bio-commandeer 0.3.0 → 0.4.0
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- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/lib/bio-commandeer/commandeer.rb +14 -3
- data/spec/bio-commandeer_spec.rb +6 -0
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 2b7559a3e351f0efdb098405a03882ea4c535b11
|
4
|
+
data.tar.gz: 443e5ea43b398f5a916bf84fb43225d0ecc7b694
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: '059e8356a0bfdad421f37a69767a7ae3e03379f3adff14a579459665d182daae75e9244e5894fb73aa8140d2902bc13d34a536612cd44fe404ffee96ada82a5e'
|
7
|
+
data.tar.gz: 48e2c1049ed3848e92e37f0c1516eac923774635a27f087245bc0a7451b4e3c1e4aa260a6c9efb534b7df42707a86ef297ff84c3162b09e95992dfa526ca9976
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.
|
1
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+
0.4.0
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@@ -1,4 +1,5 @@
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|
1
1
|
require 'systemu'
|
2
|
+
require 'timeout'
|
2
3
|
|
3
4
|
module Bio
|
4
5
|
# See #run
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@@ -9,6 +10,8 @@ module Bio
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|
9
10
|
# * options is a hash, with keys:
|
10
11
|
# :stdin: a string that is the stdin
|
11
12
|
# :log: if true, turn on logging. If given an object use it as the logger
|
13
|
+
# :timeout: number of seconds to allow the process to run for. If nil (the default),
|
14
|
+
# no timeout.
|
12
15
|
def self.run(command, options={})
|
13
16
|
obj = run_to_finish(command, options)
|
14
17
|
obj.raise_if_failed
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@@ -34,7 +37,13 @@ module Bio
|
|
34
37
|
end
|
35
38
|
res = CommandResult.new
|
36
39
|
res.command = command
|
37
|
-
|
40
|
+
begin
|
41
|
+
Timeout::timeout(options[:timeout]) do
|
42
|
+
res.status, res.stdout, res.stderr = systemu command, :stdin => options[:stdin]
|
43
|
+
end
|
44
|
+
rescue Timeout::Error => e
|
45
|
+
res.timed_out = true
|
46
|
+
end
|
38
47
|
|
39
48
|
if @log
|
40
49
|
@log.info "Command finished with exitstatus #{res.status.exitstatus}"
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@@ -44,10 +53,12 @@ module Bio
|
|
44
53
|
end
|
45
54
|
|
46
55
|
class CommandResult
|
47
|
-
attr_accessor :stdout, :stderr, :command, :status
|
56
|
+
attr_accessor :stdout, :stderr, :command, :status, :timed_out
|
48
57
|
|
49
58
|
def raise_if_failed
|
50
|
-
if @
|
59
|
+
if @timed_out
|
60
|
+
raise Bio::CommandFailedException, "Command timed out. Command run was #{command}."
|
61
|
+
elsif @status.exitstatus != 0
|
51
62
|
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}"
|
52
63
|
end
|
53
64
|
end
|
data/spec/bio-commandeer_spec.rb
CHANGED
@@ -64,4 +64,10 @@ describe "BioCommandeer" do
|
|
64
64
|
obj = Bio::Commandeer.run_to_finish("cat /definitelyNotAFile")
|
65
65
|
expect{obj.raise_if_failed}.to raise_error(Bio::CommandFailedException)
|
66
66
|
end
|
67
|
+
|
68
|
+
it 'should respect timeout' do
|
69
|
+
Bio::Commandeer.run "sleep 2"
|
70
|
+
expect { Bio::Commandeer.run "sleep 1", :timeout => 1}.
|
71
|
+
to raise_error(Bio::CommandFailedException)
|
72
|
+
end
|
67
73
|
end
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bio-commandeer
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.
|
4
|
+
version: 0.4.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Ben J. Woodcroft
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2017-08-
|
11
|
+
date: 2017-08-10 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bio-logger
|