summaryrefslogtreecommitdiff
path: root/application.rb
blob: 7c76b15db21f5a0cee8c6593c0e89dab88efcf2a (plain)
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
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
ENV["JAVA_HOME"] = "/usr/lib/jvm/java-6-sun" unless ENV["JAVA_HOME"]
ENV["JOELIB2"] = File.join File.expand_path(File.dirname(__FILE__)),"java"
deps = []
deps << "#{ENV["JAVA_HOME"]}/lib/tools.jar"
deps << "#{ENV["JAVA_HOME"]}/lib/classes.jar"
deps << "#{ENV["JOELIB2"]}"
jars = Dir[ENV["JOELIB2"]+"/*.jar"].collect {|f| File.expand_path(f) }
deps = deps + jars
ENV["CLASSPATH"] = deps.join(":")


require 'rubygems'
gem "opentox-ruby", "~> 3"
require 'opentox-ruby'
require 'profiler'
require 'rjb'

set :lock, true

@@datadir = "data"

@@idfile_path = @@datadir+"/id" 
unless File.exist?(@@idfile_path)
  id = Dir["./#{@@datadir}/*json"].collect{|f| File.basename(f.sub(/.json/,'')).to_i}.sort.last
  id = 0 if id.nil?
  open(@@idfile_path,"w") do |f|
    f.puts(id)
  end
end

helpers do
  def next_id
    open(@@idfile_path, "r+") do |f|
      f.flock(File::LOCK_EX)
      @id = f.gets.to_i + 1
      f.rewind
      f.print @id
    end
    return @id
  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(@uri, @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