solvebio 1.5.2 → 1.6.1

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Files changed (46) hide show
  1. data/.travis.yml +13 -8
  2. data/Gemfile +4 -2
  3. data/README.md +5 -3
  4. data/demo/cheatsheet.rb +31 -0
  5. data/lib/cli/auth.rb +6 -6
  6. data/lib/cli/irbrc.rb +2 -1
  7. data/lib/cli/options.rb +1 -1
  8. data/lib/client.rb +85 -83
  9. data/lib/credentials.rb +2 -2
  10. data/lib/main.rb +11 -2
  11. data/lib/query.rb +5 -6
  12. data/lib/resource/annotation.rb +23 -0
  13. data/lib/resource/apiresource.rb +241 -0
  14. data/lib/resource/dataset.rb +91 -0
  15. data/lib/resource/datasetfield.rb +37 -0
  16. data/lib/resource/depository.rb +50 -0
  17. data/lib/resource/depositoryversion.rb +69 -0
  18. data/lib/resource/main.rb +123 -0
  19. data/lib/resource/sample.rb +75 -0
  20. data/lib/{solveobject.rb → resource/solveobject.rb} +43 -22
  21. data/lib/resource/user.rb +5 -0
  22. data/lib/solvebio.rb +1 -1
  23. data/lib/util.rb +29 -0
  24. data/solvebio.gemspec +7 -4
  25. data/test/Makefile +9 -0
  26. data/test/data/sample.vcf.gz +0 -0
  27. data/test/helper.rb +9 -2
  28. data/test/test-annotation.rb +46 -0
  29. data/test/test-auth.rb +8 -4
  30. data/test/test-client.rb +6 -6
  31. data/test/test-conversion.rb +13 -0
  32. data/test/test-dataset.rb +42 -0
  33. data/test/test-depository.rb +35 -0
  34. data/test/test-netrc.rb +13 -3
  35. data/test/test-query-batch.rb +26 -46
  36. data/test/test-query-paging.rb +77 -98
  37. data/test/test-query.rb +47 -64
  38. data/test/test-resource.rb +8 -15
  39. data/test/test-sample-access.rb +59 -0
  40. data/test/test-sample-download.rb +20 -0
  41. data/test/test-tabulate.rb +27 -23
  42. data/test/{test-solveobject.rb → test-util.rb} +17 -2
  43. metadata +128 -56
  44. data/lib/apiresource.rb +0 -130
  45. data/lib/help.rb +0 -46
  46. data/lib/resource.rb +0 -414
data/test/test-query.rb CHANGED
@@ -1,87 +1,70 @@
1
1
  $VERBOSE = true
2
+ require 'socket'
2
3
  require_relative 'helper'
4
+ require_relative '../lib/resource/main'
3
5
 
4
6
  class TestQuery < Test::Unit::TestCase
7
+ def setup
8
+ @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
9
+ end
5
10
 
6
- TEST_DATASET_NAME = 'ClinVar/2.0.0-1/Variants'
11
+ # When paging is off, results.length should return the number of
12
+ # results retrieved.
13
+ def test_limit
14
+ @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
15
+ limit = 10
16
+ results = @dataset.query :paging=>false, :limit => limit
17
+ assert_equal(limit, results.length,
18
+ 'limit == results.size, paging = false')
7
19
 
8
- if SolveBio::api_key
9
20
 
10
- def setup
11
- begin
12
- @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
13
- rescue SocketError
14
- @dataset = nil
15
- end
21
+ results.each_with_index do |val, i|
22
+ assert results[i], "retrieving value at #{i}"
16
23
  end
17
24
 
18
- # When paging is off, results.length should return the number of
19
- # results retrieved.
20
- def test_limit
21
- skip('Are you connected to the Internet?') unless @dataset
22
- @dataset = SolveBio::Dataset.retrieve(TEST_DATASET_NAME)
23
- limit = 10
24
- results = @dataset.query :paging=>false, :limit => limit
25
- assert_equal(limit, results.length,
26
- 'limit == results.size, paging = false')
27
-
28
-
29
- results.each_with_index do |val, i|
30
- assert results[i], "retrieving value at #{i}"
31
- end
32
-
33
- assert_raise IndexError do
34
- puts results[limit]
35
- end
25
+ assert_raise IndexError do
26
+ puts results[limit]
36
27
  end
28
+ end
37
29
 
38
- # test Query when limit is specified and is GREATER THAN total available
39
- # results
40
- def test_limit_empty
41
- skip('Are you connected to the Internet?') unless @dataset
42
- limit = 100
43
- results = @dataset.query(:paging=>false, :limit => limit).
44
- filter({:hg19_start => 1234})
45
- assert_equal(0, results.size)
46
-
47
- assert_raise IndexError do
48
- puts results[0]
49
- end
30
+ # test Query when limit is specified and is GREATER THAN total available
31
+ # results
32
+ def test_limit_empty
33
+ limit = 100
34
+ results = @dataset.query(:paging=>false, :limit => limit).
35
+ filter({:omim_ids => 999999})
36
+ assert_equal(0, results.size)
50
37
 
51
- results = @dataset.query(:paging=>false, :limit => limit).
52
- filter :hg19_start => 148459988
53
- assert_equal(1, results.size)
38
+ assert_raise IndexError do
39
+ puts results[0]
54
40
  end
55
41
 
56
- # test Filtered Query in which limit is specified but is GREATER THAN
57
- # the number of total available results
58
- def test_limit_filter
59
- skip('Are you connected to the Internet?') unless @dataset
60
- limit = 10
61
- num_filters = 3
62
-
63
- filters3 =
64
- SolveBio::Filter.new(:hg19_start => 148459988) |
65
- SolveBio::Filter.new(:hg19_start => 148562304) |
66
- SolveBio::Filter.new(:hg19_start => 148891521)
42
+ results = @dataset.query(:paging=>false, :limit => limit).
43
+ filter :omim_ids => 123631
44
+ assert_equal(1, results.size)
45
+ end
67
46
 
68
- results = @dataset.query(:paging=>false, :limit => limit,
69
- :filters => filters3)
47
+ # test Filtered Query in which limit is specified but is GREATER THAN
48
+ # the number of total available results
49
+ def test_limit_filter
50
+ limit = 10
51
+ num_filters = 2
70
52
 
71
- num_filters.times do |i|
72
- assert results[i]
73
- end
53
+ filters =
54
+ SolveBio::Filter.new(:omim_ids => 123631) |
55
+ SolveBio::Filter.new(:omim_ids => 123670)
74
56
 
75
- assert_equal(num_filters, results.size)
57
+ results = @dataset.query(:paging=>false, :limit => limit,
58
+ :filters => filters)
76
59
 
77
- assert_raise IndexError do
78
- puts results[num_filters]
79
- end
60
+ num_filters.times do |i|
61
+ assert results[i]
80
62
  end
81
63
 
82
- else
83
- def test_skip
84
- skip 'Please set SolveBio::api_key'
64
+ assert_equal(num_filters, results.size)
65
+
66
+ assert_raise IndexError do
67
+ puts results[num_filters]
85
68
  end
86
69
  end
87
70
 
@@ -1,14 +1,14 @@
1
1
  #!/usr/bin/env ruby
2
2
  $VERBOSE = true
3
- require 'test/unit'
4
- require_relative '../lib/resource'
3
+ require_relative './helper'
4
+ require_relative '../lib/resource/main'
5
5
 
6
6
  class TestResource < Test::Unit::TestCase
7
7
 
8
8
  # Do the class FULL_NAME_REGEX contants match what the think they
9
9
  # should?
10
10
  def test_full_name_regexp
11
- assert('Clinvar/2.0.0-1/Variants' =~
11
+ assert('HGNC/1.0.0-1/HGNC' =~
12
12
  SolveBio::Dataset::FULL_NAME_REGEX,
13
13
  'Dataset regexp')
14
14
 
