rbbt-util 5.28.5 → 5.28.10
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- checksums.yaml +4 -4
- data/lib/rbbt/entity.rb +1 -1
- data/lib/rbbt/fix_width_table.rb +5 -4
- data/lib/rbbt/persist.rb +1 -0
- data/lib/rbbt/persist/tsv/adapter.rb +0 -1
- data/lib/rbbt/persist/tsv/fix_width_table.rb +5 -3
- data/lib/rbbt/tsv/accessor.rb +10 -2
- data/lib/rbbt/tsv/dumper.rb +14 -2
- data/lib/rbbt/tsv/parallel/traverse.rb +3 -0
- data/lib/rbbt/tsv/util.rb +5 -1
- data/lib/rbbt/util/cmd.rb +1 -0
- data/lib/rbbt/util/config.rb +2 -1
- data/lib/rbbt/util/misc/bgzf.rb +1 -1
- data/lib/rbbt/util/misc/inspect.rb +1 -1
- data/lib/rbbt/util/misc/system.rb +1 -1
- data/lib/rbbt/util/named_array.rb +1 -1
- data/lib/rbbt/util/open.rb +18 -17
- data/lib/rbbt/workflow.rb +1 -0
- data/lib/rbbt/workflow/accessor.rb +94 -93
- data/lib/rbbt/workflow/definition.rb +8 -4
- data/lib/rbbt/workflow/integration/ansible.rb +53 -0
- data/lib/rbbt/workflow/integration/ansible/workflow.rb +60 -0
- data/lib/rbbt/workflow/remote_workflow/driver/rest.rb +5 -1
- data/lib/rbbt/workflow/step.rb +22 -5
- data/lib/rbbt/workflow/step/accessor.rb +7 -5
- data/lib/rbbt/workflow/usage.rb +1 -1
- data/lib/rbbt/workflow/util/archive.rb +3 -0
- data/lib/rbbt/workflow/util/orchestrator.rb +228 -0
- data/lib/rbbt/workflow/util/trace.rb +182 -0
- data/share/rbbt_commands/ansible +55 -0
- data/share/rbbt_commands/purge_job +2 -5
- data/share/rbbt_commands/system/status +1 -1
- data/share/rbbt_commands/workflow/forget_deps +10 -3
- data/share/rbbt_commands/workflow/server +2 -0
- data/test/rbbt/association/test_index.rb +6 -6
- data/test/rbbt/knowledge_base/test_query.rb +3 -3
- data/test/rbbt/knowledge_base/test_registry.rb +1 -1
- data/test/rbbt/persist/tsv/test_cdb.rb +0 -7
- data/test/rbbt/persist/tsv/test_kyotocabinet.rb +2 -8
- data/test/rbbt/persist/tsv/test_leveldb.rb +0 -6
- data/test/rbbt/persist/tsv/test_lmdb.rb +0 -6
- data/test/rbbt/persist/tsv/test_tokyocabinet.rb +15 -14
- data/test/rbbt/test_entity.rb +0 -1
- data/test/rbbt/test_knowledge_base.rb +3 -4
- data/test/rbbt/test_persist.rb +10 -6
- data/test/rbbt/test_workflow.rb +17 -16
- data/test/rbbt/tsv/parallel/test_traverse.rb +14 -0
- data/test/rbbt/tsv/test_accessor.rb +11 -0
- data/test/rbbt/tsv/test_attach.rb +0 -2
- data/test/rbbt/tsv/test_index.rb +6 -7
- data/test/rbbt/tsv/test_manipulate.rb +22 -3
- data/test/rbbt/util/R/test_model.rb +2 -1
- data/test/rbbt/util/R/test_plot.rb +0 -2
- data/test/rbbt/util/concurrency/test_processes.rb +1 -1
- data/test/rbbt/util/misc/test_bgzf.rb +11 -7
- data/test/rbbt/util/misc/test_lock.rb +0 -1
- data/test/rbbt/util/misc/test_multipart_payload.rb +1 -1
- data/test/rbbt/util/misc/test_pipes.rb +0 -5
- data/test/rbbt/util/test_R.rb +1 -0
- data/test/rbbt/util/test_log.rb +4 -6
- data/test/rbbt/util/test_misc.rb +0 -2
- data/test/rbbt/util/test_open.rb +0 -1
- data/test/rbbt/util/test_python.rb +17 -1
- data/test/rbbt/workflow/test_remote_workflow.rb +1 -1
- data/test/rbbt/workflow/test_schedule.rb +0 -0
- data/test/rbbt/workflow/test_step.rb +8 -3
- data/test/rbbt/workflow/util/test_orchestrator.rb +273 -0
- metadata +11 -5
- data/lib/rbbt/workflow/schedule.rb +0 -238
- data/test/rbbt/workflow/remote/test_client.rb +0 -56
