genevalidator 1.6.12 → 2.1.3

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Files changed (91) hide show
  1. checksums.yaml +5 -5
  2. data/.gitignore +30 -1
  3. data/.ruby-version +1 -0
  4. data/.travis.yml +13 -12
  5. data/Gemfile +4 -1
  6. data/Gemfile.lock +135 -0
  7. data/README.md +104 -122
  8. data/Rakefile +377 -5
  9. data/aux/gv_results.slim +155 -0
  10. data/aux/html_files/css/gv.compiled.min.css +8 -0
  11. data/aux/{files → html_files}/css/src/bootstrap.min.css +0 -0
  12. data/aux/{files → html_files}/css/src/font-awesome.min.css +0 -0
  13. data/aux/{files → html_files}/css/src/style.css +0 -0
  14. data/aux/{files → html_files}/fonts/FontAwesome.otf +0 -0
  15. data/aux/{files → html_files}/fonts/fontawesome-webfont.eot +0 -0
  16. data/aux/{files → html_files}/fonts/fontawesome-webfont.svg +0 -0
  17. data/aux/{files → html_files}/fonts/fontawesome-webfont.ttf +0 -0
  18. data/aux/{files → html_files}/fonts/fontawesome-webfont.woff +0 -0
  19. data/aux/{files → html_files}/img/gene.png +0 -0
  20. data/aux/html_files/js/gv.compiled.min.js +1 -0
  21. data/aux/{files → html_files}/js/src/bootstrap.min.js +0 -0
  22. data/aux/{files → html_files}/js/src/d3.v3.min.js +0 -0
  23. data/aux/{files → html_files}/js/src/jquery-2.1.1.min.js +0 -0
  24. data/aux/{files → html_files}/js/src/jquery.tablesorter.min.js +0 -0
  25. data/aux/{files → html_files}/js/src/plots.js +1 -1
  26. data/aux/{files → html_files}/js/src/script.js +0 -0
  27. data/aux/{files → html_files}/json/.gitkeep +0 -0
  28. data/bin/genevalidator +393 -56
  29. data/exemplar_data/README.md +60 -0
  30. data/{data/mrna_data.fasta → exemplar_data/mrna_data.fa} +1 -1
  31. data/{data/protein_data.fasta → exemplar_data/protein_data.fa} +0 -0
  32. data/genevalidator.gemspec +35 -20
  33. data/install.sh +92 -0
  34. data/lib/genevalidator.rb +171 -56
  35. data/lib/genevalidator/arg_validation.rb +26 -55
  36. data/lib/genevalidator/blast.rb +44 -99
  37. data/lib/genevalidator/clusterization.rb +18 -22
  38. data/lib/genevalidator/exceptions.rb +17 -17
  39. data/lib/genevalidator/ext/array.rb +21 -4
  40. data/lib/genevalidator/get_raw_sequences.rb +32 -31
  41. data/lib/genevalidator/hsp.rb +31 -2
  42. data/lib/genevalidator/json_to_gv_results.rb +38 -122
  43. data/lib/genevalidator/output.rb +158 -172
  44. data/lib/genevalidator/output_files.rb +134 -0
  45. data/lib/genevalidator/pool.rb +2 -5
  46. data/lib/genevalidator/query.rb +1 -1
  47. data/lib/genevalidator/tabular_parser.rb +8 -29
  48. data/lib/genevalidator/validation.rb +48 -90
  49. data/lib/genevalidator/validation_alignment.rb +64 -75
  50. data/lib/genevalidator/validation_blast_reading_frame.rb +13 -9
  51. data/lib/genevalidator/validation_duplication.rb +85 -84
  52. data/lib/genevalidator/validation_gene_merge.rb +46 -35
