scout-gear 8.0.0 → 9.0.0
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- checksums.yaml +4 -4
- data/.vimproject +48 -9
- data/Rakefile +6 -1
- data/VERSION +1 -1
- data/bin/scout +16 -4
- data/doc/lib/scout/path.md +35 -0
- data/doc/lib/scout/workflow/task.md +13 -0
- data/lib/rbbt-scout.rb +2 -1
- data/lib/scout/cmd.rb +32 -29
- data/lib/scout/concurrent_stream.rb +36 -19
- data/lib/scout/exceptions.rb +10 -0
- data/lib/scout/indiferent_hash.rb +17 -0
- data/lib/scout/log/color.rb +11 -11
- data/lib/scout/log/progress/report.rb +8 -5
- data/lib/scout/log/progress/util.rb +3 -0
- data/lib/scout/log/trap.rb +3 -3
- data/lib/scout/log.rb +67 -36
- data/lib/scout/meta_extension.rb +34 -0
- data/lib/scout/misc/digest.rb +11 -2
- data/lib/scout/misc/filesystem.rb +2 -3
- data/lib/scout/misc/format.rb +12 -7
- data/lib/scout/misc/monitor.rb +11 -0
- data/lib/scout/misc/system.rb +48 -0
- data/lib/scout/named_array.rb +8 -0
- data/lib/scout/offsite/ssh.rb +174 -0
- data/lib/scout/offsite/step.rb +100 -0
- data/lib/scout/offsite/sync.rb +55 -0
- data/lib/scout/offsite.rb +3 -0
- data/lib/scout/open/lock.rb +5 -24
- data/lib/scout/open/remote.rb +12 -1
- data/lib/scout/open/stream.rb +109 -122
- data/lib/scout/open/util.rb +9 -0
- data/lib/scout/open.rb +12 -11
- data/lib/scout/path/find.rb +15 -10
- data/lib/scout/path/util.rb +5 -0
- data/lib/scout/path.rb +1 -1
- data/lib/scout/persist/serialize.rb +4 -4
- data/lib/scout/persist.rb +1 -1
- data/lib/scout/resource/open.rb +8 -0
- data/lib/scout/resource/path.rb +16 -9
- data/lib/scout/resource/software.rb +4 -2
- data/lib/scout/resource/util.rb +10 -4
- data/lib/scout/resource.rb +2 -0
- data/lib/scout/tsv/dumper.rb +5 -1
- data/lib/scout/tsv/index.rb +28 -86
- data/lib/scout/tsv/open.rb +35 -14
- data/lib/scout/tsv/parser.rb +22 -5
- data/lib/scout/tsv/persist/tokyocabinet.rb +2 -0
- data/lib/scout/tsv/stream.rb +204 -0
- data/lib/scout/tsv/transformer.rb +11 -0
- data/lib/scout/tsv.rb +9 -2
- data/lib/scout/work_queue/worker.rb +2 -2
- data/lib/scout/work_queue.rb +37 -12
- data/lib/scout/workflow/definition.rb +2 -1
- data/lib/scout/workflow/deployment/orchestrator.rb +254 -0
- data/lib/scout/workflow/deployment.rb +1 -0
- data/lib/scout/workflow/step/dependencies.rb +46 -14
- data/lib/scout/workflow/step/file.rb +5 -0
- data/lib/scout/workflow/step/info.rb +13 -3
- data/lib/scout/workflow/step/inputs.rb +5 -0
- data/lib/scout/workflow/step/load.rb +1 -1
- data/lib/scout/workflow/step/provenance.rb +1 -0
- data/lib/scout/workflow/step/status.rb +27 -9
- data/lib/scout/workflow/step.rb +82 -30
- data/lib/scout/workflow/task/dependencies.rb +116 -0
- data/lib/scout/workflow/task/inputs.rb +36 -17
- data/lib/scout/workflow/task.rb +12 -109
- data/lib/scout/workflow/usage.rb +57 -41
- data/lib/scout/workflow.rb +19 -13
- data/lib/scout-gear.rb +2 -0
- data/lib/scout.rb +6 -0
- data/scout-gear.gemspec +38 -7
- data/scout_commands/doc +37 -0
- data/scout_commands/find +1 -0
- data/scout_commands/offsite +30 -0
- data/scout_commands/resource/produce +66 -0
- data/scout_commands/template +52 -0
- data/scout_commands/update +29 -0
- data/scout_commands/workflow/info +15 -3
- data/scout_commands/workflow/install +105 -0
- data/scout_commands/workflow/task +46 -6
- data/share/software/install_helpers +2 -2
- data/share/templates/command +25 -0
- data/share/templates/workflow.rb +14 -0
- data/test/scout/offsite/test_ssh.rb +15 -0
- data/test/scout/offsite/test_step.rb +32 -0
- data/test/scout/offsite/test_sync.rb +36 -0
