miga-base 1.2.6.4 → 1.2.8.2
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- checksums.yaml +4 -4
- data/lib/miga/cli/action/classify_wf.rb +1 -1
- data/lib/miga/cli/action/init/daemon_helper.rb +1 -1
- data/lib/miga/cli/action/touch.rb +16 -0
- data/lib/miga/cli/base.rb +1 -0
- data/lib/miga/dataset.rb +5 -0
- data/lib/miga/version.rb +2 -2
- metadata +3 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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|
1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
|
+
metadata.gz: 6605edc35cd0b2aec6d095653ff1d9604df81d6a57e341a290cbd213bb18fee3
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4
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+
data.tar.gz: 2f811051db25da424bdf9f9c89390a4e0cac33fb3c6330e255b369d171e8a4b9
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5
5
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SHA512:
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6
|
-
metadata.gz:
|
7
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-
data.tar.gz:
|
6
|
+
metadata.gz: 252fe9abe5ce14ebe86c5250716b9ce541f1faf510bd36ae2d33f4f15f964f3ec735a66db9fa11503b74fb82f16d6a2a5c43d6df3a71b67dacec65462425d759
|
7
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+
data.tar.gz: ef734003e57818b155347ce591e9683420ecfa00cd5b4398c0ed1485fc23108a74d9bd91980d6a2bb4c2481c3d1027805b9083fb9add802b5a30f140926c996d
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@@ -56,7 +56,7 @@ class MiGA::Cli::Action::ClassifyWf < MiGA::Cli::Action
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56
56
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p = create_project(
|
57
57
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:assembly,
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58
58
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p_metadata,
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59
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-
|
59
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+
run_mytaxa_scan: false, run_distances: false
|
60
60
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)
|
61
61
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p.set_option(:ref_project, ref_db.path)
|
62
62
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p.set_option(:tax_pvalue, cli[:pvalue])
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@@ -152,7 +152,7 @@ module MiGA::Cli::Action::Init::DaemonHelper
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|
152
152
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"#{v[:type]} -q '#{queue}' -v '{{vars}}' -pe openmp {{cpus}} " \
|
153
153
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"-j y -o '{{log}}' -N '{{task_name_simple}}' -l h_vmem=9g " \
|
154
154
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"-l h_rt=12:00:00 '{{script}}' | grep . " \
|
155
|
-
"| perl -pe 's/^Your job (
|
155
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+
"| perl -pe 's/^Your job (\\S+) .*/$1/'"
|
156
156
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)
|
157
157
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else
|
158
158
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v[:cmd] = cli.ask_user(
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@@ -0,0 +1,16 @@
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1
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+
# @package MiGA
|
2
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+
# @license Artistic-2.0
|
3
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+
|
4
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+
require 'miga/cli/action'
|
5
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+
|
6
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+
class MiGA::Cli::Action::Touch < MiGA::Cli::Action
|
7
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+
def parse_cli
|
8
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+
cli.parse do |opt|
|
9
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+
cli.opt_object(opt, [:project, :dataset_opt])
|
10
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+
end
|
11
|
+
end
|
12
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+
|
13
|
+
def perform
|
14
|
+
cli.load_project_or_dataset.save!
|
15
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+
end
|
16
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+
end
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data/lib/miga/cli/base.rb
CHANGED
@@ -34,6 +34,7 @@ module MiGA::Cli::Base
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|
34
34
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# Objects (Datasets or Projects)
|
35
35
|
edit: 'Edit the metadata of a dataset or project',
|
36
36
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option: 'Get or set options of a dataset or project',
|
37
|
+
touch: 'Change the "last modified" time to now without changes',
|
37
38
|
# System
|
38
39
|
init: 'Initialize MiGA to process new projects',
|
39
40
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daemon: 'Control the daemon of a MiGA project',
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data/lib/miga/dataset.rb
CHANGED
@@ -84,6 +84,11 @@ class MiGA::Dataset < MiGA::MiGA
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|
84
84
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pull_hook :on_save
|
85
85
|
end
|
86
86
|
|
87
|
+
##
|
88
|
+
# Currently +save!+ is simply an alias of +save+, for compatibility with the
|
89
|
+
# +Project+ interface
|
90
|
+
alias :save! :save
|
91
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+
|
87
92
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##
|
88
93
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# Get the type of dataset as Symbol
|
89
94
|
def type
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data/lib/miga/version.rb
CHANGED
@@ -12,7 +12,7 @@ module MiGA
|
|
12
12
|
# - String indicating release status:
|
13
13
|
# - rc* release candidate, not released as gem
|
14
14
|
# - [0-9]+ stable release, released as gem
|
15
|
-
VERSION = [1.2,
|
15
|
+
VERSION = [1.2, 8, 2].freeze
|
16
16
|
|
17
17
|
##
|
18
18
|
# Nickname for the current major.minor version.
|
@@ -20,7 +20,7 @@ module MiGA
|
|
20
20
|
|
21
21
|
##
|
22
22
|
# Date of the current gem relese.
|
23
|
-
VERSION_DATE = Date.new(2022,
|
23
|
+
VERSION_DATE = Date.new(2022, 8, 14)
|
24
24
|
|
25
25
|
##
|
26
26
|
# References of MiGA
|
metadata
CHANGED
@@ -1,14 +1,14 @@
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|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
|
name: miga-base
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.2.
|
4
|
+
version: 1.2.8.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Luis M. Rodriguez-R
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2022-
|
11
|
+
date: 2022-08-14 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: daemons
|
@@ -170,6 +170,7 @@ files:
|
|
170
170
|
- lib/miga/cli/action/tax_index.rb
|
171
171
|
- lib/miga/cli/action/tax_set.rb
|
172
172
|
- lib/miga/cli/action/tax_test.rb
|
173
|
+
- lib/miga/cli/action/touch.rb
|
173
174
|
- lib/miga/cli/action/wf.rb
|
174
175
|
- lib/miga/cli/base.rb
|
175
176
|
- lib/miga/cli/objects_helper.rb
|