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 443812f3080048a2e39b95ceda4fda2b3f403788c4d32ae4822b0b6920ac1d1f
|
4
|
+
data.tar.gz: e586076cca9dbd72b9dae8ba8be0061269e9bef5d04163f382f2d3b3f353d1b8
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: ca6ea9a139a48dfcc76fb04b889d45881d023e9f6fda362da0bb7bd4c63b31217ca0a9bb9f4702186c78b741a1eb1b5c7ca2607512e6dced51026081bdcb8aa7
|
7
|
+
data.tar.gz: 76f021c8d565e2833506f17fb54436d0fe80d29d8bface099cece0445cb70718f8f2126e6fa6eb139f6555e33fe9382d1401339aacb100073bb4964c62f1a260
|
data/lib/rbbt/entity.rb
CHANGED
data/lib/rbbt/fix_width_table.rb
CHANGED
@@ -67,7 +67,7 @@ class FixWidthTable
|
|
67
67
|
|
68
68
|
def format(pos, value)
|
69
69
|
padding = value_size - value.length
|
70
|
-
if range
|
70
|
+
if @range
|
71
71
|
(pos + [padding, value + ("\0" * padding)]).pack("llll#{mask}")
|
72
72
|
else
|
73
73
|
[pos, padding, value + ("\0" * padding)].pack("ll#{mask}")
|
@@ -105,7 +105,7 @@ class FixWidthTable
|
|
105
105
|
|
106
106
|
def idx_value(index)
|
107
107
|
return nil if index < 0 or index >= size
|
108
|
-
@file.seek((range ? 17 : 9 ) + (record_size) * index, IO::SEEK_SET)
|
108
|
+
@file.seek((@range ? 17 : 9 ) + (record_size) * index, IO::SEEK_SET)
|
109
109
|
padding = @file.read(4).unpack("l").first+1
|
110
110
|
txt = @file.read(value_size)
|
111
111
|
str = txt.unpack(mask).first
|
@@ -277,7 +277,8 @@ class FixWidthTable
|
|
277
277
|
|
278
278
|
def [](pos)
|
279
279
|
return [] if size == 0
|
280
|
-
|
280
|
+
self.read
|
281
|
+
if @range
|
281
282
|
get_range(pos)
|
282
283
|
else
|
283
284
|
get_point(pos)
|
@@ -286,7 +287,7 @@ class FixWidthTable
|
|
286
287
|
|
287
288
|
def overlaps(pos, value = false)
|
288
289
|
return [] if size == 0
|
289
|
-
idxs = if range
|
290
|
+
idxs = if @range
|
290
291
|
get_range(pos, true)
|
291
292
|
else
|
292
293
|
get_point(pos, true)
|
data/lib/rbbt/persist.rb
CHANGED
@@ -25,6 +25,7 @@ module Persist
|
|
25
25
|
MEMORY = {} unless defined? MEMORY
|
26
26
|
MAX_FILE_LENGTH = 150
|
27
27
|
|
28
|
+
# Is 'file' newer than 'path'? return non-true if path is newer than file
|
28
29
|
def self.newer?(path, file)
|
29
30
|
return true if not Open.exists?(file)
|
30
31
|
path = path.find if Path === path
|
@@ -52,7 +52,7 @@ module Persist
|
|
52
52
|
if TSV::ENTRY_KEYS.include? key
|
53
53
|
set_metadata(key, value)
|
54
54
|
else
|
55
|
-
if range
|
55
|
+
if @range
|
56
56
|
add_range_point key, value
|
57
57
|
else
|
58
58
|
add key, value
|
@@ -61,7 +61,7 @@ module Persist
|
|
61
61
|
end
|
62
62
|
|
63
63
|
def add(key, value)
|
64
|
-
key = pos_function.call(key) if pos_function and not (range and Array === key)
|
64
|
+
key = pos_function.call(key) if pos_function and not (@range and Array === key)
|
65
65
|
super(key, value)
|
66
66
|
end
|
67
67
|
|
@@ -85,8 +85,10 @@ module Persist
|
|
85
85
|
end
|
86
86
|
|
87
87
|
def each
|
88
|
+
read
|
88
89
|
@size.times do |i|
|
89
|
-
|
90
|
+
v = idx_value(i)
|
91
|
+
yield i, v
|
90
92
|
end
|
91
93
|
end
|
92
94
|
|
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/dumper.rb
CHANGED
@@ -32,9 +32,21 @@ module TSV
|
|
32
32
|
sep + ([""] * fields.length) * sep << "\n"
|
33
33
|
end
|
34
34
|
when Array
|
35
|
-
|
35
|
+
if fields.nil?