@@ -27,18 +27,11 @@ class TestResource < Test::Unit::TestCase
27
27
  def test_Dataset_from_response
28
28
  resp = {
29
29
  'class_name' => 'Dataset',
30
- 'data_url' => 'https://api.solvebio.com/v1/datasets/25/data',
31
- 'depository' => 'ClinVar',
32
- 'depository_id' => 223,
33
- 'depository_version' => 'ClinVar/2.0.0-1',
34
- 'depository_version_id' => 15,
35
- 'description' => '',
36
- 'fields_url' => 'https://api.solvebio.com/v1/datasets/25/fields',
37
- 'full_name' => 'ClinVar/2.0.0-1/Variants',
38
- 'id' => 25,
39
- 'name' => 'Variants',
40
- 'title' => 'Variants',
41
- 'url' => 'https://api.solvebio.com/v1/datasets/25'
30
+ 'depository' => 'HGNC',
31
+ 'depository_version' => 'HGNC/1.0.0-1',
32
+ 'full_name' => 'HGNC/1.0.0-1/HGNC',
33
+ 'name' => 'HGNC',
34
+ 'title' => 'HGNC'
42
35
  }
43
36
  so = resp.to_solvebio
44
37
  assert_equal SolveBio::Dataset, so.class, 'Hash -> SolveObject'
@@ -0,0 +1,59 @@
1
+ require_relative './helper'
2
+
3
+ class TestSampleAccess < Test::Unit::TestCase
4
+
5
+ def check_response(response, expect, msg)
6
+ expect.each do |key, val|
7
+ assert_equal(val, response[key], msg)
8
+ end
9
+ end
10
+
11
+ def test_insert_delete
12
+ if SolveBio::API_HOST == 'https://api.solvebio.com'
13
+ skip "Testing only on local/dev environments"
14
+ end
15
+
16
+ all = SolveBio::Sample.all
17
+ total = all.total
18
+ vcf_url = 'http://downloads.solvebio.com/vcf/small_sample.vcf.gz'
19
+ expect = {
20
+ 'class_name' => 'Sample',
21
+ 'annotations_count' => 0,
22
+ 'description' => '',
23
+ 'genome_build' => 'GRCh37',
24
+ 'vcf_md5' => 'a03e39e96671a01208cffd234812556d',
25
+ 'vcf_size' => 12124
26
+ }
27
+
28
+ response = SolveBio::Sample.create('GRCh37', :vcf_url => vcf_url)
29
+ check_response(response, expect,
30
+ 'create sample.vcf.gz from url')
31
+ all = SolveBio::Sample.all
32
+ assert_equal(all.total, total + 1, "After uploading an url")
33
+ total = total + 1
34
+
35
+ vcf_file = File.join(File.dirname(__FILE__), 'data/sample.vcf.gz')
36
+ response = SolveBio::Sample.create('GRCh37', {:vcf_file => vcf_file})
37
+ expect = {
38
+ 'class_name' => 'Sample',
39
+ 'annotations_count' => 0,
40
+ 'description' => '',
41
+ 'genome_build' => 'GRCh37',
42
+ 'vcf_md5' => '83acd96171c72ab2bb35e9c52961afd9',
43
+ 'vcf_size' => 592
44
+ }
45
+
46
+ check_response(response, expect,
47
+ 'create sample.vcf.gz from a file')
48
+
49
+ # assert_equal(all.total, total, "After uploading a file")
50
+
51
+ # sample = SolveBio::Sample.retrieve(response.id)
52
+ # delete_response = sample.delete
53
+ # assert_equal(delete_response.deleted, true,
54
+ # 'response.deleted should be true')
55
+
56
+ # all = SolveBio::Sample.all
57
+ # assert_equal(all.total, total, "After deleting a file")
58
+ end
59
+ end
@@ -0,0 +1,20 @@
1
+ require 'fileutils'
2
+ require_relative './helper'
3
+
4
+ class TestSampleDownload < Test::Unit::TestCase
5
+
6
+ def test_sample_download
7
+ if SolveBio::API_HOST == 'https://api.solvebio.com'
8
+ skip "Testing only on local/dev environments"
9
+ end
10
+
11
+ vcf_file = File.join(File.dirname(__FILE__), 'data/sample.vcf.gz')
12
+ sample = SolveBio::Sample.create('GRCh37', {:vcf_file => vcf_file})
13
+ response = sample.download()
14
+ assert_equal(response['code'], 200,
15
+ "Download sample file status ok")
16
+ assert(File.exist?(response['filename']),
17
+ "Download sample file on filesystem")
18
+ FileUtils.rm response['filename']
19
+ end
20
+ end
@@ -63,6 +63,10 @@ class TestTabulate < Test::Unit::TestCase
63
63
  end
64
64
 
