rbbt-util 5.25.30 → 5.25.31
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- checksums.yaml +4 -4
- data/bin/rbbt +1 -1
- data/lib/rbbt/annotations.rb +3 -0
- data/lib/rbbt/tsv/parser.rb +1 -0
- data/lib/rbbt/util/misc/inspect.rb +4 -1
- data/lib/rbbt/util/simpleopt/get.rb +1 -1
- data/lib/rbbt/workflow.rb +2 -1
- data/lib/rbbt/workflow/step/run.rb +1 -0
- data/share/Rlib/util.R +4 -4
- data/share/rbbt_commands/workflow/info +1 -1
- metadata +65 -65
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: f68692725942b4b7093433ae6cd3ce2b021e6fcc
|
4
|
+
data.tar.gz: 76ec7e3c0cc49cbe6f056d5203624a31eb53192f
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 26b78cd83316c25d6326664aef707fc777e659c4655de66ddc205830833a8bba73007acbf538aee9c5c465e1e888f73e90e259bec8bc9a1f2b83b2bcdfb74953
|
7
|
+
data.tar.gz: c93486946a1b6714ecea32026c1d1b5a9d7fa25c4e491024d8b4a34da3542f154320bb47dc7ea62df0a3368264525bac8870455af046d83544a2e1bd9b642eb9
|
data/bin/rbbt
CHANGED
@@ -59,7 +59,7 @@ $ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value
|
|
59
59
|
-ck--config_keys* #{Log.color :yellow, "Override some config keys"}
|
60
60
|
EOF
|
61
61
|
|
62
|
-
if options[:
|
62
|
+
if options[:jobname_show_inputs]
|
63
63
|
ENV["RBBT_INPUT_JOBNAME"] = "true"
|
64
64
|
end
|
65
65
|
|
data/lib/rbbt/annotations.rb
CHANGED
@@ -162,6 +162,9 @@ module Annotated
|
|
162
162
|
object.respond_to?(:clean_annotations) ?
|
163
163
|
object.clean_annotations(true) :
|
164
164
|
object.inject([]){|acc,e| acc << Annotated.purge(e); acc}
|
165
|
+
when TSV
|
166
|
+
object.unnamed = true
|
167
|
+
object
|
165
168
|
when Hash
|
166
169
|
new = {}
|
167
170
|
object.each do |key, value|
|
data/lib/rbbt/tsv/parser.rb
CHANGED
@@ -176,7 +176,7 @@ module Misc
|
|
176
176
|
next if k == :monitor or k == "monitor" or k == :in_situ_persistence or k == "in_situ_persistence"
|
177
177
|
_v = hash[k]
|
178
178
|
_k = k
|
179
|
-
v = Annotated.purge(_v)
|
179
|
+
v = TSV === _v ? _v : Annotated.purge(_v)
|
180
180
|
k = Annotated.purge(k)
|
181
181
|
|
182
182
|
case
|
@@ -184,6 +184,9 @@ module Misc
|
|
184
184
|
str << k.to_s << "=>true"
|
185
185
|
when FalseClass === v
|
186
186
|
str << k.to_s << "=>false"
|
187
|
+
when TSV === v
|
188
|
+
iii :TSV
|
189
|
+
str << k.to_s << "=>" << obj2md5(v)
|
187
190
|
when Hash === v
|
188
191
|
str << k.to_s << "=>" << hash2md5(v)
|
189
192
|
when Symbol === v
|
@@ -27,7 +27,7 @@ module SOPT
|
|
27
27
|
values[input] = value
|
28
28
|
else
|
29
29
|
if value.nil? and %w(F false FALSE no).include?(args[i])
|
30
|
-
Log.warn "Boolean values
|
30
|
+
Log.warn "Boolean values are best specified as #{current}=[true|false], not #{ current } [true|false]. Token '#{args[i]}' following '#{current}' automatically assigned as value"
|
31
31
|
value = args.delete_at(i)
|
32
32
|
end
|
33
33
|
values[input] = %w(F false FALSE no).include?(value)? false : true
