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authorChristoph Helma <helma@in-silico.ch>2012-05-04 10:29:55 +0000
committerChristoph Helma <helma@in-silico.ch>2012-05-04 10:29:55 +0000
commit8a5e3d69a16fc0c7d551e000270fe243ed121c85 (patch)
tree1f3dc8f4c2b9321fcda9aa4e44f5f26ba01cdb28 /lib
parentb317039ba3e5ba10e7ea4769f256e345829ce8ff (diff)
ntriples as default format, rdfxml as fallback
Diffstat (limited to 'lib')
-rw-r--r--lib/error.rb53
-rw-r--r--lib/opentox-client.rb3
-rw-r--r--lib/opentox.rb9
-rw-r--r--lib/rest-client-wrapper.rb1
-rw-r--r--lib/task.rb12
5 files changed, 6 insertions, 72 deletions
diff --git a/lib/error.rb b/lib/error.rb
index 58b9816..64b0fb1 100644
--- a/lib/error.rb
+++ b/lib/error.rb
@@ -87,57 +87,4 @@ module OpenTox
end
end
-=begin
- # TODO: create reports directly from errors, requires modified task service
- class ErrorReport
- def initialize http_code, error
- @http_code = http_code
- @report = {}
- @report[RDF::OT.actor] = error.uri.to_s
- @report[RDF::OT.message] = error.message.to_s
- @report[RDF::OT.statusCode] = @http_code
- @report[RDF::OT.errorCode] = error.class.to_s
-
- # cut backtrace
- backtrace = caller.collect{|line| line unless line =~ /#{File.dirname(__FILE__)}/}.compact
- cut_index = backtrace.find_index{|line| line.match /sinatra|minitest/}
- cut_index ||= backtrace.size
- cut_index -= 1
- cut_index = backtrace.size-1 if cut_index < 0
- @report[RDF::OT.errorDetails] = backtrace[0..cut_index].join("\n")
- @report[RDF::OT.errorDetails] += "REST paramenters:\n#{error.request.args.inspect}" if defined? error.request
- #@report[RDF::OT.message] += "\n" + error.response.body.to_s if defined? error.response
- # TODO fix Error cause
- # should point to another errorReport, but errorReports do not have URIs
- # create a separate service?
- #report[RDF::OT.errorCause] = @report if defined?(@report)
- end
-
- # define to_ and self.from_ methods for various rdf formats
- RDF_FORMATS.each do |format|
-
- send :define_method, "to_#{format}".to_sym do
- rdf = RDF::Writer.for(format).buffer do |writer|
- # TODO: not used for turtle
- # http://rdf.rubyforge.org/RDF/Writer.html#
- writer.prefix :ot, RDF::URI('http://www.opentox.org/api/1.2#')
- writer.prefix :ot1_1, RDF::URI('http://www.opentox.org/api/1.1#')
- subject = RDF::Node.new
- @report.each do |predicate,object|
- writer << [subject, predicate, object] if object
- end
- end
- rdf
- end
-
- define_singleton_method "from_#{format}".to_sym do |rdf|
- report = ErrorReport.new
- RDF::Reader.for(format).new(rdf) do |reader|
- reader.each_statement{ |statement| report.rdf << statement }
- end
- report
- end
- end
- end
-=end
end
diff --git a/lib/opentox-client.rb b/lib/opentox-client.rb
index 0546634..8c19225 100644
--- a/lib/opentox-client.rb
+++ b/lib/opentox-client.rb
@@ -15,11 +15,8 @@ RDF::OT = RDF::Vocabulary.new 'http://www.opentox.org/api/1.2#'
RDF::OT1 = RDF::Vocabulary.new 'http://www.opentox.org/api/1.1#'
RDF::OTA = RDF::Vocabulary.new 'http://www.opentox.org/algorithmTypes.owl#'
-#CLASSES = ["Compound", "Feature", "Dataset", "Algorithm", "Model", "Validation", "Task", "ErrorReport", "Investigation"]
CLASSES = ["Generic", "Compound", "Feature", "Dataset", "Algorithm", "Model", "Validation", "Task", "Investigation"]
