Maven migration (first draft)

legacy/utilities/ISF-transition/obsoleteUris/directory_walker.rb

@@ -0,0 +1,66 @@
+require 'find'
+
+class DirectoryWalker
+  # ------------------------------------------------------------------------------------
+  private
+  # ------------------------------------------------------------------------------------
+
+  def start_walking()
+    Find.find(@directory_root) do |path|
+      if FileTest.directory?(path)
+        if File.basename(path).start_with?(".")
+          Find.prune       # Don't look any further into this directory.
+        elsif @known_exceptions.skip?(path)
+          Find.prune
+        else
+          next
+        end
+      elsif @known_exceptions.skip?(path)
+        Find.prune
+      else
+        scan_file(path)
+      end
+    end
+  end
+  
+  def scan_file(path)
+    @report.register_file(path)
+    lines = File.readlines(path)
+    lines.each_index do |index|
+      line_number = index + 1
+      line = lines[index].strip
+      scan_line(path, line_number, line) unless @known_exceptions.skip?(path, line_number)
+    end
+  end
+  
+  def scan_line(path, line_number, line)
+    @obsolete_uris.uris.each do |uri|
+#     next if @known_exceptions.skip?(path, line_number, uri)
+      @report.add_event(Event.new(path, line_number, line, uri)) if line =~ Regexp.new("\\b#{Regexp.quote(uri)}\\b") 
+    end
+    if @complete
+      @obsolete_uris.localnames.each do |localname|
+        term = ":#{localname}"
+#       next if @known_exceptions.skip?(path, line_number, term)
+        @report.add_event(Event.new(path, line_number, line, term)) if line =~ Regexp.new("#{Regexp.quote(term)}\\b") 
+      end
+    end
+  end
+
+  # ------------------------------------------------------------------------------------
+  public
+  # ------------------------------------------------------------------------------------
+
+  def initialize(directory_root, obsolete_uris, known_exceptions, report, complete)
+  	@directory_root = File.expand_path(directory_root)
+  	@obsolete_uris = obsolete_uris
+  	@known_exceptions = known_exceptions
+  	@report = report
+  	@complete = complete
+  end
+  
+  def walk()
+    start_walking()
+  end
+  
+end

legacy/utilities/ISF-transition/obsoleteUris/doit

@@ -0,0 +1,7 @@
+ruby obsoleteUriChecker.rb /Users/jeb228/git/VIVO  \
+   ../../../productMods/WEB-INF/ontologies/update/diff.tab.txt \
+   vivo_known_exceptions.txt complete > scan_VIVO_maint_branch
+ruby obsoleteUriChecker.rb /Users/jeb228/git/Vitro  \
+   ../../../productMods/WEB-INF/ontologies/update/diff.tab.txt \
+   vivo_known_exceptions.txt complete > scan_Vitro_maint_branch
+

legacy/utilities/ISF-transition/obsoleteUris/doit_old

@@ -0,0 +1,2 @@
+ruby obsoleteUriChecker.rb /Users/jeb228/Documents/Releases/VIVO\ 1.6/vivo-rel-1.6-rc1  ../../../productMods/WEB-INF/ontologies/update/diff.tab.txt vivo_known_exceptions.txt complete
+

legacy/utilities/ISF-transition/obsoleteUris/event.rb

@@ -0,0 +1,37 @@
+class Event
+  attr_reader :path
+  attr_reader :line_number
+  attr_reader :line
+  attr_reader :string
+  attr_reader :is_localname
+  
+  require 'pathname'
+
+  # ------------------------------------------------------------------------------------
+  private
+  # ------------------------------------------------------------------------------------
+  
+  def relativize(root, path)
+    Pathname.new(path).relative_path_from(Pathname.new(root)).to_s
+  end
+
+  # ------------------------------------------------------------------------------------
+  public
+  # ------------------------------------------------------------------------------------
+
+  def initialize(path, line_number, line, string)
+    @path = path
+    @line_number = line_number
+    @line = line
+    @string = string
+    @is_localname = string[0] == ?:
+  end
+  
+  def to_s(directory_root = nil)
+    if directory_root
+      "#{relativize(directory_root, @path)} \n   #{@line_number} #{@line} \n   #{@string} #{@is_localname ? "Localname" : "URI"}"
+    else
+      "#{@path} \n   #{@line_number} #{@line} \n   #{@string} #{@is_localname ? "Localname" : "URI"}"
+    end
+  end
+end

