rbbt-util 5.27.2 → 5.27.7
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- checksums.yaml +4 -4
- data/lib/rbbt/fix_width_table.rb +6 -5
- data/lib/rbbt/persist/tsv.rb +5 -5
- data/lib/rbbt/persist/tsv/adapter.rb +89 -38
- data/lib/rbbt/persist/tsv/tokyocabinet.rb +5 -3
- data/lib/rbbt/resource.rb +8 -5
- data/lib/rbbt/resource/path.rb +3 -3
- data/lib/rbbt/tsv/accessor.rb +6 -6
- data/lib/rbbt/tsv/change_id.rb +3 -1
- data/lib/rbbt/tsv/stream.rb +1 -0
- data/lib/rbbt/util/misc/exceptions.rb +8 -0
- data/lib/rbbt/util/misc/pipes.rb +37 -7
- data/lib/rbbt/workflow.rb +1 -1
- data/lib/rbbt/workflow/accessor.rb +3 -1
- data/lib/rbbt/workflow/definition.rb +6 -0
- data/lib/rbbt/workflow/remote_workflow/driver/rest.rb +9 -3
- data/lib/rbbt/workflow/remote_workflow/remote_step.rb +9 -3
- data/lib/rbbt/workflow/remote_workflow/remote_step/rest.rb +7 -1
- data/lib/rbbt/workflow/step/accessor.rb +4 -0
- data/lib/rbbt/workflow/step/dependencies.rb +11 -7
- data/lib/rbbt/workflow/step/run.rb +1 -1
- data/lib/rbbt/workflow/task.rb +1 -1
- data/lib/rbbt/workflow/util/archive.rb +30 -4
- data/share/install/software/lib/install_helpers +7 -3
- data/share/rbbt_commands/migrate_job +3 -1
- data/share/rbbt_commands/system/status +3 -2
- data/share/rbbt_commands/workflow/monitor +3 -3
- data/test/rbbt/tsv/test_stream.rb +4 -3
- data/test/rbbt/util/misc/test_pipes.rb +1 -1
- data/test/rbbt/workflow/step/test_dependencies.rb +106 -17
- data/test/rbbt/workflow/test_remote_workflow.rb +13 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 6551d632ae1f2289805a53ceaf9db01d0c0a029ea6c76176aed419e4d6a2a485
|
4
|
+
data.tar.gz: 72562729535554e718451adb87338503ff40a81874a9e0fed6f8eaf4e6aa0edc
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 0d8c3ff2861dd4bbd835e3e41826f5fd6452bdd0b40fbd8378737effdffa6da051ce221e24f4bbacaf952725ccf7da09b533c8c414a7fd10480369ae528a4259
|
7
|
+
data.tar.gz: 1790b8f38f91dfbb582a394d86953156d90351a8d724fb9535a3bc72ebac5fbbfe24e88fe10cf943e2ed91ff059af68cf581bac333f5480096f85cf6e29b8018
|
data/lib/rbbt/fix_width_table.rb
CHANGED
@@ -4,20 +4,21 @@ class FixWidthTable
|
|
4
4
|
def initialize(filename, value_size = nil, range = nil, update = false, in_memory = true)
|
5
5
|
@filename = filename
|
6
6
|
|
7
|
-
if update
|
7
|
+
if update || %w(memory stringio).include?(filename.to_s.downcase) || ! File.exist?(filename)
|
8
8
|
Log.debug "FixWidthTable create: #{ filename }"
|
9
9
|
@value_size = value_size
|
10
10
|
@range = range
|
11
11
|
@record_size = @value_size + (@range ? 16 : 8)
|
12
12
|
@write = true
|
13
13
|
|
14
|
-
if %w(memory stringio).include?
|
14
|
+
if %w(memory stringio).include?(filename.to_s.downcase)
|
15
15
|
@filename = :memory
|
16
16
|
@file = StringIO.new
|
17
17
|
else
|
18
18
|
FileUtils.rm @filename if File.exist? @filename
|
19
19
|
FileUtils.mkdir_p File.dirname(@filename) unless File.exist? @filename
|
20
|
-
|
20
|
+
#@file = File.open(@filename, 'wb')
|
21
|
+
@file = File.open(@filename, 'w:ASCII-8BIT')
|
21
22
|
end
|
22
23
|
|
23
24
|
@file.write [value_size].pack("L")
|
@@ -25,9 +26,9 @@ class FixWidthTable
|
|
25
26
|
|
26
27
|
@size = 0
|
27
28
|
else
|
28
|
-
Log.debug "FixWidthTable up-to-date: #{ filename }"
|
29
|
+
Log.debug "FixWidthTable up-to-date: #{ filename } - (in_memory:#{in_memory})"
|
29
30
|
if in_memory
|
30
|
-
@file =
|
31
|
+
@file = Open.open(@filename, :mode => 'r:ASCII-ASCII'){|f| StringIO.new f.read}
|
31
32
|
else
|
32
33
|
@file = File.open(@filename, 'r:ASCII-8BIT')
|
33
34
|
end
|
data/lib/rbbt/persist/tsv.rb
CHANGED
@@ -148,13 +148,13 @@ module Persist
|
|
148
148
|
|
149
149
|
data.write_and_read do
|
150
150
|
yield data
|
151
|
-
end
|
152
151
|
|
153
|
-
|
154
|
-
|
155
|
-
|
152
|
+
FileUtils.mv data.persistence_path, path if File.exist? data.persistence_path and not File.exist? path
|
153
|
+
tsv = CONNECTIONS[path] = CONNECTIONS.delete tmp_path
|
154
|
+
tsv.persistence_path = path
|
156
155
|
|
157
|
-
|
156
|
+
tsv.fix_io if tsv.respond_to? :fix_io
|
157
|
+
end
|
158
158
|
|
159
159
|
data
|
160
160
|
rescue Exception
|
@@ -9,25 +9,10 @@ module Persist
|
|
9
9
|
@mutex ||= Mutex.new
|
10
10
|
end
|
11
11
|
|
12
|
-
def prefix(key)
|
13
|
-
range(key, 1, key + MAX_CHAR, 1)
|
14
|
-
end
|
15
|
-
|
16
|
-
def get_prefix(key)
|
17
|
-
keys = prefix(key)
|
18
|
-
select(:key => keys)
|
19
|
-
end
|
20
|
-
|
21
12
|
def closed?
|
22
13
|
@closed
|
23
14
|
end
|
24
15
|
|
25
|
-
def close
|
26
|
-
@closed = true
|
27
|
-
super
|
28
|
-
self
|
29
|
-
end
|
30
|
-
|
31
16
|
def write?
|
32
17
|
@writable
|
33
18
|
end
|
@@ -47,8 +32,10 @@ module Persist
|
|
47
32
|
def close(*args)
|
48
33
|
begin
|
49
34
|
super(*args)
|
35
|
+
@closed = true
|
50
36
|
rescue NoMethodError
|
51
37
|
end
|
38
|
+
self
|
52
39
|
end
|
53
40
|
|
54
41
|
def read(*args)
|
@@ -58,25 +45,14 @@ module Persist
|
|
58
45
|
end
|
59
46
|
end
|
60
47
|
|
61
|
-
def collect
|
62
|
-
res = []
|
63
|
-
each do |key, value|
|
64
|
-
res << if block_given?
