Merge commit 'mguetlein/test' into development

Conflicts:

	application.rb

1 files changed, 94 insertions, 93 deletions

diff --git a/application.rb b/application.rb
index 42552f1..476445e 100755
--- a/application.rb
+++ b/application.rb
@@ -3,18 +3,19 @@ gem "opentox-ruby-api-wrapper", "= 1.6.0"
 require 'opentox-ruby-api-wrapper'
 
 class Dataset
-	include DataMapper::Resource
-	property :id, Serial
-	property :uri, String, :length => 255
-	property :file, String, :length => 255
-	property :yaml, Text, :length => 2**32-1 
-	property :owl, Text, :length => 2**32-1 
-	property :created_at, DateTime
+  include DataMapper::Resource
+  property :id, Serial
+  property :uri, String, :length => 255
+  property :file, String, :length => 255
+  property :yaml, Text, :length => 2**32-1 
+  property :owl, Text, :length => 2**32-1 
+  property :created_at, DateTime
 
-	def to_owl
-		data = YAML.load(yaml)
-		owl = OpenTox::Owl.create 'Dataset', uri
-		owl.set "title", data.title
+  def to_owl
+   
+    data = YAML.load(yaml)
+    owl = OpenTox::Owl.create 'Dataset', uri
+    owl.set "title", data.title
     owl.set "creator", data.creator
     if data.compounds
       data.compounds.each do |compound|
@@ -22,7 +23,7 @@ class Dataset
        end
     end
     owl.rdf
-	end
+  end
 
 end
 
@@ -31,44 +32,44 @@ DataMapper.auto_upgrade!
 ## REST API
 
 get '/?' do
-	response['Content-Type'] = 'text/uri-list'
-	Dataset.all(params).collect{|d| d.uri}.join("\n") + "\n"
+  response['Content-Type'] = 'text/uri-list'
+  Dataset.all(params).collect{|d| d.uri}.join("\n") + "\n"
 end
 
 get '/:id' do
-	accept = request.env['HTTP_ACCEPT']
-	accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil?
-	# workaround for browser links
-	case params[:id]
-	when /.yaml$/
-		params[:id].sub!(/.yaml$/,'')
-		accept =  'application/x-yaml'
-	when /.rdf$/
-		params[:id].sub!(/.rdf$/,'')
-		accept =  'application/rdf+xml'
-	when /.xls$/
-		params[:id].sub!(/.xls$/,'')
-		accept =  'application/vnd.ms-excel'	
-	end
-	begin
-		dataset = Dataset.get(params[:id])
+  accept = request.env['HTTP_ACCEPT']
+  accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil?
+  # workaround for browser links
+  case params[:id]
+  when /.yaml$/
+    params[:id].sub!(/.yaml$/,'')
+    accept =  'application/x-yaml'
+  when /.rdf$/
+    params[:id].sub!(/.rdf$/,'')
+    accept =  'application/rdf+xml'
+  when /.xls$/
+    params[:id].sub!(/.xls$/,'')
+    accept =  'application/vnd.ms-excel'  
+  end
+  begin
+    dataset = Dataset.get(params[:id])
     halt 404, "Dataset #{params[:id]} not found." unless dataset
-	rescue => e
-		raise e.message + e.backtrace
-		halt 404, "Dataset #{params[:id]} not found."
-	end
-	halt 404, "Dataset #{params[:id]} not found." if dataset.nil? # not sure how an empty cataset can be returned, but if this happens stale processes keep runing at 100% cpo
-	case accept
-	when /rdf/ # redland sends text/rdf instead of application/rdf+xml
-		response['Content-Type'] = 'application/rdf+xml'
-		unless dataset.owl # lazy owl creation
-			dataset.owl = dataset.to_owl
-			dataset.save
-		end
-		dataset.owl
-	when /yaml/
-		response['Content-Type'] = 'application/x-yaml'
-		dataset.yaml
+  rescue => e
+    raise e.message + e.backtrace
+    halt 404, "Dataset #{params[:id]} not found."
+  end
+  halt 404, "Dataset #{params[:id]} not found." if dataset.nil? # not sure how an empty cataset can be returned, but if this happens stale processes keep runing at 100% cpo
+  case accept
+  when /rdf/ # redland sends text/rdf instead of application/rdf+xml
+    response['Content-Type'] = 'application/rdf+xml'
+    unless dataset.owl # lazy owl creation
+      dataset.owl = dataset.to_owl
+      dataset.save
+    end
+    dataset.owl
+  when /yaml/
+    response['Content-Type'] = 'application/x-yaml'
+    dataset.yaml
   when /ms-excel/
     require 'spreadsheet'
     response['Content-Type'] = 'application/vnd.ms-excel'
@@ -81,12 +82,12 @@ get '/:id' do
     YAML.load(dataset.yaml).data.each do |line|
       begin
         smilestring = RestClient.get(line[0], :accept => 'chemical/x-daylight-smiles').to_s
-				if line[1]
-					val = line[1][0].first[1]
-					LOGGER.debug val
-					#line[1][0] ? val = line[1][0].first[1] #? "1" : "0" : val = "" 
-					sheet.update_row(i, smilestring , val)
-				end
+        if line[1]
+          val = line[1][0].first[1]
+          LOGGER.debug val
+          #line[1][0] ? val = line[1][0].first[1] #? "1" : "0" : val = "" 
+          sheet.update_row(i, smilestring , val)
+        end
         i+=1 
       rescue
       end
@@ -99,66 +100,66 @@ get '/:id' do
     end
     tmp.close!
   else
-		halt 400, "Unsupported MIME type '#{accept}'"
-	end
+    halt 400, "Unsupported MIME type '#{accept}'"
+  end
 end
 