- data/test/scout/offsite/test_task.rb +0 -0
- data/test/scout/resource/test_path.rb +6 -0
- data/test/scout/test_named_array.rb +6 -0
- data/test/scout/test_persist.rb +3 -2
- data/test/scout/test_tsv.rb +17 -0
- data/test/scout/test_work_queue.rb +64 -42
- data/test/scout/tsv/persist/test_adapter.rb +1 -1
- data/test/scout/tsv/test_index.rb +14 -0
- data/test/scout/tsv/test_parser.rb +35 -0
- data/test/scout/tsv/test_stream.rb +200 -0
- data/test/scout/tsv/test_transformer.rb +12 -0
- data/test/scout/workflow/deployment/test_orchestrator.rb +272 -0
- data/test/scout/workflow/step/test_dependencies.rb +68 -0
- data/test/scout/workflow/step/test_info.rb +17 -0
- data/test/scout/workflow/step/test_status.rb +0 -1
- data/test/scout/workflow/task/test_dependencies.rb +357 -0
- data/test/scout/workflow/task/test_inputs.rb +52 -0
- data/test/scout/workflow/test_definition.rb +18 -0
- data/test/scout/workflow/test_documentation.rb +24 -0
- data/test/scout/workflow/test_step.rb +109 -0
- data/test/scout/workflow/test_task.rb +0 -287
- data/test/test_scout.rb +9 -0
- metadata +89 -5
- data/scout_commands/workflow/task_old +0 -706
data/lib/scout/open/stream.rb
CHANGED
@@ -3,7 +3,7 @@ module Open
|
|
3
3
|
|
4
4
|
class << self
|
5
5
|
attr_accessor :sensible_write_lock_dir
|
6
|
-
|
6
|
+
|
7
7
|
def sensible_write_lock_dir
|
8
8
|
@sensible_write_lock_dir ||= Path.setup("tmp/sensible_write_locks").find
|
9
9
|
end
|
@@ -18,7 +18,7 @@ module Open
|
|
18
18
|
|
19
19
|
def self.consume_stream(io, in_thread = false, into = nil, into_close = true, &block)
|
20
20
|
return if Path === io
|
21
|
-
return unless io.respond_to? :read
|
21
|
+
return unless io.respond_to? :read
|
22
22
|
|
23
23
|
if io.respond_to? :closed? and io.closed?
|
24
24
|
io.join if io.respond_to? :join
|
@@ -46,12 +46,12 @@ module Open
|
|
46
46
|
begin
|
47
47
|
into = into.find if Path === into
|
48
48
|
|
49
|
-
if String === into
|
49
|
+
if String === into
|
50
50
|
dir = File.dirname(into)
|
51
51
|
Open.mkdir dir unless File.exist?(dir)
|
52
|
-
into_path, into = into, File.open(into, 'w')
|
52
|
+
into_path, into = into, File.open(into, 'w')
|
53
53
|
end
|
54
|
-
|
54
|
+
|
55
55
|
into_close = false unless into.respond_to? :close
|
56
56
|
|
57
57
|
while c = io.read(BLOCK_SIZE)
|
@@ -81,7 +81,7 @@ module Open
|
|
81
81
|
into.close if into.respond_to?(:closed?) && ! into.closed?
|
82
82
|
into_path = into if into_path.nil? && String === into
|
83
83
|
if into_path and File.exist?(into_path)
|
84
|
-
FileUtils.rm into_path
|
84
|
+
FileUtils.rm into_path
|
85
85
|
end
|
86
86
|
raise exception
|
87
87
|
end
|
@@ -92,7 +92,7 @@ module Open
|
|
92
92
|
force = IndiferentHash.process_options options, :force
|
93
93
|
|
94
94
|
if File.exist?(path) and not force
|
95
|
-
Open.consume_stream content
|
95
|
+
Open.consume_stream content
|
96
96
|
return
|
97
97
|
end
|
98
98
|
|
@@ -107,10 +107,11 @@ module Open
|
|
107
107
|
|
108
108
|
if File.exist? path and not force
|
109
109
|
Log.warn "Path exists in sensible_write, not forcing update: #{ path }"
|
110
|
-
Open.consume_stream content
|
110
|
+
Open.consume_stream content
|
111
111
|
else
|
112
112
|
FileUtils.mkdir_p File.dirname(tmp_path) unless File.directory?(File.dirname(tmp_path))
|
113
113
|
FileUtils.rm_f tmp_path if File.exist? tmp_path
|
114
|
+
Log.low "Sensible write stream #{Log.fingerprint content} -> #{Log.fingerprint path}" if IO === content
|
114
115
|
begin
|
115
116
|
case
|
116
117
|
when block_given?