  53. data/lib/genevalidator/validation_length_cluster.rb +18 -15
  54. data/lib/genevalidator/validation_length_rank.rb +19 -15
  55. data/lib/genevalidator/validation_maker_qi.rb +13 -12
  56. data/lib/genevalidator/validation_open_reading_frame.rb +16 -13
  57. data/lib/genevalidator/validation_report.rb +1 -1
  58. data/lib/genevalidator/validation_test.rb +1 -1
  59. data/lib/genevalidator/version.rb +1 -1
  60. data/test/overall.rb +1 -1
  61. data/test/test_all_validations.rb +36 -24
  62. data/test/test_blast.rb +39 -24
  63. data/test/test_clusterization_2d.rb +4 -4
  64. data/test/test_helper.rb +2 -2
  65. data/test/test_query.rb +16 -20
  66. data/test/test_validation_open_reading_frame.rb +122 -122
  67. data/test/test_validations.rb +12 -10
  68. metadata +94 -79
  69. data/aux/files/css/genevalidator.compiled.min.css +0 -16
  70. data/aux/files/js/genevalidator.compiled.min.js +0 -28
  71. data/aux/json_footer.erb +0 -8
  72. data/aux/json_header.erb +0 -19
  73. data/aux/json_query.erb +0 -15
  74. data/aux/template_footer.erb +0 -8
  75. data/aux/template_header.erb +0 -19
  76. data/aux/template_query.erb +0 -14
  77. data/data/README.md +0 -57
  78. data/data/mrna_data.fasta.blast_tabular +0 -3567
  79. data/data/mrna_data.fasta.blast_tabular.raw_seq +0 -53998
  80. data/data/mrna_data.fasta.blast_tabular.raw_seq.idx +0 -5440
  81. data/data/mrna_data.fasta.blast_xml +0 -39800
  82. data/data/mrna_data.fasta.blast_xml.raw_seq +0 -2554
  83. data/data/mrna_data.fasta.blast_xml.raw_seq.idx +0 -3127
  84. data/data/mrna_data.fasta.json +0 -1
  85. data/data/protein_data.fasta.blast_tabular +0 -3278
  86. data/data/protein_data.fasta.blast_tabular.raw_seq +0 -61295
  87. data/data/protein_data.fasta.blast_tabular.raw_seq.idx +0 -4438
  88. data/data/protein_data.fasta.blast_xml +0 -26228
  89. data/data/protein_data.fasta.blast_xml.raw_seq +0 -9803
  90. data/data/protein_data.fasta.blast_xml.raw_seq.idx +0 -1777
  91. data/data/protein_data.fasta.json +0 -1
data/aux/html_files/css/gv.compiled.min.css ADDED
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data/aux/{files → html_files}/js/src/plots.js RENAMED
@@ -84,7 +84,7 @@ if (!GV) {
84
84
  if (window.chrome && (window.location.protocol === 'file:')){
85
85
  $('#overview').remove();
86
86
  } else {
87
- var jsonFile = 'files/json/overview.json';
87
+ var jsonFile = $("#overview_btn").data('overviewjson');
88
88
  $.getJSON(jsonFile, function( json ) {
89
89
  var overview = $('<span>' + json.less + '</span><br>');
90
90
  var full_overview = $('<span>' + json.evaluation + '</span><br>');
data/aux/{files → html_files}/json/.gitkeep RENAMED
File without changes
data/bin/genevalidator CHANGED
@@ -2,28 +2,31 @@
2
2
  require 'optparse'
3
3
  require 'English'
4
4
 
