rbbt-rest 1.8.157 → 1.9.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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+ data.tar.gz: f2d21a95f95a61838596be12cd95a58ef3f979015be6c53b7137758f47616a4732cbc8b0eae75b9d354c20209f7244be8ad9dd3d31b3a49fb215dd3cfaf1d79c
@@ -20,10 +20,10 @@ module RbbtRESTHelpers
20
20
  def old_cache(path, check)
21
21
  return false if production?
22
22
  return false if check.nil? or check.empty?
23
- return false if not File.exists? path
23
+ return false if not File.exist? path
24
24
  check = [check] unless Array === check
25
25
  check.each do |file|
26
- if not File.exists?(file)
26
+ if not File.exist?(file)
27
27
  return true
28
28
  end
29
29
  if File.mtime(file) > File.mtime(path)
@@ -270,7 +270,7 @@ data = NULL
270
270
  if mime && mime.to_s.include?("text/html")
271
271
  halt_html txt || Open.read(fragment_file)
272
272
  else
273
- if File.exists?(fragment_file)
273
+ if File.exist?(fragment_file)
274
274
  send_file fragment_file
275
275
  else
276
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  halt 200, Open.read(fragment_file)
@@ -325,7 +325,7 @@ data = NULL
325
325
  raise RbbtRESTHelpers::Retry
326
326
  end
327
327
 
328
- #if File.exists?(step.info_file) and Time.now - File.atime(step.info_file) > 60
328
+ #if File.exist?(step.info_file) and Time.now - File.atime(step.info_file) > 60
329
329
  # Log.debug{ "Checking on #{step.info_file}" }
330
330
  # running = (not step.done?) and step.running?
331
331
  # if FalseClass === running
@@ -5,7 +5,7 @@ module RbbtRESTHelpers
5
5
  class Retry < Exception; end
6
6
 
7
7
  def check_step(step)
8
- if File.exists?(step.info_file) and Time.now - File.atime(step.info_file) > 60
8
+ if File.exist?(step.info_file) and Time.now - File.atime(step.info_file) > 60
9
9
  done = step.done?
10
10
  running = done ? false : step.running?
11
11
  Log.debug{ "Checking on #{step.info_file} (done: #{done}; running: #{running})" }
@@ -301,7 +301,7 @@ module RbbtRESTHelpers
301
301
  def permalink(path)
302
302
  id = Misc.digest(Time.now.to_s)
303
303
  dest = File.join(settings.permalink_dir, id)
304
- FileUtils.mkdir_p settings.permalink_dir unless File.exists? settings.permalink_dir
304
+ FileUtils.mkdir_p settings.permalink_dir unless File.exist? settings.permalink_dir
305
305
  FileUtils.ln_s(path, dest)
306
306
  "/permalink/#{ id }"
307
307
  end
@@ -322,36 +322,81 @@ module RbbtRESTHelpers
322
322
 
323
323
  end
324
324
 
325
- class Haml::Filters::DeferJS < Haml::Filters::Base
325
+ if $haml_6
326
+ Haml::Template.options[:escape_html] = false
326
327
 
327
- def render(text)
328
- step_path = Thread.current["step_path"]
329
- text = "" if text.nil?
330
- defer_text =<<-EOF
328
+ class Haml::Filters::DeferJS < Haml::Filters::TiltBase
329
+
330
+ def compile(node)
331
+ text = node.value[:text]
332
+ step_path = Thread.current["step_path"]
333
+ text = "" if text.nil?
334
+ defer_text =<<-EOF
331
335
  %script
332
336
  :plain
333
337
  defer(function(step_path){
334
338
 
335
339
  #{text.gsub(/^/," ")}
336
340
  }, '#{step_path}')
337
- EOF
338
- Haml::Engine.new(defer_text).to_html
341
+ EOF
342
+ node.value[:text] = defer_text
343
+ compile_with_tilt(node, 'haml')
344
+ end
339
345
  end
340
- end
341
346
 
342
- class Haml::Filters::Documentation < Haml::Filters::Base
347
+ class Haml::Filters::Documentation < Haml::Filters::TiltBase
343
348
 
344
- def render(text)
345
- text = "<br/>" if text.strip.empty?
349
+ def compile(node)
350
+ text = node.value[:text]
351
+ text = "<br/>" if text.strip.empty?
346
352
 