|
65
|
-
yield key, value
|
66
|
-
else
|
67
|
-
[key, value]
|
68
|
-
end
|
69
|
-
end
|
70
|
-
res
|
71
|
-
end
|
72
|
-
|
73
48
|
def delete(key)
|
74
49
|
out(key)
|
75
50
|
end
|
76
51
|
|
77
52
|
def lock
|
78
|
-
|
53
|
+
return yield if @locked
|
79
54
|
lock_filename = Persist.persistence_path(persistence_path, {:dir => TSV.lock_dir})
|
55
|
+
Log.stack caller if $LOG
|
80
56
|
Misc.lock(lock_filename) do
|
81
57
|
begin
|
82
58
|
@locked = true
|
@@ -87,6 +63,16 @@ module Persist
|
|
87
63
|
end
|
88
64
|
end
|
89
65
|
|
66
|
+
def lock_and_close
|
67
|
+
lock do
|
68
|
+
begin
|
69
|
+
yield
|
70
|
+
ensure
|
71
|
+
close
|
72
|
+
end
|
73
|
+
end
|
74
|
+
end
|
75
|
+
|
90
76
|
def write_and_read
|
91
77
|
if write?
|
92
78
|
begin
|
@@ -97,7 +83,7 @@ module Persist
|
|
97
83
|
end
|
98
84
|
|
99
85
|
lock do
|
100
|
-
write
|
86
|
+
write(true) if closed? || !write?
|
101
87
|
begin
|
102
88
|
yield
|
103
89
|
ensure
|
@@ -111,12 +97,12 @@ module Persist
|
|
111
97
|
begin
|
112
98
|
return yield
|
113
99
|
ensure
|
114
|
-
close
|
100
|
+
close unless @locked
|
115
101
|
end
|
116
102
|
end
|
117
103
|
|
118
104
|
lock do
|
119
|
-
write
|
105
|
+
write(true) if closed? || ! write?
|
120
106
|
res = begin
|
121
107
|
yield
|
122
108
|
rescue Exception
|
@@ -130,11 +116,12 @@ module Persist
|
|
130
116
|
end
|
131
117
|
|
132
118
|
def read_and_close
|
133
|
-
if
|
119
|
+
#return yield if @locked
|
120
|
+
if read? || write?
|
134
121
|
begin
|
135
122
|
return yield
|
136
123
|
ensure
|
137
|
-
close
|
124
|
+
close unless @locked
|
138
125
|
end
|
139
126
|
end
|
140
127
|
|
@@ -148,21 +135,85 @@ module Persist
|
|
148
135
|
end
|
149
136
|
end
|
150
137
|
|
151
|
-
|
152
138
|
def merge!(hash)
|
153
139
|
hash.each do |key,values|
|
154
140
|
self[key] = values
|
155
141
|
end
|
156
142
|
end
|
157
143
|
|
158
|
-
|
159
144
|
def range(*args)
|
160
|
-
|
145
|
+
self.read_and_close do
|
146
|
+
super(*args)
|
147
|
+
end
|
161
148
|
end
|
162
149
|
|
163
150
|
def include?(*args)
|
164
|
-
|
165
|
-
|
151
|
+
self.read_and_close do
|
152
|
+
super(*args) #- TSV::ENTRY_KEYS.to_a
|
153
|
+
end
|
154
|
+
end
|
155
|
+
|
156
|
+
def [](*args)
|
157
|
+
self.read_and_close do
|
158
|
+
super(*args) #- TSV::ENTRY_KEYS.to_a
|
159
|
+
end
|
160
|
+
end
|
161
|
+
|
162
|
+
def []=(*args)
|
163
|
+
self.write_and_close do
|
164
|
+
super(*args) #- TSV::ENTRY_KEYS.to_a
|
165
|
+
end
|
166
|
+
end
|
167
|
+
|
168
|
+
def keys(*args)
|
169
|
+
self.read_and_close do
|
170
|
+
super(*args)
|
171
|
+
end
|
172
|
+
end
|
173
|
+
|
174
|
+
|
175
|
+
def prefix(key)
|
176
|
+
self.read_and_close do
|
177
|
+
range(key, 1, key + MAX_CHAR, 1)
|
178
|
+
end
|
179
|
+
end
|
180
|
+
|
181
|
+
def get_prefix(key)
|
182
|
+
keys = prefix(key)
|
183
|
+
select(:key => keys)
|
184
|
+
end
|
185
|
+
|
186
|
+
|
187
|
+
def size(*args)
|
188
|
+
self.read_and_close do
|
189
|
+
super(*args)
|
190
|
+
end
|
191
|
+
end
|
192
|
+
|
193
|
+
def each(*args, &block)
|
194
|
+
self.read_and_close do
|
195
|
+
super(*args, &block)
|
196
|
+
end
|
197
|
+
end
|
198
|
+
|
199
|
+
def collect
|
200
|
+
res = []
|
201
|
+
each do |key, value|
|
202
|
+
res << if block_given?
|
203
|
+
yield key, value
|
204
|
+
else
|
205
|
+
[key, value]
|
206
|
+
end
|
207
|
+
end
|
208
|
+
res
|
209
|
+
end
|
210
|
+
|
211
|
+
def values_at(*keys)
|
212
|
+
self.read_and_close do
|
213
|
+
keys.collect do |k|
|
214
|
+
self[k]
|
215
|
+
end
|
216
|
+
end
|
166
217
|
end
|
167
218
|
end
|
168
219
|
end
|
@@ -16,7 +16,7 @@ module Persist
|
|
16
16
|
end
|
17
17
|
|
18
18
|
dir = File.dirname(File.expand_path(path))
|
19
|
-
|
19
|
+
File.mkdir(dir) unless File.exists?(dir)
|
20
20
|
|
21
21
|
tokyocabinet_class = TokyoCabinet::HDB if tokyocabinet_class == "HDB" or tokyocabinet_class.nil?
|
22
22
|
tokyocabinet_class = TokyoCabinet::BDB if tokyocabinet_class == "BDB"
|
@@ -87,13 +87,15 @@ module Persist
|
|
87
87
|
def self.open_tokyocabinet(path, write, serializer = nil, tokyocabinet_class = TokyoCabinet::HDB)
|
88
88
|
write = true unless File.exist? path
|
89
89
|
|
90
|
-
FileUtils.mkdir_p File.dirname(path) unless
|
90
|
+
FileUtils.mkdir_p File.dirname(path) unless File.exist?(File.dirname(path))
|
91
91
|
|
92
92
|
database = Persist::TCAdapter.open(path, write, tokyocabinet_class)
|
93
93
|
|
94
94
|
unless serializer == :clean
|
95
95
|
TSV.setup database
|
96
|
-
database.
