rbbt-util 5.20.2 → 5.20.3
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- checksums.yaml +4 -4
- data/lib/rbbt/association/index.rb +3 -4
- data/lib/rbbt/tsv/accessor.rb +1 -1
- data/lib/rbbt/tsv/manipulate.rb +0 -1
- data/lib/rbbt/tsv/parallel/traverse.rb +8 -2
- data/lib/rbbt/util/cmd.rb +1 -1
- data/lib/rbbt/util/concurrency/processes.rb +4 -3
- data/lib/rbbt/util/concurrency/processes/worker.rb +4 -2
- data/lib/rbbt/util/log/progress/util.rb +20 -1
- data/lib/rbbt/util/misc/bgzf.rb +1 -1
- data/lib/rbbt/util/misc/inspect.rb +7 -3
- data/lib/rbbt/util/misc/multipart_payload.rb +8 -8
- data/lib/rbbt/util/misc/pipes.rb +115 -51
- data/lib/rbbt/util/open.rb +1 -1
- data/lib/rbbt/workflow.rb +1 -0
- data/lib/rbbt/workflow/accessor.rb +86 -15
- data/lib/rbbt/workflow/definition.rb +10 -17
- data/lib/rbbt/workflow/step.rb +4 -16
- data/lib/rbbt/workflow/step/dependencies.rb +451 -0
- data/lib/rbbt/workflow/step/run.rb +43 -226
- data/lib/rbbt/workflow/task.rb +7 -1
- data/share/rbbt_commands/association/subset +6 -1
- data/share/rbbt_commands/workflow/task +21 -9
- data/test/rbbt/util/misc/test_pipes.rb +54 -0
- data/test/rbbt/workflow/step/test_dependencies.rb +206 -0
- metadata +5 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: c01ec7b654f4f713aaf4c9cf3b518aec087009de
|
4
|
+
data.tar.gz: 2721569f2e2a9445c97415eb5093150a6ca1850a
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: c152113e19eaea2dac605abdff6e60132137dd1eb09f797befc230d2d4eb6422ce5c9c0defaaab6d6f684e772c0d65776efc0836ffacbf680b9881d1e4a13d41
|
7
|
+
data.tar.gz: 68a251d79736a2c0d54120f50071015c96a51270886f83ea951ca460fc1c0ae48af8f07ad3a90d1ed93a81af0acbfb7d3de7b57907ebaca741610e06e3de4740
|
@@ -59,18 +59,16 @@ module Association
|
|
59
59
|
list.replace [list.first] * size if list.length == 1
|
60
60
|
end if recycle and size > 1
|
61
61
|
|
62
|
-
|
63
62
|
rest = Misc.zip_fields rest
|
64
63
|
|
65
|
-
|
66
64
|
annotations = (Array === rest.first and rest.first.length > 1) ?
|
67
65
|
targets.zip(rest) :
|
68
66
|
targets.zip(rest * targets.length)
|
69
67
|
|
68
|
+
source = source.gsub('~','-..-')
|
70
69
|
annotations.each do |target, info|
|
71
70
|
next if target.nil? or target.empty?
|
72
|
-
|
73
|
-
target.gsub!('~','-..-')
|
71
|
+
target = target.gsub('~','-..-')
|
74
72
|
key = [source, target] * "~"
|
75
73
|
|
76
74
|
if data[key].nil? or info.nil?
|
@@ -160,6 +158,7 @@ module Association
|
|
160
158
|
|
161
159
|
new.undirected = undirected
|
162
160
|
|
161
|
+
Log.tsv new
|
163
162
|
new
|
164
163
|
rescue Exception
|
165
164
|
Log.error "Deleting after error reversing database: #{ reverse_filename }"
|
data/lib/rbbt/tsv/accessor.rb
CHANGED
data/lib/rbbt/tsv/manipulate.rb
CHANGED
@@ -20,7 +20,13 @@ module TSV
|
|
20
20
|
case obj
|
21
21
|
when (defined? Step and Step)
|
22
22
|
if obj.done?
