new structure, adjusted yard doc, new routes for validation

1 files changed, 61 insertions, 0 deletions

diff --git a/lib/compound.rb b/lib/compound.rb
new file mode 100644
index 0000000..fc4ec55
--- /dev/null
+++ b/lib/compound.rb
@@ -0,0 +1,61 @@
+# Get a list of a single or all descriptors
+# @param [Header] Accept one of text/plain, application/json
+# @param [Path] Descriptor name (e.G.: Openbabel.HBA1)
+# @return [text/plain, application/json] list of all prediction models
+get "/compound/descriptor/?:descriptor?" do
+  case @accept
+  when "application/json"
+    return "#{JSON.pretty_generate OpenTox::PhysChem::DESCRIPTORS} "  unless params[:descriptor]
+    return {params[:descriptor] => OpenTox::PhysChem::DESCRIPTORS[params[:descriptor]]}.to_json
+  else
+    return OpenTox::PhysChem::DESCRIPTORS.collect{|k, v| "#{k}: #{v}\n"} unless params[:descriptor]
+    return OpenTox::PhysChem::DESCRIPTORS[params[:descriptor]]
+  end
+end
+
+post "/compound/descriptor/?" do
+  bad_request_error "Missing Parameter " unless (params[:identifier] or params[:file]) and params[:descriptor]
+  descriptor = params['descriptor'].split(',')
+  if params[:file]
+    data = OpenTox::Dataset.from_csv_file params[:file][:tempfile]
+  else
+    data = OpenTox::Compound.from_smiles params[:identifier]
+  end
+  d = Algorithm::Descriptor.physchem data, descriptor
+  csv = d.to_csv
+  csv = "SMILES,#{params[:descriptor]}\n#{params[:identifier]},#{csv}" if params[:identifier]
+  case @accept
+  when "application/csv"
+    return csv
+  when "application/json"
+    lines = CSV.parse(csv)
+    keys = lines.delete lines.first
+    data = lines.collect{|values|Hash[keys.zip(values)]}
+    return JSON.pretty_generate(data)
+  end
+end
+
+get %r{/compound/(.+)} do |inchi|
+  bad_request_error "Input parameter #{inchi} is not an InChI" unless inchi.match(/^InChI=/)
+  compound = OpenTox::Compound.from_inchi URI.unescape(inchi)
+  response['Content-Type'] = @accept
+  case @accept
+  when "application/json"
+    return JSON.pretty_generate JSON.parse(compound.to_json)
+  when "chemical/x-daylight-smiles"
+    return compound.smiles
+  when "chemical/x-inchi"
+    return compound.inchi
+  when "chemical/x-mdl-sdfile"
+    return compound.sdf
+  when "chemical/x-mdl-molfile"
+  when "image/png"
+    return compound.png
+  when "image/svg+xml"
+    return compound.svg
+  when "text/plain"
+    return "#{compound.names}\n"
+  else
+    return compound.inspect
+  end
+end
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