|
96
|
+
database.write_and_read do
|
97
|
+
database.serializer = serializer
|
98
|
+
end if serializer && database.serializer != serializer
|
97
99
|
end
|
98
100
|
|
99
101
|
database
|
data/lib/rbbt/resource.rb
CHANGED
@@ -170,10 +170,12 @@ module Resource
|
|
170
170
|
if type and not File.exist?(final_path) or force
|
171
171
|
Log.medium "Producing: #{ final_path }"
|
172
172
|
lock_filename = Persist.persistence_path(final_path, {:dir => Resource.lock_dir})
|
173
|
+
|
173
174
|
Misc.lock lock_filename do
|
174
175
|
FileUtils.rm_rf final_path if force and File.exist? final_path
|
175
|
-
|
176
|
-
|
176
|
+
|
177
|
+
if ! File.exist?(final_path) || force
|
178
|
+
|
177
179
|
begin
|
178
180
|
case type
|
179
181
|
when :string
|
@@ -291,7 +293,7 @@ url='#{url}'
|
|
291
293
|
rescue
|
292
294
|
FileUtils.rm_rf final_path if File.exist? final_path
|
293
295
|
raise $!
|
294
|
-
end
|
296
|
+
end unless (remote_server && get_from_server(path, final_path))
|
295
297
|
end
|
296
298
|
end
|
297
299
|
end
|
@@ -304,11 +306,12 @@ url='#{url}'
|
|
304
306
|
resource ||= Rbbt
|
305
307
|
(Path::STANDARD_SEARCH + resource.search_order + resource.search_paths.keys).uniq.each do |name|
|
306
308
|
pattern = resource.search_paths[name]
|
307
|
-
next if
|
309
|
+
next if pattern.nil?
|
310
|
+
pattern = pattern.sub('{PWD}', Dir.pwd)
|
308
311
|
if String === pattern and pattern.include?('{')
|
309
312
|
regexp = "^" + pattern.gsub(/{([^}]+)}/,'(?<\1>[^/]+)') + "(?:/(?<REST>.*))?/?$"
|
310
313
|
if m = path.match(regexp)
|
311
|
-
if m["PKGDIR"] == resource.pkgdir
|
314
|
+
if ! m.named_captures.include?("PKGDIR") || m["PKGDIR"] == resource.pkgdir
|
312
315
|
return self[m["TOPLEVEL"]][m["SUBPATH"]][m["REST"]]
|
313
316
|
end
|
314
317
|
end
|
data/lib/rbbt/resource/path.rb
CHANGED
@@ -199,7 +199,7 @@ module Path
|
|
199
199
|
next if res
|
200
200
|
next unless paths.include? w
|
201
201
|
path = find(w, caller_lib, paths)
|
202
|
-
res = path if File.exist?
|
202
|
+
res = path if File.exist?(path)
|
203
203
|
end if res.nil?
|
204
204
|
|
205
205
|
(paths.keys - STANDARD_SEARCH - search_order).each do |w|
|
@@ -241,8 +241,8 @@ module Path
|
|
241
241
|
sub('{REMOVE}/', '').
|
242
242
|
sub('{REMOVE}', '')
|
243
243
|
|
244
|
-
path = path + '.gz' if File.exist?
|
245
|
-
path = path + '.bgz' if File.exist?
|
244
|
+
path = path + '.gz' if File.exist?(path + '.gz')
|
245
|
+
path = path + '.bgz' if File.exist?(path + '.bgz')
|
246
246
|
|
247
247
|
self.annotate path
|
248
248
|
|
data/lib/rbbt/tsv/accessor.rb
CHANGED
@@ -243,7 +243,7 @@ module TSV
|
|
243
243
|
end
|
244
244
|
|
245
245
|
def []=(key, value, clean = false)
|
246
|
-
return super(key, value) if clean
|
246
|
+
return super(key, value) if clean || value.nil? || TSV::CleanSerializer == self.serializer_module
|
247
247
|
super(key, @serializer_module.dump(value))
|
248
248
|
end
|
249
249
|
|
@@ -366,11 +366,11 @@ module TSV
|
|
366
366
|
keys.length
|
367
367
|
end
|
368
368
|
|
369
|
-
def
|
370
|
-
|
371
|
-
|
372
|
-
|
373
|
-
end
|
369
|
+
#def _values_at(*keys)
|
370
|
+
# keys.collect do |key|
|
371
|
+
# self[key]
|
372
|
+
# end
|
373
|
+
#end
|
374
374
|
|
375
375
|
def chunked_values_at(keys, max = 5000)
|
376
376
|
Misc.ordered_divide(keys, max).inject([]) do |acc,c|
|
data/lib/rbbt/tsv/change_id.rb
CHANGED
@@ -10,7 +10,8 @@ module TSV
|
|
10
10
|
|
11
11
|
identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? and tsv.namespace
|
12
12
|
|
13
|
-
|
13
|
+
|
14
|
+
if ! tsv.fields.include?(format)
|
14
15
|
new = {}
|
15
16
|
tsv.each do |k,v|
|
16
17
|
if v === String or v === Array
|
@@ -32,6 +33,7 @@ module TSV
|
|
32
33
|
tsv = tsv.attach identifiers, :fields => [format], :persist_input => true
|
33
34
|
end
|
34
35
|
|
36
|
+
|
35
37
|
tsv = tsv.reorder(format, tsv.fields[0..-2])
|
36
38
|
|
37
39
|
tsv = tsv.to_flat if orig_type == :flat
|
data/lib/rbbt/tsv/stream.rb
CHANGED
@@ -15,6 +15,14 @@ end
|
|
15
15
|
class Aborted < StandardError; end
|
16
16
|
|
17
17
|
class TryAgain < StandardError; end
|
18
|
+
|
19
|
+
class TryThis < StandardError
|
20
|
+
attr_accessor :payload
|
21
|
+
def initialize(payload = nil)
|
22
|
+
@payload = payload
|
23
|
+
end
|
24
|
+
end
|
25
|
+
|
18
26
|
class SemaphoreInterrupted < TryAgain; end
|
19
27
|
class LockInterrupted < TryAgain; end
|
20
28
|
|
data/lib/rbbt/util/misc/pipes.rb
CHANGED
@@ -18,6 +18,8 @@ module Misc
|
|
18
18
|
|
19
19
|
BLOCK_SIZE=1024 * 8
|
20
20
|
|
21
|
+
SKIP_TAG="[SKIP TAG]"
|
22
|
+
|
21
23
|
PIPE_MUTEX = Mutex.new
|
22
24
|
|
23
25
|
OPEN_PIPE_IN = []
|
@@ -29,7 +31,7 @@ module Misc
|
|
29
31
|
|
30
32
|
[sout, sin]
|
31
33
|
end
|
32
|
-
Log.debug{"Creating pipe #{[res.last.inspect,res.first.inspect] * " => "}"}
|
34
|
+
Log.debug{"Creating pipe #{[res.last.inspect, res.first.inspect] * " => "}"}
|
33
35
|
res
|
34
36
|
end
|
35
37
|
|
@@ -255,6 +257,11 @@ module Misc
|
|
255
257
|
end
|
256
258
|
tee1, *rest = Misc.tee_stream stream_dup, num + 1
|
257
259
|
stream.reopen(tee1)
|
260
|
+
|
261
|
+
#ToDo: I can't explain why the @threads variable appears with the value of
|
262
|
+
# @filename
|
263
|
+
stream.instance_variable_set(:@threads, nil) if stream.instance_variables.include?(:@threads)
|
264
|
+
|
258
265
|
tee1.annotate(stream)
|
259
266
|
rest
|
260
267
|
end
|
@@ -537,18 +544,29 @@ module Misc
|
|
537
544
|
end
|
538
545
|
end
|
539
546
|
|
547
|
+
def self.buffer_stream(stream)
|
548
|
+
sout, sin = Misc.pipe
|
549
|
+
Misc.consume_stream(stream, true, sin)
|
550
|
+
sout
|
551
|
+
end
|
552
|
+
|
540
553
|
def self._paste_streams(streams, output, lines = nil, sep = "\t", header = nil, &block)
|
541
554
|
output.puts header if header
|
542
555
|
streams = streams.collect do |stream|
|
543
556
|
if defined? Step and Step === stream
|
544
|
-
stream.get_stream
|
557
|
+
io = stream.get_stream
|
558
|
+
if io
|
559
|
+
buffer_stream(io)
|
560
|
+
else
|
561
|
+
stream.join.path.open
|
562
|
+
end
|
545
563
|
else
|
546
564
|
stream
|
547
565
|
end
|
548
566
|
end
|
549
567
|
|
550
568
|
begin
|
551
|
-
|
569
|
+
|
552
570
|
lines ||= streams.collect{|s| s.gets }
|
553
571
|
keys = []
|
554
572
|
parts = []
|
@@ -564,6 +582,7 @@ module Misc
|
|
564
582
|
end
|
565
583
|
sizes = parts.collect{|p| p.nil? ? 0 : p.length }
|
566
584
|
last_min = nil
|
585
|
+
|
567
586
|
while lines.compact.any?
