rbbt-util 5.28.1 → 5.28.7
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc.rb +5 -2
- data/lib/rbbt/persist.rb +1 -0
- data/lib/rbbt/resource/path.rb +3 -1
- data/lib/rbbt/tsv/accessor.rb +10 -2
- data/lib/rbbt/tsv/change_id.rb +2 -2
- data/lib/rbbt/tsv/dumper.rb +10 -2
- data/lib/rbbt/tsv/parallel/traverse.rb +9 -8
- data/lib/rbbt/tsv/util.rb +25 -13
- data/lib/rbbt/util/config.rb +2 -1
- data/lib/rbbt/util/misc/inspect.rb +2 -2
- data/lib/rbbt/util/misc/system.rb +1 -1
- data/lib/rbbt/workflow.rb +1 -0
- data/lib/rbbt/workflow/accessor.rb +94 -93
- data/lib/rbbt/workflow/definition.rb +5 -3
- data/lib/rbbt/workflow/integration/cromwell.rb +10 -3
- data/lib/rbbt/workflow/remote_workflow/driver/rest.rb +5 -1
- data/lib/rbbt/workflow/step.rb +4 -3
- data/lib/rbbt/workflow/step/accessor.rb +10 -7
- data/lib/rbbt/workflow/step/dependencies.rb +2 -2
- data/lib/rbbt/workflow/usage.rb +1 -1
- data/lib/rbbt/workflow/util/archive.rb +1 -0
- data/lib/rbbt/workflow/util/orchestrator.rb +190 -0
- data/lib/rbbt/workflow/util/trace.rb +182 -0
- data/share/rbbt_commands/app/start +2 -2
- data/share/rbbt_commands/purge_job +2 -4
- data/share/rbbt_commands/system/status +1 -1
- data/share/rbbt_commands/workflow/server +2 -0
- data/test/rbbt/tsv/parallel/test_traverse.rb +35 -1
- data/test/rbbt/tsv/test_manipulate.rb +20 -0
- data/test/rbbt/workflow/test_schedule.rb +0 -0
- data/test/rbbt/workflow/util/test_orchestrator.rb +136 -0
- metadata +8 -3
- data/lib/rbbt/workflow/schedule.rb +0 -238
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: f13812c850239f7d78c94e74288ea7807663c72146002e13a13aa99babb18555
|
4
|
+
data.tar.gz: 3568f646d3095448ac6c8d99f32a5513421c80fd9d8b1f9a049a7ce512f3139d
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 644bcc769e818310492993b15a024b83de399d65a0cfc74b9dc06ee233bfd66da3c0951a26899c66ce62a8410104f00b8b84c07f77a4a1159a7fb5149befb5a1
|
7
|
+
data.tar.gz: da5fd395014feded588f223686bd032dd86e46cac0e48e4369e9d1ea2e1f0d021e0fab02539ab2be1f483efc5463b9487952783edf2e00f22d7158879b5fd32d
|
data/lib/rbbt/hpc.rb
CHANGED
@@ -451,12 +451,15 @@ EOF
|
|
451
451
|
out = CMD.cmd("tail -f '#{fout}'", :pipe => true) if File.exists?(fout) and not tail == :STDERR
|
452
452
|
err = CMD.cmd("tail -f '#{ferr}'", :pipe => true) if File.exists?(ferr)
|
453
453
|
|
454
|
-
Misc.consume_stream(err, true, STDERR) if err
|
455
|
-
Misc.consume_stream(out, true, STDOUT) if out
|
454
|
+
terr = Misc.consume_stream(err, true, STDERR) if err
|
455
|
+
tout = Misc.consume_stream(out, true, STDOUT) if out
|
456
456
|
|
457
457
|
sleep 3 while CMD.cmd("squeue --job #{job}").read.include? job.to_s
|
458
|
+
rescue Aborted
|
458
459
|
ensure
|
459
460
|
begin
|
461
|
+
terr.exit if terr
|
462
|
+
tout.exit if tout
|
460
463
|
err.close if err
|
461
464
|
err.join if err
|
462
465
|
rescue Exception
|
data/lib/rbbt/persist.rb
CHANGED
data/lib/rbbt/resource/path.rb
CHANGED
@@ -412,7 +412,9 @@ module Path
|
|
412
412
|
end
|
413
413
|
|
414
414
|
def replace_extension(new_extension = nil, multiple = false)
|
415
|
-
if multiple
|
415
|
+
if String === multiple
|
416
|
+
new_path = self.sub(/(\.[^\.\/]{1,5})(.#{multiple})?$/,'')
|
417
|
+
elsif multiple
|
416
418
|
new_path = self.sub(/(\.[^\.\/]{1,5})+$/,'')
|
417
419
|
else
|
418
420
|
new_path = self.sub(/\.[^\.\/]{1,5}$/,'')
|
data/lib/rbbt/tsv/accessor.rb
CHANGED
@@ -550,9 +550,17 @@ module TSV
|
|
550
550
|
"\t" << ([""] * fields.length) * "\t" << "\n"
|
551
551
|
end
|
552
552
|
when Array
|
553
|
-
|
553
|
+
if fields.nil? or fields.empty?