RDF_FORMATS = [:rdfxml,:ntriples,:turtle]
-#$default_rdf = "text/plain"
-$default_rdf = "application/rdf+xml"
# Regular expressions for parsing classification data
TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 2682258..f79b51b 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -21,9 +21,9 @@ module OpenTox
# Load metadata from service
def pull
- # TODO generic method for all formats
- #parse_rdfxml RestClientWrapper.get(@uri,{},{:accept => $default_rdf, :subjectid => @subjectid})
parse_ntriples RestClientWrapper.get(@uri,{},{:accept => "text/plain", :subjectid => @subjectid})
+ rescue # fall back to rdfxml
+ parse_rdfxml RestClientWrapper.get(@uri,{},{:accept => "application/rdf+xml", :subjectid => @subjectid})
end
# Get object metadata
@@ -48,8 +48,9 @@ module OpenTox
# Save object at service
def save
- #TODO: dynamic assignment
- put self.to_rdfxml, { :content_type => $default_rdf}
+ put self.to_ntriples, { :content_type => "text/plain"}
+ rescue # fall back to rdfxml
+ put self.to_rdfxml, { :content_type => "application/rdf+xml"}
end
RDF_FORMATS.each do |format|
diff --git a/lib/rest-client-wrapper.rb b/lib/rest-client-wrapper.rb
index d5d9c82..479d5a5 100644
--- a/lib/rest-client-wrapper.rb
+++ b/lib/rest-client-wrapper.rb
@@ -18,7 +18,6 @@ module OpenTox
# check input
@subjectid = headers[:subjectid] ? headers[:subjectid] : nil
bad_request_error "Invalid URI: '#{uri}'" unless URI.valid? uri
- #TODO fix for internal installations
not_found_error "URI '#{uri}' not found." unless URI.accessible?(uri, @subjectid) unless URI.ssl?(uri)
bad_request_error "Headers are not a hash: #{headers.inspect}" unless headers==nil or headers.is_a?(Hash)
# make sure that no header parameters are set in the payload
diff --git a/lib/task.rb b/lib/task.rb
index 4cdbb51..ceb6fd9 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -9,11 +9,7 @@ module OpenTox
def self.create service_uri, params={}
uri = RDF::URI.new File.join(service_uri,SecureRandom.uuid)
- #uri = RestClientWrapper.post service_uri
- #puts uri
task = Task.new uri
- #task.pull
- #puts task.to_turtle
task.rdf << RDF::Statement.new(uri, RDF.type, RDF::OT.Task)
task.rdf << RDF::Statement.new(uri, RDF::DC.date, RDF::Literal.new(DateTime.now))
task.rdf << RDF::Statement.new(uri, RDF::OT.hasStatus, RDF::Literal.new("Running"))
@@ -27,7 +23,7 @@ module OpenTox
if $!.respond_to? :to_ntriples
RestClientWrapper.put(File.join(task.uri,'Error'),:errorReport => $!.to_ntriples,:content_type => 'text/plain')
else
- RestClientWrapper.put(File.join(task.uri,'Error')) #if $!.respond_to? :report
+ RestClientWrapper.put(File.join(task.uri,'Error'))
end
task.kill
end
@@ -72,7 +68,6 @@ module OpenTox
end
def completed(uri)
- #TODO fix for https rewrites
not_found_error "Result URI \"#{uri}\" does not exist." unless URI.accessible? uri
RestClientWrapper.put(File.join(@uri,'Completed'),{:resultURI => uri})
end
@@ -111,11 +106,6 @@ module OpenTox
code >= 400 and code != 503
end
- def errorReport
- # TODO: fix rdf output at task service
- not_implemented_error "RDF output of errorReports has to be fixed at task service"
- end
-
[:hasStatus, :resultURI].each do |method|
define_method method do
response = self.[](RDF::OT[method])