65
65
  def test_tabulate
66
+ old_verbose = $VERBOSE
67
+ $VERBOSE=nil
68
+ SolveBio::Tabulate.const_set(:TTY_COLS, 80)
69
+ $VERBOSE=old_verbose
66
70
  tsv = simple_separated_format("\t")
67
71
  expected = <<-EOS
68
72
  foo 1
@@ -86,37 +90,37 @@ EOS
86
90
  expected = <<-EOS
87
91
  | Fields | Data |
88
92
  |-----------------------+-----------------------------|
89
- | rcvaccession_version | 2 |
93
+ | alternate_alleles | T |
94
+ | clinical_origin | somatic |
95
+ | clinical_significance | other |
96
+ | gene_symbols | CPB1 |
90
97
  | hg18_chromosome | 3 |
98
+ | hg19_chromosome | 3 |
91
99
  | hg19_start | 148562304 |
92
- | rcvaccession | RCV000060731 |
93
100
  | hg38_start | 148844517 |
101
+ | hgvs | NC_000003.12:g.148844517C>T |
102
+ | rcvaccession | RCV000060731 |
103
+ | rcvaccession_version | 2 |
94
104
  | reference_allele | C |
95
- | gene_symbols | CPB1 |
96
105
  | rsid | rs150241322 |
97
- | hg19_chromosome | 3 |
98
- | hgvs | NC_000003.12:g.148844517C>T |
99
- | clinical_significance | other |
100
- | alternate_alleles | T |
101
- | clinical_origin | somatic |
102
106
  | type | SNV |
103
107
  EOS
104
108
 
105
- hash = {
106
- "rcvaccession_version"=>2,
107
- "hg18_chromosome"=>"3",
108
- "hg19_start"=>148562304,
109
- "rcvaccession"=>"RCV000060731",
110
- "hg38_start"=>148844517,
111
- "reference_allele"=>"C",
112
- "gene_symbols"=>["CPB1"],
113
- "rsid"=>"rs150241322",
114
- "hg19_chromosome"=>"3",
115
- "hgvs"=>["NC_000003.12:g.148844517C>T"],
116
- "clinical_significance"=>"other",
117
- "alternate_alleles"=>["T"],
118
- "clinical_origin"=>["somatic"],
119
- "type"=>"SNV"
109
+ hash = {
110
+ "alternate_alleles" => ["T"],
111
+ "clinical_origin" => ["somatic"],
112
+ "clinical_significance"=> "other",
113
+ "gene_symbols" => ["CPB1"],
114
+ "hg18_chromosome" => "3",
115
+ "hg19_chromosome" => "3",
116
+ "hg19_start" => 148562304,
117
+ "hg38_start" => 148844517,
118
+ "hgvs" => ["NC_000003.12:g.148844517C>T"],
119
+ "rcvaccession" => "RCV000060731",
120
+ "rcvaccession_version" => 2,
121
+ "reference_allele" => "C",
122
+ "rsid" => "rs150241322",
123
+ "type" => "SNV"
120
124
  }
121
125
  assert_equal(expected.chomp, tabulate(hash.to_a,
122
126
  ['Fields', 'Data'],
@@ -1,7 +1,7 @@
1
1
  #!/usr/bin/env ruby
2
2
  $VERBOSE = true
3
3
  require 'test/unit'
4
- require_relative '../lib/solveobject'
4
+ require_relative '../lib/util'
5
5
 