5
- require 'genevalidator'
6
- require 'genevalidator/get_raw_sequences'
7
- require 'genevalidator/json_to_gv_results'
8
- require 'genevalidator/version'
9
-
10
5
  opt = {}
11
- opt_parser = OptionParser.new do |opts|
6
+
7
+ global = OptionParser.new do |opts|
12
8
  opts.banner = <<BANNER
9
+ SUMMARY:
10
+ GeneValidator - Identify problems with predicted genes
13
11
 
14
12
  USAGE:
15
- genevalidator [OPTIONS] Input_File
13
+ genevalidator [OPTIONAL ARGUMENTS] INPUT_FILE
16
14
 
17
- ARGUMENTS:
18
- Input_File: Path to the input fasta file containing the predicted sequences.
15
+ To run as a web application:
16
+
17
+ genevalidator app [OPTIONAL ARGUMENTS]
18
+
19
+ See 'genevalidator app --help' for more information
19
20
 
20
- OPTIONAL ARGUMENTS
21
21
  BANNER
22
22
 
23
+ opts.separator 'OPTIONAL ARGUMENTS'
24
+ opts.separator ' '
25
+
23
26
  opt[:validations] = ['all']
24
- opts.on('-v', '--validations <String>', Array,
27
+ opts.on('-v', '--validations [VALIDATIONS]', Array,
25
28
  'The Validations to be applied.',
26
- 'Validation Options Available (separated by coma):',
29
+ 'Validation Options Available (separated by comma):',
27
30
  ' all = All validations (default),',
28
31
  ' lenc = Length validation by clusterization,',
29
32
  ' lenr = Length validation by ranking,',
@@ -36,84 +39,297 @@ BANNER
36
39
  end
37
40
 
38
41
  opt[:db] = 'swissprot -remote'
39
- opts.on('-d', '--db [BLAST_DATABASE]',
42
+ opts.on('-d', '--db [PATH]',
40
43
  'Path to the BLAST database',
44
+ 'e.g. genevalidator -d /path/to/databasa.fa Input_File',
41
45
  'GeneValidator also supports remote databases:',
42
46
  'e.g. genevalidator -d "swissprot -remote" Input_File') do |db|
43
47
  opt[:db] = db
44
48
  end
45
49
 
46
- opts.on('-e', '--extract_raw_seqs',
47
- 'Produces a fasta file of the raw sequences of all BLAST hits in the',
48
- 'supplied BLAST output file. This fasta file can then be provided to',
49
- 'GeneValidator with the "-r", "--raw_sequences" argument') do
50
- opt[:extract_raw_seqs] = true
50
+ opts.on('-s', '--select_single_best',
51
+ 'Writes the fasta sequence of the best scoring gene to STDOUT.') do
52
+ opt[:select_single_best] = true
51
53
  end
52
54
 
53
- opts.on('-j', '--json_file [JSON_FILE]',
54
- 'Generate HTML report from a JSON file (or a subset of a JSON file)',
55
- 'produced by GeneValidator') do |json|
56
- opt[:json_file] = json
55
+ opts.separator ' '
56
+ opts.separator '# OUTPUT ARGUMENTS'
57
+ opts.separator ' '
58
+
59
+ opts.on('-o', '--output_dir [PATH]',
60
+ 'Path to the output folder.',
61
+ 'By default the output folder is in the same directory as the input',
62
+ 'file and is named as input filename, followed by the time of',
63
+ 'analysis') do |d|
64
+ opt[:output_dir] = d
65
+ end
66
+
67
+ opts.on('-f', '--force_rewrite', 'Rewrites over existing output.') do
68
+ opt[:force_rewrite] = true
57
69
  end
58
70
 
59
- opts.on('-x', '--blast_xml_file [BLAST_XML_FILE]',
71
+ opt[:output_formats] = %w[html csv json stdout summary]
72
+ opts.on('--output_formats [STRING]',
73
+ 'Output Formats to generate. This can be either: "all", "html",',
74
+ '"csv", "json", "summary" or "stdout". Multiple formats can be',
75
+ 'separated by a semi-colon e.g. "csv:json".',
76
+ 'By default, all output formats are generated.') do |f|
77
+ opt[:output_formats] = f.split(':') unless f == 'all'
78
+ end
79
+
80
+ opts.separator ' '
81
+ opts.separator '# BLAST ARGUMENTS'
82
+ opts.separator ' '
83
+
84
+ opt[:min_blast_hits] = 5
85
+ opts.on('--min_blast_hits_required [NUM]',
86
+ 'The minimum number of BLAST hits required by GeneValidator in order',
87
+ 'to carry out validations. Note: certain validations have their own',
88
+ 'set minimum (such as the multiple alignment validation, which',
89
+ ' requires a minimum of 10 BLAST hits)') do |min|
90
+ opt[:min_blast_hits] = min.to_i
91
+ end
92
+
93
+ opts.on('-b', '--blast_options [STRING]',
94
+ 'A string that is to passed to BLAST') do |blast_options|
95
+ opt[:blast_options] = blast_options
96
+ end
97
+
98
+ opts.on('-x', '--blast_xml_file [PATH]',
60
99
  'Provide GeneValidator with a pre-computed BLAST XML output',
61
100
  'file (BLAST -outfmt option 5).') do |blast_xml_file|
62
101
  opt[:blast_xml_file] = blast_xml_file
63
102
  end
64
103
 
65
- opts.on('-t', '--blast_tabular_file [BLAST_TABULAR_FILE]',
104
+ opts.on('-t', '--blast_tabular_file [PATH]',
66
105
  'Provide GeneValidator with a pre-computed BLAST tabular output',
67
106
  'file. (BLAST -outfmt option 6).') do |blast_tabular_file|
68
107
  opt[:blast_tabular_file] = blast_tabular_file
69
108
  end
70
109
 
71
110
  # default blast tabular columns
72
- opts.on('-o', '--blast_tabular_options [BLAST_TABULAR_OPTIONS]',
111
+ opts.on('--blast_tabular_options [STRING]',
73
112
  'Custom format used in BLAST -outfmt argument',
74
113
  'See BLAST+ manual pages for more details') do |blast_table_options|
75
114
  opt[:blast_tabular_options] = blast_table_options
76
115
  end
77
116
 
117
+ opts.on('--raw_sequences [PATH]',
118
+ 'Supply a fasta file of the raw sequences of all BLAST hits present',
119
+ 'in the supplied BLAST XML or BLAST tabular file.') do |raw_seq|
120
+ opt[:raw_sequences] = raw_seq
121
+ end
122
+
123
+ opts.separator ' '
124
+ opts.separator '# EXTRACT RAW SEQUENCES ARGUMENTS'
125
+ opts.separator ' '
126
+
127
+ opts.on('-e', '--extract_raw_seqs',
128
+ 'Extract a fasta file of the raw sequences of BLAST hits in the',
129
+ 'supplied BLAST output file. This fasta file can then be provided to',
130
+ 'GeneValidator with the "--raw_sequences" argument') do
131
+ opt[:extract_raw_seqs] = true
132
+ end
133
+
134
+ opts.separator ' '
135
+ opts.separator '# REPROCESS JSON ARGUMENTS'
136
+ opts.separator ' '
137
+
138
+ opts.on('-j', '--json_file [JSON_FILE]',
139
+ 'Path to json file. Re-generate the HTML report from a (filtered)',
140
+ 'JSON file that was previously produced by GeneValidator') do |json|
141
+ opt[:json_file] = json
142
+ end
143
+
144
+ opts.separator ' '
145
+ opts.separator '# GENERAL ARGUMENTS'
146
+ opts.separator ' '
147
+
78
148
  opt[:num_threads] = 1
79
- opts.on('-n', '--num_threads num_of_threads',
149
+ opts.on('-n', '--num_threads [THREADS]',
80
150
  'Specify the number of processor threads to use when running',
81
- 'BLAST and Mafft within GeneValidator.') do |num_threads|
151
+ 'BLAST and GeneValidator.') do |num_threads|
82
152
  opt[:num_threads] = num_threads
83
153
  end
84
154
 
85
- opts.on('-r', '--raw_sequences [raw_seq]',
86
- 'Supply a fasta file of the raw sequences of all BLAST hits present',
87
- 'in the supplied BLAST XML or BLAST tabular file.') do |raw_seq|
88
- opt[:raw_sequences] = raw_seq
155
+ opt[:mafft_threads] = 1
156
+ opts.on('-m', '--mafft_threads [THREADS]',
157
+ 'Specify the number of processor threads to use when running',
158
+ 'Mafft. Note Mafft is run independently in each of the threads',
159
+ 'specified in --num_threads.') do |mafft_threads|
160
+ opt[:mafft_threads] = mafft_threads
89
161
  end
90
162
 
91
- opts.on('-b', '--binaries [binaries]', Array,
163
+ opts.on('-r', '--resume [DIR]',
164
+ 'Resumes an analysis. This works by using previously generated',
165
+ 'temporary files instead of recomputing the analysis where possible.',
166
+ 'A new output directory is created where the output files are',
167
+ 'generated. This assumes that the input file is the same as that',
168
+ 'used in the analysis you are resuming from.') do |dir|
169
+ opt[:resumable] = dir
170
+ end
171
+
172
+ opts.on('--bin [DIR]', Array,
92
173
  'Path to BLAST and MAFFT bin folders (is added to $PATH variable)',
93
174
  'To be provided as follows:',
94
- 'e.g. genevalidator -b /blast/bin/path/ -b /mafft/bin/path/') do |bin|
175
+ 'e.g. genevalidator --bin /blast/bin/ --bin /mafft/bin/') do |bin|
95
176
  (opt[:bin] ||= []).concat(bin)
96
177
  end
97
178
 