|
36
|
+
sep + (values.collect{|v| Array === v ? v * "|" : v} * sep) << "\n"
|
37
|
+
elsif fields.empty?
|
38
|
+
"\n"
|
39
|
+
else
|
40
|
+
sep + (values.collect{|v| Array === v ? v * "|" : v} * sep) << "\n"
|
41
|
+
end
|
36
42
|
else
|
37
|
-
|
43
|
+
if fields.nil?
|
44
|
+
sep + values.to_s + "\n"
|
45
|
+
elsif fields.empty?
|
46
|
+
"\n"
|
47
|
+
else
|
48
|
+
sep + values.to_s << "\n"
|
49
|
+
end
|
38
50
|
end
|
39
51
|
end
|
40
52
|
|
@@ -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|
|
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
|
data/lib/rbbt/util/cmd.rb
CHANGED
@@ -98,6 +98,7 @@ module CMD
|
|
98
98
|
post = options.delete(:post)
|
99
99
|
log = options.delete(:log)
|
100
100
|
no_fail = options.delete(:no_fail)
|
101
|
+
no_fail = options.delete(:nofail) if no_fail.nil?
|
101
102
|
no_wait = options.delete(:no_wait)
|
102
103
|
|
103
104
|
dont_close_in = options.delete(:dont_close_in)
|
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]
|
data/lib/rbbt/util/misc/bgzf.rb
CHANGED
@@ -7,7 +7,7 @@ module Bgzf
|
|
7
7
|
|
8
8
|
def self.bgzip_cmd
|
9
9
|
@@bgzip_cmd ||= begin
|
10
|
-
path = `bash -c "type -p
|
10
|
+
path = `bash -c "type -p bgzip"`.strip
|
11
11
|
if path.empty?
|
12
12
|
Rbbt.claim Rbbt.software.opt.htslib, :install, Rbbt.share.install.software.HTSLIB.find(:lib)
|
13
13
|
Rbbt.software.opt.htslib.produce
|
@@ -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/util/open.rb
CHANGED
@@ -16,9 +16,9 @@ module Open
|
|
16
16
|
GREP_CMD = begin
|
17
17
|
if ENV["GREP_CMD"]
|
18
18
|
ENV["GREP_CMD"]
|
19
|
-
elsif File.
|
19
|
+
elsif File.exist?('/bin/grep')
|
20
20
|
"/bin/grep"
|
21
|
-
elsif File.
|
21
|
+
elsif File.exist?('/usr/bin/grep')
|
22
22
|
"/usr/bin/grep"
|
23
23
|
else
|
24
24
|
"grep"
|
@@ -262,7 +262,7 @@ module Open
|
|
262
262
|
if (dir_sub_path = find_repo_dir(file))
|
263
263
|
remove_from_repo(*dir_sub_path)
|
264
264
|
else
|
265
|
-
FileUtils.rm(file) if File.
|
265
|
+
FileUtils.rm(file) if File.exist?(file) or Open.broken_link?(file)
|
266
266
|
end
|
267
267
|
end
|
268
268
|
|
@@ -333,7 +333,7 @@ module Open
|
|
333
333
|
nil
|
334
334
|
else
|
335
335
|
target = target.find if Path === target
|
336
|
-
if ! File.
|
336
|
+
if ! File.exist?(target)
|
337
337
|
FileUtils.mkdir_p target
|
338
338
|
end
|
339
339
|
end
|
@@ -344,8 +344,8 @@ module Open
|
|
344
344
|
target = target.find if Path === target
|
345
345
|
|
346
346
|
target = File.join(target, File.basename(source)) if File.directory? target
|
347
|
-
FileUtils.mkdir_p File.dirname(target) unless File.
|
348
|
-
FileUtils.rm target if File.
|
347
|
+
FileUtils.mkdir_p File.dirname(target) unless File.exist?(File.dirname(target))
|
348
|
+
FileUtils.rm target if File.exist?(target)
|
349
349
|
FileUtils.ln_s source, target
|
350
350
|
end
|
351
351
|
|
@@ -353,8 +353,8 @@ module Open
|
|
353
353
|
source = source.find if Path === source
|
354
354
|
target = target.find if Path === target
|
355
355
|
|
356
|
-
FileUtils.mkdir_p File.dirname(target) unless File.
