bio-ucsc-api 0.6.3 → 0.6.4
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- checksums.yaml +4 -4
- data/Gemfile +6 -9
- data/Gemfile.lock +27 -34
- data/README.md +4 -3
- data/VERSION +1 -1
- data/bio-ucsc-api.gemspec +49 -49
- data/lib/bio-ucsc.rb +2 -4
- data/lib/bio-ucsc/ailmel1.rb +4 -4
- data/lib/bio-ucsc/anocar2.rb +4 -4
- data/lib/bio-ucsc/anogam1.rb +4 -4
- data/lib/bio-ucsc/apimel2.rb +4 -4
- data/lib/bio-ucsc/aplcal1.rb +4 -4
- data/lib/bio-ucsc/bostau4.rb +4 -4
- data/lib/bio-ucsc/braflo1.rb +4 -4
- data/lib/bio-ucsc/caejap1.rb +4 -4
- data/lib/bio-ucsc/caepb2.rb +4 -4
- data/lib/bio-ucsc/caerem3.rb +4 -4
- data/lib/bio-ucsc/caljac3.rb +4 -4
- data/lib/bio-ucsc/canfam2.rb +4 -4
- data/lib/bio-ucsc/cavpor3.rb +4 -4
- data/lib/bio-ucsc/cb3.rb +4 -4
- data/lib/bio-ucsc/ce6.rb +4 -4
- data/lib/bio-ucsc/ci2.rb +4 -4
- data/lib/bio-ucsc/danrer7.rb +4 -4
- data/lib/bio-ucsc/dm3.rb +4 -4
- data/lib/bio-ucsc/dp3.rb +4 -4
- data/lib/bio-ucsc/droana2.rb +4 -4
- data/lib/bio-ucsc/droere1.rb +4 -4
- data/lib/bio-ucsc/drogri1.rb +4 -4
- data/lib/bio-ucsc/dromoj2.rb +4 -4
- data/lib/bio-ucsc/droper1.rb +4 -4
- data/lib/bio-ucsc/drosec1.rb +4 -4
- data/lib/bio-ucsc/drosim1.rb +4 -4
- data/lib/bio-ucsc/drovir2.rb +4 -4
- data/lib/bio-ucsc/droyak2.rb +4 -4
- data/lib/bio-ucsc/equcab2.rb +4 -4
- data/lib/bio-ucsc/felcat4.rb +4 -4
- data/lib/bio-ucsc/fr2.rb +4 -4
- data/lib/bio-ucsc/galgal4.rb +4 -4
- data/lib/bio-ucsc/gasacu1.rb +4 -4
- data/lib/bio-ucsc/go.rb +4 -4
- data/lib/bio-ucsc/hg18.rb +4 -4
- data/lib/bio-ucsc/hg19.rb +4 -4
- data/lib/bio-ucsc/hg38.rb +3 -3
- data/lib/bio-ucsc/hgfixed.rb +4 -4
- data/lib/bio-ucsc/loxafr3.rb +4 -4
- data/lib/bio-ucsc/mm10.rb +3 -3
- data/lib/bio-ucsc/mm9.rb +4 -4
- data/lib/bio-ucsc/mondom5.rb +4 -4
- data/lib/bio-ucsc/ornana1.rb +4 -4
- data/lib/bio-ucsc/orycun2.rb +4 -4
- data/lib/bio-ucsc/orylat2.rb +4 -4
- data/lib/bio-ucsc/oviari1.rb +4 -4
- data/lib/bio-ucsc/pantro3.rb +4 -4
- data/lib/bio-ucsc/petmar1.rb +4 -4
- data/lib/bio-ucsc/ponabe2.rb +4 -4
- data/lib/bio-ucsc/pripac1.rb +4 -4
- data/lib/bio-ucsc/proteome.rb +4 -4
- data/lib/bio-ucsc/rhemac2.rb +4 -4
- data/lib/bio-ucsc/rn4.rb +4 -4
- data/lib/bio-ucsc/rn5.rb +4 -4
- data/lib/bio-ucsc/saccer2.rb +4 -4
- data/lib/bio-ucsc/strpur2.rb +4 -4
- data/lib/bio-ucsc/susscr2.rb +4 -4
- data/lib/bio-ucsc/taegut1.rb +4 -4
- data/lib/bio-ucsc/tetnig2.rb +4 -4
- data/lib/bio-ucsc/uniprot.rb +4 -4
- data/lib/bio-ucsc/visigene.rb +4 -4
- data/lib/bio-ucsc/xentro2.rb +4 -4
- metadata +16 -16
data/lib/bio-ucsc/hg38.rb
CHANGED
@@ -1,6 +1,6 @@
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1
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#
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2
2
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# = AUTOMATIC Table Definition of Hg38
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3
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-
# Copyright:: Copyright (C) 2011
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3
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+
# Copyright:: Copyright (C) 2011-2017
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4
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# MISHIMA, Hiroyuki
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5
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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# License:: The MIT license
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@@ -29,7 +29,7 @@ module Bio
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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-
@@db_adapter ||= '
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -40,7 +40,7 @@ module Bio
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self.abstract_class = true
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def self.default
|
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-
@@db_adapter = '
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/hgfixed.rb
CHANGED
@@ -1,9 +1,9 @@
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1
1
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#
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2
2
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# = AUTOMATIC Table Definition of HgFixed
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-
