rbbt-util 5.13.24 → 5.13.25
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- checksums.yaml +4 -4
- data/bin/rbbt +35 -5
- data/lib/rbbt/resource.rb +8 -3
- data/lib/rbbt/tsv/parallel/traverse.rb +1 -0
- data/lib/rbbt/util/log.rb +1 -1
- data/lib/rbbt/util/misc/concurrent_stream.rb +30 -7
- data/lib/rbbt/workflow/step/run.rb +1 -0
- data/share/rbbt_commands/log +32 -0
- data/share/rbbt_commands/workflow/info +2 -0
- metadata +3 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 5239dbb15f48c166b31834d3f927f4c46103dd2d
|
4
|
+
data.tar.gz: eef931195c348851b6aeb3de3ba35f4e043884f6
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 60e3af52f609fce5ac4ef7c129bc31dff0bf06576bad4b10e2dabb9840388240bc4556f01eb045b24a0bd4206b8e7dde95566d3bb7fd01d88153e37f21f9e1ed
|
7
|
+
data.tar.gz: 50a0e08c13bb120b2b111de91f6446eb9d42cd0b6ca1897e8a2308e1f547cf2bb7d4d1198eeecf89ce2c2bf457456e3234403726cbdc314c2dcd8519187ee33f
|
data/bin/rbbt
CHANGED
@@ -1,8 +1,34 @@
|
|
1
1
|
#!/usr/bin/env ruby
|
2
2
|
|
3
|
+
dev_dir = nil
|
4
|
+
if _i = ARGV.index("--dev")
|
5
|
+
dev_dir = ARGV[_i+1]
|
6
|
+
ARGV.delete "--dev"
|
7
|
+
end
|
8
|
+
|
9
|
+
if dev_dir.nil?
|
10
|
+
_s = nil
|
11
|
+
ARGV.each_with_index do |s,i|
|
12
|
+
if s.match(/^--dev(?:=(.*))?/)
|
13
|
+
dev_dir = $1
|
14
|
+
_s = s
|
15
|
+
next
|
16
|
+
end
|
17
|
+
end
|
18
|
+
ARGV.delete _s if _s
|
19
|
+
end
|
20
|
+
|
21
|
+
if dev_dir
|
22
|
+
Dir.glob(File.join(File.expand_path(dev_dir),'rbbt-*')).each do |f|
|
23
|
+
$LOAD_PATH << f
|
24
|
+
end
|
25
|
+
end
|
26
|
+
|
3
27
|
require 'rbbt'
|
4
28
|
require 'rbbt/util/simpleopt'
|
5
29
|
|
30
|
+
Log.nocolor = true if ARGV.include? "--nocolor"
|
31
|
+
|
6
32
|
options = SOPT.setup <<EOF
|
7
33
|
Ruby bioinformatics toolkit
|
8
34
|
|
@@ -10,6 +36,7 @@ $ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value
|
|
10
36
|
|
11
37
|
|
12
38
|
--log* #{Log.color :yellow, "Log level from 0 (debug) 6 (errors)"}
|
39
|
+
--dev* #{Log.color :yellow, "Find development libraries in the directory specified"}
|
13
40
|
-cd--command_dir* #{Log.color :yellow, "Directory from where to load command scripts"}
|
14
41
|
--profile #{Log.color :yellow, "Profile execution"}
|
15
42
|
--nocolor #{Log.color :yellow, "Disable colored output"}
|
@@ -17,10 +44,6 @@ $ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value
|
|
17
44
|
--locate_file #{Log.color :yellow, "Report the location of the script instead of executing it"}
|
18
45
|
EOF
|
19
46
|
|
20
|
-
if options[:nocolor]
|
21
|
-
Log.nocolor = true
|
22
|
-
end
|
23
|
-
|
24
47
|
if options.delete :nobar
|
25
48
|
ENV["RBBT_NO_PROGRESS"] = "true"
|
26
49
|
end
|
@@ -29,7 +52,14 @@ locate = options.delete :locate_file
|
|
29
52
|
|
30
53
|
if options[:log]
|
31
54
|
Log.severity = options[:log].to_i
|
32
|
-
|
55
|
+
else
|
56
|
+
global_severity = Log.get_level(Rbbt.etc.log_severity.read.strip) if Rbbt.etc.log_severity.exists?