|
23
|
-
|
23
|
+
path = obj.path
|
24
|
+
path = path.find if path.respond_to? :find
|
25
|
+
if File.exists? path
|
26
|
+
CMD.cmd("wc -l '#{path}'").read.to_i
|
27
|
+
else
|
28
|
+
nil
|
29
|
+
end
|
24
30
|
else
|
25
31
|
nil
|
26
32
|
end
|
@@ -349,7 +355,7 @@ module TSV
|
|
349
355
|
respawn = true if ENV["RBBT_RESPAWN"] and ENV["RBBT_RESPAWN"] == "true"
|
350
356
|
|
351
357
|
Log.low "Traversing in #{ num } cpus: #{respawn ? "respawn" : "no respawn"}"
|
352
|
-
q = RbbtProcessQueue.new num, cleanup, join, respawn
|
358
|
+
q = RbbtProcessQueue.new num, cleanup, join, respawn, !!bar
|
353
359
|
callback = Proc.new{ bar.tick } if callback.nil? and bar
|
354
360
|
q.callback &callback
|
355
361
|
q.init &block
|
data/lib/rbbt/util/cmd.rb
CHANGED
@@ -3,13 +3,14 @@ require 'rbbt/util/concurrency/processes/socket'
|
|
3
3
|
|
4
4
|
class RbbtProcessQueue
|
5
5
|
|
6
|
-
attr_accessor :num_processes, :processes, :queue, :process_monitor, :cleanup, :join, :reswpan
|
7
|
-
def initialize(num_processes, cleanup = nil, join = nil, reswpan = nil)
|
6
|
+
attr_accessor :num_processes, :processes, :queue, :process_monitor, :cleanup, :join, :reswpan, :offset
|
7
|
+
def initialize(num_processes, cleanup = nil, join = nil, reswpan = nil, offset = false)
|
8
8
|
@num_processes = num_processes
|
9
9
|
@processes = []
|
10
10
|
@cleanup = cleanup
|
11
11
|
@join = join
|
12
12
|
@respawn = reswpan
|
13
|
+
@offset = offset
|
13
14
|
@queue = RbbtProcessSocket.new
|
14
15
|
end
|
15
16
|
|
@@ -59,7 +60,7 @@ class RbbtProcessQueue
|
|
59
60
|
|
60
61
|
def init(&block)
|
61
62
|
num_processes.times do |i|
|
62
|
-
@processes << RbbtProcessQueueWorker.new(@queue, @callback_queue, @cleanup, @respawn, &block)
|
63
|
+
@processes << RbbtProcessQueueWorker.new(@queue, @callback_queue, @cleanup, @respawn, @offset, &block)
|
63
64
|
end
|
64
65
|
@queue.close_read
|
65
66
|
|
@@ -120,11 +120,12 @@ class RbbtProcessQueue
|
|
120
120
|
end
|
121
121
|
end
|
122
122
|
|
123
|
-
def initialize(queue, callback_queue = nil, cleanup = nil, respawn = false, &block)
|
124
|
-
@queue, @callback_queue, @cleanup, @block = queue, callback_queue, cleanup, block
|
123
|
+
def initialize(queue, callback_queue = nil, cleanup = nil, respawn = false, offset = false, &block)
|
124
|
+
@queue, @callback_queue, @cleanup, @block, @offset = queue, callback_queue, cleanup, block, offset
|
125
125
|
|
126
126
|
@pid = Process.fork do
|
127
127
|
Misc.pre_fork
|
128
|
+
Log::ProgressBar.add_offset if @offset
|
128
129
|
|
129
130
|
@cleanup.call if @cleanup
|
130
131
|
@queue.close_write
|
@@ -141,6 +142,7 @@ class RbbtProcessQueue
|
|
141
142
|
else
|
142
143
|
run
|
143
144
|
end
|
145
|
+
Log::ProgressBar.remove_offset if @offset
|
144
146
|
end
|
145
147
|
end
|
146
148
|
|
@@ -5,11 +5,30 @@ module Log
|
|
5
5
|
REMOVE = []
|
6
6
|
SILENCED = []
|
7
7
|
|
8
|
+
def self.add_offset
|
9
|
+
@@offset = offset + 1
|
10
|
+
@@offset = 0 if @@offset < 0
|
11
|
+
@@offset
|
12
|
+
end
|
13
|
+
|
14
|
+
def self.remove_offset
|
15
|
+
@@offset = offset - 1
|
16
|
+
@@offset = 0 if @@offset < 0
|
17
|
+
@@offset
|
18
|
+
end
|
19
|
+
|
20
|
+
|
21
|
+
def self.offset
|
22
|
+
@@offset ||= 0
|
23
|
+
@@offset = 0 if @@offset < 0
|
24
|
+
@@offset
|
25
|
+
end
|
26
|
+
|
8
27
|
def self.new_bar(max, options = {})
|
9
28
|
cleanup_bars
|
10
29
|
BAR_MUTEX.synchronize do
|
11
30
|
#Log::LAST.replace "new_bar" if Log::LAST == "progress"
|
12
|
-
options = Misc.add_defaults options, :depth => BARS.length
|
31
|
+
options = Misc.add_defaults options, :depth => BARS.length + Log::ProgressBar.offset
|
13
32
|
BARS << (bar = ProgressBar.new(max, options))
|
14
33
|
bar
|
15
34
|
end
|
data/lib/rbbt/util/misc/bgzf.rb
CHANGED
@@ -65,7 +65,7 @@ module Misc
|
|
65
65
|
else
|
66
66
|
new = "{"
|
67
67
|
obj.each do |k,v|
|
68
|
-
new << k
|
68
|
+
new << fingerprint(k) << '=>' << fingerprint(v) << ' '
|
69
69
|
end
|
70
70
|
if new.length > 1
|
71
71
|
new[-1] = "}"
|
@@ -249,8 +249,8 @@ module Misc
|
|
249
249
|
str
|
250
250
|
end
|
251
251
|
|
252
|
-
|
253
|
-
def self.
