1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
|
require 'rubygems'
gem "opentox-ruby", "~> 3"
require 'opentox-ruby'
require 'profiler'
set :lock, true
@@datadir = "data"
helpers do
def next_id
id = Dir["./#{@@datadir}/*json"].collect{|f| File.basename(f.sub(/.json/,'')).to_i}.sort.last
id = 0 if id.nil?
id + 1
end
def uri(id)
url_for "/#{id}", :full
end
# subjectid ist stored as memeber variable, not in params
def load_dataset(id, params,content_type,input_data)
@uri = uri id
raise "store subject-id in dataset-object, not in params" if params.has_key?(:subjectid) and @subjectid==nil
content_type = "application/rdf+xml" if content_type.nil?
dataset = OpenTox::Dataset.new(nil, @subjectid)
case content_type
when /yaml/
dataset.load_yaml(input_data)
when /json/
dataset.load_json(input_data)
when /application\/rdf\+xml/
dataset.load_rdfxml(input_data, @subjectid)
when "chemical/x-mdl-sdfile"
dataset.load_sdf(input_data, @subjectid)
when /multipart\/form-data/ , "application/x-www-form-urlencoded" # file uploads
case params[:file][:type]
when "chemical/x-mdl-sdfile"
dataset.load_sdf(input_data, @subjectid)
when /json/
dataset.load_json(params[:file][:tempfile].read)
when /yaml/
dataset.load_yaml(params[:file][:tempfile].read)
when "application/rdf+xml"
dataset.load_rdfxml_file(params[:file][:tempfile], @subjectid)
when "text/csv"
dataset.load_csv(params[:file][:tempfile].read, @subjectid)
dataset.add_metadata({
DC.title => File.basename(params[:file][:filename],".csv"),
OT.hasSource => File.basename(params[:file][:filename])
})
when /ms-excel/
extension = File.extname(params[:file][:filename])
case extension
when ".xls"
xls = params[:file][:tempfile].path + ".xls"
File.rename params[:file][:tempfile].path, xls # roo needs these endings
book = Excel.new xls
when ".xlsx"
xlsx = params[:file][:tempfile].path + ".xlsx"
File.rename params[:file][:tempfile].path, xlsx # roo needs these endings
book = Excel.new xlsx
else
raise "#{params[:file][:filename]} is not a valid Excel input file."
end
dataset.load_spreadsheet(book, @subjectid)
dataset.add_metadata({
DC.title => File.basename(params[:file][:filename],extension),
OT.hasSource => File.basename(params[:file][:filename])
})
else
raise "MIME type \"#{params[:file][:type]}\" not supported."
end
else
raise "MIME type \"#{content_type}\" not supported."
end
dataset.uri = @uri # update uri (also in metdata)
dataset.features.keys.each { |f| dataset.features[f][OT.hasSource] = dataset.metadata[OT.hasSource] unless dataset.features[f][OT.hasSource]}
File.open("#{@@datadir}/#{@id}.json","w+"){|f| f.puts dataset.to_json}
end
end
before do
@accept = request.env['HTTP_ACCEPT']
@accept = 'application/rdf+xml' if @accept == '*/*' or @accept == '' or @accept.nil?
@id = request.path_info.match(/^\/\d+/)
unless @id.nil?
@id = @id.to_s.sub(/\//,'').to_i
@uri = uri @id
@json_file = "#{@@datadir}/#{@id}.json"
raise OpenTox::NotFoundError.new "Dataset #{@id} not found." unless File.exists? @json_file
extension = File.extname(request.path_info)
unless extension.empty?
case extension
when ".html"
@accept = 'text/html'
when ".json"
@accept = 'application/json'
when ".yaml"
@accept = 'application/x-yaml'
when ".csv"
@accept = 'text/csv'
when ".rdfxml"
@accept = 'application/rdf+xml'
when ".xls"
@accept = 'application/ms-excel'
when ".sdf"
@accept = 'chemical/x-mdl-sdfile'
else
raise OpenTox::NotFoundError.new "File format #{extension} not supported."