# Copyright:: Copyright (C) 2011
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+
# Copyright:: Copyright (C) 2011-2017
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4
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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-
# License:: The
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+
# License:: The MIT licence
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#
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -29,7 +29,7 @@ module Bio
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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-
@@db_adapter ||= '
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -40,7 +40,7 @@ module Bio
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self.abstract_class = true
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def self.default
|
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-
@@db_adapter = '
|
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/loxafr3.rb
CHANGED
@@ -1,9 +1,9 @@
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1
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#
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2
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# = AUTOMATIC Table Definition of the Elephant Jul. 2009 (Broad/loxAfr3) assembly
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-
# Copyright:: Copyright (C) 2012
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+
# Copyright:: Copyright (C) 2012-2017
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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-
# License:: The
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+
# License:: The MIT licence
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#
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -30,7 +30,7 @@ module Bio
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
|
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|
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-
@@db_adapter ||= '
|
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -41,7 +41,7 @@ module Bio
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self.abstract_class = true
|
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|
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def self.default
|
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-
@@db_adapter = '
|
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+
@@db_adapter = 'mysql2'
|
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@@db_host = 'genome-mysql.cse.ucsc.edu'
|
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/mm10.rb
CHANGED
@@ -1,6 +1,6 @@
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1
1
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#
|
2
2
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# = AUTOMATIC Table Definition of mm10
|
3
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-
# Copyright:: Copyright (C) 2011
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3
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+
# Copyright:: Copyright (C) 2011-2017
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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# License:: The Ruby licence (Ryby's / GPLv2 dual)
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@@ -32,7 +32,7 @@ ChrX ChrY)
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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|
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-
@@db_adapter ||= '
|
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -43,7 +43,7 @@ ChrX ChrY)
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self.abstract_class = true
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|
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def self.default
|
46
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-
@@db_adapter = '
|
46
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+
@@db_adapter = 'mysql2'
|
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@@db_host = 'genome-mysql.cse.ucsc.edu'
|
48
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/mm9.rb
CHANGED
@@ -1,9 +1,9 @@
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|
1
1
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#
|
2
2
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# = AUTOMATIC Table Definition of mm9
|
3
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-
