rbbt-util 5.19.17 → 5.19.18
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- checksums.yaml +4 -4
- data/lib/rbbt/monitor.rb +9 -7
- data/lib/rbbt/tsv/stream.rb +1 -1
- data/lib/rbbt/util/misc/inspect.rb +1 -1
- data/lib/rbbt/util/misc/pipes.rb +4 -2
- data/lib/rbbt/workflow/accessor.rb +8 -3
- data/lib/rbbt/workflow/step/run.rb +1 -2
- data/share/rbbt_commands/system/clean +1 -1
- data/share/rbbt_commands/tsv/sort +1 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 64ccfc0af909dbc006460786c31cd03ecb5a09d4
|
4
|
+
data.tar.gz: 221e3508c946239991fbb3fa8e4f9a4649cc954a
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 585970e6c3d50f7edd9b9188e5e45a7938b821bd0d6ed69b03b08b8fd6ee893cdff167d7804005ea96c7e5f5f3dea68445e4755d6be8724b3a8d5e03e31e94e3
|
7
|
+
data.tar.gz: 3f3d63792bdd57aee6b3e7b863c7af2ed65e77706edcc55b1fda8b185dc0207bfd2e193b197d67f91bbf5afc7c8fbf0bc384654f4aeb2c510f5fde11d49e0ce5
|
data/lib/rbbt/monitor.rb
CHANGED
@@ -2,8 +2,10 @@ require 'rbbt'
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|
2
2
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|
3
3
|
module Rbbt
|
4
4
|
|
5
|
-
LOCK_DIRS = Rbbt.share.find_all + Rbbt.var.cache.persistence.find_all + Rbbt.var.jobs.find_all +
|
6
|
-
|
5
|
+
#LOCK_DIRS = Rbbt.share.find_all + Rbbt.var.cache.persistence.find_all + Rbbt.var.jobs.find_all +
|
6
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+
# Rbbt.tmp.tsv_open_locks.find_all + Rbbt.tmp.persist_locks.find_all + Rbbt.tmp.sensiblewrite_lock_dir.find_all +
|
7
|
+
# Rbbt.tmp.produce_locks.find_all + Rbbt.tmp.step_info_locks.find_all
|
8
|
+
LOCK_DIRS = Rbbt.tmp.tsv_open_locks.find_all + Rbbt.tmp.persist_locks.find_all + Rbbt.tmp.sensiblewrite_lock_dir.find_all +
|
7
9
|
Rbbt.tmp.produce_locks.find_all + Rbbt.tmp.step_info_locks.find_all
|
8
10
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|
9
11
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SENSIBLE_WRITE_DIRS = Misc.sensiblewrite_dir.find_all
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@@ -48,7 +50,7 @@ module Rbbt
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|
48
50
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def self.locks(dirs = LOCK_DIRS)
|
49
51
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dirs.collect do |dir|
|
50
52
|
next unless Open.exists? dir
|
51
|
-
`find "#{ dir }" -name "*.lock"`.split "\n"
|
53
|
+
`find "#{ dir }" -name "*.lock" 2>/dev/null`.split "\n"
|
52
54
|
end.compact.flatten
|
53
55
|
end
|
54
56
|
|
@@ -67,7 +69,7 @@ module Rbbt
|
|
67
69
|
lock_info[f][:ppid] = info[:ppid]
|
68
70
|
end
|
69
71
|
rescue Exception
|
70
|
-
Log.exception $!
|
72
|
+
#Log.exception $!
|
71
73
|
end
|
72
74
|
end
|
73
75
|
lock_info
|
@@ -78,7 +80,7 @@ module Rbbt
|
|
78
80
|
def self.sensiblewrites(dirs = SENSIBLE_WRITE_DIRS)
|
79
81
|
dirs.collect do |dir|
|
80
82
|
next unless Open.exists? dir
|
81
|
-
`find "#{ dir }" -not -name "*.lock" -not -type d`.split "\n"
|
83
|
+
`find "#{ dir }" -not -name "*.lock" -not -type d 2>/dev/null`.split "\n"
|
82
84
|
end.compact.flatten
|
83
85
|
end
|
84
86
|
|
@@ -100,7 +102,7 @@ module Rbbt
|
|
100
102
|
def self.persists(dirs = PERSIST_DIRS)
|
101
103
|
dirs.collect do |dir|
|
102
104
|
next unless Open.exists? dir
|
103
|
-
`find "#{ dir }" -name "*.persist"`.split "\n"
|
105
|
+
`find "#{ dir }" -name "*.persist" 2>/dev/null`.split "\n"
|
104
106
|
end.compact.flatten
|
105
107
|
end
|
106
108
|
|
@@ -140,7 +142,7 @@ module Rbbt
|
|
140
142
|
task = File.basename(taskdir)
|
141
143
|
next if tasks and not tasks.include? task
|
142
144
|
|
143
|
-
files = `find "#{ taskdir }/" -not -type d -not -path "*/*.files/*"`.split("\n").sort
|
145
|
+
files = `find "#{ taskdir }/" -not -type d -not -path "*/*.files/*" 2>/dev/null`.split("\n").sort
|
144
146
|
_files = Set.new files
|
145
147
|
TSV.traverse files, :type => :array, :into => jobs do |file|
|
146
148
|
if m = file.match(/(.*).info$/)
|
data/lib/rbbt/tsv/stream.rb
CHANGED