|
252
|
+
|
253
|
+
def self.obj2digest(obj)
|
254
254
|
str = obj2str(obj)
|
255
255
|
|
256
256
|
if str.empty?
|
@@ -259,4 +259,8 @@ module Misc
|
|
259
259
|
digest(str)
|
260
260
|
end
|
261
261
|
end
|
262
|
+
|
263
|
+
def self.obj2md5(obj)
|
264
|
+
obj2digest(obj)
|
265
|
+
end
|
262
266
|
end
|
@@ -22,7 +22,7 @@ module RbbtMutiplartPayload
|
|
22
22
|
EOL = "\r\n"
|
23
23
|
|
24
24
|
def self.mutex
|
25
|
-
|
25
|
+
@@mutex ||= Mutex.new
|
26
26
|
end
|
27
27
|
|
28
28
|
def self.input_header(name, filename = nil)
|
@@ -47,17 +47,19 @@ module RbbtMutiplartPayload
|
|
47
47
|
|
48
48
|
def self.add_stream(io, name, content, filename = nil)
|
49
49
|
header = input_header(name, filename)
|
50
|
-
io.write "--" + BOUNDARY + EOL + header + EOL
|
50
|
+
io.write "--" + BOUNDARY + EOL + header + EOL
|
51
51
|
|
52
|
-
|
53
|
-
|
52
|
+
begin
|
53
|
+
while c = content.readpartial(Misc::BLOCK_SIZE)
|
54
|
+
io.write c
|
55
|
+
end
|
56
|
+
rescue EOFError
|
54
57
|
end
|
55
58
|
content.close
|
56
59
|
end
|
57
60
|
|
58
61
|
def self.close_stream(io)
|
59
62
|
io.write "--" + BOUNDARY + "--" + EOL + EOL
|
60
|
-
io.write EOL
|
61
63
|
io.close
|
62
64
|
end
|
63
65
|
|
@@ -121,8 +123,7 @@ module RbbtMutiplartPayload
|
|
121
123
|
req.body = sout.read
|
122
124
|
end
|
123
125
|
|
124
|
-
Misc.open_pipe
|
125
|
-
sleep rand(10).to_f / 5
|
126
|
+
Misc.open_pipe do |sin|
|
126
127
|
Net::HTTP.start(uri.hostname, uri.port) do |http|
|
127
128
|
http.request(req) do |res|
|
128
129
|
url_path = res["RBBT-STREAMING-JOB-URL"]
|
@@ -139,7 +140,6 @@ module RbbtMutiplartPayload
|
|
139
140
|
sin.puts "BULK" if report_type
|
140
141
|
sin.write res.body
|
141
142
|
end
|
142
|
-
sin.close
|
143
143
|
end
|
144
144
|
end
|
145
145
|
end
|
data/lib/rbbt/util/misc/pipes.rb
CHANGED
@@ -16,6 +16,8 @@ module Misc
|
|
16
16
|
end
|
17
17
|
end
|
18
18
|
|
19
|
+
BLOCK_SIZE=1024 * 8
|
20
|
+
|
19
21
|
PIPE_MUTEX = Mutex.new
|
20
22
|
|
21
23
|
OPEN_PIPE_IN = []
|
@@ -87,70 +89,136 @@ module Misc
|
|
87
89
|
sout
|
88
90
|
end
|
89
91
|
|
90
|
-
def self.tee_stream_thread(stream)
|
91
|
-
|
92
|
-
|
92
|
+
#def self.tee_stream_thread(stream)