# Copyright:: Copyright (C) 2011
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3
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+
# Copyright:: Copyright (C) 2011-2017
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# MISHIMA, Hiroyuki
|
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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-
# License:: The
|
6
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+
# License:: The MIT licence
|
7
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#
|
8
8
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -34,7 +34,7 @@ ChrX ChrY)
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include SafeAttributes
|
35
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self.inheritance_column = 'dummy_not_to_use'
|
36
36
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|
37
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-
@@db_adapter ||= '
|
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+
@@db_adapter ||= 'mysql2'
|
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
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@@db_username ||= 'genome'
|
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@@db_password ||= ''
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@@ -45,7 +45,7 @@ ChrX ChrY)
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self.abstract_class = true
|
46
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|
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def self.default
|
48
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-
@@db_adapter = '
|
48
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+
@@db_adapter = 'mysql2'
|
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@@db_host = 'genome-mysql.cse.ucsc.edu'
|
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/mondom5.rb
CHANGED
@@ -1,9 +1,9 @@
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1
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#
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# = AUTOMATIC Table Definition of the Opossum Oct. 2006 (Broad/monDom5) assembly
|
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-
# Copyright:: Copyright (C) 2011
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+
# Copyright:: Copyright (C) 2011-2017
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4
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# MISHIMA, Hiroyuki
|
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5
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
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-
# License:: The
|
6
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+
# License:: The MIT licence
|
7
7
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#
|
8
8
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|
9
9
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -31,7 +31,7 @@ module Bio
|
|
31
31
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include SafeAttributes
|
32
32
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self.inheritance_column = 'dummy_not_to_use'
|
33
33
|
|
34
|
-
@@db_adapter ||= '
|
34
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+
@@db_adapter ||= 'mysql2'
|
35
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
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@@db_username ||= 'genome'
|
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@@db_password ||= ''
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@@ -42,7 +42,7 @@ module Bio
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|
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self.abstract_class = true
|
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|
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def self.default
|
45
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-
@@db_adapter = '
|
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
|
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/ornana1.rb
CHANGED
@@ -1,9 +1,9 @@
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1
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#
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2
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# = AUTOMATIC Table Definition of the Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1)
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-