legacy/utilities/ISF-transition/obsoleteUris/known_exceptions.rb

@@ -0,0 +1,101 @@
+require 'pathname'
+
+class KnownExceptionsError < StandardError; end
+
+class GlobSkipper
+  def initialize(root_path, glob)
+    @root_path = root_path
+    @glob = glob
+  end
+  
+  def relativize(path)
+    Pathname.new(path).relative_path_from(Pathname.new(@root_path)).to_s
+  end
+
+  def skip?(path, line, uri)
+    return File.fnmatch(@glob, relativize(path))
+  end
+end
+
+class ExtensionSkipper
+  def initialize(extension)
+    @extension = extension
+  end
+
+  def skip?(path, line, uri)
+    return File.extname(path) == @extension
+  end
+end 
+
+class PathSkipper
+  def initialize(root_path, relative_path)
+    @root_path = root_path
+    @absolute_path = File.expand_path(relative_path, @root_path)
+  end
+  
+  def skip?(path, line, uri)
+    return @absolute_path == File.expand_path(path, @root_path)
+  end
+end
+
+class LineSkipper
+  def initialize(root_path, relative_path, line_number)
+    @inner = PathSkipper.new(root_path, relative_path)
+    @line_number = line_number
+  end
+  
+  def skip?(path, line, uri)
+    return @inner.skip?(path, line, uri) && line == @line_number
+  end
+end
+
+class KnownExceptions
+  # ------------------------------------------------------------------------------------
+  private
+  # ------------------------------------------------------------------------------------
+  
+  def parse_file(file)
+    skippers = []
+    File.readlines(file).each do |line|
+      # ignore blank lines, and lines starting with '#' or '!'.
+      line.strip!
+      next if line.length == 0 || line[0..0] == '#' || line[0] == ?!
+
+#      if line =~ /^\.[^\/]*$/
+#        skippers << ExtensionSkipper.new(line)
+      if line =~ /^(\S+)\s*$/
+#        skippers << PathSkipper.new(@root_path, $1)
+        skippers << GlobSkipper.new(@root_path, $1)
+      elsif line =~ /^(\S+)\s*(\d+)\s*$/
+        skippers << LineSkipper.new(@root_path, $1, $2.to_i)
+      else
+        raise "BOGUS line in known_exceptions file: '#{line}'"
+      end
+    end
+    skippers
+  end
+  
+  # ------------------------------------------------------------------------------------
+  public
+  # ------------------------------------------------------------------------------------
+
+  def initialize(root_path, file)
+    @root_path = File.expand_path(root_path)
+    @skippers = parse_file(file)
+  end
+  
+  def skip?(file, line_number = -1, string = "@!#IMPOSSIBLE#!@")
+    @skippers.each() do |skipper|
+      if line_number == -1
+        next if skipper.is_a?(LineSkipper)
+      else
+        next if skipper.is_a?(ExtensionSkipper) || skipper.is_a?(PathSkipper) || skipper.is_a?(GlobSkipper)
+      end
+
+      if skipper.skip?(file, line_number, string)
+        return true
+      end
+    end
+    false
+  end
+end

