sequenceserver 1.1.0.beta11 → 1.1.0.beta12

Sign up to get free protection for your applications and to get access to all the features.

Potentially problematic release.

This version of sequenceserver might be problematic. Click here for more details.

Files changed (30) hide show
  1. checksums.yaml +4 -4
  2. data/.rubocop.yml +14 -9
  3. data/Rakefile +1 -1
  4. data/bin/sequenceserver +79 -89
  5. data/lib/sequenceserver.rb +21 -18
  6. data/lib/sequenceserver/api_errors.rb +10 -11
  7. data/lib/sequenceserver/blast/constants.rb +6 -6
  8. data/lib/sequenceserver/blast/formatter.rb +3 -4
  9. data/lib/sequenceserver/blast/hit.rb +5 -2
  10. data/lib/sequenceserver/blast/hsp.rb +8 -5
  11. data/lib/sequenceserver/blast/job.rb +14 -13
  12. data/lib/sequenceserver/blast/query.rb +5 -3
  13. data/lib/sequenceserver/blast/report.rb +25 -23
  14. data/lib/sequenceserver/config.rb +26 -6
  15. data/lib/sequenceserver/database.rb +4 -3
  16. data/lib/sequenceserver/doctor.rb +22 -22
  17. data/lib/sequenceserver/exceptions.rb +17 -24
  18. data/lib/sequenceserver/job.rb +7 -7
  19. data/lib/sequenceserver/links.rb +11 -12
  20. data/lib/sequenceserver/logger.rb +1 -1
  21. data/lib/sequenceserver/pool.rb +0 -2
  22. data/lib/sequenceserver/report.rb +0 -1
  23. data/lib/sequenceserver/routes.rb +16 -16
  24. data/lib/sequenceserver/sequence.rb +24 -20
  25. data/lib/sequenceserver/server.rb +8 -8
  26. data/lib/sequenceserver/version.rb +1 -1
  27. data/public/js/search.js +2 -12
  28. data/public/sequenceserver-search.min.js +2 -2
  29. data/sequenceserver.gemspec +18 -17
  30. metadata +55 -55
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: sequenceserver
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.1.0.beta11
4
+ version: 1.1.0.beta12
5
5
  platform: ruby
6
6
  authors:
7
7
  - Anurag Priyam
@@ -11,68 +11,68 @@ authors:
11
11
  autorequire:
12
12
  bindir: bin
13
13
  cert_chain: []
14
- date: 2018-07-10 00:00:00.000000000 Z
14
+ date: 2018-09-10 00:00:00.000000000 Z
15
15
  dependencies:
16
16
  - !ruby/object:Gem::Dependency
17
- name: sinatra
17
+ name: json_pure
18
18
  requirement: !ruby/object:Gem::Requirement
19
19
  requirements:
20
20
  - - "~>"
21
21
  - !ruby/object:Gem::Version
22
- version: '2.0'
22
+ version: '1.8'
23
23
  - - ">="
24
24
  - !ruby/object:Gem::Version
25
- version: 2.0.0
25
+ version: 1.8.2
26
26
  type: :runtime
27
27
  prerelease: false
28
28
  version_requirements: !ruby/object:Gem::Requirement
29
29
  requirements:
30
30
  - - "~>"
31
31
  - !ruby/object:Gem::Version
32
- version: '2.0'
32
+ version: '1.8'
33
33
  - - ">="
34
34
  - !ruby/object:Gem::Version
35
- version: 2.0.0
35
+ version: 1.8.2
36
36
  - !ruby/object:Gem::Dependency
37
- name: json_pure
37
+ name: ox
38
38
  requirement: !ruby/object:Gem::Requirement
39
39
  requirements:
40
40
  - - "~>"
41
41
  - !ruby/object:Gem::Version
42
- version: '1.8'
42
+ version: '2.1'
43
43
  - - ">="
44
44
  - !ruby/object:Gem::Version
45
- version: 1.8.2
45
+ version: 2.1.1
46
46
  type: :runtime
47
47
  prerelease: false
48
48
  version_requirements: !ruby/object:Gem::Requirement
49
49
  requirements:
50
50
  - - "~>"
51
51
  - !ruby/object:Gem::Version
52
- version: '1.8'
52
+ version: '2.1'
53
53
  - - ">="
54
54