|
93
|
+
# stream_out1, stream_in1 = Misc.pipe
|
94
|
+
# stream_out2, stream_in2 = Misc.pipe
|
95
|
+
|
96
|
+
# splitter_thread = Thread.new(Thread.current) do |parent|
|
97
|
+
# begin
|
98
|
+
|
99
|
+
# skip1 = skip2 = false
|
100
|
+
# while block = stream.read(1024)
|
101
|
+
|
102
|
+
# begin
|
103
|
+
# stream_in1.write block;
|
104
|
+
# rescue IOError
|
105
|
+
# Log.medium("Tee stream 1 #{Misc.fingerprint stream} IOError: #{$!.message}");
|
106
|
+
# skip1 = true
|
107
|
+
# end unless skip1
|
108
|
+
|
109
|
+
# begin
|
110
|
+
# stream_in2.write block
|
111
|
+
# rescue IOError
|
112
|
+
# Log.medium("Tee stream 2 #{Misc.fingerprint stream} IOError: #{$!.message}");
|
113
|
+
# skip2 = true
|
114
|
+
# end unless skip2
|
115
|
+
|
116
|
+
# end
|
117
|
+
|
118
|
+
# stream_in1.close unless stream_in1.closed?
|
119
|
+
# stream.join if stream.respond_to? :join
|
120
|
+
# stream_in2.close unless stream_in2.closed?
|
121
|
+
# rescue Aborted, Interrupt
|
122
|
+
# stream_out1.abort if stream_out1.respond_to? :abort
|
123
|
+
# stream.abort if stream.respond_to? :abort
|
124
|
+
# stream_out2.abort if stream_out2.respond_to? :abort
|
125
|
+
# Log.medium "Tee aborting #{Misc.fingerprint stream}"
|
126
|
+
# raise $!
|
127
|
+
# rescue Exception
|
128
|
+
# stream_out1.abort if stream_out1.respond_to? :abort
|
129
|
+
# stream.abort if stream.respond_to? :abort
|
130
|
+
# stream_out2.abort if stream_out2.respond_to? :abort
|
131
|
+
# Log.medium "Tee exception #{Misc.fingerprint stream}"
|
132
|
+
# raise $!
|
133
|
+
# end
|
134
|
+
# end
|
135
|
+
|
136
|
+
# ConcurrentStream.setup stream_out1, :threads => splitter_thread
|
137
|
+
# ConcurrentStream.setup stream_out2, :threads => splitter_thread
|
138
|
+
|
139
|
+
# [stream_out1, stream_out2]
|
140
|
+
#end
|
141
|
+
|
142
|
+
def self.tee_stream_thread_multiple(stream, num = 2)
|
143
|
+
in_pipes = []
|
144
|
+
out_pipes = []
|
145
|
+
num.times do
|
146
|
+
sout, sin = Misc.pipe
|
147
|
+
in_pipes << sin
|
148
|
+
out_pipes << sout
|
149
|
+
end
|
93
150
|
|
94
151
|
splitter_thread = Thread.new(Thread.current) do |parent|
|
95
152
|
begin
|
96
153
|
|
97
|
-
|
98
|
-
|
99
|
-
|
100
|
-
|
101
|
-
|
102
|
-
|
103
|
-
|
104
|
-
|
105
|
-
|
106
|
-
|
107
|
-
|
108
|
-
|
109
|
-
|
110
|
-
|
111
|
-
skip2 = true
|
112
|
-
end unless skip2
|
113
|
-
|
154
|
+
skip = [false] * num
|
155
|
+
begin
|
156
|
+
while block = stream.readpartial(BLOCK_SIZE)
|
157
|
+
|
158
|
+
in_pipes.each_with_index do |sin,i|
|
159
|
+
begin
|
160
|
+
sin.write block;
|
161
|
+
rescue IOError
|
162
|
+
Log.medium("Tee stream #{i} #{Misc.fingerprint stream} IOError: #{$!.message}");
|
163
|
+
skip[i] = true
|
164
|
+
end unless skip[i]
|
165
|
+
end
|
166
|
+
end
|
167
|
+
rescue IOError
|
114
168
|
end
|
115
169
|
|
116
|
-
|
170
|
+
in_pipes.each do |sin|
|
171
|
+
sin.close unless sin.closed?
|
172
|
+
end
|
117
173
|
stream.join if stream.respond_to? :join
|
118
|
-
stream_in2.close unless stream_in2.closed?
|
119
174
|
rescue Aborted, Interrupt
|
120
|
-
stream_out1.abort if stream_out1.respond_to? :abort
|
121
175
|
stream.abort if stream.respond_to? :abort
|
122
|
-
|
176
|
+
out_pipes.each do |sout|
|
177
|
+
sout.abort if sout.respond_to? :abort
|
178
|
+
end
|
123
179
|
Log.medium "Tee aborting #{Misc.fingerprint stream}"
|
124
180
|
raise $!