98
- opts.on('--version', 'The version of GeneValidator that you are running.') do
99
- puts GeneValidator::VERSION
179
+ opts.on('-h', '--help', 'Show this screen.') do
180
+ puts global
100
181
  exit
101
182
  end
102
183
 
103
- opts.on('-h', '--help', 'Show this screen.') do
104
- $stderr.puts opt_parser
184
+ opts.on('-v', '--version',
185
+ 'The version of GeneValidator that you are running.') do
186
+ require 'genevalidator/version'
187
+ puts GeneValidator::VERSION
105
188
  exit
106
189
  end
107
190
  end
108
191
 
192
+ subcommands = {
193
+ 'app' => OptionParser.new do |opts|
194
+ opts.banner = <<BANNER
195
+ SUMMARY:
196
+ Launch GeneValidator as a web application
197
+
198
+ USAGE:
199
+ $ genevalidator app [options]
200
+
201
+ Examples:
202
+ # Launch GeneValidatorApp with the given config file
203
+ $ genevalidator app --config ~/.genevalidatorapp.conf
204
+
205
+ # Launch GeneValidatorApp with 8 threads at port 8888
206
+ $ genevalidator app --num_threads 8 --port 8888
207
+
208
+ # Create a config file with the other arguments
209
+ $ genevalidator app -s -d ~/database_dir
210
+
211
+ BANNER
212
+
213
+ opts.separator 'MANDATORY ARGUMENTS'
214
+ opts.separator ' '
215
+
216
+ # attempt to set the database dir to GV_BLAST_DB_DIR if it exists
217
+ opt[:database_dir] = ENV.fetch('GV_BLAST_DB_DIR') { nil }
218
+ opts.on('-d', '--database_dir [PATH]',
219
+ 'Path to the directory containing BLAST database') do |path|
220
+ opt[:database_dir] = path
221
+ end
222
+
223
+ opts.separator ' '
224
+ opts.separator 'OPTIONAL ARGUMENTS'
225
+ opts.separator ' '
226
+
227
+ opts.on('-c', '--config_file [PATH]',
228
+ 'Path to the directory containing BLAST database') do |path|
229
+ opt[:config_file] = path
230
+ end
231
+
232
+ opts.on('-g', '--gv_public_dir [PATH]',
233
+ 'The public directory that is served to the web application') do |path|
234
+ opt[:gv_public_dir] = path
235
+ end
236
+
237
+ opts.on('-b', '--bin [PATH]', Array,
238
+ 'Path to BLAST and MAFFT bin folders (is added to $PATH variable)',
239
+ 'To be provided as follows:',
240
+ 'e.g. genevalidator -b /blast/bin/path/ -b /mafft/bin/path/') do |bin|
241
+ (opt[:bin] ||= []).concat(bin)
242
+ end
243
+
244
+ opts.on('-f', '--default_database_path [PATH]',
245
+ 'Path to the default BLAST database') do |path|
246
+ opt[:default_database_path] = path
247
+ end
248
+
249
+ opts.on('-H', '--host [HOST]',
250
+ 'Host to run GeneValidatorApp on') do |host|
251
+ opt[:host] = host
252
+ end
253
+
254
+ opts.on('-p', '--port [PORT]',
255
+ 'Port to run GeneValidatorApp on') do |port|
256
+ opt[:port] = port
257
+ end
258
+
259
+ opts.on('-s', '--set',
260
+ 'Set configuration value in default or given config file') do
261
+ opt[:set] = true
262
+ end
263
+
264
+ opts.on('-l', '--list_databases',
265
+ 'List found BLAST databases') do
266
+ opt[:list_databases] = true
267
+ end
268
+
269
+ opt[:num_threads] = 1
270
+ opts.on('-n', '--num_threads [THREADS]',
271
+ 'Number of threads to use to running the app') do |num_threads|
272
+ opt[:num_threads] = num_threads
273
+ end
274
+
275
+ opts.on('-D', '--devel',
276
+ 'Start GeneValidatorApp in development mode') do
277
+ opt[:devel] = true
278
+ end
279
+
280
+ opts.on('-h', '--help', 'Show this screen.') do
281
+ puts subcommands['app']
282
+ exit
283
+ end
284
+ end,
285
+ 'serve' => OptionParser.new do |opts|
286
+ opts.banner = <<BANNER
287
+ SUMMARY:
288
+ Create a web server for viewing results
289
+
290
+ USAGE:
291
+ $ genevalidator serve [options] OUTPUT_DIR
292
+
293
+ ARGUMENTS:
294
+ BANNER
295
+ opt[:file_server_port] = 6789
296
+ opts.on('-p', '--port [PORT]',
297
+ 'Port to run the server on') do |port|
298
+ opt[:file_server_port] = port
299
+ end
300
+
301
+ opts.on('-h', '--help', 'Show this screen.') do
302
+ puts subcommands['serve']
303
+ exit
304
+ end
305
+ end
306
+ }
307
+
109
308
  begin
110
- opt_parser.parse!(ARGV)
111
- if ARGV.length > 1
112
- $stderr.puts 'Error: you must specify a single fasta input file instead' \
113
- ' of ' + ARGV.length.to_s + ".\n"
309
+ global.order!
310
+ first_arg = ARGV.shift
311
+ if subcommands.key?(first_arg)
312
+ command = first_arg
313
+ subcommands[command].order! unless subcommands[command].nil?
314
+ else
315
+ opt[:input_fasta_file] = first_arg
316
+ end
317
+ if opt[:input_fasta_file].nil? && command.nil? &&
318
+ ((opt[:extract_raw_seqs] && opt[:raw_sequences].nil?) ||
319
+ opt[:json_file].nil?)
320
+ warn # a blank line
321
+ warn '==> Error: Input Fasta file required.'
322
+ warn # a blank line
323
+ warn # a blank line
324
+ puts global
114
325
  exit 1
115
- elsif ARGV.length == 0 && opt[:extract_raw_seqs].nil? && opt[:json_file].nil?
116
- $stderr.puts opt_parser
326
+ end
327
+ if opt[:database_dir].nil? && command == 'app'
328
+ warn # a blank line
329
+ warn '==> Error: Database directory containing BLAST databases required.'
330
+ warn # a blank line
331
+ warn # a blank line
332
+ puts subcommands['app']
117
333
  exit 1
118
334
  end
119
335
  rescue OptionParser::ParseError
@@ -121,23 +337,144 @@ rescue OptionParser::ParseError
121
337
  exit 1
122
338
  end
123
339
 
