rbbt-util 5.23.26 → 5.23.27
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- checksums.yaml +4 -4
- data/lib/rbbt/persist.rb +1 -0
- data/lib/rbbt/resource.rb +11 -1
- data/lib/rbbt/util/open.rb +7 -1
- data/lib/rbbt/workflow/accessor.rb +1 -1
- data/share/rbbt_commands/stat/heatmap +1 -1
- data/share/rbbt_commands/workflow/prov +6 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 727fd7ea14a972a4bbd10a93b3d5ff270f049d7d
|
4
|
+
data.tar.gz: 8f60c11ea14eca70d231e8a4e55208a51207d989
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 4bfcfd6f510295128945a4f3a759b755777063776f5b9478e3c94865854ecbc755714d61a9bb783b5beb18fd88f85ce03b4e87aa26f4bf794e40acee282f3972
|
7
|
+
data.tar.gz: 9c7d620f5acd24e129c210fe35476b8f055bb5170ce5698217b90406fc314b3b9a02d2d80142a5c744f5817f0c84ccdae6a1dd4a57b34703aa47a4a6b70ba8c9
|
data/lib/rbbt/persist.rb
CHANGED
data/lib/rbbt/resource.rb
CHANGED
@@ -132,7 +132,17 @@ module Resource
|
|
132
132
|
rake_dir, content = rake_for(path)
|
133
133
|
rake_dir = Path.setup(rake_dir.dup, self.pkgdir, self)
|
134
134
|
else
|
135
|
-
|
135
|
+
begin
|
136
|
+
if path !~ /\.(gz|bgz)$/
|
137
|
+
begin
|
138
|
+
produce(path + '.gz', force)
|
139
|
+
rescue
|
140
|
+
produce(path + '.bgz', force)
|
141
|
+
end
|
142
|
+
end
|
143
|
+
rescue
|
144
|
+
raise "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
|
145
|
+
end
|
136
146
|
end
|
137
147
|
|
138
148
|
if path.respond_to?(:find)
|
data/lib/rbbt/util/open.rb
CHANGED
@@ -2,6 +2,7 @@ require 'rbbt/util/cmd'
|
|
2
2
|
require 'rbbt/util/tmpfile'
|
3
3
|
require 'rbbt/util/misc'
|
4
4
|
require 'rbbt/util/misc/bgzf'
|
5
|
+
require 'pathname'
|
5
6
|
|
6
7
|
require 'zlib'
|
7
8
|
|
@@ -710,7 +711,12 @@ module Open
|
|
710
711
|
get_time_from_repo(*dir_sub_path)
|
711
712
|
else
|
712
713
|
file = file.find if Path === file
|
713
|
-
File.
|
714
|
+
file = Pathname.new(file).realpath.to_s if File.symlink?(file)
|
715
|
+
begin
|
716
|
+
File.mtime(file)
|
717
|
+
rescue
|
718
|
+
nil
|
719
|
+
end
|
714
720
|
end
|
715
721
|
end
|
716
722
|
|
@@ -945,7 +945,7 @@ module Workflow
|
|
945
945
|
all_d = (real_dependencies + real_dependencies.flatten.collect{|d| d.rec_dependencies} ).flatten.compact.uniq
|
946
946
|
|
947
947
|
_inputs = assign_dep_inputs(_inputs, options, all_d, workflow.task_info(dep_task))
|
948
|
-
jobname = _inputs
|
948
|
+
jobname = _inputs.delete :jobname if _inputs.include? :jobname
|
949
949
|
|
950
950
|
job = workflow._job(dep_task, jobname, _inputs)
|
951
951
|
ComputeDependency.setup(job, compute) if compute
|
@@ -70,7 +70,12 @@ def report_msg(status, name, path, info = nil)
|
|
70
70
|
task, status, workflow = Log.color(:yellow, info[:task_name]), Log.color(:blue, "file"), Log.color(:magenta, "-")
|
71
71
|
end
|
72
72
|
|
73
|
-
|
73
|
+
path_mtime = begin
|
74
|
+
Open.mtime(path)
|
75
|
+
rescue
|
76
|
+
nil
|
77
|
+
end
|
78
|
+
str = if not Open.remote?(path) and (Open.exists?(path) and $main_mtime and path_mtime and ($main_mtime - path_mtime) < 0)
|
74
79
|
status_msg(status.to_s) << " " << [workflow, task, path].compact * " " << " (#{Log.color(:red, "Mtime out of sync") })"
|
75
80
|
else
|
76
81
|
status_msg(status.to_s) << " " << [workflow, task, path].compact * " "
|
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: 5.23.
|
4
|
+
version: 5.23.27
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2018-10-
|
11
|
+
date: 2018-10-24 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|