From a5ff12a57811fbaa116ec19c54b8a029a7630cd7 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Fri, 26 Oct 2012 10:55:43 +0200
Subject: Added ds speed doc

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 doc/dsspeed.md | 126 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 126 insertions(+)
 create mode 100644 doc/dsspeed.md

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diff --git a/doc/dsspeed.md b/doc/dsspeed.md
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+Filename: `dsspeed.pdf`  
+Description: A benchmark comparison of different dataset implementations.  
+Author: Andreas Maunz `<andreas@maunz.de>`  
+Date: 10/2012
+
+# Request per row
+
+(Old) implementation with one query for data entries **per compound**.
+
+    @compounds.each_with_index do |compound,i|
+      query = RDF::Query.new do
+        pattern [:data_entry, RDF::OLO.index, i]
+        pattern [:data_entry, RDF::OT.values, :values]
+        pattern [:values, RDF::OT.feature, :feature]
+        pattern [:feature, RDF::OLO.index, :feature_idx]
+        pattern [:values, RDF::OT.value, :value]
+      end
+      values = query.execute(@rdf).sort_by{|s| s.feature_idx}.collect do |s|
+        (numeric_features[s.feature_idx] and s.value.to_s != "") ? \
+         s.value.to_s.to_f : s.value.to_s
+      end
+      @data_entries << values.collect{|v| v == "" ? nil : v}
+    end
+
+Timings for reading a BBRC feature dataset (85 compounds, 53 features. Repeated three times, median reported):
+
+                     user     system      total        real
+    ds reading   6.640000   0.090000   6.730000 (  7.429505)
+
+
+# Single Table
+
+Now some optimized versions that retrieve entries all at once. A few variables have been renamed for clarity in the query:
+
+    query = RDF::Query.new do
+      # compound index: now a free variable
+      pattern [:data_entry, RDF::OLO.index, :cidx] 
+      pattern [:data_entry, RDF::OT.values, :vals]
+      pattern [:vals, RDF::OT.feature, :f]
+      pattern [:f, RDF::OLO.index, :fidx]
+      pattern [:vals, RDF::OT.value, :val]
+    end
+
+Also `RDF::Query::Solutions#order_by` is used instead of the generic `Enumerable#sort_by`, which may have advantages (not tested seperately).
+
+## 'Row Slicing' Version
+
+Results are sorted by compound, then by feature. The long array is sliced into rows.
+
+    @data_entries = query.execute(@rdf).order_by(:cidx, :fidx).collect { |entry| 
+      entry.val.to_s.blank? ? nil : \
+      (numeric_features[entry.fidx] ? entry.val.to_s.to_f : entry.val.to_s)
+    }.each_slice(@features.size).to_a
+
+Timings:
+
+                     user     system      total        real
+    ds reading   3.850000   0.090000   3.940000 (  4.643435)
+
+## 'Fill Table' Version
+
+A modification that avoids lookup operations where possible. Also pre-allocates `@data_entries`.
+
+    clim=(@compounds.size-1)
+    cidx=0
+    fidx=0
+    num=numeric_features[fidx]
+    @data_entries = \
+    (Array.new(@compounds.size*@features.size)).each_slice(@features.size).to_a
+    # order by feature index as to compute numeric status less frequently
+    query.execute(@rdf).order_by(:fidx, :cidx).each { |entry| 
+      val = entry.val.to_s
+      unless val.blank?
+        @data_entries[cidx][fidx] = (num ? val.to_f : val)
+      end
+      if (cidx < clim)
+        cidx+=1
+      else
+        cidx=0
+        fidx+=1
+        num=numeric_features[fidx]
+      end
+    }
+
+Timings:
+
+                     user     system      total        real
+    ds reading   3.820000   0.040000   3.860000 (  4.540800)
+
+
+# Dataset Tests
+
+Test runtimes changed as follows:
+
+Test             old     new     
+---------------- ------- ------- 
+dataset.rb       6.998s  7.406s  
+dataset_large.rb 64.230s 25.231s 
+
+Table: Runtimes
+
+
+## Conclusions
+
+Based on the results I implemented the 'Fill Table' variant.
+
+
+## Note
+
+A further modification that avoids querying compounds separately made runtimes much worse again.
+The idea was to get the compound together with each data entry:
+
+    #<RDF::Query::Solution:0x24f41cc(
+      {
+        :compound=>#<RDF::URI:0x2638c68(http://loca [...]
+        :cidx=>#<RDF::Literal::Integer:0x2639190("3 [...]
+        :data_entry=>#<RDF::Node:0x2639618(_:b1324f [...]
+        :vals=>#<RDF::Node:0x17699d0(_:b32bf4000000 [...]
+        :f=>#<RDF::URI:0x1638ed0(http://localhost:8 [...]
+        :fidx=>#<RDF::Literal::Integer:0x271c170("0 [...]
+        :val=>#<RDF::Literal::Integer:0x176879c("0" [...]
+      }
+    )>
+
+One would add compounds to `@compounds` only for the first run through column no '1'.
+
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