|
554
|
+
"\n"
|
555
|
+
else
|
556
|
+
"\t" << values.collect{|v| Array === v ? v * "|" : v} * "\t" << "\n"
|
557
|
+
end
|
554
558
|
else
|
555
|
-
|
559
|
+
if fields.nil? or fields.empty?
|
560
|
+
"\n"
|
561
|
+
else
|
562
|
+
"\t" << values.to_s << "\n"
|
563
|
+
end
|
556
564
|
end
|
557
565
|
end
|
558
566
|
|
data/lib/rbbt/tsv/change_id.rb
CHANGED
@@ -58,13 +58,13 @@ module TSV
|
|
58
58
|
|
59
59
|
identifiers, persist_input, compact = Misc.process_options options, :identifiers, :persist, :compact
|
60
60
|
identifiers = tsv.identifier_files.first if identifiers.nil?
|
61
|
-
identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil?
|
61
|
+
identifiers = Organism.identifiers(tsv.namespace) if defined?(Organism) && identifiers.nil? && tsv.namespace && Organism.identifiers(tsv.namespace).exists?
|
62
62
|
identifiers.namespace ||= tsv.namespace
|
63
63
|
|
64
64
|
fields = (identifiers and identifiers.all_fields.include?(field))? [field] : nil
|
65
65
|
#index = identifiers.index :target => format, :fields => fields, :persist => persist_input, :order => true
|
66
66
|
|
67
|
-
grep = Organism.blacklist_genes(tsv.namespace).list if identifiers.namespace
|
67
|
+
grep = Organism.blacklist_genes(tsv.namespace).list if defined?(Organism) && identifiers.namespace && Organism.blacklist_genes(tsv.namespace).exists?
|
68
68
|
if fields.nil?
|
69
69
|
index = identifiers.index(:data_tsv_grep => grep, :data_invert_grep => true, :target => format, :persist => true, :order => true, :unnamed => true, :data_persist => true)
|
70
70
|
else
|
data/lib/rbbt/tsv/dumper.rb
CHANGED
@@ -32,9 +32,17 @@ module TSV
|
|
32
32
|
sep + ([""] * fields.length) * sep << "\n"
|
33
33
|
end
|
34
34
|
when Array
|
35
|
-
|
35
|
+
if fields.nil? or fields.empty?
|
36
|
+
"\n"
|
37
|
+
else
|
38
|
+
sep + (values.collect{|v| Array === v ? v * "|" : v} * sep) << "\n"
|
39
|
+
end
|
36
40
|
else
|
37
|
-
|
41
|
+
if fields.nil? or fields.empty?
|
42
|
+
"\n"
|
43
|
+
else
|
44
|
+
sep + values.to_s << "\n"
|
45
|
+
end
|
38
46
|
end
|
39
47
|
end
|
40
48
|
|
@@ -101,8 +101,8 @@ module TSV
|
|
101
101
|
error = true
|
102
102
|
raise $!