legacy/utilities/ISF-transition/obsoleteUris/obsoleteUriChecker.rb

@@ -0,0 +1,120 @@
+=begin
+--------------------------------------------------------------------------------
+
+A utility that scans the code base for the presence of URIs that were made 
+obsolete by the ISF transition.
+
+Accept a file of obsolete URIs.
+	Blank lines or lines beginning with '#' are comments. 
+	Each non-comment line contains an obsolete URI.
+
+Accept a file of known exceptions.
+	Blank lines or lines beginning with '#' are comments.
+	Each non-comment line is in one of these forms:
+		.xxx - denotes an extension that is exempt from scanning
+		[filepath] - denotes a path, relative to the codebase root, of a 
+				file that should not be scanned.
+		[filepath] [line number] - denotes a particular line in a file for
+				which no error should be reported. 
+		[filepath] [line number] [uri] - denotes a particular line in a file
+				on which the given uri will not be reported.
+	
+The command line will look like this:
+	ruby obsoleteUriChecker.rb <directory_root> <obsolete_uri_file> <known_exceptions_file> [complete]
+Where:
+	directory_root - the path to the top if the directory tree we are scanning
+	obsolete_uri_file - the path to the file that lists the obsolete URIs
+	known_exceptions_file - the path to the file that lists the events that we should ignore
+	complete - optional parameter; if present, check for :localname as well as for the full URL.
+	 
+E.g.:
+	ruby obsoleteUriChecker.rb ../../.. ../../../productMods/WEB-INF/ontologies/update/diff.tab.txt known_exceptions.txt complete 
+
+--------------------------------------------------------------------------------
+=end
+
+$: << File.dirname(File.expand_path(__FILE__))
+require 'known_exceptions'
+require 'obsolete_uris'
+require 'report'
+require 'event'
+require 'directory_walker'
+
+class UsageError < StandardError; end
+
+class ObsoleteUriChecker
+  # ------------------------------------------------------------------------------------
+  private
+  # ------------------------------------------------------------------------------------
+
+  #
+  # Parse the arguments and complain if they don't make sense.
+  #
+  def parse_arguments(args)
+    raise UsageError, "usage is: obsoleteUriChecker.rb <directory_root> <obsolete_uri_file> <known_exceptions_file> [complete]" unless (3..4).include?(args.length)
+
+	if args[3]
+		raise UsageError, "If provided, the 4th argument must be 'complete'" unless args[3].downcase == 'complete'
+		complete = true
+	else
+		complete = false
+	end
+	
+    directory_root = args[0]
+    raise UsageError, "Directory '#{directory_root}' does not exist." unless File.exist?(directory_root)
+    raise UsageError, "Directory '#{directory_root}' is not a directory." unless File.directory?(directory_root)
+
+    obsolete_uri_file = args[1]
+    raise UsageError, "File '#{obsolete_uri_file}' does not exist." unless File.exist?(obsolete_uri_file)
+    obsolete_uris = ObsoleteUris.new(obsolete_uri_file)
+
+    known_exceptions_file = args[2]
+    raise UsageError, "File '#{known_exceptions_file}' does not exist." unless File.exist?(known_exceptions_file)
+    known_exceptions = KnownExceptions.new(directory_root, known_exceptions_file)
+
+    return directory_root, obsolete_uris, known_exceptions, complete
+  end
+  
+  # ------------------------------------------------------------------------------------
+  public
+  # ------------------------------------------------------------------------------------
+
+  def initialize(args)
+    @directory_root, @obsolete_uris, @known_exceptions, @complete = parse_arguments(args)
+    @report = Report.new(args, @directory_root) 
+  rescue UsageError => e
+    puts "\n----------------\nUsage error\n----------------\n\n#{e}\n\n----------------\n\n"
+    exit
+  rescue ObsoleteUrisError => e
+    puts "\n----------------\nObsolete Uris file is invalid\n----------------\n\n#{e}\n\n----------------\n\n"
+    exit
+  rescue KnownExceptionsError => e
+    puts "\n----------------\Known Exceptions file is invalid\n----------------\n\n#{e}\n\n----------------\n\n"
+    exit
+  end
+
+  def scan()
+    walker = DirectoryWalker.new(@directory_root, @obsolete_uris, @known_exceptions, @report, @complete)
+    walker.walk
+  end
+
+  def report()
+    @report.report()
+  end
+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__)
+  checker = ObsoleteUriChecker.new(ARGV)
+  checker.scan()
+  checker.report()
+end