# Copyright:: Copyright (C) 2011
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+
# Copyright:: Copyright (C) 2011-2017
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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6
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-
# License:: The
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6
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+
# License:: The MIT licence
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7
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#
|
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8
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -29,7 +29,7 @@ module Bio
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include SafeAttributes
|
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self.inheritance_column = 'dummy_not_to_use'
|
31
31
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|
32
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-
@@db_adapter ||= '
|
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+
@@db_adapter ||= 'mysql2'
|
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
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@@db_username ||= 'genome'
|
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@@db_password ||= ''
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@@ -40,7 +40,7 @@ module Bio
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self.abstract_class = true
|
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def self.default
|
43
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-
@@db_adapter = '
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/orycun2.rb
CHANGED
@@ -1,9 +1,9 @@
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1
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#
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# = AUTOMATIC Table Definition of the Rabbit Apr. 2009 (Broad/oryCun2) assembly
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-
# Copyright:: Copyright (C) 2011
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+
# Copyright:: Copyright (C) 2011-2017
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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-
# License:: The
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6
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+
# License:: The MIT licence
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#
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -32,7 +32,7 @@ Chr20 Chr21 ChrX)
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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34
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|
35
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-
@@db_adapter ||= '
|
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -43,7 +43,7 @@ Chr20 Chr21 ChrX)
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self.abstract_class = true
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|
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def self.default
|
46
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-
@@db_adapter = '
|
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
|
48
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/orylat2.rb
CHANGED
@@ -1,9 +1,9 @@
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|
1
1
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#
|
2
2
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# = AUTOMATIC Table Definition of the Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) assembly
|
3
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-
# Copyright:: Copyright (C) 2011
|
3
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+
# Copyright:: Copyright (C) 2011-2017
|
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4
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# MISHIMA, Hiroyuki
|
5
5
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
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-
# License:: The
|
6
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+
# License:: The MIT licence
|
7
7
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#
|
8
8
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -33,7 +33,7 @@ chr21 chr22 chr23 chr24)
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include SafeAttributes
|
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self.inheritance_column = 'dummy_not_to_use'