|
@@ -122,7 +123,7 @@ module Open
|
|
122
123
|
while block = content.read(BLOCK_SIZE)
|
123
124
|
f.write block
|
124
125
|
break if content.closed?
|
125
|
-
end
|
126
|
+
end
|
126
127
|
end
|
127
128
|
else
|
128
129
|
File.open(tmp_path, 'wb') do |f| end
|
@@ -139,8 +140,7 @@ module Open
|
|
139
140
|
Open.touch path if File.exist? path
|
140
141
|
content.join if content.respond_to?(:join) and not Path === content and not (content.respond_to?(:joined?) && content.joined?)
|
141
142
|
|
142
|
-
Open.notify_write(path)
|
143
|
-
Log.debug "Done sensible write: [#{Process.pid}] -- #{ path }"
|
143
|
+
Open.notify_write(path)
|
144
144
|
rescue Aborted
|
145
145
|
Log.low "Aborted sensible_write -- #{ Log.reset << path }"
|
146
146
|
content.abort if content.respond_to? :abort
|
@@ -174,7 +174,7 @@ module Open
|
|
174
174
|
|
175
175
|
[sout, sin]
|
176
176
|
end
|
177
|
-
Log.
|
177
|
+
Log.low{"Creating pipe #{[Log.fingerprint(res.last), Log.fingerprint(res.first)] * " -> "}"}
|
178
178
|
res
|
179
179
|
end
|
180
180
|
|
@@ -214,14 +214,13 @@ module Open
|
|
214
214
|
|
215
215
|
if do_fork
|
216
216
|
|
217
|
-
#parent_pid = Process.pid
|
218
217
|
pid = Process.fork {
|
219
218
|
begin
|
220
219
|
purge_pipes(sin)
|
221
220
|
sout.close
|
222
221
|
|
223
222
|
yield sin
|
224
|
-
sin.close if close and not sin.closed?
|
223
|
+
sin.close if close and not sin.closed?
|
225
224
|
|
226
225
|
rescue Exception
|
227
226
|
Log.exception $!
|
@@ -237,34 +236,20 @@ module Open
|
|
237
236
|
ConcurrentStream.setup sin, :pair => sout
|
238
237
|
ConcurrentStream.setup sout, :pair => sin
|
239
238
|
|
240
|
-
thread = Thread.new do
|
239
|
+
thread = Thread.new do
|
241
240
|
begin
|
242
|
-
|
243
|
-
|
244
|
-
|
245
|
-
yield sin
|
241
|
+
ConcurrentStream.process_stream(sin, :message => "Open pipe") do
|
242
|
+
Thread.current.report_on_exception = false
|
243
|
+
Thread.current["name"] = "Pipe input #{Log.fingerprint sin} => #{Log.fingerprint sout}"
|
246
244
|
|
247
|
-
|
248
|
-
rescue Aborted
|
249
|
-
Log.low "Aborted open_pipe: #{$!.message}"
|
250
|
-
raise $!
|
251
|
-
rescue Exception
|
252
|
-
Log.low "Exception in open_pipe: #{$!.message}"
|
253
|
-
begin
|
254
|
-
sout.threads.delete(Thread.current)
|
255
|
-
sout.pair = []
|
256
|
-
sout.abort($!) if sout.respond_to?(:abort)
|
257
|
-
sin.threads.delete(Thread.current)
|
258
|
-
sin.pair = []
|
259
|
-
sin.abort($!) if sin.respond_to?(:abort)
|
260
|
-
ensure
|
261
|
-
raise $!