|
568
587
|
if block_given?
|
569
588
|
min = keys.compact.sort(&block).first
|
@@ -571,14 +590,23 @@ module Misc
|
|
571
590
|
min = keys.compact.sort.first
|
572
591
|
end
|
573
592
|
str = []
|
593
|
+
threads = []
|
574
594
|
keys.each_with_index do |key,i|
|
575
595
|
case key
|
576
596
|
when min
|
577
|
-
|
597
|
+
if parts[i] == [SKIP_TAG]
|
598
|
+
str << [sep * (sizes[i]-1)] if sizes[i] > 0
|
599
|
+
else
|
600
|
+
str << [parts[i] * sep]
|
601
|
+
end
|
602
|
+
|
578
603
|
line = lines[i] = streams[i].gets
|
579
|
-
|
604
|
+
|
605
|
+
if line.nil?
|
580
606
|
keys[i] = nil
|
581
607
|
parts[i] = nil
|
608
|
+
streams[i].close unless streams[i].closed?
|
609
|
+
streams[i].join if streams[i].respond_to?(:join)
|
582
610
|
else
|
583
611
|
k, *p = line.chomp.split(sep, -1)
|
584
612
|
keys[i] = k
|
@@ -589,10 +617,12 @@ module Misc
|
|
589
617
|
end
|
590
618
|
end
|
591
619
|
|
592
|
-
output.puts [min, str*sep] * sep
|
620
|
+
output.puts [min, str.flatten*sep] * sep
|
593
621
|
end
|
622
|
+
|
594
623
|
streams.each do |stream|
|
595
|
-
stream.
|
624
|
+
stream.close unless stream.closed?
|
625
|
+
stream.join if stream.respond_to?(:join)
|
596
626
|
end
|
597
627
|
rescue
|
598
628
|
Log.exception $!
|
data/lib/rbbt/workflow.rb
CHANGED
@@ -35,6 +35,7 @@ module Workflow
|
|
35
35
|
input_use = rec_input_use(name)
|
36
36
|
input_defaults = rec_input_defaults(name)
|
37
37
|
input_options = rec_input_options(name)
|
38
|
+
extension = task.extension
|
38
39
|
export = case
|
39
40
|
when (synchronous_exports.include?(name.to_sym) or synchronous_exports.include?(name.to_s))
|
40
41
|
:synchronous
|
@@ -60,7 +61,8 @@ module Workflow
|
|
60
61
|
:input_use => input_use,
|
61
62
|
:result_type => result_type,
|
62
63
|
:result_description => result_description,
|
63
|
-
:dependencies => dependencies
|
64
|
+
:dependencies => dependencies,
|
65
|
+
:extension => extension
|
64
66
|
}
|
65
67
|
end
|
66
68
|
end
|
@@ -18,6 +18,7 @@ module Workflow
|
|
18
18
|
:description => "",
|
19
19
|
:result_type => nil,
|
20
20
|
:result_description => "",
|
21
|
+
:resumable => false,
|
21
22
|
:extension => nil)
|
22
23
|
|
23
24
|
|
@@ -33,6 +34,10 @@ module Workflow
|
|
33
34
|
@extension = extension
|
34
35
|
end
|
35
36
|
|
37
|
+
def resumable
|
38
|
+
@resumable = true
|
39
|
+
end
|
40
|
+
|
36
41
|
def returns(description)
|
37
42
|
@result_description = description
|
38
43
|
end
|
@@ -118,6 +123,7 @@ module Workflow
|
|
118
123
|
:input_descriptions => consume_input_descriptions,
|
119
124
|
:required_inputs => consume_required_inputs,
|
120
125
|
:extension => consume_extension,
|
126
|
+
:resumable => consume_resumable,
|
121
127
|
:input_options => consume_input_options
|
122
128
|
}
|
123
129
|
|
@@ -137,13 +137,15 @@ class RemoteWorkflow
|
|
137
137
|
|
138
138
|
post_thread = Thread.new(Thread.current) do |parent|
|
139
139
|
bl = lambda do |rok|
|
140
|
-
if Net::HTTPOK === rok
|
140
|
+
if Net::HTTPOK === rok
|
141
141
|
_url = rok["RBBT-STREAMING-JOB-URL"]
|
142
142
|
@url = File.join(task_url, File.basename(_url)) if _url
|
143
143
|
rok.read_body do |c,_a, _b|
|
144
144
|
sin.write c
|
145
145
|
end
|
146
146
|
sin.close
|
147
|
+
elsif Net::HTTPSeeOther === rok
|
148
|
+
raise TryThis.new(rok)
|
147
149
|
else
|
148
150
|
err = StringIO.new
|
149
151
|
rok.read_body do |c,_a, _b|
|
@@ -156,7 +158,7 @@ class RemoteWorkflow
|
|
156
158
|
err.rewind
|
157
159
|
err.read
|
158
160
|
end
|
159
|
-
ne =
|
161
|
+
ne = RemoteWorkflow.parse_exception text
|
160
162
|
case ne
|
161
163
|
when String
|
162
164
|
parent.raise e.class, ne
|
@@ -173,7 +175,11 @@ class RemoteWorkflow
|
|
173
175
|
end
|
174
176
|
|
175
177
|
Log.debug{ "RestClient execute: #{ task_url } - #{Misc.fingerprint task_params}" }
|
176
|
-
|
178
|
+
begin
|
179
|
+
RestClient::Request.execute(:method => :post, :url => task_url, :payload => task_params, :block_response => bl)
|
180
|
+
rescue TryThis
|
181
|
+
RestClient::Request.execute(:method => :get, :url => $!.payload.header[:location], :block_response => bl)
|
182
|
+
end
|
177
183
|
end
|
178
184
|
|
179
185
|
# It seems like now response body are now decoded by Net::HTTP after 2.1
|
@@ -25,8 +25,13 @@ class RemoteStep < Step
|
|
25
25
|
end
|
26
26
|
|
27
27
|
def cache_file
|
28
|
-
|
29
|
-
|
28
|
+
begin
|
29
|
+
digest = Misc.obj2digest([base_url, task, base_name, inputs])
|
30
|
+
Rbbt.var.cache.REST[[task, clean_name, digest].compact * "."].find
|
31
|
+
rescue
|
32
|
+
Log.exception $!