6
6
  class TestSolveObject < Test::Unit::TestCase
7
7
 
@@ -20,8 +20,23 @@ class TestSolveObject < Test::Unit::TestCase
20
20
  ]
21
21
  data.each do |triple|
22
22
  assert_equal(triple[1],
23
- camelcase_to_underscore(triple[0]),
23
+ SolveBio::camelcase_to_underscore(triple[0]),
24
24
  triple[2])
25
25
  end
26
26
  end
27
+
28
+ def test_pluralize
29
+ data =
30
+ [
31
+ ['depository', 'depositories', "ends in 'y'"],
32
+ ['dataset', 'datasets', "simply adds an 's'"]
33
+ ]
34
+ data.each do |triple|
35
+ assert_equal(triple[1],
36
+ SolveBio::pluralize(triple[0]),
37
+ triple[2])
38
+ end
39
+
40
+ end
41
+
27
42
  end
metadata CHANGED
@@ -1,66 +1,116 @@
1
- --- !ruby/object:Gem::Specification
1
+ --- !ruby/object:Gem::Specification
2
2
  name: solvebio
3
- version: !ruby/object:Gem::Version
3
+ version: !ruby/object:Gem::Version
4
+ version: 1.6.1
4
5
  prerelease:
5
- version: 1.5.2
6
6
  platform: ruby
7
- authors:
7
+ authors:
8
8
  - solvebio.com
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
-
13
- date: 2014-10-01 00:00:00 Z
14
- dependencies:
15
- - !ruby/object:Gem::Dependency
12
+ date: 2014-11-05 00:00:00.000000000 Z
13
+ dependencies:
14
+ - !ruby/object:Gem::Dependency
16
15
  name: netrc
16
+ requirement: !ruby/object:Gem::Requirement
17
+ none: false
18
+ requirements:
19
+ - - ! '>='
20
+ - !ruby/object:Gem::Version
21
+ version: 0.7.7
22
+ type: :runtime
17
23
  prerelease: false
18
- requirement: &id001 !ruby/object:Gem::Requirement
24
+ version_requirements: !ruby/object:Gem::Requirement
19
25
  none: false
20
- requirements:
21
- - - ">="
22
- - !ruby/object:Gem::Version
26
+ requirements:
27
+ - - ! '>='
28
+ - !ruby/object:Gem::Version
23
29
  version: 0.7.7
30
+ - !ruby/object:Gem::Dependency
31
+ name: rest_client
32
+ requirement: !ruby/object:Gem::Requirement
33
+ none: false
34
+ requirements:
35
+ - - ! '>='
36
+ - !ruby/object:Gem::Version
37
+ version: 1.8.1
24
38
  type: :runtime
25
- version_requirements: *id001
26
- - !ruby/object:Gem::Dependency
27
- name: rake
28
39
  prerelease: false
29
- requirement: &id002 !ruby/object:Gem::Requirement
40
+ version_requirements: !ruby/object:Gem::Requirement
41
+ none: false
