(Bio::CommandFailedException)
   end
+
+  it 'should respect timeout' do
+    Bio::Commandeer.run "sleep 2"
+    expect { Bio::Commandeer.run "sleep 1", :timeout => 1}.
+      to raise_error(Bio::CommandFailedException)
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-commandeer
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.4.0
 platform: ruby
 authors:
 - Ben J. Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-08-07 00:00:00.000000000 Z
+date: 2017-08-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger