bio-ucsc-api 0.6.3 → 0.6.4

Sign up to get free protection for your applications and to get access to all the features.
Files changed (70) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +6 -9
  3. data/Gemfile.lock +27 -34
  4. data/README.md +4 -3
  5. data/VERSION +1 -1
  6. data/bio-ucsc-api.gemspec +49 -49
  7. data/lib/bio-ucsc.rb +2 -4
  8. data/lib/bio-ucsc/ailmel1.rb +4 -4
  9. data/lib/bio-ucsc/anocar2.rb +4 -4
  10. data/lib/bio-ucsc/anogam1.rb +4 -4
  11. data/lib/bio-ucsc/apimel2.rb +4 -4
  12. data/lib/bio-ucsc/aplcal1.rb +4 -4
  13. data/lib/bio-ucsc/bostau4.rb +4 -4
  14. data/lib/bio-ucsc/braflo1.rb +4 -4
  15. data/lib/bio-ucsc/caejap1.rb +4 -4
  16. data/lib/bio-ucsc/caepb2.rb +4 -4
  17. data/lib/bio-ucsc/caerem3.rb +4 -4
  18. data/lib/bio-ucsc/caljac3.rb +4 -4
  19. data/lib/bio-ucsc/canfam2.rb +4 -4
  20. data/lib/bio-ucsc/cavpor3.rb +4 -4
  21. data/lib/bio-ucsc/cb3.rb +4 -4
  22. data/lib/bio-ucsc/ce6.rb +4 -4
  23. data/lib/bio-ucsc/ci2.rb +4 -4
  24. data/lib/bio-ucsc/danrer7.rb +4 -4
  25. data/lib/bio-ucsc/dm3.rb +4 -4
  26. data/lib/bio-ucsc/dp3.rb +4 -4
  27. data/lib/bio-ucsc/droana2.rb +4 -4
  28. data/lib/bio-ucsc/droere1.rb +4 -4
  29. data/lib/bio-ucsc/drogri1.rb +4 -4
  30. data/lib/bio-ucsc/dromoj2.rb +4 -4
  31. data/lib/bio-ucsc/droper1.rb +4 -4
  32. data/lib/bio-ucsc/drosec1.rb +4 -4
  33. data/lib/bio-ucsc/drosim1.rb +4 -4
  34. data/lib/bio-ucsc/drovir2.rb +4 -4
  35. data/lib/bio-ucsc/droyak2.rb +4 -4
  36. data/lib/bio-ucsc/equcab2.rb +4 -4
  37. data/lib/bio-ucsc/felcat4.rb +4 -4
  38. data/lib/bio-ucsc/fr2.rb +4 -4
  39. data/lib/bio-ucsc/galgal4.rb +4 -4
  40. data/lib/bio-ucsc/gasacu1.rb +4 -4
  41. data/lib/bio-ucsc/go.rb +4 -4
  42. data/lib/bio-ucsc/hg18.rb +4 -4
  43. data/lib/bio-ucsc/hg19.rb +4 -4
  44. data/lib/bio-ucsc/hg38.rb +3 -3
  45. data/lib/bio-ucsc/hgfixed.rb +4 -4
  46. data/lib/bio-ucsc/loxafr3.rb +4 -4
  47. data/lib/bio-ucsc/mm10.rb +3 -3
  48. data/lib/bio-ucsc/mm9.rb +4 -4
  49. data/lib/bio-ucsc/mondom5.rb +4 -4
  50. data/lib/bio-ucsc/ornana1.rb +4 -4
  51. data/lib/bio-ucsc/orycun2.rb +4 -4
  52. data/lib/bio-ucsc/orylat2.rb +4 -4
  53. data/lib/bio-ucsc/oviari1.rb +4 -4
  54. data/lib/bio-ucsc/pantro3.rb +4 -4
  55. data/lib/bio-ucsc/petmar1.rb +4 -4
  56. data/lib/bio-ucsc/ponabe2.rb +4 -4
  57. data/lib/bio-ucsc/pripac1.rb +4 -4
  58. data/lib/bio-ucsc/proteome.rb +4 -4
  59. data/lib/bio-ucsc/rhemac2.rb +4 -4
  60. data/lib/bio-ucsc/rn4.rb +4 -4
  61. data/lib/bio-ucsc/rn5.rb +4 -4
  62. data/lib/bio-ucsc/saccer2.rb +4 -4
  63. data/lib/bio-ucsc/strpur2.rb +4 -4
  64. data/lib/bio-ucsc/susscr2.rb +4 -4
  65. data/lib/bio-ucsc/taegut1.rb +4 -4
  66. data/lib/bio-ucsc/tetnig2.rb +4 -4
  67. data/lib/bio-ucsc/uniprot.rb +4 -4
  68. data/lib/bio-ucsc/visigene.rb +4 -4
  69. data/lib/bio-ucsc/xentro2.rb +4 -4
  70. metadata +16 -16
data/lib/bio-ucsc/aplcal1.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the Sea hare Sept. 2008 (Broad 2.0/aplCal1) 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 Ruby licence (Ryby's / GPLv2 dual)
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 ||= 'mysql'
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 = 'mysql'
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/bostau4.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of he Cow Oct. 2007 (Baylor 4.0/bosTau4) 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 Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
9
  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -32,7 +32,7 @@ Chr21 Chr22 Chr23 Chr24 Chr25 Chr26 Chr27 Chr28 Chr29 ChrX)
32
32
  include SafeAttributes
33
33
  self.inheritance_column = 'dummy_not_to_use'
34
34
 
35
- @@db_adapter ||= 'mysql'
35
+ @@db_adapter ||= 'mysql2'
36
36
  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
37
37
  @@db_username ||= 'genome'
38
38
  @@db_password ||= ''
@@ -43,7 +43,7 @@ Chr21 Chr22 Chr23 Chr24 Chr25 Chr26 Chr27 Chr28 Chr29 ChrX)
43
43
  self.abstract_class = true
44
44
 
45
45
  def self.default
46
- @@db_adapter = 'mysql'
46
+ @@db_adapter = 'mysql2'
47
47
  @@db_host = 'genome-mysql.cse.ucsc.edu'
48
48
  @@db_username = 'genome'
49
49
  @@db_password = ''
data/lib/bio-ucsc/braflo1.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the Lancelet Mar. 2006 (JGI 1.0/braFlo1) 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 Ruby licence (Ryby's / GPLv2 dual)
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 ||= 'mysql'
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 = 'mysql'
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/caejap1.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the C. japonica Mar. 2008 (WUGSC 3.0.2/caeJap1) 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 Ruby licence (Ryby's / GPLv2 dual)
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 ||= 'mysql'
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 = 'mysql'
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/caepb2.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the C. brenneri Feb. 2008 (WUGSC 6.0.1/caePb2) assembly
3
- # Copyright:: Copyright (C) 2011, 2012
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 Ruby licence (Ryby's / GPLv2 dual)
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 ||= 'mysql'
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 = 'mysql'
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/caerem3.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the C. remanei May 2007 (WUGSC 15.0.1/caeRem3) 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 Ruby licence (Ryby's / GPLv2 dual)
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 ||= 'mysql'
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 = 'mysql'
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/caljac3.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the Marmoset March 2009 (WUGSC 3.2/calJac3) assembly
3
- # Copyright:: Copyright (C) 2011, 2012
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 Ruby licence (Ryby's / GPLv2 dual)
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 ||= 'mysql'
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 = 'mysql'
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/canfam2.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the Dog May 2005 (Broad/canFam2) 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 Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
9
  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -33,7 +33,7 @@ Chr30 Chr31 Chr32 Chr33 Chr34 Chr35 Chr36 Chr37 Chr38 ChrX)
33
33
  include SafeAttributes
34
34
  self.inheritance_column = 'dummy_not_to_use'
35
35
 
36
- @@db_adapter ||= 'mysql'
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 @@ Chr30 Chr31 Chr32 Chr33 Chr34 Chr35 Chr36 Chr37 Chr38 ChrX)
44
44
  self.abstract_class = true
45
45
 