|
245
|
+
yield sin
|
262
246
|
end
|
263
247
|
end
|
264
248
|
end
|
265
249
|
|
266
250
|
sin.threads = [thread]
|
267
251
|
sout.threads = [thread]
|
252
|
+
|
268
253
|
Thread.pass until thread["name"]
|
269
254
|
end
|
270
255
|
|
@@ -274,12 +259,14 @@ module Open
|
|
274
259
|
def self.tee_stream_thread_multiple(stream, num = 2)
|
275
260
|
in_pipes = []
|
276
261
|
out_pipes = []
|
277
|
-
num.times do
|
262
|
+
num.times do
|
278
263
|
sout, sin = Open.pipe
|
279
264
|
in_pipes << sin
|
280
265
|
out_pipes << sout
|
281
266
|
end
|
282
267
|
|
268
|
+
Log.low("Tee stream #{Log.fingerprint stream} -> #{Log.fingerprint out_pipes}")
|
269
|
+
|
283
270
|
filename = stream.filename if stream.respond_to? :filename
|
284
271
|
|
285
272
|
splitter_thread = Thread.new(Thread.current) do |parent|
|
@@ -291,7 +278,7 @@ module Open
|
|
291
278
|
while block = stream.read(BLOCK_SIZE)
|
292
279
|
|
293
280
|
in_pipes.each_with_index do |sin,i|
|
294
|
-
begin
|
281
|
+
begin
|
295
282
|
sin.write block
|
296
283
|
rescue IOError
|
297
284
|
Log.warn("Tee stream #{i} #{Log.fingerprint stream} IOError: #{$!.message} (#{Log.fingerprint sin})");
|
@@ -299,13 +286,12 @@ module Open
|
|
299
286
|
rescue
|
300
287
|
Log.warn("Tee stream #{i} #{Log.fingerprint stream} Exception: #{$!.message} (#{Log.fingerprint sin})");
|
301
288
|
raise $!
|
302
|
-
end unless skip[i]
|
289
|
+
end unless skip[i]
|
303
290
|
end
|
304
291
|
break if stream.closed?
|
305
292
|
end
|
306
293
|
|
307
294
|
stream.join if stream.respond_to? :join
|
308
|
-
stream.close unless stream.closed?
|
309
295
|
in_pipes.first.close unless in_pipes.first.closed?
|
310
296
|
rescue Aborted, Interrupt
|
311
297
|
stream.abort if stream.respond_to?(:abort) && ! stream.aborted?
|
@@ -348,18 +334,32 @@ module Open
|
|
348
334
|
end
|
349
335
|
end
|
350
336
|
|
351
|
-
out_pipes.each do |sout|
|
352
|
-
ConcurrentStream.setup sout, :threads => splitter_thread, :filename => filename, :pair => stream
|
353
|
-
end
|
354
337
|
Thread.pass until splitter_thread["name"]
|
355
338
|
|
356
339
|
main_pipe = out_pipes.first
|
357
|
-
main_pipe.autojoin = true
|
358
340
|
|
359
|
-
main_pipe
|
360
|
-
|
361
|
-
|
362
|
-
|
341
|
+
ConcurrentStream.setup(main_pipe, :threads => [splitter_thread], :filename => filename, :autojoin => true)
|
342
|
+
|
343
|
+
out_pipes[1..-1].each do |sout|
|
344
|
+
ConcurrentStream.setup sout, :filename => filename, :threads => [splitter_thread]
|
345
|
+
end
|
346
|
+
|
347
|
+
main_pipe.callback = proc do
|
348
|
+
begin
|
349
|
+
stream.join if stream.respond_to?(:join) && ! stream.joined?
|
350
|
+
in_pipes[1..-1].each do |sin|
|
351
|
+
sin.close unless sin.closed?
|
352
|
+
end
|
353
|
+
rescue
|
354
|
+
main_pipe.abort_callback.call($!)
|
355
|
+
raise $!
|
356
|
+
end
|
357
|
+
end
|
358
|
+
|
359
|
+
main_pipe.abort_callback = proc do |exception|
|
360
|
+
stream.abort(exception)
|
361
|
+
out_pipes[1..-1].each do |sout|
|
362
|
+
sout.abort(exception)
|
363
363
|
end
|
364
364
|
end
|
365
365
|
|
@@ -378,7 +378,7 @@ module Open
|
|
378
378
|
str = nil
|
379
379
|
Thread.pass while IO.select([stream],nil,nil,1).nil?
|
380
380
|
while not str = stream.read(size)
|
381
|
-
IO.select([stream],nil,nil,1)
|
381
|
+
IO.select([stream],nil,nil,1)
|
382
382
|
Thread.pass
|
383
383
|
raise ClosedStream if stream.eof?
