bsi-pipeline 0.0.5 → 0.0.6
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- checksums.yaml +4 -4
- data/lib/bsi-pipeline/importer.rb +15 -11
- data/lib/bsi-pipeline/version.rb +1 -1
- data/spec/add_batch_spec.rb +1 -0
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
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2
2
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SHA1:
|
3
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-
metadata.gz:
|
4
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-
data.tar.gz:
|
3
|
+
metadata.gz: 50e0b28ec4df04a63b0d9c6a530b36c30e7072b7
|
4
|
+
data.tar.gz: 58b68121e0ea1345f0321d00d46ef63f2f3b1a9c
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5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 67ba71b202d5062375f2585f580f2dd589d520217ffe039b01de598e2877092b70078b56e7e1fbfea3d35872c41501b5570e2cf13c3d894f3e629f9c2d0353aa
|
7
|
+
data.tar.gz: aeb9871c95343cc74790eee7bb9661dc280715d412d790be1dcab265504c6eb115b36ec15c3d326ababb59f363858ee530f41103a615855abf5fee5e32ee8c96
|
@@ -56,7 +56,7 @@ module Pipeline
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56
56
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specimen_family.each_with_index do |spec, i|
|
57
57
|
# Assign sample and sequence numbers
|
58
58
|
spec.sample_id = family_sample_id
|
59
|
-
spec.sequence
|
59
|
+
spec.sequence = i+1
|
60
60
|
end
|
61
61
|
end
|
62
62
|
end
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@@ -81,21 +81,25 @@ module Pipeline
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|
81
81
|
|
82
82
|
def import(all_specimens, options={})
|
83
83
|
@specimens = all_specimens
|
84
|
+
study_ids = @specimens.map{|e| e.study_id}.uniq
|
84
85
|
subject_ids = @specimens.map{|e| e.subject_id}.uniq
|
85
86
|
|
86
|
-
|
87
|
-
|
88
|
-
|
87
|
+
study_ids.each do |study|
|
88
|
+
subject_ids.each_with_index do |sid, i|
|
89
|
+
# Filter by subject_id and study_id
|
90
|
+
subset = @specimens.select{|e| e.study_id == study && e.subject_id == sid}
|
89
91
|
|
90
|
-
|
91
|
-
|
92
|
-
|
92
|
+
batch_properties = {
|
93
|
+
'batch.description' => "Subject: #{sid}",
|
94
|
+
'batch.study_id' => study.to_s
|
95
|
+
}
|
93
96
|
|
94
|
-
|
95
|
-
|
96
|
-
|
97
|
+
@batch = AddBatch.new(@bsi, batch_properties)
|
98
|
+
@batch.add_specimens(subset)
|
99
|
+
@batch.commit if options['commit']
|
97
100
|
|
98
|
-
|
101
|
+
@batches << @batch
|
102
|
+
end
|
99
103
|
end
|
100
104
|
|
101
105
|
@bsi.common.logoff
|
data/lib/bsi-pipeline/version.rb
CHANGED
data/spec/add_batch_spec.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bsi-pipeline
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
|
+
version: 0.0.6
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Elijah Christensen
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2014-07-
|
11
|
+
date: 2014-07-31 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundler
|