From 3a11ba2918795821600b7113d0758415718d263a Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 11 Jun 2018 12:46:06 +0200
Subject: combine gui with rest

---
 lib/compound.rb | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 lib/compound.rb

(limited to 'lib/compound.rb')

diff --git a/lib/compound.rb b/lib/compound.rb
new file mode 100644
index 0000000..01ba036
--- /dev/null
+++ b/lib/compound.rb
@@ -0,0 +1,64 @@
+# Get a list of a single or all descriptors
+# @param [Header] Accept one of text/plain, application/json
+# @param [Path] Descriptor name or descriptor ID (e.G.: Openbabel.HBA1, 5755f8eb3cf99a00d8fedf2f)
+# @return [text/plain, application/json] list of all prediction models
+get "/compound/descriptor/?:descriptor?" do
+  case @accept
+  when "application/json"
+    return "#{JSON.pretty_generate PhysChem::DESCRIPTORS} "  unless params[:descriptor]
+    return PhysChem.find_by(:name => params[:descriptor]).to_json if PhysChem::DESCRIPTORS.include?(params[:descriptor])
+    return PhysChem.find(params[:descriptor]).to_json if PhysChem.find(params[:descriptor])
+  else
+    return PhysChem::DESCRIPTORS.collect{|k, v| "#{k}: #{v}\n"} unless params[:descriptor]
+    return PhysChem::DESCRIPTORS[params[:descriptor]] if PhysChem::DESCRIPTORS.include?(params[:descriptor])
+    return "#{PhysChem.find(params[:descriptor]).name}: #{PhysChem.find(params[:descriptor]).description}" if PhysChem.find(params[:descriptor])
+  end
+end
+
+post "/compound/descriptor/?" do
+  bad_request_error "Missing Parameter " unless params[:identifier] && params[:descriptor]
+  descriptors = params['descriptor'].split(',')
+  compound = Compound.from_smiles params[:identifier]
+  physchem_descriptors = []
+  descriptors.each do |descriptor|
+    physchem_descriptors << PhysChem.find_by(:name => descriptor)
+  end
+  result = compound.calculate_properties physchem_descriptors
+  csv = (0..result.size-1).collect{|i| "\"#{physchem_descriptors[i].name}\",#{result[i]}"}.join("\n")
+  csv = "SMILES,\"#{params[:identifier]}\"\n#{csv}" if params[:identifier]
+  case @accept
+  when "text/csv","application/csv"
+    return csv
+  when "application/json"
+    result_hash = (0..result.size-1).collect{|i| {"#{physchem_descriptors[i].name}" => "#{result[i]}"}}
+    data = {"compound" => {"SMILES" => "#{params[:identifier]}"}}
+    data["compound"]["InChI"] = "#{compound.inchi}" if compound.inchi
+    data["compound"]["results"] = result_hash
+    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 = 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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