|
384
384
|
end
|
@@ -403,102 +403,89 @@ module Open
|
|
403
403
|
str
|
404
404
|
end
|
405
405
|
|
406
|
-
def self.sort_stream(stream, header_hash
|
407
|
-
Open.open_pipe do |sin|
|
408
|
-
|
409
|
-
while line =~ /^#{header_hash}/ do
|
410
|
-
sin.puts line
|
406
|
+
def self.sort_stream(stream, header_hash: "#", cmd_args: "-u", memory: false)
|
407
|
+
sout = Open.open_pipe do |sin|
|
408
|
+
ConcurrentStream.process_stream(stream) do
|
411
409
|
line = stream.gets
|
412
|
-
|
410
|
+
while line && line.start_with?(header_hash) do
|
411
|
+
sin.puts line
|
412
|
+
line = stream.gets
|
413
|
+
end
|
413
414
|
|
414
|
-
|
415
|
-
|
416
|
-
begin
|
415
|
+
line_stream = Open.open_pipe do |line_stream_in|
|
416
|
+
line_stream_in.puts line if line
|
417
417
|
Open.consume_stream(stream, false, line_stream_in)
|
418
|
-
rescue
|
419
|
-
raise $!
|
420
418
|
end
|
421
|
-
|
419
|
+
Log.low "Sub-sort stream #{Log.fingerprint stream} -> #{Log.fingerprint line_stream}"
|
422
420
|
|
423
|
-
|
424
|
-
|
425
|
-
|
426
|
-
|
427
|
-
|
428
|
-
|
429
|
-
|
430
|
-
sorted.raise($!) if sorted.respond_to? :raise
|
431
|
-
stream.raise($!) if stream.respond_to? :raise
|
432
|
-
ensure
|
433
|
-
raise $!
|
421
|
+
if memory
|
422
|
+
line_stream.read.split("\n").sort.each do |line|
|
423
|
+
sin.puts line
|
424
|
+
end
|
425
|
+
else
|
426
|
+
io = CMD.cmd("env LC_ALL=C sort #{cmd_args || ""}", :in => line_stream, :pipe => true)
|
427
|
+
Open.consume_stream(io, false, sin)
|
434
428
|
end
|
435
429
|
end
|
436
430
|
end
|
431
|
+
Log.low "Sort #{Log.fingerprint stream} -> #{Log.fingerprint sout}"
|
432
|
+
sout
|
437
433
|
end
|
438
434
|
|
439
|
-
def self.
|
440
|
-
|
441
|
-
|
442
|
-
s.close if s.respond_to?(:close) && ! s.closed?
|
443
|
-
s.join if s.respond_to?(:join)
|
444
|
-
rescue
|
445
|
-
s.abort($!) if s.respond_to? :abort
|
446
|
-
raise $!
|
447
|
-
end
|
448
|
-
end
|
449
|
-
|
435
|
+
#def self.sort_stream(stream, header_hash = "#", cmd_args = "-u")
|
436
|
+
# StringIO.new stream.read.split("\n").sort.uniq * "\n"
|
437
|
+
#end
|
450
438
|
|
451
439
|
def self.collapse_stream(s, line: nil, sep: "\t", header: nil, &block)
|
452
440
|
sep ||= "\t"
|
453
441
|
Open.open_pipe do |sin|
|
442
|
+
|
454
443
|
sin.puts header if header
|
455
|
-
process_stream(s) do |s|
|
456
|
-
line ||= s.gets
|
457
444
|
|
458
|
-
|
459
|
-
|
460
|
-
|
461
|
-
|
462
|
-
|
463
|
-
|
464
|
-
|
465
|
-
|
466
|
-
|
467
|
-
|
468
|
-
|
469
|
-
|
470
|
-
|
471
|
-
|
472
|
-
|
445
|
+
line ||= s.gets
|
446
|
+
|
447
|
+
current_parts = []
|
448
|
+
while line
|
449
|
+
key, *parts = line.chomp.split(sep, -1)
|
450
|
+
case
|
451
|
+
when key.nil?
|
452
|
+
when current_parts.nil?
|
453
|
+
current_parts = parts
|
454
|
+
current_key = key
|
455
|
+
when current_key == key
|
456
|
+
parts.each_with_index do |part,i|
|
457
|
+
if current_parts[i].nil?
|
458
|
+
current_parts[i] = "|" << part
|
459
|
+
else
|
460
|
+
current_parts[i] = current_parts[i] << "|" << part
|
473
461
|
end
|
462
|
+
end
|
474
463
|
|
475
|
-
|
476
|
-
|
477
|
-
end
|
478
|
-
when current_key.nil?
|
479
|
-
current_key = key
|
480
|
-
current_parts = parts
|
481
|
-
when current_key != key
|
482
|
-
if block_given?
|
483
|
-
res = block.call(current_parts)
|
484
|
-
sin.puts [current_key, res] * sep
|
485
|
-
else
|
486
|
-
sin.puts [current_key, current_parts].flatten * sep
|
487
|
-
end
|
488
|
-
current_key = key
|
489
|
-
current_parts = parts
|
464
|
+
(parts.length..current_parts.length-1).to_a.each do |pos|
|
465
|
+
current_parts[pos] = current_parts[pos] << "|" << ""
|
490
466
|
end
|
491
|
-
|
467
|
+
when current_key.nil?