347
- doc_text =<<-EOF
353
+ doc_text =<<-EOF
348
354
  %section.documentation#{ text.gsub(/\s/,'').length < 80 * 10 ? '.short' : ''}
349
355
  :markdown
350
356
  #{text.gsub(/^/," ")}
351
- EOF
357
+ EOF
352
358
 
353
- Haml::Engine.new(doc_text).to_html
359
+ node.value[:text] = doc_text
360
+ compile_with_tilt(node, 'haml')
361
+ end
354
362
  end
355
363
 
356
- end
364
+ class Haml::Filters
365
+ register :deferjs, Haml::Filters::DeferJS
366
+ register :documentation, Haml::Filters::Documentation
367
+ end
368
+ else
369
+ module Haml::Filters::DeferJS
370
+ include Haml::Filters::Base
371
+
372
+ def render(text)
373
+ step_path = Thread.current["step_path"]
374
+ text = "" if text.nil?
375
+ defer_text =<<-EOF
376
+ %script
377
+ :plain
378
+ defer(function(step_path){
379
+ #{text.gsub(/^/," ")}
380
+ }, '#{step_path}')
381
+ EOF
382
+ Haml::Engine.new(defer_text).to_html
383
+ end
384
+ end
385
+
386
+ module Haml::Filters::Documentation
387
+ include Haml::Filters::Base
388
+
389
+ def render(text)
390
+ text = "<br/>" if text.strip.empty?
357
391
 
392
+ doc_text =<<-EOF
393
+ %section.documentation#{ text.gsub(/\s/,'').length < 80 * 10 ? '.short' : ''}
394
+ :markdown
395
+ #{text.gsub(/^/," ")}
396
+ EOF
397
+
398
+ Haml::Engine.new(doc_text).to_html
399
+ end
400
+
401
+ end
402
+ end
@@ -3,7 +3,6 @@ require 'rbbt/rest/common/cache'
3
3
  require 'tilt'
4
4
 
5
5
  Tilt::SYMBOL_ARRAY_SORTABLE = false
6
-
7
6
  module RbbtRESTHelpers
8
7
  def error_for(job, layout = nil)
9
8
  if ex = job.info[:exception]
@@ -153,7 +152,8 @@ module RbbtRESTHelpers
153
152
  end
154
153
  end
155
154
  Log.low("Fragment started: #{ fragment_file } - #{Process.pid}")
156
- res = capture_haml fragment_code, &block
155
+ #res = capture_haml fragment_code, &block
156
+ res = $haml_6 ? capture(&block) : capture_haml(&block)
157
157
  Log.low("Fragment writing: #{ fragment_file } - #{Process.pid}")
158
158
  Open.write(fragment_file, res)
159
159
  Log.low("Fragment done: #{ fragment_file } - #{Process.pid}")
@@ -196,7 +196,7 @@ module RbbtRESTHelpers
196
196
  end
197
197
  end
198
198
  else
199
- capture_haml &block
199
+ $haml_6 ? capture(&block) : capture_haml(&block)
200
200
  end
201
201
  else
202
202
  if link =~ / class=/
@@ -294,7 +294,8 @@ module RbbtRESTHelpers
294
294
  def reveal(text, id = nil, options = nil, &block)
295
295
  id ||= "rbbt_reveal_" << (rand * 10000).to_i.to_s
296
296
 
297
- content_html = capture_haml(&block)
297
+ #content_html = capture_haml(&block)
298
+ content_html = $haml_6 ? capture(&block) : capture_haml(&block)
298
299
 
299
300
  options = {} if options.nil?
300
301
  options = {:href => "#", "data-reveal-id" => 'modal1', 'attr-reveal_id' => id}.merge(options)
@@ -40,7 +40,7 @@ module RbbtRESTHelpers
40
40
  md5 = Misc.digest(recorded_js_files * ",")
41
41
  filename = settings.file_dir["all_js-#{md5}.js"].find
42
42
 
43
- if not File.exists?(filename)
43
+ if not File.exist?(filename)
44
44
  Log.debug{ "Regenerating JS Compressed file: #{ filename }" }
45
45
 
46
46
  text = recorded_js_files.collect{|file|
@@ -53,7 +53,7 @@ module RbbtRESTHelpers
53
53
  "//FILE: #{ File.basename(path) }\n" + Open.read(path)
54
54
  } * "\n"
55
55
 
56
- FileUtils.mkdir_p File.dirname(filename) unless File.exists? File.dirname(filename)
56
+ FileUtils.mkdir_p File.dirname(filename) unless File.exist? File.dirname(filename)
57
57
  Open.write(filename, Uglifier.compile(text))
58
58
  end
59
59
 