124
- opt[:input_fasta_file] = ARGV[0]
125
-
126
- start = Time.now
127
-
128
- if opt[:extract_raw_seqs] && opt[:raw_sequences].nil?
340
+ if command.nil? && opt[:extract_raw_seqs] && opt[:raw_sequences].nil?
341
+ require 'genevalidator/get_raw_sequences'
129
342
  GeneValidator.opt = opt
130
343
  GeneValidator.config = {}
131
- # GVArgValidation.run_raw_seqs
132
344
  GeneValidator::RawSequences.run
133
- elsif opt[:json_file]
134
- GeneValidator.opt = opt
135
- # GVArgValidation.run_json_to_gv_results
345
+ elsif command.nil? && opt[:json_file]
346
+ start = Time.now
347
+ require 'genevalidator/json_to_gv_results'
348
+ GeneValidator::JsonToGVResults.init(opt)
136
349
  GeneValidator::JsonToGVResults.run
137
- else
350
+ warn "Total running time: #{(Time.now - start).round(3)}s"
351
+ warn # a blank line
352
+ elsif command.nil?
353
+ start = Time.now
354
+ require 'genevalidator'
355
+ opt[:output_formats] = 'fasta' if opt[:select_single_best]
138
356
  GeneValidator.init(opt)
139
357
  GeneValidator.run
140
- end
358
+ warn "Total running time: #{(Time.now - start).round(3)}s"
359
+ warn # a blank line
360
+ elsif command == 'serve'
361
+ require 'rack'
362
+
363
+ # Uses `open` on Mac or `xdg-open` on Linux to opens the search form in
364
+ # user's default browser. Errors, if any, are silenced.
365
+ def open_in_browser(server_url)
366
+ return if using_ssh?
367
+ if RUBY_PLATFORM =~ /linux/ && xdg?
368
+ system "xdg-open #{server_url}"
369
+ elsif RUBY_PLATFORM =~ /darwin/
370
+ system "open #{server_url}"
371
+ end
372
+ rescue StandardError
373
+ # fail silently
374
+ end
141
375
 