|
468
|
+
current_key = key
|
469
|
+
current_parts = parts
|
470
|
+
when current_key != key
|
471
|
+
if block_given?
|
472
|
+
res = block.call(current_parts)
|
473
|
+
sin.puts [current_key, res] * sep
|
474
|
+
else
|
475
|
+
sin.puts [current_key, current_parts].flatten * sep
|
476
|
+
end
|
477
|
+
current_key = key
|
478
|
+
current_parts = parts
|
492
479
|
end
|
493
|
-
|
494
|
-
if block_given?
|
495
|
-
res = block.call(current_parts)
|
496
|
-
sin.puts [current_key, res] * sep
|
497
|
-
else
|
498
|
-
sin.puts [current_key, current_parts].flatten * sep
|
499
|
-
end unless current_key.nil?
|
480
|
+
line = s.gets
|
500
481
|
end
|
482
|
+
|
483
|
+
if block_given?
|
484
|
+
res = block.call(current_parts)
|
485
|
+
sin.puts [current_key, res] * sep
|
486
|
+
else
|
487
|
+
sin.puts [current_key, current_parts].flatten * sep
|
488
|
+
end unless current_key.nil?
|
501
489
|
end
|
502
490
|
end
|
503
|
-
|
504
491
|
end
|
data/lib/scout/open/util.rb
CHANGED
@@ -68,6 +68,15 @@ module Open
|
|
68
68
|
!! (file =~ /\.zip$/)
|
69
69
|
end
|
70
70
|
|
71
|
+
def self.is_stream?(obj)
|
72
|
+
IO === obj || StringIO === obj
|
73
|
+
end
|
74
|
+
|
75
|
+
def self.has_stream?(obj)
|
76
|
+
obj.respond_to?(:stream)
|
77
|
+
end
|
78
|
+
|
79
|
+
|
71
80
|
def self.notify_write(file)
|
72
81
|
begin
|
73
82
|
notification_file = file + '.notify'
|
data/lib/scout/open.rb
CHANGED
@@ -20,19 +20,21 @@ module Open
|
|
20
20
|
end
|
21
21
|
end
|
22
22
|
|
23
|
-
def self.get_stream(file, mode = 'r')
|
23
|
+
def self.get_stream(file, mode = 'r', options = {})
|
24
|
+
return file if Open.is_stream?(file)
|
25
|
+
return file.stream if Open.has_stream?(file)
|
24
26
|
file = file.find if Path === file
|
25
27
|
|
26
|
-
return Open.ssh(file) if Open.ssh?(file)
|
27
|
-
return Open.wget(file) if Open.remote?(file)
|
28
|
+
return Open.ssh(file, options) if Open.ssh?(file)
|
29
|
+
return Open.wget(file, options) if Open.remote?(file)
|
28
30
|
|
29
31
|
File.open(file, mode)
|
30
32
|
end
|
31
33
|
|
32
|
-
def self.file_open(file, grep = false, mode = 'r', invert_grep = false)
|
34
|
+
def self.file_open(file, grep = false, mode = 'r', invert_grep = false, options = {})
|
33
35
|
Open.mkdir File.dirname(file) if mode.include? 'w'
|
34
36
|
|
35
|
-
stream = get_stream(file, mode)
|
37
|
+
stream = get_stream(file, mode, options)
|
36
38
|
|
37
39
|
if grep
|
38
40
|
grep(stream, grep, invert_grep)
|
@@ -56,11 +58,11 @@ module Open
|
|
56
58
|
def self.open(file, options = {})
|
57
59
|
if IO === file || StringIO === file
|
58
60
|
if block_given?
|
59
|
-
res = yield file
|
61
|
+
res = yield file, options
|
60
62
|
file.close
|
61
63
|
return res
|
62
64
|
else
|
63
|
-
return file
|
65
|
+
return file
|
64
66
|
end
|
65
67
|
end
|
66
68
|
|
@@ -70,7 +72,7 @@ module Open
|
|
70
72
|
|
71
73
|
options[:noz] = true if mode.include? "w"
|
72
74
|
|
73
|
-
io = file_open(file, options[:grep], mode, options[:invert_grep])
|
75
|
+
io = file_open(file, options[:grep], mode, options[:invert_grep], options)
|
74
76
|
|
75
77
|
io = unzip(io) if ((String === file and zip?(file)) and not options[:noz]) or options[:zip]
|
76
78
|
io = gunzip(io) if ((String === file and gzip?(file)) and not options[:noz]) or options[:gzip]
|
@@ -86,7 +88,7 @@ module Open
|
|
86
88
|
rescue DontClose
|
87
89
|
res = $!.payload
|
88
90
|
rescue Exception
|
89
|
-
io.abort if io.respond_to? :abort
|
91
|
+
io.abort $! if io.respond_to? :abort
|
90
92
|
io.join if io.respond_to? :join
|
91
93
|
raise $!