@@ -146,6 +146,32 @@ Quality
146
146
  end
147
147
 
148
148
  module RbbtRESTHelpers
149
+
150
+ def capture(*args, &block)
151
+
152
+ variables = block.binding.local_variables
153
+ #variables.each do |v|
154
+ # iif [v, block.binding.local_variable_get(v)]
155
+ #end
156
+ buff_var = variables.select{|v| v.to_s =~ /^_module\d+$/}.sort_by{|v| v.to_s.scan(/\d+/).first.to_i}.last
157
+ buff_was = block.binding.local_variable_get(buff_var) if variables.include? buff_var
158
+ block.binding.local_variable_set(buff_var,'') if buff_var
159
+ begin
160
+ raw = block.call(*args)
161
+ #variables = block.binding.local_variables
162
+ #iii variables
163
+ #variables.each do |v|
164
+ # iif [v, block.binding.local_variable_get(v)]
165
+ #end
166
+ captured = block.binding.local_variable_get(buff_var) if block.binding.local_variables.include?(buff_var)
167
+ captured = "" if captured.nil?
168
+ captured = raw if captured.empty?
169
+ captured
170
+ ensure
171
+ block.binding.local_variable_set(buff_var, buff_was) if buff_was
172
+ end
173
+ end
174
+
149
175
  def tsv_rows_full(tsv)
150
176
  case tsv.type
151
177
  when :single
@@ -390,7 +416,7 @@ module RbbtRESTHelpers
390
416
  tsv = TSV.open(Open.open(file))
391
417
  end
392
418
 
393
- table_options = File.exists?(file + '.table_options') ? YAML.load_file(file + '.table_options') : {}
419
+ table_options = File.exist?(file + '.table_options') ? YAML.load_file(file + '.table_options') : {}
394
420
  tsv.entity_options = table_options[:tsv_entity_options]
395
421
  headers = table_options[:headers]
396
422
  headers.each{|field,p| tsv.entity_templates[field] = Misc.prepare_entity("TEMPLATE", p.first, (tsv.entity_options || {}).merge(p.last)) } unless headers.nil?
@@ -402,10 +428,12 @@ module RbbtRESTHelpers
402
428
  RbbtRESTHelpers.load_tsv(*args)
403
429
  end
404
430
 
405
- def table(options = {})
431
+ def table(options = {},&block)
406
432
  options = {} if options.nil?
407
433
 
408
- tsv = yield
434
+ tsv = $haml_6 ? capture(&block) : block.call
435
+
436
+ raise "Use next to return the table" if String === tsv
409
437
 
410
438
  table_code = options[:table_id] || (rand * 100000).to_i.to_s
411
439
  table_code = Entity::REST.clean_element(table_code)
@@ -1,6 +1,7 @@
1
-
2
1
  module RbbtRESTHelpers
3
2
  class Tabs
3
+ include RbbtRESTHelpers
4
+
4
5
  attr_accessor :headers, :codes, :content, :classes, :tab_classes
5
6
  def initialize(page)
6
7
  @page = page
@@ -13,7 +14,7 @@ module RbbtRESTHelpers
13
14
  @content ||= {}
14
15
 
15
16
  if block_given?
16
- html = @page.capture_haml &block
17
+ html = $haml_6 ? capture(&block) : @page.capture_haml(&block)
17
18
  else
18
19
  html = nil
19
20
  end
@@ -57,10 +57,10 @@ module Entity
57
57
 
58
58
  def self.load_list(entity_type, id, user = nil)
59
59
  path = list_file(entity_type, id, user)
60
- path = list_file(entity_type, id, :public) unless path != nil and File.exists? path
61
- path = list_file(entity_type, id) unless path != nil and File.exists? path
60
+ path = list_file(entity_type, id, :public) unless path != nil and File.exist? path
61
+ path = list_file(entity_type, id) unless path != nil and File.exist? path
62
62
 
63
- raise "List not found: #{ id }" if path.nil? or not File.exists? path
63
+ raise "List not found: #{ id }" if path.nil? or not File.exist? path
64
64
 
65
65
  begin
66
66
  list = Annotated.load_tsv TSV.open(path)
@@ -79,7 +79,7 @@ module Entity
79
79
  begin
80
80
  Open.write(path, Annotated.tsv(list, :all).to_s)
81
81
  rescue
82
- FileUtils.rm path if File.exists? path
82
+ FileUtils.rm path if File.exist? path
83
83
  raise $!
84
84
  end
85
85
  end
@@ -88,11 +88,11 @@ module Entity
88
88
  def self.delete_list(entity_type, id, user)
89
89
  path = list_file(entity_type, id, user)
90
90
 
91
- "This list does not belong to #{ user }: #{[entity_type, id] * ": "}" unless File.exists? path
91
+ "This list does not belong to #{ user }: #{[entity_type, id] * ": "}" unless File.exist? path
92
92
 
93
93
  Misc.lock path do
94
94
  begin
95
- FileUtils.rm path if File.exists? path
95
+ FileUtils.rm path if File.exist? path
96
96
  rescue
97
97
  raise $!
98
98
  end
@@ -39,7 +39,7 @@ module EntityRESTHelpers
39
39
  path.annotate check_file
40
40
  return false unless check_file.exists?
41
41
  else
42
- return false unless File.exists?(check_file)
42
+ return false unless File.exist?(check_file)
43
43
  end
44
44
 
45
45
  reject?(check_file, binding)
@@ -57,8 +57,8 @@ module Entity
57
57
 
58
58
  def self.load_map(entity_type, column, id, user = nil)
59
59
  path = map_file(entity_type, column, id, user)
60
- path = map_file(entity_type, column, id, :public) unless path != nil and File.exists? path
61
- path = map_file(entity_type, column, id) unless path != nil and File.exists? path
60
+ path = map_file(entity_type, column, id, :public) unless path != nil and File.exist? path
61
+ path = map_file(entity_type, column, id) unless path != nil and File.exist? path
62
62
 
63
63
  begin
64
64
  RbbtRESTHelpers.load_tsv(path).first
@@ -75,7 +75,7 @@ module Entity
75
75
  begin
76
76
  RbbtRESTHelpers.save_tsv(map, path)
77
77
  rescue
78
- FileUtils.rm path if path and File.exists? path
78
+ FileUtils.rm path if path and File.exist? path
79
79
  raise $!
80
80
  end
81
81
  end
@@ -84,11 +84,11 @@ module Entity
84
84
  def self.delete_map(entity_type, column, id, user)
85
85
  path = map_file(entity_type, column, id, user)
86
86
 
87
- "This map does not belong to #{ user }: #{[entity_type, column, id] * ": "}" unless File.exists? path
87
+ "This map does not belong to #{ user }: #{[entity_type, column, id] * ": "}" unless File.exist? path
88
88
 
89
89
  Misc.lock path do
90
90
  begin
91
- FileUtils.rm path if File.exists? path
91
+ FileUtils.rm path if File.exist? path
92
92
  rescue
93
93
  raise $!
94
94
  end
@@ -189,7 +189,7 @@ module Entity
189
189
  reuse = options.delete("reuse") if reuse.nil?
190
190
  reuse = true if reuse.nil?
191
191
 
192
- Entity::List.save_list(entity_type.to_s, id, self) unless reuse and File.exists?(Entity::List.list_file(entity_type.to_s, id))
192
+ Entity::List.save_list(entity_type.to_s, id, self) unless reuse and File.exist?(Entity::List.list_file(entity_type.to_s, id))
193
193
 
194
194
  klasses = self.klasses
195
195
  klasses << 'entity_list'
@@ -212,7 +212,7 @@ module Entity
212
212
  reuse = options.delete("reuse") if reuse.nil?
213
213
  reuse = true if reuse.nil?
214
214
 
215
- Entity::List.save_list(entity_type.to_s, id, self) unless reuse and File.exists? Entity::List.list_file(entity_type.to_s, id, self)
215
+ Entity::List.save_list(entity_type.to_s, id, self) unless reuse and File.exist? Entity::List.list_file(entity_type.to_s, id, self)
216
216
 
217
217
  klasses = self.klasses
218
218
  klasses << 'entity_list_action'
@@ -134,10 +134,10 @@ module Sinatra
134
134
  when :raw, :literal
135
135
  content_type "text/tab-separated-values"
136
136
  user_file = Entity::List.list_file(entity_type.split(":").first, list_id, user)
137
- send_file user_file if File.exists? user_file
137
+ send_file user_file if File.exist? user_file
138
138
 
139
139
  global_file = Entity::List.list_file(entity_type.split(":").first, list_id, nil)
140
- send_file global_file if File.exists? global_file
140
+ send_file global_file if File.exist? global_file
141
141
 
142
142
  raise "List file not found: #{ list_id }"
143
143
  when :json
@@ -296,21 +296,21 @@ module Sinatra
296
296
  case @format
297
297
  when :name
298
298
  file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
299
- file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
299
+ file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
300
300
  new = TSV.open(file).change_key "Associated Gene Name"
301
301
  new_id = map_id << " [Names]"
302
302
  Entity::Map.save_map(entity_type, column, new_id, new, user)
303
303
  redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
304
304
  when :ensembl
305
305
  file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
306
- file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
306
+ file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
307
307
  new = TSV.open(file).change_key "Ensembl Gene ID"
308
308
  new_id = map_id << " [Ensembl]"
309
309
  Entity::Map.save_map(entity_type, column, new_id, new, user)
310
310
  redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
311
311
  when :pvalue_score
312
312
  file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
313
- file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
313
+ file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
314
314
  tsv = TSV.open(file)
315
315
  tsv.process tsv.fields.first do |value|
316
316
  value = value.flatten.first if Array === value
@@ -325,7 +325,7 @@ module Sinatra
325
325
  redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
326
326
  when :ranks
327
327
  file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
328
- file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
328
+ file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
329
329
  tsv = TSV.open(file, :cast => :to_f)
330
330
  new = tsv.ranks_for(tsv.fields.first)
331
331
  new_id = map_id << " [Ranks]"
@@ -334,7 +334,7 @@ module Sinatra
334
334
  redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
335
335
  when :invert_ranks
336
336
  file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
337
- file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
337
+ file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
338
338
  tsv = TSV.open(file)
339
339
  size = tsv.size
340
340
  tsv.process "Rank" do |v|
@@ -351,15 +351,15 @@ module Sinatra
351
351
  when :raw, :literal
352
352
  content_type "text/tab-separated-values"
353
353
  user_file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
354
- send_file user_file if File.exists? user_file
354
+ send_file user_file if File.exist? user_file
355
355
 
356
356
  global_file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil)
357
- send_file global_file if File.exists? global_file
357
+ send_file global_file if File.exist? global_file
358
358
 
359
359
  raise "Map file not found: #{ map_id }"
360
360
  when :json
361
361
  file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, user)
362
- file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exists? file
362
+ file = Entity::Map.map_file(entity_type.split(":").first, column, map_id, nil) unless File.exist? file
363
363
 
364
364
  content_type "application/json"
365
365
  tsv = TSV.open(file)
@@ -413,13 +413,13 @@ module Sinatra
413
413
  column = Entity::REST.restore_element(column)
414
414
 
415
415
  file1 = Entity::Map.map_file(entity_type.split(":").first, column, map1, user)
416
- file1 = Entity::Map.map_file(entity_type.split(":").first, column, map1, nil) unless File.exists? file1
417
- raise "Map not found: #{ map1 }" unless File.exists? file1
416
+ file1 = Entity::Map.map_file(entity_type.split(":").first, column, map1, nil) unless File.exist? file1
417
+ raise "Map not found: #{ map1 }" unless File.exist? file1
418
418
  tsv1 = TSV.open(file1, :cast => :to_f)
419
419
 
420
420
  file2 = Entity::Map.map_file(entity_type.split(":").first, column2, map2, user)
421
- file2 = Entity::Map.map_file(entity_type.split(":").first, column2, map2, nil) unless File.exists? file2
422
- raise "Map not found: #{ map2 } - #{ file2 }" unless File.exists? file2
421
+ file2 = Entity::Map.map_file(entity_type.split(":").first, column2, map2, nil) unless File.exist? file2
422
+ raise "Map not found: #{ map2 } - #{ file2 }" unless File.exist? file2
423
423
  tsv2 = TSV.open(file2, :cast => :to_f)
424
424
 
425
425
  tsv1 = tsv1.select :key => tsv2.keys
@@ -1,3 +1,6 @@
1
+ require 'haml'
2
+ $haml_6 = Gem::Version.new(Haml::VERSION) >= Gem::Version.new("6.0.0")
3
+
1
4
  require 'rbbt/rest/common/locate'
2
5
  require 'rbbt/rest/common/resources'
3
6
  require 'rbbt/rest/common/users'
@@ -14,6 +17,7 @@ require 'json'
14
17
  require 'nakayoshi_fork'
15
18
 