|
125
181
|
rescue Exception
|
126
|
-
stream_out1.abort if stream_out1.respond_to? :abort
|
127
182
|
stream.abort if stream.respond_to? :abort
|
128
|
-
|
183
|
+
out_pipes.each do |sout|
|
184
|
+
sout.abort if sout.respond_to? :abort
|
185
|
+
end
|
129
186
|
Log.medium "Tee exception #{Misc.fingerprint stream}"
|
130
187
|
raise $!
|
131
188
|
end
|
132
189
|
end
|
133
190
|
|
134
|
-
|
135
|
-
|
191
|
+
out_pipes.each do |sout|
|
192
|
+
ConcurrentStream.setup sout, :threads => splitter_thread
|
193
|
+
end
|
136
194
|
|
137
|
-
|
138
|
-
|
195
|
+
out_pipes
|
196
|
+
end
|
139
197
|
|
140
|
-
|
141
|
-
|
198
|
+
def self.tee_stream_thread(stream)
|
199
|
+
tee_stream_thread_multiple(stream, 2)
|
200
|
+
end
|
142
201
|
|
143
|
-
|
202
|
+
def self.dup_stream_multiple(stream, num = 1)
|
203
|
+
stream_dup = stream.dup
|
204
|
+
if stream.respond_to? :annotate
|
205
|
+
stream.annotate stream_dup
|
206
|
+
stream.clear
|
207
|
+
end
|
208
|
+
tee1, *rest = Misc.tee_stream stream_dup, num + 1
|
209
|
+
stream.reopen(tee1)
|
210
|
+
rest
|
144
211
|
end
|
145
212
|
|
146
213
|
class << self
|
147
|
-
alias tee_stream
|
214
|
+
alias tee_stream tee_stream_thread_multiple
|
215
|
+
alias dup_stream dup_stream_multiple
|
148
216
|
end
|
149
217
|
|
150
218
|
def self.read_full_stream(io)
|
151
219
|
str = ""
|
152
220
|
begin
|
153
|
-
while block = io.read(
|
221
|
+
while block = io.read(BLOCK_SIZE)
|
154
222
|
str << block
|
155
223
|
end
|
156
224
|
io.join if io.respond_to? :join
|
@@ -182,10 +250,17 @@ module Misc
|
|
182
250
|
begin
|
183
251
|
into = into.find if Path === into
|
184
252
|
into = Open.open(into, :mode => 'w') if String === into
|
185
|
-
into.sync
|
186
|
-
|
187
|
-
|
253
|
+
into.sync = true if IO === into
|
254
|
+
into_close = false unless into.respond_to? :close
|
255
|
+
io.sync = true
|
256
|
+
|
257
|
+
begin
|
258
|
+
while block = io.readpartial(BLOCK_SIZE)
|
259
|
+
into << block if into
|
260
|
+
end
|
261
|
+
rescue EOFError
|
188
262
|
end
|
263
|
+
|
189
264
|
io.join if io.respond_to? :join
|
190
265
|
io.close unless io.closed?
|
191
266
|
into.close if into and into_close and not into.closed?
|
@@ -256,7 +331,7 @@ module Misc
|
|
256
331
|
|
257
332
|
Open.write(tmp_path) do |f|
|
258
333
|
f.sync = true
|
259
|
-
while block = content.read(
|
334
|
+
while block = content.read(BLOCK_SIZE)
|
260
335
|
f.write block
|
261
336
|
end
|
262
337
|
end
|
@@ -340,7 +415,7 @@ module Misc
|
|
340
415
|
|
341
416
|
sorted = CMD.cmd("env LC_ALL=C sort #{cmd_args || ""}", :in => line_stream, :pipe => true)
|
342
417
|
|
343
|
-
while block = sorted.read(
|
418
|
+
while block = sorted.read(BLOCK_SIZE)
|
344
419
|
sin.write block
|
345
420
|
end
|
346
421
|
|
@@ -476,17 +551,6 @@ module Misc
|
|
476
551
|
end
|
477
552
|
end
|
478
553
|
|
479
|
-
def self.dup_stream(stream)
|
480
|
-
stream_dup = stream.dup
|
481
|
-
if stream.respond_to? :annotate
|
482
|
-
stream.annotate stream_dup
|
483
|
-
stream.clear
|
484
|
-
end
|
485
|
-
tee1, tee2 = Misc.tee_stream stream_dup
|
486
|
-
stream.reopen(tee1)
|
487
|
-
tee2
|
488
|
-
end
|
489
|
-
|
490
554
|
def self.save_stream(file, stream)
|
491
555
|
out, save = Misc.tee_stream stream
|
492
556
|
out.filename = file
|