 get '/:id/features/:feature_id/?' do
-	OpenTox::Dataset.find(url_for("/#{params[:id]}", :full)).feature(params[:feature_id])
+  OpenTox::Dataset.find(url_for("/#{params[:id]}", :full)).feature(params[:feature_id])
 end
 
 get '/:id/features/?' do
-	YAML.load(Dataset.get(params[:id]).yaml).features.join("\n") + "\n"
+  YAML.load(Dataset.get(params[:id]).yaml).features.join("\n") + "\n"
 end
 
 get '/:id/compounds/?' do
-	YAML.load(Dataset.get(params[:id]).yaml).compounds.join("\n") + "\n"
+  YAML.load(Dataset.get(params[:id]).yaml).compounds.join("\n") + "\n"
 end
 
 post '/?' do
 
-		dataset = Dataset.new
-		dataset.save
-		dataset.uri = url_for("/#{dataset.id}", :full)
-		content_type = request.content_type
-		content_type = "application/rdf+xml" if content_type.nil?
-		case request.content_type
-		when /yaml/
-			dataset.yaml =	request.env["rack.input"].read
-		#when /csv/
-			#dataset.yaml =	csv2yaml request.env["rack.input"].read
-		#when "application/rdf+xml"
-			#dataset.yaml =	owl2yaml request.env["rack.input"].read
-		else
-			halt 404, "MIME type \"#{request.content_type}\" not supported."
-		end
-		begin
-			#dataset.owl = d.rdf
+    dataset = Dataset.new
+    dataset.save
+    dataset.uri = url_for("/#{dataset.id}", :full)
+    content_type = request.content_type
+    content_type = "application/rdf+xml" if content_type.nil?
+    case request.content_type
+    when /yaml/
+      dataset.yaml =  request.env["rack.input"].read
+#    when /csv/
+#      dataset.yaml =  csv2yaml request.env["rack.input"].read
+    when "application/rdf+xml"
+      dataset.yaml = YAML.load(OpenTox::Dataset.owl_to_yaml(request.env["rack.input"].read,dataset.uri))
+    else
+      halt 404, "MIME type \"#{request.content_type}\" not supported."
+    end
+    begin
+      #dataset.owl = d.rdf
       #dataset.uri = uri 
-			raise "saving failed: "+dataset.errors.inspect unless dataset.save
-		rescue => e
-			LOGGER.error e.message
-			LOGGER.info e.backtrace
-			halt 500, "Could not save dataset #{dataset.uri}."
-		end
-		LOGGER.debug "#{dataset.uri} saved."
-	response['Content-Type'] = 'text/uri-list'
-	dataset.uri + "\n"
+      raise "saving failed: "+dataset.errors.inspect unless dataset.save
+    rescue => e
+      LOGGER.error e.message
+      LOGGER.info e.backtrace
+      halt 500, "Could not save dataset #{dataset.uri}."
+    end
+    LOGGER.debug "#{dataset.uri} saved."
+  response['Content-Type'] = 'text/uri-list'
+  dataset.uri + "\n"
 end
 
 delete '/:id/?' do
-	begin
-		dataset = Dataset.get(params[:id])
-		dataset.destroy!
-		response['Content-Type'] = 'text/plain'
-		"Dataset #{params[:id]} deleted."
-	rescue
-		halt 404, "Dataset #{params[:id]} does not exist."
-	end
+  begin
+    dataset = Dataset.get(params[:id])
+    dataset.destroy!
+    response['Content-Type'] = 'text/plain'
+    "Dataset #{params[:id]} deleted."
+  rescue
+    halt 404, "Dataset #{params[:id]} does not exist."
+  end
 end
 
 delete '/?' do
   Dataset.auto_migrate!
-	response['Content-Type'] = 'text/plain'
-	"All datasets deleted."
+  response['Content-Type'] = 'text/plain'
+  "All datasets deleted."
 end