summaryrefslogtreecommitdiff
path: root/application.rb
blob: de11313ecf99f1652ceeee78de5f8b1ee90a131a (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
require 'rubygems'
gem "opentox-ruby", "~> 0"
require 'opentox-ruby'

set :lock, true

helpers do
        def next_id
	  id = Dir["./public/*yaml"].collect{|f| File.basename(f.sub(/.yaml/,'')).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 /application\/rdf\+xml/
            dataset.load_rdfxml(input_data)

          when /multipart\/form-data/ , "application/x-www-form-urlencoded" # file uploads

            case params[:file][:type]

            when /yaml/
              dataset.load_yaml(params[:file][:tempfile].read)

            when "application/rdf+xml"
              dataset.load_rdfxml_file(params[:file][:tempfile])

            when "text/csv"
              dataset = OpenTox::Dataset.new @uri
              dataset.load_csv(params[:file][:tempfile].read)
              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)
              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("public/#{@id}.yaml","w+"){|f| f.puts dataset.to_yaml}
        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
    @yaml_file = "public/#{@id}.yaml"
    halt 404, "Dataset #{@id} not found." unless File.exists? @yaml_file

    extension = File.extname(request.path_info)
    #extension = File.extname(params[:id]).sub(/\./,'')
    unless extension.empty?
     #request.path_info.sub!(/\.#{extension}$/,'')
     case extension
     when "html"
       @accept = 'text/html'
     when "yaml"
       @accept = 'application/x-yaml'
     when "csv"
       @accept = 'text/csv'
     when "rdfxml"
       @accept = 'application/rdf+xml'
     when "xls"
       @accept = 'application/ms-excel'
     else
       halt 404, "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
  response['Content-Type'] = 'text/uri-list'
  Dir["./public/*yaml"].collect{|f| File.basename(f.sub(/.yaml/,'')).to_i}.sort.collect{|n| uri n}.join("\n") + "\n"
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 = "public/#{params[:id]}.rdfxml"
    unless File.exists? file # lazy rdfxml generation
      dataset = YAML.load_file(@yaml_file)
      File.open(file,"w+") { |f| f.puts dataset.to_rdfxml }
    end
    response['Content-Type'] = 'application/rdf+xml'
    File.read(file)

  when /yaml/
    response['Content-Type'] = 'application/x-yaml'
    File.read(@yaml_file)

   when /html/
    response['Content-Type'] = 'text/html'
    OpenTox.text_to_html File.read(@yaml_file) 

  when "text/csv"
    response['Content-Type'] = 'text/csv'
    YAML.load_file(@yaml_file).to_csv

  when /ms-excel/
    file = "public/#{params[:id]}.xls"
    YAML.load_file(@yaml_file).to_xls.write(file) unless File.exists? file # lazy xls generation
    response['Content-Type'] = 'application/ms-excel'
    File.open(file).read

  else
    halt 404, "Content-type #{@accept} not supported."
  end
end

# Get metadata of the dataset
# @return [application/rdf+xml] Metadata OWL-DL
get '/:id/metadata' do

  metadata = YAML.load_file(@yaml_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
  @yaml_file = "public/#{@id}.yaml"
  feature_uri = url_for("/#{@id}/feature/#{URI.encode(feature)}",:full) # work around  racks internal uri decoding
  metadata = YAML.load_file(@yaml_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
  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 = YAML.load_file(@yaml_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 "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'
  YAML.load_file(@yaml_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
  @yaml_file = "public/#{@id}.yaml"
  if params.size == 0 and input_data.size==0
    File.open(@yaml_file,"w+"){|f| f.puts OpenTox::Dataset.new(@uri).to_yaml}
    OpenTox::Authorization.check_policy(@uri, @subjectid) if File.exists? @yaml_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? @yaml_file
      @uri
    end
    halt 503,task.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 
  LOGGER.debug @uri
  response['Content-Type'] = 'text/uri-list'
  task = OpenTox::Task.create("Converting and saving dataset ", @uri) do 
    FileUtils.rm Dir["public/#{@id}.*"]
    load_dataset @id, params, request.content_type, request.env["rack.input"].read 
    @uri
  end
  halt 503,task.uri+"\n" if task.status == "Cancelled"
  halt 202,task.uri.to_s+"\n"
end

# Delete a dataset
# @return [text/plain] Status message
delete '/:id' do
  LOGGER.debug "deleting dataset with id "+@id.to_s
  begin
    FileUtils.rm Dir["public/#{@id}.*"]
    if @subjectid and !File.exists? @yaml_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
    halt 404, "Dataset #{@id} does not exist."
  end
end

# Delete all datasets
# @return [text/plain] Status message
delete '/?' do
  FileUtils.rm Dir["public/*.rdfxml"]
  FileUtils.rm Dir["public/*.xls"]
  FileUtils.rm Dir["public/*.yaml"]
  response['Content-Type'] = 'text/plain'
  "All datasets deleted."
end