142
- $stderr.puts "Total running time: #{(Time.now - start).round(3)}s"
143
- $stderr.puts # a blank line
376
+ def using_ssh?
377
+ true if ENV['SSH_CLIENT'] || ENV['SSH_TTY'] || ENV['SSH_CONNECTION']
378
+ end
379
+
380
+ def xdg?
381
+ true if ENV['DISPLAY'] && command?('xdg-open')
382
+ end
383
+
384
+ dir = ARGV[0]
385
+ index_file = File.basename(Dir[File.join(dir, '*.html')].min)
386
+ app = Rack::Static.new nil, urls: [''], root: dir, index: index_file
387
+ Rack::Server.start app: app, port: opt[:file_server_port], StartCallback: proc {
388
+ open_in_browser("http://localhost:#{opt[:file_server_port]}")
389
+ }
390
+ elsif command == 'app'
391
+ ENV['RACK_ENV'] = 'development' if opt[:devel]
392
+
393
+ # Exit gracefully on SIGINT.
394
+ stty = `stty -g`.chomp
395
+ trap('INT') do
396
+ warn ''
397
+ warn 'Aborted.'
398
+ system('stty', stty)
399
+ exit
400
+ end
401
+
402
+ require 'genevalidatorapp'
403
+
404
+ begin
405
+ GeneValidatorApp.init opt
406
+
407
+ # The aim of following error recovery scenarios is to guide user to a
408
+ # working GeneValidatorApp installation. We expect to land following
409
+ # error scenarios either when creating a new GeneValidatorApp (first
410
+ # time or later), or updating config values using -s CLI option.
411
+ rescue GeneValidatorApp::CONFIG_FILE_ERROR => e
412
+ warn e
413
+ exit!
414
+ rescue GeneValidatorApp::NUM_THREADS_INCORRECT => e
415
+ warn e
416
+
417
+ if opt[:num_threads].nil?
418
+ warn 'You can set the correct value by running:'
419
+ warn
420
+ warn ' genevalidatorapp -s -n <value>'
421
+ warn
422
+ end
423
+
424
+ exit!
425
+ rescue GeneValidatorApp::BIN_DIR_NOT_FOUND => e
426
+ warn e
427
+
428
+ if opt[:bin].nil?
429
+ warn 'You can set the correct value by running:'
430
+ warn
431
+ warn ' genevalidatorapp -s -b <value>'
432
+ warn
433
+ end
434
+
435
+ exit!
436
+ rescue GeneValidatorApp::DATABASE_DIR_NOT_FOUND => e
437
+ warn e
438
+
439
+ if opt[:database_dir].nil?
440
+ warn 'You can set the correct value by running:'
441
+ warn
442
+ warn ' genevalidatorapp -s -d <value>'
443
+ warn
444
+ end
445
+
446
+ exit!
447
+ rescue GeneValidatorApp::BLAST_DATABASE_ERROR => e
448
+ warn e
449
+ exit!
450
+ rescue StandardError => e
451
+ # This will catch any unhandled error and some very special errors.
452
+ # Ideally we will never hit this block. If we do, there's a bug in
453
+ # GeneValidatorApp or something really weird going on. If we hit this
454
+ # error block we show the stacktrace to the user requesting them to
455
+ # post the same to our Google Group.
456
+ warn <<MSG
457
+ Something went wonky
458
+
459
+ Looks like you have encountered a bug in GeneValidatorApp. Please could you
460
+ report this incident here -
461
+ https://github.com/wurmlab/genevalidator/issues
462
+
463
+ Error:
464
+ #{e.backtrace.unshift(e.message).join("\n")}
465
+ MSG
466
+ exit!
467
+ end
468
+
469
+ if opt[:list_databases]
470
+ puts GeneValidatorApp::Database.all
471
+ exit
472
+ end
473
+
474
+ if opt[:set]
475
+ GeneValidatorApp.config.write_config_file
476
+ exit
477
+ end
478
+
479
+ GeneValidatorApp.run
480
+ end