rbbt-util 5.34.23 → 5.34.24
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- checksums.yaml +4 -4
- data/lib/rbbt/util/log.rb +24 -0
- data/lib/rbbt/workflow/step/dependencies.rb +3 -3
- data/share/Rlib/util.R +10 -2
- data/share/rbbt_commands/tsv/read +2 -0
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
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2
2
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SHA256:
|
3
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-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 7359f3a8ce8bde23107f23515557f47eb7bb65ee094c64419ba5542378af1c8c
|
4
|
+
data.tar.gz: 0a030eb0b6f9648a60c11abaac383fe33b24845c288ddd7a28eb8e9aa8d8ac1c
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: dce1b81193d5d0d7ad86140e7287228b4a9d83fe99f08c4a431e34491d3c2a6057054cc9d80a76be9d4ac34b422c8203470d53579c4ba84bee8a804b6f12a2dd
|
7
|
+
data.tar.gz: 5b1d4e2aa040b183a92ea7b3ccb45fef2e3467a7d94203fd5214a366cbc87bfd6944095888f68c0ca6c8da6d2442cd0f6685b381e4be2e5b68c07bc68365ae72
|
data/lib/rbbt/util/log.rb
CHANGED
@@ -131,6 +131,30 @@ module Log
|
|
131
131
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end
|
132
132
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end
|
133
133
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|
134
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+
def self._ignore_stdout
|
135
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+
begin
|
136
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+
File.open('/dev/null', 'w') do |f|
|
137
|
+
backup_stdout = STDOUT.dup
|
138
|
+
STDOUT.reopen(f)
|
139
|
+
begin
|
140
|
+
yield
|
141
|
+
ensure
|
142
|
+
STDOUT.reopen backup_stdout
|
143
|
+
backup_stdout.close
|
144
|
+
end
|
145
|
+
end
|
146
|
+
rescue Errno::ENOENT
|
147
|
+
yield
|
148
|
+
end
|
149
|
+
end
|
150
|
+
|
151
|
+
|
152
|
+
def self.ignore_stdout(&block)
|
153
|
+
LOG_MUTEX.synchronize do
|
154
|
+
_ignore_stdout &block
|
155
|
+
end
|
156
|
+
end
|
157
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+
|
134
158
|
def self.get_level(level)
|
135
159
|
case level
|
136
160
|
when Numeric
|
@@ -577,20 +577,20 @@ class Step
|
|
577
577
|
|
578
578
|
return [] if dependencies.nil? or dependencies.empty?
|
579
579
|
|
580
|
-
new_dependencies = []
|
581
580
|
if self.overriden?
|
582
581
|
archived_deps = []
|
583
582
|
else
|
584
583
|
archived_deps = self.info[:archived_info] ? self.info[:archived_info].keys : []
|
585
584
|
end
|
586
585
|
|
586
|
+
new_dependencies = []
|
587
587
|
dependencies.each{|step|
|
588
588
|
#next if self.done? && Open.exists?(info_file) && info[:dependencies] && info[:dependencies].select{|task,name,path| path == step.path }.empty?
|
589
589
|
next if archived_deps.include? step.path
|
590
|
-
next if seen.include? step
|
590
|
+
next if seen.include? step
|
591
591
|
next if self.done? && connected && ! updatable?
|
592
592
|
|
593
|
-
r = step.rec_dependencies(connected, new_dependencies
|
593
|
+
r = step.rec_dependencies(connected, new_dependencies)
|
594
594
|
new_dependencies.concat r
|
595
595
|
new_dependencies << step
|
596
596
|
}
|
data/share/Rlib/util.R
CHANGED
@@ -185,9 +185,17 @@ rbbt.tsv <- function(filename, sep = "\t", comment.char ="#", row.names=1, check
|
|
185
185
|
}
|
186
186
|
|
187
187
|
columns = rbbt.tsv.columns(filename, sep, comment.char=comment.char)
|
188
|
+
if (! is.null(comment.char))
|
189
|
+
columns[1] = substring(columns[1],length(comment.char) + 1)
|
190
|
+
|
188
191
|
if (! is.null(columns)){
|
189
|
-
names(data) <- columns[2:length(columns)];
|
190
|
-
|
192
|
+
#names(data) <- columns[2:length(columns)];
|
193
|
+
if (! is.null(row.names)){
|
194
|
+
names(data) <- columns[c(-row.names)];
|
195
|
+
}else{
|
196
|
+
names(data) <- columns
|
197
|
+
}
|
198
|
+
attributes(data)$key.field = columns[1];
|
191
199
|
}
|
192
200
|
|
193
201
|
return(data);
|
@@ -37,6 +37,8 @@ when options[:tokyocabinet_bd]
|
|
37
37
|
exit
|
38
38
|
end
|
39
39
|
|
40
|
+
options[:fields] = options[:fields].split(/,\s*/) if options[:fields]
|
41
|
+
|
40
42
|
parser = TSV::Parser.new TSV.get_stream(file), options
|
41
43
|
|
42
44
|
dumper = TSV::Dumper.new parser.options.merge(:sep => "\t", :sep2 => '|')
|
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: 5.34.
|
4
|
+
version: 5.34.24
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2022-
|
11
|
+
date: 2022-12-09 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|