rbbt-util 5.16.1 → 5.16.2
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- checksums.yaml +4 -4
- data/lib/rbbt/association/index.rb +3 -1
- data/lib/rbbt/resource.rb +5 -1
- data/lib/rbbt/tsv/index.rb +1 -0
- data/test/rbbt/association/test_database.rb +15 -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
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 34f1d517fbcc392d6fb628b06c1803ccc741c5c7
|
4
|
+
data.tar.gz: 37a629ea804ba0fe4dddfd113ea58b4334de99d8
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 468a5f0148cdbaee168e98d356e3d05989ff6a28b3ed146dec47ed53a470e36e5309170cf474ffff52ab91ce664585dfdec9bb07ea54349faf8c6bd677f12c4c
|
7
|
+
data.tar.gz: 462e3776be3b24f57a61c3d24316d8f60858859c145590f2d3303494f3e5d28729c44e5cfee7dca49c775c537e82c2d371518226c4441c49a4c7a25740b0ad41
|
@@ -59,9 +59,11 @@ module Association
|
|
59
59
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list.replace [list.first] * size if list.length == 1
|
60
60
|
end if recycle and size > 1
|
61
61
|
|
62
|
+
|
62
63
|
rest = Misc.zip_fields rest
|
63
64
|
|
64
|
-
|
65
|
+
|
66
|
+
annotations = (Array === rest.first and rest.first.length > 1) ?
|
65
67
|
targets.zip(rest) :
|
66
68
|
targets.zip(rest * targets.length)
|
67
69
|
|
data/lib/rbbt/resource.rb
CHANGED
@@ -74,7 +74,11 @@ module Resource
|
|
74
74
|
begin
|
75
75
|
@server_missing_resource_cache ||= Set.new
|
76
76
|
raise "Resource Not Found" if @server_missing_resource_cache.include? url
|
77
|
-
|
77
|
+
|
78
|
+
#lock_filename = Persist.persistence_path(final_path, {:dir => Resource.lock_dir})
|
79
|
+
|
80
|
+
lock_filename = nil # it seems like this was locked already.
|
81
|
+
|
78
82
|
Misc.lock lock_filename do
|
79
83
|
Net::HTTP.get_response URI(url) do |response|
|
80
84
|
case response
|
data/lib/rbbt/tsv/index.rb
CHANGED
@@ -61,4 +61,19 @@ TP53 NFKB1|GLI1 activation|activation true|true
|
|
61
61
|
def test_gene_ages
|
62
62
|
assert Association.database('/home/mvazquezg/git/workflows/genomics/share/gene_ages', :source => "FamilyAge", :merge => true, :target => "Ensembl Gene ID", :persist => false).values.first.length > 1
|
63
63
|
end
|
64
|
+
|
65
|
+
def __test_reorder_multiple_mismatch
|
66
|
+
|
67
|
+
text =<<-EOF
|
68
|
+
#: :filename=BLADDER_11_and_12#:namespace=Hsa/feb2014#:type=:double
|
69
|
+
#Genomic Mutation Ensembl Gene ID affected damaged splicing broken Sample
|
70
|
+
12:54423561:A ENSG00000273049|ENSG00000197757|ENSG00000198353|ENSG00000273046 false|true|false|false false|true|false|false false|false|false|false false|true|false|false 51106212
|
71
|
+
EOF
|
72
|
+
|
73
|
+
tsv = TSV.open(StringIO.new(text))
|
74
|
+
|
75
|
+
index = Association.index(tsv, :source => "Sample", :target => "Genomic Mutation", :merge => true, :persist_update => true)
|
76
|
+
assert_equal 4, index["51106212~12:54423561:A"][0].split(";;").length
|
77
|
+
|
78
|
+
end
|
64
79
|
end
|
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: 5.16.
|
4
|
+
version: 5.16.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2015-01-
|
11
|
+
date: 2015-01-30 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|