|
33
|
+
raise $!
|
34
|
+
end
|
30
35
|
end
|
31
36
|
|
32
37
|
def cache_files
|
@@ -62,7 +67,6 @@ class RemoteStep < Step
|
|
62
67
|
no_load ? Misc.add_GET_param(path, "_format", "raw") : @result
|
63
68
|
end
|
64
69
|
|
65
|
-
|
66
70
|
def self.get_streams(inputs, stream_input = nil)
|
67
71
|
new_inputs = {}
|
68
72
|
inputs.each do |k,v|
|
@@ -240,6 +244,7 @@ class RemoteStep < Step
|
|
240
244
|
return true if cache_files.any?
|
241
245
|
init_job unless @url
|
242
246
|
Log.debug{ "Joining RemoteStep: #{path}" }
|
247
|
+
|
243
248
|
if IO === @result
|
244
249
|
res = @result
|
245
250
|
@result = nil
|
@@ -253,6 +258,7 @@ class RemoteStep < Step
|
|
253
258
|
sleep 1 unless self.done? || self.aborted? || self.error?
|
254
259
|
while not (self.done? || self.aborted? || self.error?)
|
255
260
|
sleep 3
|
261
|
+
iif [self.done?, self.status, self.info]
|
256
262
|
end
|
257
263
|
end
|
258
264
|
|
@@ -129,7 +129,7 @@ class RemoteStep
|
|
129
129
|
end
|
130
130
|
end
|
131
131
|
|
132
|
-
def _run_job(cache_type = :
|
132
|
+
def _run_job(cache_type = :asynchronous)
|
133
133
|
get_streams
|
134
134
|
|
135
135
|
task_url = URI.encode(File.join(base_url, task.to_s))
|
@@ -142,7 +142,13 @@ class RemoteStep
|
|
142
142
|
else
|
143
143
|
@adaptor.execute_job(base_url, task, task_params, cache_type)
|
144
144
|
end
|
145
|
+
end
|
146
|
+
|
145
147
|
|
148
|
+
def produce(*args)
|
149
|
+
@started = true
|
150
|
+
_run_job
|
146
151
|
end
|
152
|
+
|
147
153
|
end
|
148
154
|
end
|
@@ -92,7 +92,7 @@ class Step
|
|
92
92
|
(job.done? && job.dirty?) || (job.error? && job.dirty?) ||
|
93
93
|
(!(job.noinfo? || job.done? || job.error? || job.aborted? || job.running?))
|
94
94
|
|
95
|
-
job.clean
|
95
|
+
job.clean unless job.resumable? && (job.updated? && ! job.dirty?)
|
96
96
|
job.set_info :status, :cleaned
|
97
97
|
end
|
98
98
|
|
@@ -144,14 +144,18 @@ class Step
|
|
144
144
|
|
145
145
|
dependency.status_lock.synchronize do
|
146
146
|
if dependency.aborted? || (dependency.error? && dependency.recoverable_error? && ! canfail_paths.include?(dependency.path) && ! already_failed.include?(dependency.path)) || (!Open.remote?(dependency.path) && dependency.missing?)
|
147
|
-
|
148
|
-
|
149
|
-
|
150
|
-
|
147
|
+
if dependency.resumable?
|
148
|
+
dependency.status = :resume
|
149
|
+
else
|
150
|
+
Log.warn "Cleaning dep. on exec #{Log.color :blue, dependency.path} (missing: #{dependency.missing?}; error #{dependency.error?})"
|
151
|
+
dependency.clean
|
152
|
+
already_failed << dependency.path
|
153
|
+
raise TryAgain
|
154
|
+
end
|
151
155
|
end
|
152
156
|
end
|
153
157
|
|
154
|
-
if ! (dependency.started? || dependency.error?)
|
158
|
+
if dependency.status == :resume || ! (dependency.started? || dependency.error?)
|
155
159
|
log_dependency_exec(dependency, :starting)
|
156
160
|
dependency.run(true)
|
157
161
|
raise TryAgain
|
@@ -362,7 +366,7 @@ class Step
|
|
362
366
|
(step.dependencies + step.input_dependencies).each do |step_dep|
|
363
367
|
next if step_dep.done? or step_dep.running? or (ComputeDependency === step_dep and (step_dep.compute == :nodup or step_dep.compute == :ignore))
|
364
368
|
dep_step[step_dep.path] ||= []
|
365
|
-
dep_step[step_dep.path] <<
|
369
|
+
dep_step[step_dep.path] << step
|
366
370
|
end
|
367
371
|
end
|
368
372
|
|
data/lib/rbbt/workflow/task.rb
CHANGED
@@ -2,7 +2,7 @@ require 'rbbt/util/misc'
|
|
2
2
|
require 'rbbt/persist'
|
3
3
|
|
4
4
|
module Task
|
5
|
-
attr_accessor :inputs, :input_types, :result_type, :input_defaults, :input_descriptions, :input_options, :required_inputs, :description, :name, :result_description, :extension, :workflow
|
5
|
+
attr_accessor :inputs, :input_types, :result_type, :input_defaults, :input_descriptions, :input_options, :required_inputs, :description, :name, :result_description, :extension, :workflow, :resumable
|
6
6
|
|
7
7
|
def self.setup(options = {}, &block)
|
8
8
|
block.extend Task
|
@@ -125,6 +125,7 @@ class Step
|
|
125
125
|
def self.migrate(path, search_path, options = {})
|
126
126
|
resource=Rbbt
|
127
127
|
|
128
|
+
orig_path = path
|
128
129
|
other_rsync_args = options[:rsync]
|
129
130
|
|
130
131
|
recursive = options[:recursive]
|
@@ -154,6 +155,7 @@ puts files * "\n"
|
|
154
155
|
else
|
155
156
|
if File.exists?(path)
|
156
157
|
path = resource.identify(path)
|
158
|
+
raise "Resource #{resource} could not identify #{orig_path}" if path.nil?