42
+ requirements:
43
+ - - ! '>='
44
+ - !ruby/object:Gem::Version
45
+ version: 1.8.1
46
+ - !ruby/object:Gem::Dependency
47
+ name: addressable
48
+ requirement: !ruby/object:Gem::Requirement
30
49
  none: false
31
- requirements:
32
- - - ">="
33
- - !ruby/object:Gem::Version
34
- version: "0"
50
+ requirements:
51
+ - - ! '>='
52
+ - !ruby/object:Gem::Version
53
+ version: 2.3.6
54
+ type: :runtime
55
+ prerelease: false
56
+ version_requirements: !ruby/object:Gem::Requirement
57
+ none: false
58
+ requirements:
59
+ - - ! '>='
60
+ - !ruby/object:Gem::Version
61
+ version: 2.3.6
62
+ - !ruby/object:Gem::Dependency
63
+ name: rake
64
+ requirement: !ruby/object:Gem::Requirement
65
+ none: false
66
+ requirements:
67
+ - - ! '>='
68
+ - !ruby/object:Gem::Version
69
+ version: '0'
35
70
  type: :development
36
- version_requirements: *id002
37
- - !ruby/object:Gem::Dependency
38
- name: rdoc
39
71
  prerelease: false
40
- requirement: &id003 !ruby/object:Gem::Requirement
72
+ version_requirements: !ruby/object:Gem::Requirement
41
73
  none: false
42
- requirements:
43
- - - ">="
44
- - !ruby/object:Gem::Version
45
- version: "0"
74
+ requirements:
75
+ - - ! '>='
76
+ - !ruby/object:Gem::Version
77
+ version: '0'
78
+ - !ruby/object:Gem::Dependency
79
+ name: rdoc
80
+ requirement: !ruby/object:Gem::Requirement
81
+ none: false
82
+ requirements:
83
+ - - ! '>='
84
+ - !ruby/object:Gem::Version
85
+ version: '0'
46
86
  type: :development
47
- version_requirements: *id003
48
- description: |
49
- SolveBio is a platform for biomedical datasets. With SolveBio you can
87
+ prerelease: false
88
+ version_requirements: !ruby/object:Gem::Requirement
89
+ none: false
90
+ requirements:
91
+ - - ! '>='
92
+ - !ruby/object:Gem::Version
93
+ version: '0'
94
+ description: ! 'SolveBio is a platform for biomedical datasets. With SolveBio you
95
+ can
96
+
50
97
  forget about parsing complex flat files and sifting through cryptic
98
+
51
99
  datasets. Just use the Ruby Client and API to explore massive
100
+
52
101
  datasets and automate just about any bioinformatics workflow.
53
-
102
+
103
+
54
104
  See https://www.solvebio.com/docs/api/ for more information.
55
105
 
