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authorChristoph Helma <helma@in-silico.ch>2013-07-16 17:45:08 +0200
committerChristoph Helma <helma@in-silico.ch>2013-07-16 17:45:08 +0200
commit80c1821e3a55b0d9c1ee51537e109dff3bc79423 (patch)
treeb77873e557b016d265c97cbc212b73f700453712 /lib/dataset.rb
parent10ffab4d032e3e5584c318a45521e774d49bd3d7 (diff)
subjectid handled by RestClientWrapper
Diffstat (limited to 'lib/dataset.rb')
-rw-r--r--lib/dataset.rb16
1 files changed, 8 insertions, 8 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb
index cb64406..4fad05b 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -7,8 +7,8 @@ module OpenTox
attr_writer :features, :compounds, :data_entries
- def initialize uri=nil, subjectid=SUBJECTID
- super uri, subjectid
+ def initialize uri=nil
+ super uri
@features = []
@compounds = []
@data_entries = []
@@ -21,9 +21,9 @@ module OpenTox
if @metadata.empty? or force_update
uri = File.join(@uri,"metadata")
begin
- parse_ntriples RestClientWrapper.get(uri,{},{:accept => "text/plain", :subjectid => @subjectid})
+ parse_ntriples RestClientWrapper.get(uri,{},{:accept => "text/plain"})
rescue # fall back to rdfxml
- parse_rdfxml RestClientWrapper.get(uri,{},{:accept => "application/rdf+xml", :subjectid => @subjectid})
+ parse_rdfxml RestClientWrapper.get(uri,{},{:accept => "application/rdf+xml"})
end
@metadata = @rdf.to_hash[RDF::URI.new(@uri)].inject({}) { |h, (predicate, values)| h[predicate] = values.collect{|v| v.to_s}; h }
end
@@ -34,7 +34,7 @@ module OpenTox
def features force_update=false
if @features.empty? or force_update
uri = File.join(@uri,"features")
- uris = RestClientWrapper.get(uri,{},{:accept => "text/uri-list", :subjectid => @subjectid}).split("\n") # ordered datasets return ordered features
+ uris = RestClientWrapper.get(uri,{},{:accept => "text/uri-list"}).split("\n") # ordered datasets return ordered features
@features = uris.collect{|uri| Feature.new(uri)}
end
@features
@@ -44,7 +44,7 @@ module OpenTox
def compounds force_update=false
if @compounds.empty? or force_update
uri = File.join(@uri,"compounds")
- uris = RestClientWrapper.get(uri,{},{:accept => "text/uri-list", :subjectid => @subjectid}).split("\n") # ordered datasets return ordered compounds
+ uris = RestClientWrapper.get(uri,{},{:accept => "text/uri-list"}).split("\n") # ordered datasets return ordered compounds
@compounds = uris.collect{|uri| Compound.new(uri)}
end
@compounds
@@ -61,7 +61,7 @@ module OpenTox
<#{RDF::OT.value}> ?value .
?f <#{RDF::OLO.index}> ?fidx.
} ORDER BY ?fidx ?cidx"
- RestClientWrapper.get(service_uri,{:query => sparql},{:accept => "text/uri-list", :subjectid => @subjectid}).split("\n").each do |row|
+ RestClientWrapper.get(service_uri,{:query => sparql},{:accept => "text/uri-list"}).split("\n").each do |row|
r,c,v = row.split("\t")
@data_entries[r.to_i] ||= []
# adjust value class depending on feature type, StringFeature takes precedence over NumericFeature
@@ -135,7 +135,7 @@ module OpenTox
# @param filename [String]
# @return [String] dataset uri
def upload filename, wait=true
- uri = RestClientWrapper.put(@uri, {:file => File.new(filename)}, {:subjectid => @subjectid})
+ uri = RestClientWrapper.put(@uri, {:file => File.new(filename)})
wait_for_task uri if URI.task?(uri) and wait
compounds true
features true