|
data/lib/rbbt/workflow.rb
CHANGED
@@ -386,7 +386,8 @@ module Workflow
|
|
386
386
|
|
387
387
|
task_info = task_info(taskname)
|
388
388
|
task_inputs = task_info[:inputs]
|
389
|
-
|
389
|
+
persist_inputs = inputs.values_at(*task_inputs)
|
390
|
+
Persist.memory("STEP", :taskname => taskname, :jobname => jobname, :inputs => persist_inputs, :repo => step_cache) do
|
390
391
|
__job(taskname, jobname, inputs)
|
391
392
|
end
|
392
393
|
end
|
data/share/Rlib/util.R
CHANGED
@@ -188,12 +188,12 @@ rbbt.tsv2matrix <- function(data){
|
|
188
188
|
return(new);
|
189
189
|
}
|
190
190
|
|
191
|
-
rbbt.tsv.write <- function(filename, data, key.field = NULL, extra_headers = NULL){
|
191
|
+
rbbt.tsv.write <- function(filename, data, key.field = NULL, extra_headers = NULL, eol="\n", ...){
|
192
192
|
|
193
193
|
if (is.null(key.field)){ key.field = attributes(data)$key.field;}
|
194
194
|
if (is.null(key.field)){ key.field = "ID";}
|
195
195
|
|
196
|
-
f = file(filename, '
|
196
|
+
f = file(filename, 'wb');
|
197
197
|
|
198
198
|
if (!is.null(extra_headers)){
|
199
199
|
extra_headers = paste("#: ", extra_headers, "\n", sep="");
|
@@ -205,9 +205,9 @@ rbbt.tsv.write <- function(filename, data, key.field = NULL, extra_headers = NUL
|
|
205
205
|
header = paste(header, "\n", sep="");
|
206
206
|
cat(header, file=f);
|
207
207
|
|
208
|
-
|
208
|
+
write.table(data, file=f, quote=FALSE, append=TRUE, col.names=FALSE, row.names=TRUE, sep="\t", eol="\n", ...);
|
209
209
|
|
210
|
-
|
210
|
+
close(f);
|
211
211
|
|
212
212
|
return(NULL);
|
213
213
|
}
|
@@ -148,7 +148,7 @@ end
|
|
148
148
|
if recursive
|
149
149
|
inputs = step.info[:inputs]
|
150
150
|
inputs = {}
|
151
|
-
deps = step.info[:dependencies].collect{|v| get_step v.last }
|
151
|
+
deps = (step.info[:dependencies] || []).collect{|v| get_step v.last }
|
152
152
|
|
153
153
|
while deps.any? do
|
154
154
|
dep = deps.shift
|
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: 5.25.
|
4
|
+
version: 5.25.31
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2019-03-
|
11
|
+
date: 2019-03-04 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|
@@ -511,90 +511,90 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
511
511
|
version: '0'
|
512
512
|
requirements: []
|
513
513
|
rubyforge_project:
|
514
|
-
rubygems_version: 2.
|
514
|
+
rubygems_version: 2.6.13
|
515
515
|
signing_key:
|
516
516
|
specification_version: 4
|
517
517
|
summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
|
518
518
|
test_files:
|
519
|
-
- test/rbbt/
|
520
|
-
- test/rbbt/
|
521
|
-
- test/rbbt/
|
522
|
-
- test/rbbt/
|
523
|
-
- test/rbbt/
|
524
|
-
- test/rbbt/
|
525
|
-
- test/rbbt/
|
526
|
-
- test/rbbt/util/misc/test_multipart_payload.rb
|
519
|
+
- test/rbbt/test_entity.rb
|
520
|
+
- test/rbbt/workflow/test_doc.rb
|
521
|
+