|
35
35
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|
36
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-
@@db_adapter ||= '
|
36
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+
@@db_adapter ||= 'mysql2'
|
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
38
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@@db_username ||= 'genome'
|
39
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@@db_password ||= ''
|
@@ -44,7 +44,7 @@ chr21 chr22 chr23 chr24)
|
|
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self.abstract_class = true
|
45
45
|
|
46
46
|
def self.default
|
47
|
-
@@db_adapter = '
|
47
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+
@@db_adapter = 'mysql2'
|
48
48
|
@@db_host = 'genome-mysql.cse.ucsc.edu'
|
49
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@@db_username = 'genome'
|
50
50
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@@db_password = ''
|
data/lib/bio-ucsc/oviari1.rb
CHANGED
@@ -1,9 +1,9 @@
|
|
1
1
|
#
|
2
2
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# = AUTOMATIC Table Definition of the Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly
|
3
|
-
# Copyright:: Copyright (C) 2011
|
3
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+
# Copyright:: Copyright (C) 2011-2017
|
4
4
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# MISHIMA, Hiroyuki
|
5
5
|
# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
|
-
# License:: The
|
6
|
+
# License:: The MIT licence
|
7
7
|
#
|
8
8
|
|
9
9
|
require "#{::File.dirname(__FILE__)}/table_class_detector"
|
@@ -33,7 +33,7 @@ Chr21 Chr22 Chr23 Chr24 Chr25 Chr26 ChrX)
|
|
33
33
|
include SafeAttributes
|
34
34
|
self.inheritance_column = 'dummy_not_to_use'
|
35
35
|
|
36
|
-
@@db_adapter ||= '
|
36
|
+
@@db_adapter ||= 'mysql2'
|
37
37
|
@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
38
38
|
@@db_username ||= 'genome'
|
39
39
|
@@db_password ||= ''
|
@@ -44,7 +44,7 @@ Chr21 Chr22 Chr23 Chr24 Chr25 Chr26 ChrX)
|
|
44
44
|
self.abstract_class = true
|
45
45
|
|
46
46
|
def self.default
|
47
|
-
@@db_adapter = '
|
47
|
+
@@db_adapter = 'mysql2'
|
48
48
|
@@db_host = 'genome-mysql.cse.ucsc.edu'
|
49
49
|
@@db_username = 'genome'
|
50
50
|
@@db_password = ''
|
data/lib/bio-ucsc/pantro3.rb
CHANGED
@@ -1,9 +1,9 @@
|
|
1
1
|
#
|
2
2
|
# = AUTOMATIC Table Definition of the Chimp Oct. 2010 (CGSC 2.1.3/panTro3) assembly
|
3
|
-
# Copyright:: Copyright (C) 2011
|
3
|
+
# Copyright:: Copyright (C) 2011-2017
|
4
4
|
# MISHIMA, Hiroyuki
|
5
5
|
# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
|
-
# License:: The
|
6
|
+
# License:: The MIT licence
|
7
7
|
#
|
8
8
|
|
9
9
|
require "#{::File.dirname(__FILE__)}/table_class_detector"
|
@@ -33,7 +33,7 @@ chr21 chr22 chrX chrY)
|
|
33
33
|
include SafeAttributes
|
34
34
|
self.inheritance_column = 'dummy_not_to_use'
|
35
35
|
|
36
|
-
@@db_adapter ||= '
|
36
|
+
@@db_adapter ||= 'mysql2'
|
37
37
|
@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
38
38
|
@@db_username ||= 'genome'
|
39
39
|
@@db_password ||= ''
|
@@ -44,7 +44,7 @@ chr21 chr22 chrX chrY)
|
|
44
44
|
self.abstract_class = true
|
45
45
|
|
46
46
|
def self.default
|
47
|
-
@@db_adapter = '
|
47
|
+
@@db_adapter = 'mysql2'
|
48
48
|
@@db_host = 'genome-mysql.cse.ucsc.edu'
|
49
49
|
@@db_username = 'genome'
|
50
50
|
@@db_password = ''
|
data/lib/bio-ucsc/petmar1.rb
CHANGED
@@ -1,9 +1,9 @@
|
|
1
1
|
#
|
2
2
|
# = AUTOMATIC Table Definition of the Lamprey Mar. 2007 (WUGSC 3.0/petMar1) assembly
|
3
|
-
# Copyright:: Copyright (C) 2011
|
3
|
+
# Copyright:: Copyright (C) 2011-2017
|
4
4
|
# MISHIMA, Hiroyuki
|
5
5
|
# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
|
-
# License:: The
|
6
|
+
# License:: The MIT licence
|
7
7
|
#
|
8
8
|
|
9
9
|
require "#{::File.dirname(__FILE__)}/table_class_detector"
|
@@ -30,7 +30,7 @@ module Bio
|
|
30
30
|
include SafeAttributes
|
31
31
|
self.inheritance_column = 'dummy_not_to_use'
|
32
32
|
|
33
|
-
@@db_adapter ||= '
|
33
|
+
@@db_adapter ||= 'mysql2'
|
34
34
|
@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
35
35
|
@@db_username ||= 'genome'
|
36
36
|
@@db_password ||= ''
|
@@ -41,7 +41,7 @@ module Bio
|
|
41
41
|
self.abstract_class = true
|
42
42
|
|
43
43
|
def self.default
|
44
|
-
@@db_adapter = '
|
44
|
+
@@db_adapter = 'mysql2'
|
45
45
|
@@db_host = 'genome-mysql.cse.ucsc.edu'
|
46
46
|
@@db_username = 'genome'