|
157
159
|
else
|
158
160
|
path = Path.setup(path)
|
159
161
|
end
|
@@ -178,7 +180,7 @@ puts resource[path].find(search_path)
|
|
178
180
|
subpath_files = {}
|
179
181
|
paths.sort.each do |path|
|
180
182
|
parts = path.split("/")
|
181
|
-
subpath = parts[0..-4] * "/"
|
183
|
+
subpath = parts[0..-4] * "/" + "/"
|
182
184
|
|
183
185
|
if subpath_files.keys.any? && subpath.start_with?(subpath_files.keys.last)
|
184
186
|
subpath = subpath_files.keys.last
|
@@ -190,6 +192,7 @@ puts resource[path].find(search_path)
|
|
190
192
|
subpath_files[subpath] << source
|
191
193
|
end
|
192
194
|
|
195
|
+
synced_files = []
|
193
196
|
subpath_files.each do |subpath, files|
|
194
197
|
if options[:target]
|
195
198
|
CMD.cmd("ssh #{options[:target]} mkdir -p '#{File.dirname(target)}'")
|
@@ -204,11 +207,15 @@ puts resource[path].find(search_path)
|
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|
end
|
205
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|
target = [options[:target], target] * ":" if options[:target]
|
206
209
|
|
210
|
+
next if File.exists?(source) && File.exists?(target) && File.expand_path(source) == File.expand_path(target)
|
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|
+
|
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212
|
files_and_dirs = Set.new( files )
|
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|
files.each do |file|
|
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|
+
synced_files << File.join(subpath, file)
|
215
|
+
|
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216
|
parts = file.split("/")[0..-2].reject{|p| p.empty?}
|
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217
|
while parts.any?
|
211
|
-
files_and_dirs <<
|
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+
files_and_dirs << parts * "/"
|
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|
parts.pop
|
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220
|
end
|
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221
|
end
|
@@ -218,8 +225,7 @@ puts resource[path].find(search_path)
|
|
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225
|
|
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226
|
cmd = "rsync #{MAIN_RSYNC_ARGS} --progress #{test_str} --files-from='#{tmp_include_file}' #{source}/ #{target}/ #{other_rsync_args}"
|
220
227
|
|
221
|
-
cmd << " && rm -Rf #{source}" if options[:delete]
|
222
|
-
|
228
|
+
#cmd << " && rm -Rf #{source}" if options[:delete]
|
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229
|
if options[:print]
|
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|
ppp Open.read(tmp_include_file)
|
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|
puts cmd
|
@@ -228,6 +234,26 @@ puts resource[path].find(search_path)
|
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234
|
end
|
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235
|
end
|
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|
end
|
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|
+
|
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|
+
if options[:delete] && synced_files.any?
|
239
|
+
puts Log.color :magenta, "About to erase these files:"
|
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|
+
synced_files.each do |p|
|
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|
+
puts Log.color :red, p
|
242
|
+
end
|
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|
+
|
244
|
+
if options[:non_interactive]
|
245
|
+
response = 'yes'
|
246
|
+
else
|
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|
+
puts Log.color :magenta, "Type 'yes' if you are sure:"
|
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|
+
response = STDIN.gets.chomp
|
249
|
+
end
|
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|
+
|
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|
+
if response == 'yes'
|
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|
+
synced_files.each do |p|
|
253
|
+
Open.rm p
|
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|
+
end
|
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|
+
end
|
256
|
+
end
|
231
257
|
end
|
232
258
|
|
233
259
|
def self.purge(path, recursive = false)
|
@@ -71,7 +71,7 @@ get_pkg(){
|
|
71
71
|
local url="$2"
|
72
72
|
|
73
73
|
if [ ! -f "$OPT_SRC_DIR/$name.pkg" ]; then
|
74
|
-
|
74
|
+
wget "$url" -O "$OPT_SRC_DIR/$name.pkg" || wget "$url" -O "$OPT_SRC_DIR/$name.pkg" --no-check-certificate || (rm -f "$OPT_SRC_DIR/$name.pkg"; echo "Error downloading"; exit -1)
|
75
75
|
fi
|
76
76
|
}
|
77
77
|
|
@@ -85,7 +85,7 @@ uncompress_pkg(){
|
|
85
85
|
mkdir -p "$OPT_BUILD_DIR"
|
86
86
|
cd "$OPT_BUILD_DIR"
|
87
87
|
|
88
|
-
(tar xvfz $pkg || tar xvfJ $pkg || tar xvfj $pkg || unzip $pkg || echo "Error decompressing") 2> /dev/null
|
88
|
+
(tar xvfz $pkg || tar xvfJ $pkg || tar xvfj $pkg || unzip $pkg || (echo "Error decompressing" & cd & rmdir "$OPT_BUILD_DIR" & exit -1 ) ) 2> /dev/null
|
89
89
|
|
90
90
|
cd "$old_pwd"
|
91
91
|
}
|
@@ -207,6 +207,8 @@ prepare_make(){
|
|
207
207
|
|
208
208
|
[ -d src -a ! -e CMakeLists.txt -a ! -e Makefile -a ! -e configure ] && cd src
|
209
209
|
|
210
|
+
[ -f bootstrap ] && (./bootstrap || exit -1)
|
211
|
+
|
210
212
|
if [ -f config/m4 ]; then
|
211
213
|
libtoolize --force
|
212
214
|
aclocal
|
@@ -275,6 +277,8 @@ build_make(){
|
|
275
277
|
setup "$name"
|
276
278
|
clean_build
|
277
279
|
fi
|
280
|
+
|
281
|
+
cd "$old_pwd"
|
278
282
|
}
|
279
283
|
|
280
284
|
buid_cmake(){
|
@@ -489,7 +493,7 @@ install_jar(){
|
|
489
493
|
local url="$2"
|
490
494
|
|
491
495
|
[ -d "$OPT_DIR/$name/" ] || mkdir -p "$OPT_DIR/$name/"
|
492
|
-
wget "$url" -O "$OPT_DIR/$name/$name.jar" --no-check-certificate
|
496
|
+
wget "$url" -O "$OPT_DIR/jars/$name.jar" || wget "$url" -O "$OPT_DIR/jars/$name.jar" --no-check-certificate || (rm "$OPT_DIR/jars/$name.jar"; exit -1)
|
493
497
|
link "$OPT_DIR/$name/$name.jar" "$OPT_JAR_DIR/$name.jar"
|
494
498
|
}
|
495
499
|
|
@@ -3,7 +3,7 @@
|
|
3
3
|
require 'rbbt-util'
|
4
4
|
require 'rbbt/util/simpleopt'
|
5
5
|
require 'rbbt/workflow'
|
6
|
-
require 'rbbt/workflow/
|
6
|
+
require 'rbbt/workflow/remote_workflow'
|
7
7
|
|
8
8
|
$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
|
9
9
|
|
@@ -34,4 +34,6 @@ end
|
|
34
34
|
|
35
35
|
path, search_path, _sep, *other = ARGV
|
36
36
|
|
37
|
+
search_path = 'user' if search_path.nil?
|
38
|
+
|
37
39
|
Step.migrate(path, search_path, options)
|
@@ -187,7 +187,7 @@ workflows.sort.each do |workflow,tasks|
|
|
187
187
|
if info_fields and info_fields.any?