- test/rbbt/workflow/test_step.rb
|
522
|
+
- test/rbbt/workflow/step/test_dependencies.rb
|
523
|
+
- test/rbbt/workflow/test_task.rb
|
524
|
+
- test/rbbt/resource/test_path.rb
|
525
|
+
- test/rbbt/util/test_colorize.rb
|
527
526
|
- test/rbbt/util/misc/test_omics.rb
|
528
|
-
- test/rbbt/util/misc/test_bgzf.rb
|
529
|
-
- test/rbbt/util/misc/test_lock.rb
|
530
527
|
- test/rbbt/util/misc/test_pipes.rb
|
531
|
-
- test/rbbt/util/
|
532
|
-
- test/rbbt/util/
|
533
|
-
- test/rbbt/util/
|
534
|
-
- test/rbbt/util/
|
535
|
-
- test/rbbt/util/
|
536
|
-
- test/rbbt/util/
|
528
|
+
- test/rbbt/util/misc/test_lock.rb
|
529
|
+
- test/rbbt/util/misc/test_multipart_payload.rb
|
530
|
+
- test/rbbt/util/misc/test_bgzf.rb
|
531
|
+
- test/rbbt/util/test_concurrency.rb
|
532
|
+
- test/rbbt/util/test_cmd.rb
|
533
|
+
- test/rbbt/util/R/test_plot.rb
|
537
534
|
- test/rbbt/util/R/test_eval.rb
|
538
535
|
- test/rbbt/util/R/test_model.rb
|
539
|
-
- test/rbbt/util/
|
540
|
-
- test/rbbt/util/test_excel2tsv.rb
|
541
|
-
- test/rbbt/util/test_open.rb
|
542
|
-
- test/rbbt/util/test_colorize.rb
|
543
|
-
- test/rbbt/util/concurrency/processes/test_socket.rb
|
544
|
-
- test/rbbt/util/concurrency/test_threads.rb
|
545
|
-
- test/rbbt/util/concurrency/test_processes.rb
|
546
|
-
- test/rbbt/util/test_cmd.rb
|
536
|
+
- test/rbbt/util/test_config.rb
|
547
537
|
- test/rbbt/util/test_log.rb
|
548
538
|
- test/rbbt/util/test_simpleDSL.rb
|
549
539
|
- test/rbbt/util/log/test_progress.rb
|
550
540
|
- test/rbbt/util/test_tmpfile.rb
|
541
|
+
- test/rbbt/util/test_R.rb
|
542
|
+
- test/rbbt/util/test_excel2tsv.rb
|
551
543
|
- test/rbbt/util/test_misc.rb
|
552
|
-
- test/rbbt/util/
|
553
|
-
- test/rbbt/util/test_concurrency.rb
|
554
|
-
- test/rbbt/util/test_filecache.rb
|
544
|
+
- test/rbbt/util/test_open.rb
|
555
545
|
- test/rbbt/util/test_simpleopt.rb
|
556
|
-
- test/rbbt/
|
557
|
-
- test/rbbt/
|
546
|
+
- test/rbbt/util/simpleopt/test_parse.rb
|
547
|
+
- test/rbbt/util/simpleopt/test_setup.rb
|
548
|
+
- test/rbbt/util/simpleopt/test_get.rb
|
549
|
+
- test/rbbt/util/test_filecache.rb
|
550
|
+
- test/rbbt/util/concurrency/test_processes.rb
|
551
|
+
- test/rbbt/util/concurrency/test_threads.rb
|
552
|
+
- test/rbbt/util/concurrency/processes/test_socket.rb
|
553
|
+
- test/rbbt/util/test_semaphore.rb
|
554
|
+
- test/rbbt/util/test_chain_methods.rb
|
555
|
+
- test/rbbt/test_resource.rb
|
556
|
+
- test/rbbt/test_packed_index.rb
|
557
|
+
- test/rbbt/tsv/test_change_id.rb
|
558
558
|
- test/rbbt/tsv/test_attach.rb
|
559
|
-
- test/rbbt/tsv/
|
560
|
-
- test/rbbt/tsv/
|
561
|
-
- test/rbbt/tsv/parallel/test_through.rb
|
562
|
-
- test/rbbt/tsv/parallel/test_traverse.rb
|
563
|
-
- test/rbbt/tsv/test_index.rb
|
564
|
-
- test/rbbt/tsv/test_matrix.rb
|
565
|
-
- test/rbbt/tsv/test_parallel.rb
|
566
|
-
- test/rbbt/tsv/test_util.rb
|
559
|
+