16
19
  Rbbt.add_version(__FILE__)
20
+
17
21
  module Sinatra
18
22
  module RbbtRESTMain
19
23
 
@@ -121,7 +125,7 @@ module Sinatra
121
125
  printer = RubyProf::MultiPrinter.new(result)
122
126
  dir = TmpFile.tmp_file
123
127
  dir = settings.file_dir
124
- FileUtils.mkdir_p dir unless File.exists? dir
128
+ FileUtils.mkdir_p dir unless File.exist? dir
125
129
  printer.print(:path => dir, :profile => 'profile')
126
130
  Log.info{ "Profile saved at #{ dir }: #{@uri}" }
127
131
  end
@@ -151,7 +151,7 @@ module WorkflowRESTHelpers
151
151
  if job.path
152
152
  if Open.remote? job.path
153
153
  Open.open(job.path, :nocache => true)
154
- elsif File.exists? job.path
154
+ elsif File.exist? job.path
155
155
  send_file(job.path, :filename => (params[:filename] || File.basename(job.path)))
156
156
  else
157
157
  halt 200, job.load
@@ -41,7 +41,7 @@ module Sinatra
41
41
  workflow.export *workflow.tasks.keys
42
42
  end
43
43
 
44
- self.instance_eval workflow.libdir.lib['sinatra.rb'].read, workflow.libdir.lib['sinatra.rb'].find if workflow.respond_to?(:libdir) and File.exists? workflow.libdir.lib['sinatra.rb']
44
+ self.instance_eval workflow.libdir.lib['sinatra.rb'].read, workflow.libdir.lib['sinatra.rb'].find if workflow.respond_to?(:libdir) and File.exist? workflow.libdir.lib['sinatra.rb']
45
45
 
46
46
  get "/#{workflow.to_s}" do
47
47
  case format
@@ -30,7 +30,7 @@
30
30
  - pvalue = pvalue.collect{|p| p == 0 ? 0.000000000000000000001 : p }
31
31
  = resource map_id + '.qqplot.png', nil, :image do |file|
32
32
  = fragment do
33
- - FileUtils.mkdir_p File.dirname(file) unless File.exists? File.dirname(file)
33
+ - FileUtils.mkdir_p File.dirname(file) unless File.exist? File.dirname(file)
34
34
  :ruby
35
35
  script =<<-EOF
36
36
  library(ggplot2)
@@ -31,7 +31,7 @@
31
31
  - name = File.basename(example_dir)
32
32
  - task_info = workflow.task_info task
33
33
  - inputs = Workflow.load_inputs(example_dir, task_info[:inputs], task_info[:input_types])
34
- - inputs.each{|k,v| v.replace Open.read(v) if String === v and File.exists? v }
34
+ - inputs.each{|k,v| v.replace Open.read(v) if String === v and File.exist? v }
35
35
  - new = {}
36
36
  - inputs.each{|k,v| v.filename = nil if TSV === v ; v = v * "\n" if Array === v; new[k] = v.to_s }
37
37
  - inputs = new
@@ -4,7 +4,7 @@
4
4
  - page = result.size > 50 ? "1" : nil
5
5
 
6
6
  = table :table_id => table_id, :page => page, :table_class => table_class, :row_ids => :use, :table_url => jobname ? to(File.join('/', workflow.to_s, task, jobname)) : nil do
7
- - result
7
+ - next result
8
8
 
9
9
  -#
10
10
  - begin
@@ -66,7 +66,7 @@
66
66
  $('.step.progress').progress({label: 'ratio',text:{ratio: '{value}'}})
67
67
 
68
68
  %hr
69
- - if defined? job.info_file and File.exists? job.info_file and @uri.include? job.name
69
+ - if defined? job.info_file and File.exist? job.info_file and @uri.include? job.name
70
70
  - abort_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "abort")
71
71
  %a.ui.button.red.abort(href=abort_url) Abort
72
72
  -#- clean_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "clean")
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: rbbt-rest
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.8.157
4
+ version: 1.9.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Miguel Vazquez
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2023-03-07 00:00:00.000000000 Z
11
+ date: 2023-03-17 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: modular-scale
@@ -1853,7 +1853,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
1853
1853
  - !ruby/object:Gem::Version
1854
1854
  version: '0'
1855
1855
  requirements: []
1856
- rubygems_version: 3.1.4
1856
+ rubygems_version: 3.4.8
1857
1857
  signing_key:
1858
1858
  specification_version: 4
1859
1859
  summary: Rbbt Web and REST interfaces