46
46
  def self.default
47
- @@db_adapter = 'mysql'
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/cavpor3.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the Guinea pig Feb. 2008 (Broad/cavPor3) assembly
3
- # Copyright:: Copyright (C) 2011, 2012
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 Ruby licence (Ryby's / GPLv2 dual)
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 ||= 'mysql'
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 = 'mysql'
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/cb3.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the C. briggsae Jan. 2007 (WUGSC 1.0/cb3) 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 Ruby licence (Ryby's / GPLv2 dual)
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 ||= 'mysql'
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 = 'mysql'
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/ce6.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of ce6
3
- # Copyright:: Copyright (C) 2011, 2012
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 Ruby licence (Ryby's / GPLv2 dual)
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 ||= 'mysql'
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 = 'mysql'
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/ci2.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the C. intestinalis Mar. 2005 (JGI 2.1/ci2) 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 Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
9
  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -32,7 +32,7 @@ chr09p chr09q chr10p chr10q chr12p chr12q chr13q chr14p chr14q)
32
32
  include SafeAttributes
33
33
  self.inheritance_column = 'dummy_not_to_use'
34
34
 
35
- @@db_adapter ||= 'mysql'
35
+ @@db_adapter ||= 'mysql2'
36
36
  @@db_host ||= 'genome-mysql.cse.ucsc.edu'
37
37
  @@db_username ||= 'genome'
38
38
  @@db_password ||= ''
@@ -43,7 +43,7 @@ chr09p chr09q chr10p chr10q chr12p chr12q chr13q chr14p chr14q)
43
43
  self.abstract_class = true
44
44
 
45
45
  def self.default
46
- @@db_adapter = 'mysql'
46
+ @@db_adapter = 'mysql2'
47
47
  @@db_host = 'genome-mysql.cse.ucsc.edu'
48
48
  @@db_username = 'genome'
49
49
  @@db_password = ''
data/lib/bio-ucsc/danrer7.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the Zebrafish Jul. 2010 (Zv9/danRer7) 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 Ruby licence (Ryby's / GPLv2 dual)
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 Chr23 Chr24 Chr25)
33
33
  include SafeAttributes
34
34
  self.inheritance_column = 'dummy_not_to_use'
35
35
 
36
- @@db_adapter ||= 'mysql'
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 Chr23 Chr24 Chr25)
44
44
  self.abstract_class = true
45
45
 
46
46
  def self.default
47
- @@db_adapter = 'mysql'
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/dm3.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of D. melanogaster Apr. 2006 (BDGP R5/dm3)
3
- # Copyright:: Copyright (C) 2011, 2012
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 Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
9
  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -31,7 +31,7 @@ chr4 chrX chrXHet chrYHet chrU chrUextra chrM)
31
31
  include SafeAttributes
32
32
  self.inheritance_column = 'dummy_not_to_use'
33
33
 
34
- @@db_adapter ||= 'mysql'
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 @@ chr4 chrX chrXHet chrYHet chrU chrUextra chrM)
42
42
  self.abstract_class = true
43
43
 
44
44
  def self.default
45
- @@db_adapter = 'mysql'
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/dp3.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the D. pseudoobscura Nov. 2004 (FlyBase 1.03/dp3) assembly
3
- # Copyright:: Copyright (C) 2011, 2012
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 Ruby licence (Ryby's / GPLv2 dual)
6
+ # License:: The MIT licence
7
7
  #
8
8
 
9
9
  require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -33,7 +33,7 @@ chrXR_group5 chrXR_group6 chrXR_group8 chrXR_group9 chrU)
33
33
  include SafeAttributes
34
34
  self.inheritance_column = 'dummy_not_to_use'
35
35
 
36
- @@db_adapter ||= 'mysql'
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 @@ chrXR_group5 chrXR_group6 chrXR_group8 chrXR_group9 chrU)
44
44
  self.abstract_class = true
45
45
 
46
46
  def self.default
47
- @@db_adapter = 'mysql'
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/droana2.rb CHANGED
@@ -1,9 +1,9 @@
1
1
  #
2
2
  # = AUTOMATIC Table Definition of the D. ananassae Aug. 2005 (Agencourt prelim/droAna2) assembly
3
- # Copyright:: Copyright (C) 2011, 2012
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 Ruby licence (Ryby's / GPLv2 dual)
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 ||= 'mysql'
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 = 'mysql'
44
+ @@db_adapter = 'mysql2'
45
45
  @@db_host = 'genome-mysql.cse.ucsc.edu'
46
46
  @@db_username = 'genome'
47
47
  @@db_password = ''