|
57
|
+
if ENV["RBBT_LOG"]
|
58
|
+
Log.severity = ENV["RBBT_LOG"].to_i
|
59
|
+
else
|
60
|
+
global_severity = Log.get_level(Rbbt.etc.log_severity.read.strip) if Rbbt.etc.log_severity.exists?
|
61
|
+
Log.severity = global_severity.to_i if global_severity
|
62
|
+
end
|
33
63
|
end
|
34
64
|
|
35
65
|
if options[:command_dir]
|
data/lib/rbbt/resource.rb
CHANGED
@@ -65,7 +65,8 @@ module Resource
|
|
65
65
|
begin
|
66
66
|
@server_missing_resource_cache ||= Set.new
|
67
67
|
raise "Resource Not Found" if @server_missing_resource_cache.include? url
|
68
|
-
|
68
|
+
Misc.lock final_path do
|
69
|
+
Net::HTTP.get_response URI(url) do |response|
|
69
70
|
case response
|
70
71
|
when Net::HTTPSuccess, Net::HTTPOK
|
71
72
|
Misc.sensiblewrite(final_path) do |file|
|
@@ -77,15 +78,19 @@ module Resource
|
|
77
78
|
location = response['location']
|
78
79
|
Log.debug("Feching directory from: #{location}. Into: #{final_path}")
|
79
80
|
FileUtils.mkdir_p final_path unless File.exists? final_path
|
80
|
-
|
81
|
-
|
81
|
+
TmpFile.with_file do |tmp_dir|
|
82
|
+
Misc.in_dir tmp_dir do
|
83
|
+
CMD.cmd('tar xvfz -', :in => Open.open(location, :nocache => true))
|
84
|
+
end
|
82
85
|
end
|
86
|
+
File.utils tmp_dir, final_path
|
83
87
|
when Net::HTTPInternalServerError
|
84
88
|
@server_missing_resource_cache << url
|
85
89
|
raise "Resource Not Found"
|
86
90
|
else
|
87
91
|
raise "Response not understood: #{response.inspect}"
|
88
92
|
end
|
93
|
+
end
|
89
94
|
end
|
90
95
|
rescue
|
91
96
|
Log.warn "Could not retrieve (#{self.to_s}) #{ path } from #{ remote_server }"
|
data/lib/rbbt/util/log.rb
CHANGED
@@ -54,10 +54,6 @@ module ConcurrentStream
|
|
54
54
|
if @threads and @threads.any?
|
55
55
|
@threads.each do |t|
|
56
56
|
t.join unless t == Thread.current
|
57
|
-
#begin
|
58
|
-
#ensure
|
59
|
-
# t.join unless t == Thread.current
|
60
|
-
#end
|
61
57
|
end
|
62
58
|
@threads = []
|
63
59
|
end
|
@@ -94,7 +90,33 @@ module ConcurrentStream
|
|
94
90
|
end
|
95
91
|
|
96
92
|
def abort_threads
|
97
|
-
@threads.
|
93
|
+
Log.medium "Aborting threads (#{Thread.current.inspect}) #{@threads.collect{|t| t.inspect } * ", "}"
|
94
|
+
|
95
|
+
@threads.each do |t|
|
96
|
+
@aborted = false if t == Thread.current
|
97
|
+
next if t == Thread.current
|
98
|
+
Log.medium "Aborting thread #{t.inspect}"
|
99
|
+
t.raise Aborted.new "Hey"
|
100
|
+
end if @threads
|
101
|
+
|
102
|
+
sleeped = false
|
103
|
+
@threads.each do |t|
|
104
|
+
next if t == Thread.current
|
105
|
+
if t.alive?