|
47
47
|
@@db_password = ''
|
data/lib/bio-ucsc/ponabe2.rb
CHANGED
@@ -1,9 +1,9 @@
|
|
1
1
|
#
|
2
2
|
# = AUTOMATIC Table Definition of the Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) assembly
|
3
|
-
# Copyright:: Copyright (C) 2011
|
3
|
+
# Copyright:: Copyright (C) 2011-2017
|
4
4
|
# MISHIMA, Hiroyuki
|
5
5
|
# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
|
-
# License:: The
|
6
|
+
# License:: The MIT licence
|
7
7
|
#
|
8
8
|
|
9
9
|
require "#{::File.dirname(__FILE__)}/table_class_detector"
|
@@ -33,7 +33,7 @@ Chr20 Chr21 Chr22 ChrX ChrY)
|
|
33
33
|
include SafeAttributes
|
34
34
|
self.inheritance_column = 'dummy_not_to_use'
|
35
35
|
|
36
|
-
@@db_adapter ||= '
|
36
|
+
@@db_adapter ||= 'mysql2'
|
37
37
|
@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
38
38
|
@@db_username ||= 'genome'
|
39
39
|
@@db_password ||= ''
|
@@ -44,7 +44,7 @@ Chr20 Chr21 Chr22 ChrX ChrY)
|
|
44
44
|
self.abstract_class = true
|
45
45
|
|
46
46
|
def self.default
|
47
|
-
@@db_adapter = '
|
47
|
+
@@db_adapter = 'mysql2'
|
48
48
|
@@db_host = 'genome-mysql.cse.ucsc.edu'
|
49
49
|
@@db_username = 'genome'
|
50
50
|
@@db_password = ''
|
data/lib/bio-ucsc/pripac1.rb
CHANGED
@@ -1,9 +1,9 @@
|
|
1
1
|
#
|
2
2
|
# = AUTOMATIC Table Definition of the P. pacificus Feb. 2007 (WUGSC 5.0/priPac1) assembly
|
3
|
-
# Copyright:: Copyright (C) 2011
|
3
|
+
# Copyright:: Copyright (C) 2011-2017
|
4
4
|
# MISHIMA, Hiroyuki
|
5
5
|
# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
|
-
# License:: The
|
6
|
+
# License:: The MIT licence
|
7
7
|
#
|
8
8
|
|
9
9
|
require "#{::File.dirname(__FILE__)}/table_class_detector"
|
@@ -31,7 +31,7 @@ module Bio
|
|
31
31
|
include SafeAttributes
|
32
32
|
self.inheritance_column = 'dummy_not_to_use'
|
33
33
|
|
34
|
-
@@db_adapter ||= '
|
34
|
+
@@db_adapter ||= 'mysql2'
|
35
35
|
@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
36
36
|
@@db_username ||= 'genome'
|
37
37
|
@@db_password ||= ''
|
@@ -42,7 +42,7 @@ module Bio
|
|
42
42
|
self.abstract_class = true
|
43
43
|
|
44
44
|
def self.default
|
45
|
-
@@db_adapter = '
|
45
|
+
@@db_adapter = 'mysql2'
|
46
46
|
@@db_host = 'genome-mysql.cse.ucsc.edu'
|
47
47
|
@@db_username = 'genome'
|
48
48
|
@@db_password = ''
|
data/lib/bio-ucsc/proteome.rb
CHANGED
@@ -1,9 +1,9 @@
|
|
1
1
|
#
|
2
2
|
# = AUTOMATIC Table Definition of Proteome
|
3
|
-
# Copyright:: Copyright (C) 2011
|
3
|
+
# Copyright:: Copyright (C) 2011-2017
|
4
4
|
# MISHIMA, Hiroyuki
|
5
5
|
# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
|
-
# License:: The
|
6
|
+
# License:: The MIT licence
|
7
7
|
#
|
8
8
|
|
9
9
|
require "#{::File.dirname(__FILE__)}/table_class_detector"
|
@@ -29,7 +29,7 @@ module Bio
|
|
29
29
|
include SafeAttributes
|
30
30
|
self.inheritance_column = 'dummy_not_to_use'
|
31
31
|
|
32
|
-
@@db_adapter ||= '
|
32
|
+
@@db_adapter ||= 'mysql2'
|
33
33
|
@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
34
34
|
@@db_username ||= 'genome'
|
35
35
|
@@db_password ||= ''
|
@@ -40,7 +40,7 @@ module Bio
|
|
40
40
|
self.abstract_class = true
|
41
41
|
|
42
42
|
def self.default
|
43
|
-
@@db_adapter = '
|
43
|
+
@@db_adapter = 'mysql2'
|
44
44
|
@@db_host = 'genome-mysql.cse.ucsc.edu'
|
45
45
|
@@db_username = 'genome'
|
46
46
|
@@db_password = ''
|
data/lib/bio-ucsc/rhemac2.rb
CHANGED
@@ -1,9 +1,9 @@
|
|
1
1
|
#
|
2
2
|
# = AUTOMATIC Table Definition of the Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly
|
3
|
-
# Copyright:: Copyright (C) 2011
|
3
|
+
# Copyright:: Copyright (C) 2011-2017
|
4
4
|
# MISHIMA, Hiroyuki
|
5
5
|
# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
|
-
# License:: The
|
6
|
+
# License:: The MIT licence
|
7
7
|
#
|
8
8
|
|
9
9
|
require "#{::File.dirname(__FILE__)}/table_class_detector"
|
@@ -33,7 +33,7 @@ Chr20 ChrX)
|
|
33
33
|
include SafeAttributes
|
34
34
|
self.inheritance_column = 'dummy_not_to_use'
|
35
35
|
|
36
|
-
@@db_adapter ||= '
|
36
|
+
@@db_adapter ||= 'mysql2'
|
37
37
|
@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
38
38
|
@@db_username ||= 'genome'
|
39
39
|
@@db_password ||= ''
|
@@ -44,7 +44,7 @@ Chr20 ChrX)
|
|
44
44
|
self.abstract_class = true
|
45
45
|
|
46
46
|
def self.default
|
47
|
-
@@db_adapter = '
|
47
|
+
@@db_adapter = 'mysql2'
|
48
48
|
@@db_host = 'genome-mysql.cse.ucsc.edu'
|
49
49
|
@@db_username = 'genome'
|
50
50
|
@@db_password = ''
|