  - !ruby/object:Gem::Version
55
- version: 1.8.2
55
+ version: 2.1.1
56
56
  - !ruby/object:Gem::Dependency
57
- name: ox
57
+ name: sinatra
58
58
  requirement: !ruby/object:Gem::Requirement
59
59
  requirements:
60
60
  - - "~>"
61
61
  - !ruby/object:Gem::Version
62
- version: '2.1'
62
+ version: '2.0'
63
63
  - - ">="
64
64
  - !ruby/object:Gem::Version
65
- version: 2.1.1
65
+ version: 2.0.0
66
66
  type: :runtime
67
67
  prerelease: false
68
68
  version_requirements: !ruby/object:Gem::Requirement
69
69
  requirements:
70
70
  - - "~>"
71
71
  - !ruby/object:Gem::Version
72
- version: '2.1'
72
+ version: '2.0'
73
73
  - - ">="
74
74
  - !ruby/object:Gem::Version
75
- version: 2.1.1
75
+ version: 2.0.0
76
76
  - !ruby/object:Gem::Dependency
77
77
  name: slop
78
78
  requirement: !ruby/object:Gem::Requirement
@@ -94,148 +94,148 @@ dependencies:
94
94
  - !ruby/object:Gem::Version
95
95
  version: 3.6.0
96
96
  - !ruby/object:Gem::Dependency
97
- name: rake
97
+ name: capybara
98
98
  requirement: !ruby/object:Gem::Requirement
99
99
  requirements:
100
100
  - - "~>"
101
101
  - !ruby/object:Gem::Version
102
- version: '10.3'
102
+ version: '2.18'
103
103
  - - ">="
104
104
  - !ruby/object:Gem::Version
105
- version: 10.3.2
105
+ version: 2.18.0
106
106
  type: :development
107
107
  prerelease: false
108
108
  version_requirements: !ruby/object:Gem::Requirement
109
109
  requirements:
110
110
  - - "~>"
111
111
  - !ruby/object:Gem::Version
112
- version: '10.3'
112
+ version: '2.18'
113
113
  - - ">="
114
114
  - !ruby/object:Gem::Version
115
- version: 10.3.2
115
+ version: 2.18.0
116
116
  - !ruby/object:Gem::Dependency
117
- name: rspec
117
+ name: codeclimate-test-reporter
118
118
  requirement: !ruby/object:Gem::Requirement
119
119
  requirements:
120
120
  - - "~>"
121
121
  - !ruby/object:Gem::Version
122
- version: '3.7'
122
+ version: '1.0'
123
123
  - - ">="
124
124
  - !ruby/object:Gem::Version
125
- version: 3.7.0
125
+ version: 1.0.8
126
126
  type: :development
127
127
  prerelease: false
128
128
  version_requirements: !ruby/object:Gem::Requirement
129
129
  requirements:
130
130
  - - "~>"
131
131
  - !ruby/object:Gem::Version
132
- version: '3.7'
132
+ version: '1.0'
133
133
  - - ">="
134
134
  - !ruby/object:Gem::Version
135
- version: 3.7.0
135
+ version: 1.0.8
136
136
  - !ruby/object:Gem::Dependency
137
- name: capybara
137
+ name: rack-test
138
138
  requirement: !ruby/object:Gem::Requirement
139
139
  requirements:
140
140
  - - "~>"
141
141
  - !ruby/object:Gem::Version
142
- version: '2.18'
142
+ version: '1.0'
143
143
  - - ">="
144
144
  - !ruby/object:Gem::Version
145
- version: 2.18.0
145
+ version: 1.0.0
146
146
  type: :development
147
147
  prerelease: false
148
148
  version_requirements: !ruby/object:Gem::Requirement
149
149
  requirements:
150
150
  - - "~>"
151
151
  - !ruby/object:Gem::Version
152
- version: '2.18'
152
+ version: '1.0'
153
153
  - - ">="
154
154
  - !ruby/object:Gem::Version
155
- version: 2.18.0
155
+ version: 1.0.0
156
156
  - !ruby/object:Gem::Dependency
157
- name: rack-test
157
+ name: rake
158
158
  requirement: !ruby/object:Gem::Requirement
159
159
  requirements:
160
160
  - - "~>"
161
161
  - !ruby/object:Gem::Version
162
- version: '1.0'
162
+ version: '10.3'
163
163
  - - ">="
164
164
  - !ruby/object:Gem::Version
165
- version: 1.0.0
165
+ version: 10.3.2
166
166
  type: :development
167
167
  prerelease: false
168
168
  version_requirements: !ruby/object:Gem::Requirement
169
169
  requirements:
170
170
  - - "~>"
171
171
  - !ruby/object:Gem::Version
172
- version: '1.0'
172
+ version: '10.3'
173
173
  - - ">="
174
174
  - !ruby/object:Gem::Version
175
- version: 1.0.0
175
+ version: 10.3.2
176
176
  - !ruby/object:Gem::Dependency
177
- name: sauce_whisk
177
+ name: rspec
178
178
  requirement: !ruby/object:Gem::Requirement
179
179
  requirements:
180
180
  - - "~>"
181
181
  - !ruby/object:Gem::Version
182
- version: '0.0'
182
+ version: '3.7'
183
183
  - - ">="
184
184
  - !ruby/object:Gem::Version
185
- version: 0.0.19
185
+ version: 3.7.0
186
186
  type: :development
187
187
  prerelease: false
188
188
  version_requirements: !ruby/object:Gem::Requirement
189
189
  requirements:
190
190
  - - "~>"
191
191
  - !ruby/object:Gem::Version
192
- version: '0.0'
192
+ version: '3.7'
193
193
  - - ">="
194
194
  - !ruby/object:Gem::Version
195
- version: 0.0.19
195
+ version: 3.7.0
196
196
  - !ruby/object:Gem::Dependency
197
- name: selenium-webdriver
197
+ name: sauce_whisk
198
198
  requirement: !ruby/object:Gem::Requirement
199
199
  requirements:
200
200
  - - "~>"
201
201
  - !ruby/object:Gem::Version
202
- version: '3.11'
202
+ version: '0.0'
203
203
  - - ">="
204
204
  - !ruby/object:Gem::Version
205
- version: 3.11.0
205
+ version: 0.0.19
206
206
  type: :development
207
207
  prerelease: false
208
208
  version_requirements: !ruby/object:Gem::Requirement
209
209
  requirements:
210
210
  - - "~>"
211
211
  - !ruby/object:Gem::Version
212
- version: '3.11'
212
+ version: '0.0'
213
213
  - - ">="
214
214
  - !ruby/object:Gem::Version
215
- version: 3.11.0
215
+ version: 0.0.19
216
216
  - !ruby/object:Gem::Dependency
217
- name: codeclimate-test-reporter
217
+ name: selenium-webdriver
218
218
  requirement: !ruby/object:Gem::Requirement
219
219
  requirements:
220
220
  - - "~>"
221
221
  - !ruby/object:Gem::Version
222
- version: '1.0'
222
+ version: '3.11'
223
223
  - - ">="
224
224
  - !ruby/object:Gem::Version
225
- version: 1.0.8
225
+ version: 3.11.0
226
226
  type: :development
227
227
  prerelease: false
228
228
  version_requirements: !ruby/object:Gem::Requirement
229
229
  requirements:
230
230
  - - "~>"
231
231
  - !ruby/object:Gem::Version
232
- version: '1.0'
232
+ version: '3.11'
233
233
  - - ">="
234
234
  - !ruby/object:Gem::Version
235
- version: 1.0.8
235
+ version: 3.11.0
236
236
  description: |
237
- SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
238
- interface for use locally or over the web.
237
+ SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
238
+ user interface for use locally or over the web.
239
239
  email:
240
240
  - anurag08priyam@gmail.com
241
241
  - b.woodcroft@uq.edu.au
@@ -3825,7 +3825,7 @@ metadata: {}
3825
3825
  post_install_message: |2+
3826
3826
 
3827
3827
  ------------------------------------------------------------------------
3828
- Thank you for installing SequenceServer :)!
3828
+ Thank you for installing SequenceServer :)
3829
3829
 
3830
3830
  To launch SequenceServer execute 'sequenceserver' from command line.
3831
3831