|
92
94
|
ensure
|
@@ -163,7 +165,6 @@ module Open
|
|
163
165
|
raise "Content unknown #{Log.fingerprint content}"
|
164
166
|
end
|
165
167
|
|
166
|
-
notify_write(file)
|
168
|
+
notify_write(file)
|
167
169
|
end
|
168
|
-
|
169
170
|
end
|
data/lib/scout/path/find.rb
CHANGED
@@ -34,6 +34,7 @@ module Path
|
|
34
34
|
|
35
35
|
def self.follow(path, map, map_name = nil)
|
36
36
|
file = map.sub('{PKGDIR}', path.pkgdir.respond_to?(:pkgdir) ? path.pkgdir.pkgdir || Path.default_pkgdir : path.pkgdir || Path.default_pkgdir).
|
37
|
+
sub('{HOME}', ENV["HOME"]).
|
37
38
|
sub('{RESOURCE}', path.pkgdir.to_s).
|
38
39
|
sub('{PWD}', FileUtils.pwd).
|
39
40
|
sub('{TOPLEVEL}', path._toplevel).
|
@@ -59,16 +60,17 @@ module Path
|
|
59
60
|
|
60
61
|
def self.path_maps
|
61
62
|
@@path_maps ||= IndiferentHash.setup({
|
62
|
-
:current =>
|
63
|
-
:user =>
|
64
|
-
:global =>
|
65
|
-
:usr =>
|
66
|
-
:local =>
|
67
|
-
:fast =>
|
68
|
-
:cache =>
|
69
|
-
:bulk =>
|
70
|
-
:lib =>
|
71
|
-
:
|
63
|
+
:current => "{PWD}/{TOPLEVEL}/{SUBPATH}",
|
64
|
+
:user => "{HOME}/.{PKGDIR}/{TOPLEVEL}/{SUBPATH}",
|
65
|
+
:global => '/{TOPLEVEL}/{PKGDIR}/{SUBPATH}',
|
66
|
+
:usr => '/usr/{TOPLEVEL}/{PKGDIR}/{SUBPATH}',
|
67
|
+
:local => '/usr/local/{TOPLEVEL}/{PKGDIR}/{SUBPATH}',
|
68
|
+
:fast => '/fast/{TOPLEVEL}/{PKGDIR}/{SUBPATH}',
|
69
|
+
:cache => '/cache/{TOPLEVEL}/{PKGDIR}/{SUBPATH}',
|
70
|
+
:bulk => '/bulk/{TOPLEVEL}/{PKGDIR}/{SUBPATH}',
|
71
|
+
:lib => '{LIBDIR}/{TOPLEVEL}/{SUBPATH}',
|
72
|
+
:scout_gear => File.join(Path.caller_lib_dir(__FILE__), "{TOPLEVEL}/{SUBPATH}"),
|
73
|
+
:tmp => '/tmp/{PKGDIR}/{TOPLEVEL}/{SUBPATH}',
|
72
74
|
:default => :user
|
73
75
|
})
|
74
76
|
end
|
@@ -127,6 +129,9 @@ module Path
|
|
127
129
|
def follow(map_name = :default, annotate = true)
|
128
130
|
IndiferentHash.setup(path_maps)
|
129
131
|
map = path_maps[map_name] || Path.path_maps[map_name]
|
132
|
+
if map.nil? && String === map_name
|
133
|
+
map = File.join(map_name, '{TOPLEVEL}/{SUBPATH}')
|
134
|
+
end
|
130
135
|
raise "Map not found #{Log.fingerprint map_name} not in #{Log.fingerprint path_maps.keys}" if map.nil?
|
131
136
|
while Symbol === map
|
132
137
|
map_name = map
|
data/lib/scout/path/util.rb
CHANGED
@@ -82,6 +82,11 @@ module Path
|
|
82
82
|
self.annotate(self + ".#{extension}")
|
83
83
|
end
|
84
84
|
|
85
|
+
def unset_extension
|
86
|
+
self.annotate(self.split(".")[0..-2] * ".")