@@ -78,7 +78,7 @@ module TSV
|
|
78
78
|
else
|
79
79
|
fields = fields.compact.flatten
|
80
80
|
end
|
81
|
-
options = options.merge(input_options.first)
|
81
|
+
options = options.merge(input_options.first || {})
|
82
82
|
options[:type] = :list if options[:type] == :single
|
83
83
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options[:type] = :double if fix_flat
|
84
84
|
|
@@ -37,7 +37,7 @@ module Misc
|
|
37
37
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":" << obj.to_s
|
38
38
|
when String
|
39
39
|
if obj.length > 100
|
40
|
-
"'" << obj.slice(0,30) << "<...#{obj.length}...>" << obj.slice(-10,30)
|
40
|
+
"'" << obj.slice(0,30) << "<...#{obj.length}...>" << obj.slice(-10,30)<< "'"
|
41
41
|
else
|
42
42
|
"'" << obj << "'"
|
43
43
|
end
|
data/lib/rbbt/util/misc/pipes.rb
CHANGED
@@ -256,7 +256,9 @@ module Misc
|
|
256
256
|
end
|
257
257
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|
258
258
|
begin
|
259
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-
|
259
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+
Misc.insist do
|
260
|
+
Open.mv tmp_path, path, lock_options
|
261
|
+
end
|
260
262
|
rescue Exception
|
261
263
|
raise $! unless File.exists? path
|
262
264
|
end
|
@@ -273,7 +275,7 @@ module Misc
|
|
273
275
|
content.abort if content.respond_to? :abort
|
274
276
|
Open.rm path if File.exists? path
|
275
277
|
rescue Exception
|
276
|
-
Log.medium "Exception in sensiblewrite: #{$!.message} -- #{ Log.color :blue, path }"
|
278
|
+
Log.medium "Exception in sensiblewrite: [#{Process.pid}] #{$!.message} -- #{ Log.color :blue, path }"
|
277
279
|
Log.exception $!
|
278
280
|
content.abort if content.respond_to? :abort
|
279
281
|
Open.rm path if File.exists? path
|
@@ -84,7 +84,7 @@ class Step
|
|
84
84
|
begin
|
85
85
|
Misc.insist do
|
86
86
|
begin
|
87
|
-
return @info_cache if @info_cache and File.ctime(info_file) < @info_cache_time
|
87
|
+
return @info_cache if @info_cache and @info_cache_time and File.ctime(info_file) < @info_cache_time
|
88
88
|
rescue Exception
|
89
89
|
raise $!
|
90
90
|
end
|
@@ -94,8 +94,13 @@ class Step
|
|
94
94
|
Misc.insist(2, 1, info_file) do
|
95
95
|
Misc.insist(3, 0.2, info_file) do
|
96
96
|
raise TryAgain, "Info locked" if check_lock and info_lock.locked?
|
97
|
-
|
98
|
-
|
97
|
+
info_lock.lock if check_lock and false
|
98
|
+
begin
|
99
|
+
Open.open(info_file) do |file|
|
100
|
+
INFO_SERIALIAZER.load(file) #|| {}
|
101
|
+
end
|
102
|
+
ensure
|
103
|
+
info_lock.unlock if check_lock and false
|
99
104
|
end
|
100
105
|
end
|
101
106
|
end
|
@@ -164,7 +164,7 @@ class Step
|
|
164
164
|
end
|
165
165
|
else
|
166
166
|
Log.info "#{Log.color :cyan, "dependency"} #{Log.color :yellow, task.name.to_s || ""} => #{Log.color :yellow, dependency.task_name.to_s || ""} starting -- #{Log.color :blue, dependency.path}"
|
167
|
-
dependency.run(true)
|
167
|
+
dependency.run(true).grace
|
168
168
|
end
|
169
169
|
else
|
170
170
|
Log.info "#{Log.color :cyan, "dependency"} #{Log.color :yellow, task.name.to_s || ""} => #{Log.color :yellow, dependency.task_name.to_s || ""} done -- #{Log.color :blue, dependency.path}"
|
@@ -215,7 +215,6 @@ class Step
|
|
215
215
|
raise $!
|
216
216
|
end
|
217
217
|
|
218
|
-
|
219
218
|
set_info :inputs, Misc.remove_long_items(Misc.zip2hash(task.inputs, @inputs)) unless task.inputs.nil?
|
220
219
|
|
221
220
|
set_info :started, (start_time = Time.now)
|
@@ -29,7 +29,7 @@ if field =~ /^\d+$/
|
|
29
29
|
else
|
30
30
|
parser = TSV.parse_header(file, options)
|
31
31
|
field_pos = parser.all_fields.index(field) + 1
|
32
|
-
saved_line = parser.
|
32
|
+
saved_line = parser.first_line
|
33
33
|
end
|
34
34
|
|
35
35
|
rest = ARGV.inject("-t\"\t\" -g -k#{field_pos}"){|acc,e| acc << " '#{e}'" }
|
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: 5.19.
|
4
|
+
version: 5.19.18
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2016-02-
|
11
|
+
date: 2016-02-27 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|