|
188
188
|
info = begin
|
189
189
|
Open.open(i[:info_file]) do |f|
|
190
|
-
Step::
|
190
|
+
Step::INFO_SERIALIZER.load(f)
|
191
191
|
end
|
192
192
|
rescue
|
193
193
|
{:status => :noinfo}
|
@@ -198,9 +198,10 @@ workflows.sort.each do |workflow,tasks|
|
|
198
198
|
else
|
199
199
|
info = begin
|
200
200
|
Open.open(i[:info_file]) do |f|
|
201
|
-
Step::
|
201
|
+
Step::INFO_SERIALIZER.load(f)
|
202
202
|
end
|
203
203
|
rescue
|
204
|
+
Log.exception $!
|
204
205
|
{:status => :noinfo}
|
205
206
|
end
|
206
207
|
IndiferentHash.setup(info)
|
@@ -41,7 +41,7 @@ def list_jobs(options)
|
|
41
41
|
clean_file = file.sub('.info','')
|
42
42
|
begin
|
43
43
|
next if File.exist? clean_file and $quick
|
44
|
-
info = Step::
|
44
|
+
info = Step::INFO_SERIALIZER.load(Open.read(file, :mode => 'rb'))
|
45
45
|
next if (File.exist?(clean_file) or info[:status] == :done) and (info[:children_pids].nil? or info[:children_done] or info[:children_pids].select{|pid| Misc.pid_exists? pid}.empty?)
|
46
46
|
rescue Exception
|
47
47
|
puts "Error parsing info file: #{ file }"
|
@@ -86,7 +86,7 @@ def clean_jobs(options)
|
|
86
86
|
info = nil
|
87
87
|
next if File.exist? clean_file
|
88
88
|
begin
|
89
|
-
info = Step::
|
89
|
+
info = Step::INFO_SERIALIZER.load(Open.read(file, :mode => 'rb'))
|
90
90
|
rescue Exception
|
91
91
|
Log.debug "Error process #{ file }"
|
92
92
|
remove_job file if options[:errors]
|
@@ -117,7 +117,7 @@ begin
|
|
117
117
|
end
|
118
118
|
else
|
119
119
|
if options[:file]
|
120
|
-
info = Step::
|
120
|
+
info = Step::INFO_SERIALIZER.load(Open.read(options[:file], :mode => 'rb'))
|
121
121
|
print_job options[:file], info
|
122
122
|
else
|
123
123
|
list_jobs options
|
@@ -4,6 +4,7 @@ require 'rbbt/tsv/stream'
|
|
4
4
|
require 'rbbt'
|
5
5
|
|
6
6
|
class TestStream < Test::Unit::TestCase
|
7
|
+
|
7
8
|
def test_collapse_stream
|
8
9
|
text=<<-EOF
|
9
10
|
#: :sep=" "
|
@@ -65,7 +66,7 @@ row3 AAA BBB CCC
|
|
65
66
|
|
66
67
|
text2=<<-EOF
|
67
68
|
#: :sep=" "
|
68
|
-
#Row Labela Labelb
|
69
|
+
#Row Labela Labelb
|
69
70
|
row1 a b
|
70
71
|
row3 aaa bbb
|
71
72
|
row2 aa bb
|
@@ -100,7 +101,7 @@ row1 A B C
|
|
100
101
|
|
101
102
|
text2=<<-EOF
|
102
103
|
#: :sep=" "
|
103
|
-
#Row Labela Labelb
|
104
|
+
#Row Labela Labelb
|
104
105
|
row2 aa bb
|
105
106
|
EOF
|
106
107
|
|
@@ -132,7 +133,7 @@ row1 A B C
|
|
132
133
|
|
133
134
|
text2=<<-EOF
|
134
135
|
#: :sep=" "
|
135
|
-
#Row Labela Labelb
|
136
|
+
#Row Labela Labelb
|
136
137
|
row2 aa bb
|
137
138
|
EOF
|
138
139
|
|
@@ -4,6 +4,27 @@ require 'rbbt/workflow'
|
|
4
4
|
module DepWorkflow
|
5
5
|
extend Workflow
|
6
6
|
|
7
|
+
input :input_file, :file, "Input file", nil, :stream => true
|
8
|
+
task :s1 => :array do |input_file|
|
9
|
+
TSV.traverse input_file, :type => :array, :into => :stream, :bar => "Task1" do |line|
|
10
|
+
line + "\t" << "Task1"
|
11
|
+
end
|
12
|
+
end
|
13
|
+
|
14
|
+
dep :s1
|
15
|
+
task :s2 => :array do |input_file|
|
16
|
+
TSV.traverse step(:s1), :type => :array, :into => :stream, :bar => "Task2" do |line|
|
17
|
+
next [line.split("\t").first, Misc::SKIP_TAG] * "\t" if rand < 0.9
|
18
|
+
line + "\t" << "Task2"
|
19
|
+
end
|
20
|
+
end
|
21
|
+
|
22
|
+
dep :s1
|
23
|
+
dep :s2
|
24
|
+
task :s3 => :array do |input_file|
|
25
|
+
Misc.paste_streams(dependencies.reverse)
|
26
|
+
end
|
27
|
+
|
7
28
|
input :input_file, :file, "Input file", nil, :stream => true
|
8
29
|
task :task1 => :array do |input_file|
|
9
30
|
TSV.traverse input_file, :type => :array, :into => :stream, :bar => "Task1" do |line|
|
@@ -28,9 +49,7 @@ module DepWorkflow
|
|
28
49
|
dep :task2
|
29
50
|
dep :task3
|
30
51
|
task :task4 => :array do
|
31
|
-
|
32
|
-
s2 = TSV.get_stream step(:task3)
|
33
|
-
Misc.paste_streams([s1, s2])
|
52
|
+
Misc.paste_streams(dependencies)
|
34
53
|
end
|
35
54
|
|
36
55
|
dep :task4
|
@@ -43,9 +62,7 @@ module DepWorkflow
|
|
43
62
|
dep :task2
|
44
63
|
dep :task5
|
45
64
|
task :task6 => :array do
|
46
|
-
|
47
|
-
s2 = TSV.get_stream step(:task5)
|
48
|
-
Misc.paste_streams([s1, s2])
|
65
|
+
Misc.paste_streams(dependencies)
|
49
66
|
end
|
50
67
|
|
51
68
|
input :stream_file, :file, "Streamed file", nil, :stream => true
|
@@ -81,6 +98,26 @@ module ComputeWorkflow
|
|
81
98
|
|
82
99
|
end
|
83
100
|
|
101
|
+
module ResumeWorkflow
|
102
|
+
extend Workflow
|
103
|
+
|
104
|
+
resumable
|
105
|
+
task :resume => :string do
|
106
|
+
if file('foo').exists?