|
106
|
+
sleep 1 unless sleeped
|
107
|
+
sleeped = true
|
108
|
+
Log.medium "Kill thread #{t.inspect}"
|
109
|
+
t.kill
|
110
|
+
end
|
111
|
+
begin
|
112
|
+
Log.medium "Join thread #{t.inspect}"
|
113
|
+
t.join unless t == Thread.current
|
114
|
+
rescue Aborted
|
115
|
+
rescue Exception
|
116
|
+
Log.exception $!
|
117
|
+
end
|
118
|
+
end
|
119
|
+
Log.medium "Aborted threads (#{Thread.current.inspect}) #{@threads.collect{|t| t.inspect } * ", "}"
|
98
120
|
end
|
99
121
|
|
100
122
|
def abort_pids
|
@@ -103,9 +125,9 @@ module ConcurrentStream
|
|
103
125
|
end
|
104
126
|
|
105
127
|
def abort
|
106
|
-
Log.medium "Aborting stream #{Misc.fingerprint self} -- #{@abort_callback} [#{@aborted}]"
|
107
128
|
return if @aborted
|
108
|
-
@aborted
|
129
|
+
Log.medium "Aborting stream #{Misc.fingerprint self} -- #{@abort_callback} [#{@aborted}]"
|
130
|
+
@aborted = true
|
109
131
|
begin
|
110
132
|
@callback = nil
|
111
133
|
@abort_callback.call if @abort_callback
|
@@ -115,6 +137,7 @@ module ConcurrentStream
|
|
115
137
|
abort_threads
|
116
138
|
abort_pids
|
117
139
|
end
|
140
|
+
Log.medium "Aborted stream #{Misc.fingerprint self} -- #{@abort_callback} [#{@aborted}]"
|
118
141
|
end
|
119
142
|
|
120
143
|
def super(*args)
|
@@ -0,0 +1,32 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
|
3
|
+
require 'rbbt-util'
|
4
|
+
require 'rbbt/util/simpleopt'
|
5
|
+
|
6
|
+
$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
|
7
|
+
|
8
|
+
options = SOPT.setup <<EOF
|
9
|
+
|
10
|
+
Change log level
|
11
|
+
|
12
|
+
$ rbbt log <level>
|
13
|
+
|
14
|
+
DEBUG
|
15
|
+
LOW
|
16
|
+
MEDIUM
|
17
|
+
HIGH
|
18
|
+
INFO
|
19
|
+
WARN
|
20
|
+
ERROR
|
21
|
+
|
22
|
+
-h--help Print this help
|
23
|
+
|
24
|
+
EOF
|
25
|
+
rbbt_usage and exit 0 if options[:help]
|
26
|
+
if ARGV.empty?
|
27
|
+
puts Rbbt.etc.log_severity.read
|
28
|
+
else
|
29
|
+
Open.write(Rbbt.etc.log_severity, ARGV[0].upcase)
|
30
|
+
end
|
31
|
+
|
32
|
+
|
@@ -55,6 +55,8 @@ if inputs and inputs.any?
|
|
55
55
|
puts Log.color(:magenta, "Inputs")
|
56
56
|
inputs.each do |input,value|
|
57
57
|
case value
|
58
|
+
when nil
|
59
|
+
puts " " << Misc.format_definition_list_item(input, 'nil', 80, 20, :blue)
|
58
60
|
when Array
|
59
61
|
puts " " << Misc.format_definition_list_item(input, value[0..5]*"\n", 80, 20, :blue)
|
60
62
|
when TrueClass, FalseClass
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.13.
|
4
|
+
version: 5.13.25
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2014-05-
|
11
|
+
date: 2014-05-30 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|
@@ -236,6 +236,7 @@ files:
|
|
236
236
|
- share/rbbt_commands/file_server/add
|
237
237
|
- share/rbbt_commands/file_server/list
|
238
238
|
- share/rbbt_commands/file_server/remove
|
239
|
+
- share/rbbt_commands/log
|
239
240
|
- share/rbbt_commands/resource/exists
|
240
241
|
- share/rbbt_commands/resource/find
|
241
242
|
- share/rbbt_commands/resource/get
|