|
357
|
-
FileUtils.rm target if File.
|
356
|
+
FileUtils.mkdir_p File.dirname(target) unless File.exist?(File.dirname(target))
|
357
|
+
FileUtils.rm target if File.exist?(target)
|
358
358
|
FileUtils.ln source, target
|
359
359
|
end
|
360
360
|
|
@@ -362,8 +362,8 @@ module Open
|
|
362
362
|
source = source.find if Path === source
|
363
363
|
target = target.find if Path === target
|
364
364
|
|
365
|
-
FileUtils.mkdir_p File.dirname(target) unless File.
|
366
|
-
FileUtils.rm target if File.
|
365
|
+
FileUtils.mkdir_p File.dirname(target) unless File.exist?(File.dirname(target))
|
366
|
+
FileUtils.rm target if File.exist?(target)
|
367
367
|
begin
|
368
368
|
CMD.cmd("ln -L '#{ source }' '#{ target }'")
|
369
369
|
rescue ProcessFailed
|
@@ -397,7 +397,7 @@ module Open
|
|
397
397
|
if dir_sub_path_source.nil? and dir_sub_path_target.nil?
|
398
398
|
FileUtils.mkdir_p File.dirname(target) unless File.exist? File.dirname(target)
|
399
399
|
tmp_target = File.join(File.dirname(target), '.tmp_mv.' + File.basename(target))
|
400
|
-
FileUtils.
|
400
|
+
FileUtils.cp_r source, tmp_target
|
401
401
|
FileUtils.mv tmp_target, target
|
402
402
|
return
|
403
403
|
end
|
@@ -475,6 +475,7 @@ module Open
|
|
475
475
|
File.exist?(file) #|| File.symlink?(file)
|
476
476
|
end
|
477
477
|
end
|
478
|
+
|
478
479
|
class << self
|
479
480
|
alias exist? exists?
|
480
481
|
end
|
@@ -747,7 +748,7 @@ module Open
|
|
747
748
|
if (dir_sub_path = find_repo_dir(path))
|
748
749
|
writable_repo?(*dir_sub_path)
|
749
750
|
else
|
750
|
-
if File.
|
751
|
+
if File.exist?(path)
|
751
752
|
File.writable?(path)
|
752
753
|
else
|
753
754
|
File.writable?(File.dirname(File.expand_path(path)))
|
@@ -776,14 +777,14 @@ module Open
|
|
776
777
|
file = file.find if Path === file
|
777
778
|
begin
|
778
779
|
if File.symlink?(file) || File.stat(file).nlink > 1
|
779
|
-
if File.
|
780
|
+
if File.exist?(file + '.info') && defined?(Step)
|
780
781
|
done = Step::INFO_SERIALIZER.load(Open.open(file + '.info'))[:done]
|
781
782
|
return done if done
|
782
783
|
end
|
783
784
|
|
784
785
|
file = Pathname.new(file).realpath.to_s
|
785
786
|
end
|
786
|
-
return nil unless File.
|
787
|
+
return nil unless File.exist?(file)
|
787
788
|
File.mtime(file)
|
788
789
|
rescue
|
789
790
|
nil
|
@@ -793,7 +794,7 @@ module Open
|
|
793
794
|
|
794
795
|
def self.update_mtime(path, target)
|
795
796
|
if File.symlink?(target) || File.stat(target).nlink > 1
|
796
|
-
if File.
|
797
|
+
if File.exist?(target + '.info')
|
797
798
|
target = target + '.info'
|
798
799
|
else
|
799
800
|
target = Pathname.new(target).realpath.to_s
|
@@ -801,7 +802,7 @@ module Open
|
|
801
802
|
end
|
802
803
|
|
803
804
|
CMD.cmd("touch -r '#{path}' '#{target}'")
|
804
|
-
CMD.cmd("touch -r '#{path}.info' '#{target}'") if File.
|
805
|
+
CMD.cmd("touch -r '#{path}.info' '#{target}'") if File.exist?(path + '.info')
|
805
806
|
end
|
806
807
|
|
807
808
|
def self.atime(file)
|
@@ -823,7 +824,7 @@ module Open
|
|
823
824
|
end
|
824
825
|
|
825
826
|
def self.broken_link?(path)
|
826
|
-
File.symlink?(path) && ! File.
|
827
|
+
File.symlink?(path) && ! File.exist?(File.readlink(path))
|
827
828
|
end
|
828
829
|
|
829
830
|
def self.download(url, path)
|
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)
|