|
107
|
+
'done'
|
108
|
+
else
|
109
|
+
Open.mkdir files_dir
|
110
|
+
Open.touch(file('foo'))
|
111
|
+
raise
|
112
|
+
end
|
113
|
+
end
|
114
|
+
|
115
|
+
dep :resume
|
116
|
+
task :reverse => :string do
|
117
|
+
step(:resume).load.reverse
|
118
|
+
end
|
119
|
+
end
|
120
|
+
|
84
121
|
class TestWorkflowDependency < Test::Unit::TestCase
|
85
122
|
def test_task1
|
86
123
|
size = 10000
|
@@ -114,8 +151,25 @@ class TestWorkflowDependency < Test::Unit::TestCase
|
|
114
151
|
end
|
115
152
|
end
|
116
153
|
|
154
|
+
def test_task3
|
155
|
+
size = 100000
|
156
|
+
content = (0..size).to_a.collect{|num| "Line #{num}" } * "\n"
|
157
|
+
TmpFile.with_file(content) do |input_file|
|
158
|
+
job = DepWorkflow.job(:task3, "TEST", :input_file => input_file)
|
159
|
+
io = TSV.get_stream job.run(:stream)
|
160
|
+
last_line = nil
|
161
|
+
while line = io.gets
|
162
|
+
last_line = line.strip
|
163
|
+
end
|
164
|
+
io.join
|
165
|
+
|
166
|
+
assert_equal "Line #{size}\tTask1\tTask3", last_line
|
167
|
+
end
|
168
|
+
end
|
169
|
+
|
117
170
|
def test_task4
|
118
|
-
size =
|
171
|
+
size = 100000
|
172
|
+
Log.severity = 0
|
119
173
|
content = (0..size).to_a.collect{|num| "Line #{num}" } * "\n"
|
120
174
|
last_line = nil
|
121
175
|
TmpFile.with_file(content) do |input_file|
|
@@ -131,7 +185,7 @@ class TestWorkflowDependency < Test::Unit::TestCase
|
|
131
185
|
end
|
132
186
|
|
133
187
|
def test_task5
|
134
|
-
size =
|
188
|
+
size = 10000
|
135
189
|
content = (0..size).to_a.collect{|num| "Line #{num}" } * "\n"
|
136
190
|
last_line = nil
|
137
191
|
TmpFile.with_file(content) do |input_file|
|
@@ -145,20 +199,44 @@ class TestWorkflowDependency < Test::Unit::TestCase
|
|
145
199
|
assert_equal "Line #{size}\tTask1\tTask2\tTask1\tTask3\tTask5", last_line
|
146
200
|
end
|
147
201
|
|
148
|
-
def
|
202
|
+
def test_s3
|
149
203
|
size = 100000
|
150
|
-
content = (
|
204
|
+
content = (1..size).to_a.collect{|num| "Line #{num}" } * "\n"
|
151
205
|
last_line = nil
|
152
206
|
Log.severity = 0
|
153
207
|
TmpFile.with_file(content) do |input_file|
|
154
208
|
begin
|
155
|
-
|
156
|
-
|
157
|
-
|
158
|
-
|
159
|
-
|
209
|
+
job = DepWorkflow.job(:s3, "TEST", :input_file => input_file)
|
210
|
+
job.recursive_clean
|
211
|
+
job.run(:stream)
|
212
|
+
io = TSV.get_stream job
|
213
|
+
while line = io.gets
|
214
|
+
last_line = line.strip
|
215
|
+
end
|
216
|
+
io.join if io.respond_to? :join
|
217
|
+
rescue Exception
|
218
|
+
job.abort
|
219
|
+
raise $!
|
160
220
|
end
|
161
|
-
|
221
|
+
end
|
222
|
+
assert last_line.include? "Line #{size}"
|
223
|
+
end
|
224
|
+
|
225
|
+
def test_task6
|
226
|
+
size = 100000
|
227
|
+
content = (1..size).to_a.collect{|num| "Line #{num}" } * "\n"
|
228
|
+
last_line = nil
|
229
|
+
Log.severity = 0
|
230
|
+
TmpFile.with_file(content) do |input_file|
|
231
|
+
begin
|
232
|
+
job = DepWorkflow.job(:task6, "TEST", :input_file => input_file)
|
233
|
+
job.recursive_clean
|
234
|
+
job.run(:stream)
|
235
|
+
io = TSV.get_stream job
|
236
|
+
while line = io.gets
|
237
|
+
last_line = line.strip
|
238
|
+
end
|
239
|
+
io.join
|
162
240
|
rescue Exception
|
163
241
|
job.abort
|
164
242
|
raise $!
|
@@ -168,7 +246,7 @@ class TestWorkflowDependency < Test::Unit::TestCase
|
|
168
246
|
end
|
169
247
|
|
170
248
|
def test_task8
|
171
|
-
size =
|
249
|
+
size = 10000
|
172
250
|
content = (0..size).to_a.collect{|num| "Line #{num}" } * "\n"
|
173
251
|
last_line = nil
|
174
252
|
Log.severity = 0
|
@@ -204,5 +282,16 @@ class TestWorkflowDependency < Test::Unit::TestCase
|
|
204
282
|
assert_equal "Line #{size}\tTask1\tTask2", last_line
|
205
283
|
end
|
206
284
|
end
|
285
|
+
|
286
|
+
def test_resume
|
287
|
+
Log.severity = 0
|
288
|
+
job = ResumeWorkflow.job(:reverse)
|
289
|
+
job.recursive_clean
|
290
|
+
assert_raise do
|
291
|
+
job.run
|
292
|
+
end
|
293
|
+
assert job.dependencies.first.file('foo').exists?
|
294
|
+
assert_equal 'done'.reverse, job.run
|
295
|
+
end
|
207
296
|
end
|
208
297
|
|
@@ -61,6 +61,18 @@ class TestRemoteWorkflow < Test::Unit::TestCase
|
|
61
61
|
def test_rest
|
62
62
|
Log.with_severity 0 do
|
63
63
|
|
64
|
+
remote_workflow_server(TestWFRest) do |client|
|
65
|
+
job = client.job(:hi, nil, {})
|
66
|
+
job.clean
|
67
|
+
job = client.job(:hi, nil, {})
|
68
|
+
assert ! job.done?
|
69
|
+
job.run
|
70
|
+
job.produce
|
71
|
+
job = client.job(:hi, nil, {})
|
72
|
+
assert job.done?
|
73
|
+
sleep 1
|
74
|
+
end
|
75
|
+
|
64
76
|
remote_workflow_server(TestWFRest) do |client|
|
65
77
|
assert_equal "Hello World", client.job(:hi, nil, {}).run.chomp
|
66
78
|
assert_equal "Hello Miguel", client.job(:hi, nil, {:name => :Miguel}).run.chomp
|
@@ -78,7 +90,7 @@ class TestRemoteWorkflow < Test::Unit::TestCase
|
|
78
90
|
|
79
91
|
def _test_ssh
|
80
92
|
Log.severity = 0
|
81
|
-
client = RemoteWorkflow.new "ssh
|
93
|
+
client = RemoteWorkflow.new "ssh://#{ENV["HOSTNAME"]}:Translation", "Translation"
|
82
94
|
job = client.job("translate", "SSH-TEST-1", :genes => ["TP53","KRAS"])
|
83
95
|
assert_equal 2, job.run.select{|l| l =~ /ENSG/}.length
|
84
96
|
end
|
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: 5.27.
|
4
|
+
version: 5.27.7
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2020-04
|
11
|
+
date: 2020-06-04 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|