|
103
103
|
ensure
|
104
|
-
Log::ProgressBar.remove_bar(bar) if bar
|
105
104
|
join.call(error) if join
|
105
|
+
Log::ProgressBar.remove_bar(bar) if bar
|
106
106
|
end
|
107
107
|
end
|
108
108
|
|
@@ -137,8 +137,8 @@ module TSV
|
|
137
137
|
error = true
|
138
138
|
raise $!
|
139
139
|
ensure
|
140
|
-
Log::ProgressBar.remove_bar(bar) if bar
|
141
140
|
join.call(error) if join
|
141
|
+
Log::ProgressBar.remove_bar(bar) if bar
|
142
142
|
end
|
143
143
|
end
|
144
144
|
|
@@ -177,8 +177,8 @@ module TSV
|
|
177
177
|
error = true
|
178
178
|
raise $!
|
179
179
|
ensure
|
180
|
-
Log::ProgressBar.remove_bar(bar) if bar
|
181
180
|
join.call(error) if join
|
181
|
+
Log::ProgressBar.remove_bar(bar) if bar
|
182
182
|
end
|
183
183
|
end
|
184
184
|
|
@@ -219,8 +219,8 @@ module TSV
|
|
219
219
|
error = true
|
220
220
|
raise $!
|
221
221
|
ensure
|
222
|
-
Log::ProgressBar.remove_bar(bar) if bar
|
223
222
|
join.call(error) if join
|
223
|
+
Log::ProgressBar.remove_bar(bar) if bar
|
224
224
|
end
|
225
225
|
end
|
226
226
|
|
@@ -273,8 +273,8 @@ module TSV
|
|
273
273
|
error = true
|
274
274
|
raise $!
|
275
275
|
ensure
|
276
|
-
Log::ProgressBar.remove_bar(bar) if bar
|
277
276
|
join.call(error) if join
|
277
|
+
Log::ProgressBar.remove_bar(bar) if bar
|
278
278
|
end
|
279
279
|
end
|
280
280
|
|
@@ -318,8 +318,8 @@ module TSV
|
|
318
318
|
error = true
|
319
319
|
raise $!
|
320
320
|
ensure
|
321
|
-
Log::ProgressBar.remove_bar(bar) if bar
|
322
321
|
join.call(error) if join
|
322
|
+
Log::ProgressBar.remove_bar(bar) if bar
|
323
323
|
end
|
324
324
|
end
|
325
325
|
|
@@ -377,6 +377,7 @@ module TSV
|
|
377
377
|
obj.run(true) unless obj.done? || obj.started? || obj.result
|
378
378
|
|
379
379
|
stream = obj.get_stream
|
380
|
+
options = {:type => :array}.merge(options) if obj.result_type == :array
|
380
381
|
|
381
382
|
if stream
|
382
383
|
traverse_obj(stream, options, &block)
|
@@ -623,6 +624,8 @@ module TSV
|
|
623
624
|
def self.traverse(obj, options = {}, &block)
|
624
625
|
into = options[:into]
|
625
626
|
|
627
|
+
into = options[:into] = Open.open(into, :mode => "w") if Misc.is_filename?(into)
|
628
|
+
|
626
629
|
case into
|
627
630
|
when :stream
|
628
631
|
sout = Misc.open_pipe false, false do |sin|
|
@@ -727,8 +730,6 @@ module TSV
|
|
727
730
|
Log.exception $!
|
728
731
|
abort_stream(into, $!)
|
729
732
|
raise $!
|
730
|
-
ensure
|
731
|
-
Log::ProgressBar.remove_bar(bar) if bar
|
732
733
|
end
|
733
734
|
|
734
735
|
into
|
data/lib/rbbt/tsv/util.rb
CHANGED
@@ -184,7 +184,11 @@ module TSV
|
|
184
184
|
str = ""
|
185
185
|
str << preamble.strip << "\n" if preamble and not preamble.empty?
|
186
186
|
if fields
|
187
|
-
|
187
|
+
if fields.empty?