- test/rbbt/tsv/test_filter.rb
|
560
|
+
- test/rbbt/tsv/test_parser.rb
|
567
561
|
- test/rbbt/tsv/test_accessor.rb
|
562
|
+
- test/rbbt/tsv/test_matrix.rb
|
568
563
|
- test/rbbt/tsv/test_field_index.rb
|
564
|
+
- test/rbbt/tsv/test_util.rb
|
565
|
+
- test/rbbt/tsv/test_index.rb
|
566
|
+
- test/rbbt/tsv/test_parallel.rb
|
569
567
|
- test/rbbt/tsv/test_manipulate.rb
|
570
|
-
- test/rbbt/tsv/
|
571
|
-
- test/rbbt/tsv/
|
572
|
-
- test/rbbt/tsv/
|
573
|
-
- test/rbbt/
|
574
|
-
- test/rbbt/
|
568
|
+
- test/rbbt/tsv/test_excel.rb
|
569
|
+
- test/rbbt/tsv/parallel/test_through.rb
|
570
|
+
- test/rbbt/tsv/parallel/test_traverse.rb
|
571
|
+
- test/rbbt/tsv/test_stream.rb
|
572
|
+
- test/rbbt/test_association.rb
|
573
|
+
- test/rbbt/association/test_database.rb
|
574
|
+
- test/rbbt/association/test_item.rb
|
575
|
+
- test/rbbt/association/test_open.rb
|
576
|
+
- test/rbbt/association/test_util.rb
|
577
|
+
- test/rbbt/association/test_index.rb
|
578
|
+
- test/rbbt/test_knowledge_base.rb
|
579
|
+
- test/rbbt/persist/tsv/test_kyotocabinet.rb
|
580
|
+
- test/rbbt/persist/tsv/test_cdb.rb
|
581
|
+
- test/rbbt/persist/tsv/test_lmdb.rb
|
582
|
+
- test/rbbt/persist/tsv/test_sharder.rb
|
583
|
+
- test/rbbt/persist/tsv/test_leveldb.rb
|
584
|
+
- test/rbbt/persist/tsv/test_tokyocabinet.rb
|
585
|
+
- test/rbbt/persist/test_tsv.rb
|
586
|
+
- test/rbbt/test_tsv.rb
|
575
587
|
- test/rbbt/test_annotations.rb
|
576
|
-
- test/rbbt/
|
588
|
+
- test/rbbt/test_fix_width_table.rb
|
589
|
+
- test/rbbt/test_workflow.rb
|
590
|
+
- test/rbbt/entity/test_identifiers.rb
|
577
591
|
- test/rbbt/annotations/test_util.rb
|
578
|
-
- test/rbbt/
|
579
|
-
- test/rbbt/
|
580
|
-
- test/rbbt/
|
581
|
-
- test/rbbt/
|
592
|
+
- test/rbbt/test_monitor.rb
|
593
|
+
- test/rbbt/test_persist.rb
|
594
|
+
- test/rbbt/knowledge_base/test_entity.rb
|
595
|
+
- test/rbbt/knowledge_base/test_registry.rb
|
582
596
|
- test/rbbt/knowledge_base/test_syndicate.rb
|
583
|
-
- test/rbbt/knowledge_base/test_enrichment.rb
|
584
597
|
- test/rbbt/knowledge_base/test_query.rb
|
598
|
+
- test/rbbt/knowledge_base/test_enrichment.rb
|
585
599
|
- test/rbbt/knowledge_base/test_traverse.rb
|
586
|
-
- test/rbbt/knowledge_base/test_entity.rb
|
587
|
-
- test/rbbt/knowledge_base/test_registry.rb
|
588
|
-
- test/rbbt/test_resource.rb
|
589
|
-
- test/rbbt/test_tsv.rb
|
590
|
-
- test/rbbt/resource/test_path.rb
|
591
|
-
- test/rbbt/test_entity.rb
|
592
|
-
- test/rbbt/test_monitor.rb
|
593
|
-
- test/rbbt/persist/tsv/test_tokyocabinet.rb
|
594
|
-
- test/rbbt/persist/tsv/test_leveldb.rb
|
595
|
-
- test/rbbt/persist/tsv/test_lmdb.rb
|
596
|
-
- test/rbbt/persist/tsv/test_kyotocabinet.rb
|
597
|
-
- test/rbbt/persist/tsv/test_cdb.rb
|
598
|
-
- test/rbbt/persist/tsv/test_sharder.rb
|
599
|
-
- test/rbbt/persist/test_tsv.rb
|
600
600
|
- test/test_helper.rb
|