end
end
end
# make sure subjectid is not included in params, subjectid is set as member variable
params.delete(:subjectid)
end
## REST API
# Get a list of available datasets
# @return [text/uri-list] List of available datasets
get '/?' do
uri_list = Dir["./#{@@datadir}/*json"].collect{|f| File.basename(f.sub(/.json/,'')).to_i}.sort.collect{|n| uri n}.join("\n") + "\n"
case @accept
when /html/
response['Content-Type'] = 'text/html'
OpenTox.text_to_html uri_list
else
response['Content-Type'] = 'text/uri-list'
uri_list
end
end
# Get a dataset representation
# @param [Header] Accept one of `application/rdf+xml, application-x-yaml, text/csv, application/ms-excel` (default application/rdf+xml)
# @return [application/rdf+xml, application-x-yaml, text/csv, application/ms-excel] Dataset representation
get '/:id' do
case @accept
when /rdf/ # redland sends text/rdf instead of application/rdf+xml
file = "#{@@datadir}/#{params[:id]}.rdfxml"
unless File.exists? file # lazy rdfxml generation
dataset = OpenTox::Dataset.from_json File.read(@json_file)
File.open(file,"w+") { |f| f.puts dataset.to_rdfxml }
end
send_file file, :type => 'application/rdf+xml'
when /json/
send_file @json_file, :type => 'application/x-yaml'
when /yaml/
file = "#{@@datadir}/#{params[:id]}.yaml"
unless File.exists? file # lazy yaml generation
dataset = OpenTox::Dataset.from_json File.read(@json_file)
File.open(file,"w+") { |f| f.puts dataset.to_yaml }
end
send_file file, :type => 'application/x-yaml'
when /html/
response['Content-Type'] = 'text/html'
OpenTox.text_to_html JSON.pretty_generate(JSON.parse(File.read(@json_file)))
when "text/csv"
response['Content-Type'] = 'text/csv'
OpenTox::Dataset.from_json(File.read(@json_file)).to_csv
when /ms-excel/
file = "#{@@datadir}/#{params[:id]}.xls"
OpenTox::Dataset.from_json(File.read(@json_file)).to_xls.write(file) unless File.exists? file # lazy xls generation
send_file file, :type => 'application/ms-excel'
when /sdfile/
response['Content-Type'] = 'chemical/x-mdl-sdfile'
OpenTox::Dataset.from_json(File.read(@json_file)).to_sdf
# when /uri-list/
# response['Content-Type'] = 'text/uri-list'
# Yajl::Parser.parse(File.read(@json_file)).to_urilist
else
raise OpenTox::NotFoundError.new "Content-type #{@accept} not supported."
end
end
# Get metadata of the dataset
# @return [application/rdf+xml] Metadata OWL-DL
get '/:id/metadata' do
metadata = OpenTox::Dataset.from_json(File.read(@json_file)).metadata
case @accept
when /rdf/ # redland sends text/rdf instead of application/rdf+xml
response['Content-Type'] = 'application/rdf+xml'
serializer = OpenTox::Serializer::Owl.new
serializer.add_metadata url_for("/#{params[:id]}",:full), metadata
serializer.to_rdfxml
when /yaml/
response['Content-Type'] = 'application/x-yaml'
metadata.to_yaml
end
end
# Get a dataset feature
# @param [Header] Accept one of `application/rdf+xml or application-x-yaml` (default application/rdf+xml)
# @return [application/rdf+xml,application/x-yaml] Feature metadata
get %r{/(\d+)/feature/(.*)$} do |id,feature|
@id = id
@uri = uri @id
@json_file = "#{@@datadir}/#{@id}.json"
feature_uri = url_for("/#{@id}/feature/#{URI.encode(feature)}",:full) # work around racks internal uri decoding
metadata = OpenTox::Dataset.from_json(File.read(@json_file)).features[feature_uri]
case @accept
when /rdf/ # redland sends text/rdf instead of application/rdf+xml
response['Content-Type'] = 'application/rdf+xml'
serializer = OpenTox::Serializer::Owl.new
serializer.add_feature feature_uri, metadata
serializer.to_rdfxml
when /yaml/
response['Content-Type'] = 'application/x-yaml'
metadata.to_yaml
when /json/
response['Content-Type'] = 'application/json'
Yajl::Encoder.encode(metadata)
end
end
# Get a list of all features
# @param [Header] Accept one of `application/rdf+xml, application-x-yaml, text/uri-list` (default application/rdf+xml)
# @return [application/rdf+xml, application-x-yaml, text/uri-list] Feature list
get '/:id/features' do
features = OpenTox::Dataset.from_json(File.read(@json_file)).features
case @accept
when /rdf/ # redland sends text/rdf instead of application/rdf+xml
response['Content-Type'] = 'application/rdf+xml'
serializer = OpenTox::Serializer::Owl.new
features.each { |feature,metadata| serializer.add_feature feature, metadata }
serializer.to_rdfxml
when /yaml/
response['Content-Type'] = 'application/x-yaml'
features.to_yaml
when /json/
response['Content-Type'] = 'application/json'
Yajl::Encoder.encode(features)
when "text/uri-list"
response['Content-Type'] = 'text/uri-list'
features.keys.join("\n") + "\n"
end
end
# Get a list of all compounds
# @return [text/uri-list] Feature list
get '/:id/compounds' do
response['Content-Type'] = 'text/uri-list'
OpenTox::Dataset.from_json(File.read(@json_file)).compounds.join("\n") + "\n"
end
# Create a new dataset.
#
# Posting without parameters creates and saves an empty dataset (with assigned URI).
# Posting with parameters creates and saves a new dataset.
# Data can be submitted either
# - in the message body with the appropriate Content-type header or
# - as file uploads with Content-type:multipart/form-data and a specified file type
# @example
# curl -X POST -F "file=@training.csv;type=text/csv" http://webservices.in-silico.ch/dataset
# @param [Header] Content-type one of `application/x-yaml, application/rdf+xml, multipart/form-data/`
# @param [BODY] - string with data in selected Content-type
# @param [optional] file, for file uploads, Content-type should be multipart/form-data, please specify the file type `application/rdf+xml, application-x-yaml, text/csv, application/ms-excel`
# @return [text/uri-list] Task URI or Dataset URI (empty datasets)
post '/?' do
response['Content-Type'] = 'text/uri-list'
# it could be that the read function works only once!, store in varible
input_data = request.env["rack.input"].read
@id = next_id
@uri = uri @id
@json_file = "#{@@datadir}/#{@id}.json"
if params.size == 0 and input_data.size==0
File.open(@json_file,"w+"){|f| f.puts OpenTox::Dataset.new(@uri).to_json}
OpenTox::Authorization.check_policy(@uri, @subjectid) if File.exists? @json_file
@uri
else
task = OpenTox::Task.create("Converting and saving dataset ", @uri) do
load_dataset @id, params, request.content_type, input_data
OpenTox::Authorization.check_policy(@uri, @subjectid) if File.exists? @json_file
@uri
end
raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
halt 202,task.uri+"\n"
end
end
# Save a dataset, will overwrite all existing data
#
# Data can be submitted either
# - in the message body with the appropriate Content-type header or
# - as file uploads with Content-type:multipart/form-data and a specified file type
# @example
# curl -X POST -F "file=@training.csv;type=text/csv" http://webservices.in-silico.ch/dataset/1
# @param [Header] Content-type one of `application/x-yaml, application/rdf+xml, multipart/form-data/`
# @param [BODY] - string with data in selected Content-type
# @param [optional] file, for file uploads, Content-type should be multipart/form-data, please specify the file type `application/rdf+xml, application-x-yaml, text/csv, application/ms-excel`
# @return [text/uri-list] Task ID
post '/:id' do
response['Content-Type'] = 'text/uri-list'
task = OpenTox::Task.create("Converting and saving dataset ", @uri) do
FileUtils.rm Dir["#{@@datadir}/#{@id}.*"]
load_dataset @id, params, request.content_type, request.env["rack.input"].read
@uri
end
raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
halt 202,task.uri.to_s+"\n"
end
# Deletes datasets that have been created by a crossvalidatoin that does not exist anymore
# (This can happen if a crossvalidation fails unexpectedly)
delete '/cleanup' do
Dir["./#{@@datadir}/*json"].each do |file|
dataset = OpenTox::Dataset.from_json File.read(file)
if dataset.metadata[DC.creator] && dataset.metadata[DC.creator] =~ /crossvalidation\/[0-9]/
begin
cv = OpenTox::Crossvalidation.find(dataset.metadata[DC.creator],@subjectid)
raise unless cv
rescue
LOGGER.debug "deleting #{dataset.uri}, crossvalidation missing: #{dataset.metadata[DC.creator]}"
begin
dataset.delete @subjectid
rescue
end
end
end
end
"cleanup done"
end
# Delete a dataset
# @return [text/plain] Status message
delete '/:id' do
LOGGER.debug "deleting dataset with id #{@id}"
begin
FileUtils.rm Dir["#{@@datadir}/#{@id}.*"]
if @subjectid and !File.exists? @json_file and @uri
begin
res = OpenTox::Authorization.delete_policies_from_uri(@uri, @subjectid)
LOGGER.debug "Policy deleted for Dataset URI: #{@uri} with result: #{res}"
rescue
LOGGER.warn "Policy delete error for Dataset URI: #{@uri}"
end
end
response['Content-Type'] = 'text/plain'
"Dataset #{@id} deleted."
rescue
raise OpenTox::NotFoundError.new "Dataset #{@id} does not exist."
end
end
# Delete all datasets
# @return [text/plain] Status message
delete '/?' do
FileUtils.rm Dir["#{@@datadir}/*.rdfxml"]
FileUtils.rm Dir["#{@@datadir}/*.xls"]
FileUtils.rm Dir["#{@@datadir}/*.yaml"]
FileUtils.rm Dir["#{@@datadir}/*.json"]
response['Content-Type'] = 'text/plain'
"All datasets deleted."
end
|