|
188
|
+
str << header_hash << (key_field || "ID").to_s << "\n"
|
189
|
+
else
|
190
|
+
str << header_hash << (key_field || "ID").to_s << sep << (fields * sep) << "\n"
|
191
|
+
end
|
188
192
|
end
|
189
193
|
|
190
194
|
str
|
@@ -316,22 +320,30 @@ module TSV
|
|
316
320
|
|
317
321
|
def to_single
|
318
322
|
new = {}
|
319
|
-
|
320
|
-
|
321
|
-
through do |k,v|
|
322
|
-
new[k] = v.first.first
|
323
|
-
end
|
324
|
-
when :flat
|
323
|
+
|
324
|
+
if block_given?
|
325
325
|
through do |k,v|
|
326
|
-
new[k] = v
|
326
|
+
new[k] = yield v
|
327
327
|
end
|
328
|
-
|
329
|
-
|
330
|
-
|
331
|
-
|
332
|
-
|
328
|
+
else
|
329
|
+
case type
|
330
|
+
when :double
|
331
|
+
through do |k,v|
|
332
|
+
new[k] = v.first.first
|
333
|
+
end
|
334
|
+
when :flat
|
335
|
+
through do |k,v|
|
336
|
+
new[k] = v.first
|
337
|
+
end
|
338
|
+
when :single
|
339
|
+
return self
|
340
|
+
when :list
|
341
|
+
through do |k,v|
|
342
|
+
new[k] = v.first
|
343
|
+
end
|
333
344
|
end
|
334
345
|
end
|
346
|
+
|
335
347
|
self.annotate(new)
|
336
348
|
new.type = :single
|
337
349
|
new.fields = [new.fields.first] if new.fields.length > 1
|
data/lib/rbbt/util/config.rb
CHANGED
@@ -15,7 +15,7 @@ module Rbbt::Config
|
|
15
15
|
end
|
16
16
|
|
17
17
|
def self.load_file(file)
|
18
|
-
Log.debug "Loading file: #{ file }"
|
18
|
+
Log.debug "Loading config file: #{ file }"
|
19
19
|
TSV.traverse file, :type => :array do |line|
|
20
20
|
next if line =~ /^#/
|
21
21
|
key, value, *tokens = line.strip.split(/\s/)
|
@@ -85,6 +85,7 @@ module Rbbt::Config
|
|
85
85
|
priorities
|
86
86
|
end
|
87
87
|
|
88
|
+
# For equal priorities the matching prioritizes tokens ealier in the list
|
88
89
|
def self.get(key, *tokens)
|
89
90
|
options = tokens.pop if Hash === tokens.last
|
90
91
|
default = options.nil? ? nil : options[:default]
|
@@ -292,7 +292,7 @@ module Misc
|
|
292
292
|
files = obj.glob("**/*")
|
293
293
|
"directory: #{Misc.fingerprint(files)}"
|
294
294
|
else
|
295
|
-
"file: " << obj << "--" << mtime_str(obj)
|
295
|
+
"file: " << Open.realpath(obj) << "--" << mtime_str(obj)
|
296
296
|
end
|
297
297
|
else
|
298
298
|
obj + " (file missing)"
|
@@ -401,7 +401,7 @@ module Misc
|
|
401
401
|
|
402
402
|
def self.scan_version_text(text, cmd = nil)
|
403
403
|
cmd = "NOCMDGIVE" if cmd.nil? || cmd.empty?
|
404
|
-
m = text.match(/(?:version.*?|#{cmd}.*?|#{cmd.split(/[-_.]/).first}.*?|v)((?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
|
404
|
+
m = text.match(/(?:version.*?|#{cmd}.*?|#{cmd.to_s.split(/[-_.]/).first}.*?|v)((?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
|
405
405
|
return nil if m.nil?
|
406
406
|
m[1]
|
407
407
|
end
|
@@ -113,7 +113,7 @@ end
|
|
113
113
|
end
|
114
114
|
|
115
115
|
def self.is_filename?(string)
|
116
|
-
return true if defined?
