A utility script that will help to analyze SPARQL query timings.

utilities/performance-measurement/README.txt

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+Ruby scripts for analyzing the SPARQL queries that were written to the log by RDFServiceLogger.
+
+Run VIVO, enable logging of SPARQL queries, through the Developer panel, load the page of interest.
+Then, run the script to summarize the results.
+
+Run it like this:
+./scan_query_times.rb partitions /Users/jeb228/Development/Performance/Weill/tomcat/logs/vivo.all.log overlap unmatched
+where:
+   "partitions" is the file that defines how the timings will be broken down. Check the "partitions"
+        file in this directory for an example
+   "......vivo.all.log" is the VIVO log file to be analyzed.
+   "overlap" is the file where the queries are written to, if they match more than one criterion.
+   "unmatched" is the file where queries are written if they match no criteria.
+
+Read the comments in scan_query_times.rb for more information.
+

utilities/performance-measurement/partition.rb

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+class Criterion
+  attr_accessor :expression
+  attr_accessor :count
+  attr_accessor :total_time
+  def initialize(expr)
+    @expression = Regexp.new(expr, Regexp::MULTILINE)
+    @count = 0
+    @total_time = 0.0
+  end
+
+  def add(log_record)
+    @count += 1
+    @total_time += log_record.time
+  end
+
+  def to_s()
+    "#{self.class}: count=#{@count}, total_time=#{format("%.3f", @total_time)}, expression='#{@expression}'"
+  end
+end
+
+class QueryCriterion < Criterion
+  def test(log_record)
+    if expression.match(log_record.query)
+      add(log_record)
+      return true
+    end
+  end
+end
+
+class StackCriterion < Criterion
+  def test(log_record)
+    if expression.match(log_record.stack.join())
+      add(log_record)
+      return true
+    end
+  end
+end
+
+class WritingCriterion < Criterion
+  def initialize(expr, filename)
+    super(expr)
+    @file = File.new(filename, "w")
+  end
+
+  def add(log_record)
+    super
+    @file.write("#{@expression}\n\n--------------------------\n\n")
+    @file.write(log_record.to_s)
+    @file.write("\n--------------------------\n\n")
+  end
+end
+
+class UnmatchedCriterion < WritingCriterion
+  def initialize(filename)
+    super("UNMATCHED", filename)
+  end
+end
+
+class OverlapCriterion < WritingCriterion
+  def initialize(filename)
+    super("OVERLAP", filename)
+  end
+end
+
+class Partition
+  # ------------------------------------------------------------------------------------
+  private
+  # ------------------------------------------------------------------------------------
+  #
+  def parse_partition_file(partition_file)
+    @criteria = []
+    File.open(partition_file).each() do |line|
+      next if line.strip().empty? || line.start_with?('#')
+      if line.start_with?("QUERY ")
+        @criteria << QueryCriterion.new(line.slice(6..-1).strip)
+      elsif line.start_with?("STACK ")
+        @criteria << StackCriterion.new(line.slice(6..-1).strip)
+      else
+        raise "Invalid line in partition file: '#{line}'"
+      end
+    end
+  end
+
+  def match_against_criteria(log_record)
+    matches = 0
+    @criteria.each do |c|
+      matches += c.test(log_record) ? 1 : 0
+    end
+    if matches == 0
+      @unmatched.add(log_record)
+    elsif matches > 1
+      @overlap.add(log_record)
+    end
+  end
+
+  # ------------------------------------------------------------------------------------
+  public
+  # ------------------------------------------------------------------------------------
+
+  def initialize(partition_file, overlap_file, unmatched_file)
+    parse_partition_file(partition_file)
+    @overlap = OverlapCriterion.new(overlap_file)
+    @unmatched = UnmatchedCriterion.new(unmatched_file)
+  end
+
+  def accumulate(log_record)
+    match_against_criteria(log_record)
+  end
+
+  def report
+    puts "#{@criteria.join("\n")}\n#{@overlap}\n#{@unmatched}"
+  end
+
+end

utilities/performance-measurement/partitions

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+STACK AjaxVisualizationController
+#STACK IndividualRequestAnalysisContextImpl
+#STACK IndividualResponseBuilder
+# STACK BaseIndividualTemplateModel
+#STACK \WIndividualTemplateModel
+#STACK FileServingServlet
+#QUERY authorshipValue
+#QUERY infoResourceValue
+#QUERY editorObj
+#QUERY IAO_0000030

utilities/performance-measurement/scan_query_times.rb

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+#!/usr/bin/ruby
+=begin
+--------------------------------------------------------------------------------
+
+A utility that reads query times from a VIVO log file, and sums them based on a
+list of partitioning expressions.
+
+1) The file of partitioning expressions is parsed and stored.
+2) The log file is scanned for records from the RDFServiceLogger, which are
+   accumulated in the program storage.
+3) The partitioning expressions are tested against each log record, and matches
+   are recorded.
+4) For each partioning expression, report:
+    a) the expression
+    b) how many queries matched it
+    c) the total time spent in those queries
+5) As errors, report:
+    a) how many queries (and how much time) matched no expression. Dump a few of
+       them to the error file.
+    b) how many queries (and how much time) matched multiple expressions. Dump a
+       few of them to the error file.
+
+--------------------------------------------------------------------------------
+
+Command line: scan_query_times.rb [partition_file] [log_file] [overlap_file] [unmatched_file]
+   If the wrong number of arguments, abort.
+   If either file does not exist, abort.
+
+--------------------------------------------------------------------------------
+
+Partitioning expressions: parse the lines in the file
+   If a line is empty, ignore it.
+   If a line begins with a #, ignore it.
+   If a line begins with the word "STACK ", then the remainder of the line
+      (trimmed) is a regular expression to be matched against the stack trace of
+      each log record.
+   If a line begins with the word "QUERY ", then the remainder of the line
+      (trimmed) is a regular expression to be matched against the query text of
+      each log record.
+   Otherwise, abort.
+
+--------------------------------------------------------------------------------
+
+A log record begins like this:
+   2014-04-29 14:26:00,798 INFO  [RDFServiceLogger]    0.001 sparqlAskQuery [ASK {...
+
+   The timestamp is ignored.
+   The log leve is ignored.
+   The logging class must be "RDFServiceLogger"
+   The time is recorded.
+   The method name is ignored.
+   The remainder of the text on that line (trimmed) is recorded as the query.
+   Any subsequent lines are the stack trace.
+
+The end of the log record is a line that does not begin with whitespace.
+
+--------------------------------------------------------------------------------
+=end
+
+$: << File.dirname(File.expand_path(__FILE__))
+
+require 'partition'
+require 'scanner'
+
+class UsageError < StandardError; end
+
+#
+# Parse the arguments and complain if they don't make sense.
+#
+def parse_args(args)
+  raise UsageError, "usage is: scan_query_times.rb <partition_file> <log_file> <overlap_file> <unmatched_file>" unless (args.length == 4)
+
+  partition_file = args[0]
+  raise UsageError, "File '#{partition_file}' does not exist." unless File.exist?(partition_file)
+  log_file = args[1]
+  raise UsageError, "File '#{log_file}' does not exist." unless File.exist?(log_file)
+  overlap_file = args[2]
+  raise UsageError, "File '#{overlap_file}' does not exist." unless File.exist?(overlap_file)
+  unmatched_file = args[3]
+  raise UsageError, "File '#{unmatched_file}' does not exist." unless File.exist?(unmatched_file)
+
+  return partition_file, log_file, overlap_file, unmatched_file
+end
+
+#
+#
+# ------------------------------------------------------------------------------------
+# Standalone calling.
+#
+# Do this if this program was called from the command line. That is, if the command
+# expands to the path of this file.
+# ------------------------------------------------------------------------------------
+#
+
+if File.expand_path($0) == File.expand_path(__FILE__)
+  begin
+    partition_file, log_file, overlap_file, unmatched_file = parse_args(ARGV)
+    partition = Partition.new(partition_file, overlap_file, unmatched_file)
+    scanner = Scanner.new(partition)
+    scanner.process(log_file)
+    partition.report
+  rescue UsageError => e
+    puts "\n----------------\nUsage error\n----------------\n\n#{e}\n\n----------------\n\n"
+    exit
+  end
+end

utilities/performance-measurement/scanner.rb

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+class LogRecord
+  attr_accessor :time
+  attr_accessor :method
+  attr_accessor :query
+  attr_accessor :stack
+  def to_s
+    "LogRecord: time=#{@time}\n   query: #{@query}\n   stack - #{@stack.size} lines:\n    #{@stack.join("    ")}"
+  end
+end
+
+class LogFileParser
+  # ------------------------------------------------------------------------------------
+  private
+  # ------------------------------------------------------------------------------------
+  #
+  def get_line()
+    if @line_buffer
+      line = @line_buffer
+      @line_buffer = nil
+      return line
+    elsif @file.eof?
+      return nil
+    else
+      @lines += 1
+      return @file.readline
+    end
+  end
+
+  def unget_line(line)
+    @line_buffer = line
+  end
+
+  def parse_first_line(line)
+    match = /\[RDFServiceLogger\]\s+([0-9.]+).*\[(\w*, )?(.+)\]\s*$/.match(line)
+    return nil unless match
+
+    log_record = LogRecord.new
+    log_record.time = match[1].to_f
+    log_record.query = match[3].strip
+    log_record.stack = []
+    return log_record
+  end
+
+  def is_stack_line(line)
+    return false unless line
+    return line.start_with?(' ')
+  end
+
+  def next_record()
+    while true
+      first_line = get_line
+      return nil unless first_line
+      log_record = parse_first_line(first_line)
+      break if log_record
+    end
+
+    while true
+      stack_line = get_line
+      if is_stack_line(stack_line)
+        log_record.stack << stack_line
+      else
+        unget_line(stack_line)
+        return log_record
+      end
+    end
+  end
+
+  # ------------------------------------------------------------------------------------
+  public
+
+  # ------------------------------------------------------------------------------------
+  #
+  def parse_records()
+    @file = File.new(@log_file)
+    begin
+      while true
+        record = next_record()
+        break unless record
+        yield record
+      end
+    ensure
+      @file.close
+    end
+  end
+
+  def initialize(log_file)
+    @log_file = log_file
+    @line_buffer = nil
+    @lines = 0
+  end
+  
+  def report()
+    puts "LogFileParser: read #{@lines} lines from '#{@log_file}'"
+  end
+end
+
+class Scanner
+  # ------------------------------------------------------------------------------------
+  private
+  # ------------------------------------------------------------------------------------
+
+  # ------------------------------------------------------------------------------------
+  public
+  # ------------------------------------------------------------------------------------
+  def initialize(partition)
+    @partition = partition
+  end
+
+  def process(log_file)
+    lfp = LogFileParser.new(log_file)
+    lfp.parse_records() do | log_record |
+      @partition.accumulate(log_record)
+    end
+    lfp.report
+  end
+end