|
87
|
+
end
|
88
|
+
|
89
|
+
|
85
90
|
# Is 'file' newer than 'path'? return non-true if path is newer than file
|
86
91
|
def self.newer?(path, file, by_link = false)
|
87
92
|
return true if not Open.exists?(file)
|
data/lib/scout/path.rb
CHANGED
@@ -32,7 +32,7 @@ module Path
|
|
32
32
|
prevpath = prevpath.to_s if Symbol === prevpath
|
33
33
|
|
34
34
|
subpath = File.join(prevpath.to_s, subpath) if prevpath
|
35
|
-
new = self.empty? ? subpath : File.join(self, subpath)
|
35
|
+
new = self.empty? ? subpath.dup : File.join(self, subpath)
|
36
36
|
self.annotate(new)
|
37
37
|
new
|
38
38
|
end
|
@@ -20,7 +20,7 @@ module Persist
|
|
20
20
|
type = type.to_sym if String === type
|
21
21
|
type = SERIALIZER if type == :serializer
|
22
22
|
case type
|
23
|
-
when nil, :string, :integer, :float, :boolean, :file, :path, :select, :folder
|
23
|
+
when nil, :string, :text, :integer, :float, :boolean, :file, :path, :select, :folder, :binary
|
24
24
|
if IO === content || StringIO === content
|
25
25
|
content.read
|
26
26
|
else
|
@@ -49,7 +49,7 @@ module Persist
|
|
49
49
|
type = SERIALIZER if type == :serializer
|
50
50
|
|
51
51
|
case type
|
52
|
-
when nil, :string, :file, :stream, :select, :folder
|
52
|
+
when nil, :string, :text, :file, :stream, :select, :folder
|
53
53
|
serialized
|
54
54
|
when :path
|
55
55
|
Path.setup(serialized)
|
@@ -58,7 +58,7 @@ module Persist
|
|
58
58
|
when :float
|
59
59
|
serialized.to_f
|
60
60
|
when :boolean
|
61
|
-
TRUE_STRINGS.include? serialized
|
61
|
+
TRUE_STRINGS.include? serialized.strip
|
62
62
|
when :array
|
63
63
|
serialized.split("\n")
|
64
64
|
when :yaml
|
@@ -104,7 +104,7 @@ module Persist
|
|
104
104
|
|
105
105
|
if type == :binary
|
106
106
|
content.force_encoding("ASCII-8BIT") if content.respond_to? :force_encoding
|
107
|
-
Open.open(
|
107
|
+
Open.open(file, :mode => 'wb') do |f|
|
108
108
|
f.puts content
|
109
109
|
end
|
110
110
|
content
|
data/lib/scout/persist.rb
CHANGED
data/lib/scout/resource/path.rb
CHANGED
@@ -3,7 +3,7 @@ module Path
|
|
3
3
|
return self if ! force && (Open.exist?(self) || @produced)
|
4
4
|
begin
|
5
5
|
if Resource === self.pkgdir
|
6
|
-
self.pkgdir.produce self
|
6
|
+
self.pkgdir.produce self, force
|
7
7
|
else
|
8
8
|
false
|
9
9
|
end
|
@@ -13,7 +13,7 @@ module Path
|
|
13
13
|
message = $!.message
|
14
14
|
message = "No exception message" if message.nil? || message.empty?
|
15
15
|
Log.warn "Error producing #{self}: #{message}"
|
16
|
-
|
16
|
+
raise $!
|
17
17
|
ensure
|
18
18
|
@produced = true
|
19
19
|
end
|
@@ -33,13 +33,16 @@ module Path
|
|
33
33
|
end
|
34
34
|
|
35
35
|
def produce_and_find(extension = nil, *args)
|
36
|
-
if extension
|
37
|
-
|
38
|
-
|
39
|
-
|
40
|
-
|
41
|
-
|
42
|
-
|
36
|
+
found = if extension
|
37
|
+
found = find_with_extension(extension, *args)
|
38
|
+
found.exists? ? found : produce_with_extension(extension, *args)
|
39
|
+
else
|
40
|
+
found = find
|
41
|
+
found.exists? ? found : produce(*args)
|
42
|
+
end
|
43
|
+
raise "Not found: #{self}" unless found
|
44
|
+
|
45
|
+
found
|
43
46
|
end
|
44
47
|
|
45
48
|
def relocate
|
@@ -47,6 +50,10 @@ module Path
|
|
47
50
|
Resource.relocate(self)
|
48
51
|
end
|
49
52
|
|
53
|
+
def identify
|
54
|
+
Resource.identify(self)
|
55
|
+
end
|
56
|
+
|
50
57
|
def open(*args, &block)
|
51
58
|
produce
|
52
59
|
Open.open(self, *args, &block)
|