|
116
|
+
return true if defined? Path and Path === string
|
117
117
|
return true if string.respond_to? :exists
|
118
118
|
return true if String === string and string.length < 265 and File.exist?(string)
|
119
119
|
return false
|
data/lib/rbbt/workflow.rb
CHANGED
@@ -364,6 +364,7 @@ module Workflow
|
|
364
364
|
raise ParameterException, "Inputs #{Misc.humanize_list(missing_inputs)} are required but were not provided or are nil"
|
365
365
|
end
|
366
366
|
|
367
|
+
# jobname => true sets the value of the input to the name of the job
|
367
368
|
if task.input_options
|
368
369
|
jobname_input = task.input_options.select{|i,o| o[:jobname]}.collect{|i,o| i }.first
|
369
370
|
else
|
@@ -26,105 +26,106 @@ module Workflow
|
|
26
26
|
raise "No '#{name}' task in '#{self.to_s}' Workflow" if task.nil?
|
27
27
|
id = File.join(self.to_s, name.to_s)
|
28
28
|
@task_info ||= {}
|
29
|
-
@task_info[id] ||= begin
|
30
|
-
|
31
|
-
|
32
|
-
|
33
|
-
|
34
|
-
|
35
|
-
|
36
|
-
|
37
|
-
|
38
|
-
|
39
|
-
|
40
|
-
|
41
|
-
|
42
|
-
|
43
|
-
|
44
|
-
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
|
49
|
-
|
50
|
-
|
29
|
+
@task_info[id] ||= begin
|
30
|
+
description = task.description
|
31
|
+
result_description = task.result_description
|
32
|
+
result_type = task.result_type
|
33
|
+
inputs = rec_inputs(name).uniq
|
34
|
+
input_types = rec_input_types(name)
|
35
|
+
input_descriptions = rec_input_descriptions(name)
|
36
|
+
input_use = rec_input_use(name)
|
37
|
+
input_defaults = rec_input_defaults(name)
|
38
|
+
input_options = rec_input_options(name)
|
39
|
+
extension = task.extension
|
40
|
+
export = case
|
41
|
+
when (synchronous_exports.include?(name.to_sym) or synchronous_exports.include?(name.to_s))
|
42
|
+
:synchronous
|
43
|
+
when (asynchronous_exports.include?(name.to_sym) or asynchronous_exports.include?(name.to_s))
|
44
|
+
:asynchronous
|
45
|
+
when (exec_exports.include?(name.to_sym) or exec_exports.include?(name.to_s))
|
46
|
+
:exec
|
47
|
+
when (stream_exports.include?(name.to_sym) or stream_exports.include?(name.to_s))
|
48
|
+
:stream
|
49
|
+
else
|
50
|
+
:none
|
51
|
+
end
|
51
52
|
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
57
|
-
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
|
65
|
-
|
66
|
-
|
67
|
-
|
53
|
+
dependencies = task_dependencies[name].select{|dep| String === dep or Symbol === dep}
|
54
|
+
{ :id => id,
|
55
|
+
:description => description,
|
56
|
+
:export => export,
|
57
|
+
:inputs => inputs,
|
58
|
+
:input_types => input_types,
|
59
|
+
:input_descriptions => input_descriptions,
|
60
|
+
:input_defaults => input_defaults,
|
61
|
+
:input_options => input_options,
|
62
|
+
:input_use => input_use,
|
63
|
+
:result_type => result_type,
|
64
|
+
:result_description => result_description,
|
65
|
+
:dependencies => dependencies,
|
66
|
+
:extension => extension