106
+ '
56
107
  email: contact@solvebio.com
57
- executables:
108
+ executables:
58
109
  - solvebio.rb
59
110
  extensions: []
60
-
61
- extra_rdoc_files:
111
+ extra_rdoc_files:
62
112
  - LICENSE
63
- files:
113
+ files:
64
114
  - .gitignore
65
115
  - .travis.yml
66
116
  - Gemfile
@@ -71,6 +121,7 @@ files:
71
121
  - Rakefile
72
122
  - bin/solvebio.rb
73
123
  - demo/README.md
124
+ - demo/cheatsheet.rb
74
125
  - demo/dataset/facets.rb
75
126
  - demo/dataset/field.rb
76
127
  - demo/depository/README.md
@@ -81,7 +132,6 @@ files:
81
132
  - demo/query/query.rb
82
133
  - demo/query/range-filter.rb
83
134
  - demo/test-api.rb
84
- - lib/apiresource.rb
85
135
  - lib/cli/auth.rb
86
136
  - lib/cli/help.rb
87
137
  - lib/cli/irb.rb
@@ -91,19 +141,33 @@ files:
91
141
  - lib/credentials.rb
92
142
  - lib/errors.rb
93
143
  - lib/filter.rb
94
- - lib/help.rb
95
144
  - lib/locale.rb
96
145
  - lib/main.rb
97
146
  - lib/query.rb
98
- - lib/resource.rb
147
+ - lib/resource/annotation.rb
148
+ - lib/resource/apiresource.rb
149
+ - lib/resource/dataset.rb
150
+ - lib/resource/datasetfield.rb
151
+ - lib/resource/depository.rb
152
+ - lib/resource/depositoryversion.rb
153
+ - lib/resource/main.rb
154
+ - lib/resource/sample.rb
155
+ - lib/resource/solveobject.rb
156
+ - lib/resource/user.rb
99
157
  - lib/solvebio.rb
100
- - lib/solveobject.rb
101
158
  - lib/tabulate.rb
159
+ - lib/util.rb
102
160
  - solvebio.gemspec
161
+ - test/Makefile
103
162
  - test/data/netrc-save
163
+ - test/data/sample.vcf.gz
104
164
  - test/helper.rb
165
+ - test/test-annotation.rb
105
166
  - test/test-auth.rb
106
167
  - test/test-client.rb
168
+ - test/test-conversion.rb
169
+ - test/test-dataset.rb
170
+ - test/test-depository.rb
107
171
  - test/test-error.rb
108
172
  - test/test-filter.rb
109
173
  - test/test-netrc.rb
@@ -112,40 +176,46 @@ files:
112
176
  - test/test-query-paging.rb
113
177
  - test/test-query.rb
114
178
  - test/test-resource.rb
115
- - test/test-solveobject.rb
179
+ - test/test-sample-access.rb
180
+ - test/test-sample-download.rb
116
181
  - test/test-tabulate.rb
182
+ - test/test-util.rb
117
183
  homepage: https://www.solvebio.com
118
184
  licenses: []
119
-
120
185
  post_install_message:
121
- rdoc_options:
186
+ rdoc_options:
122
187
  - --charset=UTF-8
123
- require_paths:
188
+ require_paths:
124
189
  - lib
125
- required_ruby_version: !ruby/object:Gem::Requirement
190
+ required_ruby_version: !ruby/object:Gem::Requirement
126
191
  none: false
127
- requirements:
128
- - - ">="
129
- - !ruby/object:Gem::Version
192
+ requirements:
193
+ - - ! '>='
194
+ - !ruby/object:Gem::Version
130
195
  version: 1.9.0
131
- required_rubygems_version: !ruby/object:Gem::Requirement
196
+ required_rubygems_version: !ruby/object:Gem::Requirement
132
197
  none: false
133
- requirements:
134
- - - ">="
135
- - !ruby/object:Gem::Version
136
- version: "0"
198
+ requirements:
199
+ - - ! '>='
200
+ - !ruby/object:Gem::Version
201
+ version: '0'
137
202
  requirements: []
138
-
139
203
  rubyforge_project:
140
204
  rubygems_version: 1.8.23
141
205
  signing_key:
142
206
  specification_version: 2
143
207
  summary: SolveBio Ruby bindings.
144
- test_files:
208
+ test_files:
209
+ - test/Makefile
145
210
  - test/data/netrc-save
211
+ - test/data/sample.vcf.gz
146
212
  - test/helper.rb
213
+ - test/test-annotation.rb
147
214
  - test/test-auth.rb
148
215
  - test/test-client.rb
216
+ - test/test-conversion.rb
217
+ - test/test-dataset.rb
218
+ - test/test-depository.rb
149
219
  - test/test-error.rb
150
220
  - test/test-filter.rb
151
221
  - test/test-netrc.rb
@@ -154,5 +224,7 @@ test_files:
154
224
  - test/test-query-paging.rb
155
225
  - test/test-query.rb
156
226
  - test/test-resource.rb
157
- - test/test-solveobject.rb
227
+ - test/test-sample-access.rb
228
+ - test/test-sample-download.rb
158
229
  - test/test-tabulate.rb
230
+ - test/test-util.rb