sushi_fabric 1.1.4 → 1.1.8
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- checksums.yaml +4 -4
- data/lib/sushi_fabric/sushiApp.rb +18 -5
- data/lib/sushi_fabric/version.rb +1 -1
- metadata +6 -6
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
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+
metadata.gz: 9fcb6060694f934b06aaa331d68ce7494a4db25f310cfdf771249d19af201176
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4
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+
data.tar.gz: 0f97798abd3e030a36878d009cae200c285da65544d108446cd56ffb45fb1997
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: f2644586e02507a2af9d6130a5e15b13ef3f8571a1ea3caac2d0b5f8bc71e6758bd5e8fb52c74e76015492b40704fca56835c26c24fe20bc25807dbea0238665
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7
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+
data.tar.gz: 4e5569562947413786252375c7819628a31b16be8f14ca032cd1969f1d2db7e0dabeea8fa2c8ec0b4ea71fd23fe4136296d5f1162cc175413ef5ef29fb2d5c96
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@@ -1,6 +1,6 @@
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1
1
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#!/usr/bin/env ruby
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2
2
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# encoding: utf-8
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3
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-
# Version = '
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3
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+
# Version = '20220217-160253'
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4
4
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5
5
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require 'csv'
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6
6
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require 'fileutils'
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@@ -116,7 +116,9 @@ class ::Hash
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116
116
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if v
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117
117
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@defaults[k] = v
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118
118
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else
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119
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-
@defaults
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119
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+
if @defaults
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120
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+
@defaults[k]
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121
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+
end
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120
122
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end
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121
123
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end
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122
124
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def data_type(k)
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@@ -252,7 +254,7 @@ class SushiApp
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252
254
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end
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253
255
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def set_input_dataset
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254
256
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if @dataset_tsv_file
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255
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-
dataset_tsv = CSV.readlines(@dataset_tsv_file,
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257
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+
dataset_tsv = CSV.readlines(@dataset_tsv_file, :headers=>true, :col_sep=>"\t")
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256
258
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@dataset_hash = []
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257
259
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@dataset = []
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258
260
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dataset_tsv.each do |row|
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@@ -365,7 +367,9 @@ class SushiApp
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365
367
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end
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366
368
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end
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367
369
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(@params.keys - headers).each do |key|
|
368
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-
@params[key]
|
370
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+
unless @params[key]
|
371
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+
@params[key] = @params.default_value(key)
|
372
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+
end
|
369
373
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end
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370
374
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end
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371
375
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@params
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@@ -587,8 +591,10 @@ rm -rf #{@scratch_dir} || exit 1
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587
591
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out << ["sushi_app", self.class.name]
|
588
592
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@output_params.each do |key, value|
|
589
593
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if @output_params[key, 'file_upload']
|
590
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-
uploaded_file_path = File.join(@
|
594
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+
uploaded_file_path = File.join(@result_dir, "uploaded", File.basename(value))
|
591
595
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out << [key, uploaded_file_path]
|
596
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+
@params[key] = uploaded_file_path
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597
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+
@output_params[key] = uploaded_file_path
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592
598
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else
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593
599
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out << [key, value]
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594
600
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end
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@@ -805,6 +811,12 @@ rm -rf #{@scratch_dir} || exit 1
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805
811
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data_set.id
|
806
812
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end
|
807
813
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end
|
814
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+
def save_parameters_in_sushi_db
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815
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+
if @next_dataset_id and next_dataset = DataSet.find_by_id(@next_dataset_id)
|
816
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+
next_dataset.job_parameters = @output_params
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817
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+
next_dataset.save
|
818
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+
end
|
819
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+
end
|
808
820
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def main(mock=false)
|
809
821
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## sushi writes creates the job scripts and builds the result data set that is to be generated
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810
822
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@result_dataset = []
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@@ -851,6 +863,7 @@ rm -rf #{@scratch_dir} || exit 1
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851
863
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unless NO_ROR
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852
864
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@current_user ||= nil
|
853
865
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@next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, @current_user, @child)
|
866
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+
save_parameters_in_sushi_db
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854
867
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855
868
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unless @off_bfabric_registration
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856
869
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if next_dataset = DataSet.find_by_id(@next_dataset_id)
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data/lib/sushi_fabric/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: sushi_fabric
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3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 1.1.
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4
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+
version: 1.1.8
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Functional Genomics Center Zurich
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8
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-
autorequire:
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8
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+
autorequire:
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9
9
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bindir: bin
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10
10
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cert_chain: []
|
11
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-
date:
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11
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+
date: 2022-02-17 00:00:00.000000000 Z
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12
12
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dependencies:
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13
13
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- !ruby/object:Gem::Dependency
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14
14
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name: bundler
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@@ -69,7 +69,7 @@ homepage: ''
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|
69
69
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licenses:
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70
70
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- MIT
|
71
71
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metadata: {}
|
72
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-
post_install_message:
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72
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+
post_install_message:
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73
73
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rdoc_options: []
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74
74
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require_paths:
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75
75
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- lib
|
@@ -84,8 +84,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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|
84
84
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- !ruby/object:Gem::Version
|
85
85
|
version: '0'
|
86
86
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requirements: []
|
87
|
-
rubygems_version: 3.
|
88
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-
signing_key:
|
87
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+
rubygems_version: 3.2.32
|
88
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+
signing_key:
|
89
89
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specification_version: 4
|
90
90
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summary: workflow manager client.
|
91
91
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test_files:
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