|
67
|
+
}
|
68
|
+
end
|
68
69
|
end
|
69
70
|
|
70
71
|
def rec_dependencies(taskname)
|
71
72
|
@rec_dependencies ||= {}
|
72
73
|
@rec_dependencies[taskname] ||= begin
|
73
|
-
|
74
|
-
|
75
|
-
|
76
|
-
|
77
|
-
|
78
|
-
|
79
|
-
|
80
|
-
|
81
|
-
|
82
|
-
|
83
|
-
|
84
|
-
|
85
|
-
|
86
|
-
|
87
|
-
|
88
|
-
|
89
|
-
|
90
|
-
|
91
|
-
|
92
|
-
|
93
|
-
|
94
|
-
|
95
|
-
|
96
|
-
|
97
|
-
|
98
|
-
|
99
|
-
|
100
|
-
|
101
|
-
|
102
|
-
|
103
|
-
|
104
|
-
|
105
|
-
|
74
|
+
if task_dependencies.include? taskname
|
75
|
+
|
76
|
+
deps = task_dependencies[taskname]
|
77
|
+
|
78
|
+
#all_deps = deps.select{|dep| String === dep or Symbol === dep or Array === dep}
|
79
|
+
|
80
|
+
all_deps = []
|
81
|
+
deps.each do |dep|
|
82
|
+
if DependencyBlock === dep
|
83
|
+
all_deps << dep.dependency if dep.dependency
|
84
|
+
else
|
85
|
+
all_deps << dep unless Proc === dep
|
86
|
+
end
|
87
|
+
|
88
|
+
begin
|
89
|
+
case dep
|
90
|
+
when Array
|
91
|
+
wf, t, o = dep
|
92
|
+
|
93
|
+
wf.rec_dependencies(t.to_sym).each do |d|
|
94
|
+
if Array === d
|
95
|
+
new = d.dup
|
96
|
+
else
|
97
|
+
new = [dep.first, d]
|
98
|
+
end
|
99
|
+
|
100
|
+
if Hash === o and not o.empty?
|
101
|
+
if Hash === new.last
|
102
|
+
hash = new.last.dup
|
103
|
+
o.each{|k,v| hash[k] ||= v}
|
104
|
+
new[new.length-1] = hash
|
105
|
+
else
|
106
|
+
new.push o.dup
|
107
|
+
end
|
108
|
+
end
|
109
|
+
|
110
|
+
all_deps << new
|
111
|
+
end if wf && t
|
112
|
+
|
113
|
+
when String, Symbol
|
114
|
+
rec_deps = rec_dependencies(dep.to_sym)
|
115
|
+
all_deps.concat rec_deps
|
116
|
+
when DependencyBlock
|
117
|
+
dep = dep.dependency
|
118
|
+
raise TryAgain
|
119
|
+
end
|
120
|
+
rescue TryAgain
|
121
|
+
retry
|
122
|
+
end
|
106
123
|
end
|
124
|
+
all_deps.uniq
|
125
|
+
else
|
126
|
+
[]
|
107
127
|
end
|
108
|
-
|
109
|
-
all_deps << new
|
110
|
-
end if wf && t
|
111
|
-
|
112
|
-
when String, Symbol
|
113
|
-
rec_deps = rec_dependencies(dep.to_sym)
|
114
|
-
all_deps.concat rec_deps
|
115
|
-
when DependencyBlock
|
116
|
-
dep = dep.dependency
|
117
|
-
raise TryAgain
|
118
|
-
end
|
119
|
-
rescue TryAgain
|
120
|
-
retry
|
121
|
-
end
|
122
|
-
end
|
123
|
-
all_deps.uniq
|
124
|
-
else
|
125
|
-
[]
|
126
|
-
end
|
127
|
-
end
|
128
|
+
end
|
128
129
|
end
|
129
130
|
|
130
131
|
def task_from_dep(dep)
|
@@ -182,7 +183,7 @@ module Workflow
|
|
182
183
|
acc
|
183
184
|
}.tap{|h| IndiferentHash.setup(h)}
|
184
185
|
end
|
185
|
-
|
186
|
+
|
186
187
|
def rec_input_use(taskname)
|
187
188
|
task = task_from_dep(taskname)
|
188
189
|
deps = rec_dependencies(taskname)
|
@@ -474,7 +475,7 @@ module Workflow
|
|
474
475
|
else
|
475
476
|
workdir_find = workdir
|
476
477
|
end
|
477
|
-
|
478
|
+
|
478
479
|
workdir_find = File.expand_path(workdir_find)
|
479
480
|
path = File.expand_path(path)
|
480
481
|
dir = File.dirname(path)
|