legacy/utilities/ISF-transition/obsoleteUris/obsolete_uris.rb

@@ -0,0 +1,42 @@
+class ObsoleteUrisError < StandardError; end
+
+class ObsoleteUris
+  # ------------------------------------------------------------------------------------
+  private
+  # ------------------------------------------------------------------------------------
+
+  def get_localname(uri)
+    delimiter = uri.rindex(/[\/#]/)
+    return uri[delimiter+1..-1] if delimiter
+    raise "BOGUS URI in obsolete_uris file -- no localname: '#{uri}'"
+  end
+  
+  # ------------------------------------------------------------------------------------
+  public
+  # ------------------------------------------------------------------------------------
+
+  def initialize(file)
+    @uris = []
+    @localnames = []
+    File.read(file).split(/[\r\n]+/).each do |line|
+      # ignore blank lines, and lines starting with '#' or '!'.
+      line.strip!
+      next if line.length == 0 || line[0..0] == '#' || line[0] == ?!
+
+      if line =~ /^(\S+)/
+        @uris << $1
+        @localnames << get_localname($1)
+      else
+        raise "BOGUS line in obsolete_uris file: '#{line}'"
+      end
+    end
+  end
+  
+  def uris()
+    @uris
+  end
+
+  def localnames()
+    @localnames
+  end
+end

legacy/utilities/ISF-transition/obsoleteUris/report.rb

@@ -0,0 +1,78 @@
+class Report
+  # ------------------------------------------------------------------------------------
+  private
+  # ------------------------------------------------------------------------------------
+
+  def relativize(path)
+    Pathname.new(path).relative_path_from(Pathname.new(@directory_root)).to_s
+  end
+
+  def state_arguments()
+  	puts
+  	puts "-----------------------------------------------------------------"
+  	puts " directory to scan = #{@args[0]}"
+  	puts " obsolete_uris_file = #{@args[1]}"
+  	puts " known exceptions file = #{@args[2]}"
+  	puts " complete = #{!@args[3].nil?}"
+  	puts "-----------------------------------------------------------------"
+  	puts
+  end
+  
+  def file_summary()
+    puts " scanned #{@file_count} files"
+    @extensions_count.sort.each do |pair|
+      puts "    #{pair[0]}  #{pair[1]}"
+    end
+    puts "-----------------------------------------------------------------"
+    puts
+  end
+ 
+  def collate_and_list_events()
+    hash = Hash.new{|h, k| []}
+    @events.each do |event|
+      hash[event.path] = hash[event.path] << event
+    end
+    
+    hash.sort.each do |path, events|
+      puts "#{relativize(path)}"
+      events.sort{|a, b| a.line_number <=> b.line_number }.each do |e|
+        trimmed = 
+          if e.line.size <= 100
+            e.line 
+          else
+            e.line[0..97] << "..."
+          end
+        puts "   #{e.line_number} #{trimmed}"
+        puts "       #{e.is_localname ? "Localname" : "URI"} #{e.string}"
+      end
+      puts "--------------------"
+    end
+  end 
+    
+  # ------------------------------------------------------------------------------------
+  public
+  # ------------------------------------------------------------------------------------
+
+  def initialize(args, directory_root)
+  	@args = args;
+  	@directory_root = directory_root
+    @file_count = 0
+    @extensions_count = Hash.new(0)
+    @events = []
+  end
+  
+  def register_file(path)
+    @file_count += 1
+    @extensions_count[File.extname(path)] += 1
+  end
+  
+  def add_event(event)
+    @events << event
+  end
+  
+  def report()
+  	state_arguments()
+  	file_summary()
+  	collate_and_list_events()
+  end
+end

legacy/utilities/ISF-transition/obsoleteUris/vivo_known_exceptions.txt

@@ -0,0 +1,68 @@
+
+bin
+utilities/ISF-transition/obsoleteUris
+
+*.GIF
+*.as
+*.class
+*.fla
+*.gif
+*.gz
+*.ico
+*.jar
+*.jpg
+*.psd
+*.png
+*.swf
+*.war
+*.zip
+
+**/.*
+
+#
+# first_pass: no excluded files. everything was duplicated in the .bin directory, and
+#          probably in the .build directory also. Ran against the repository, so VIVO
+#          only.
+#
+#    7498   89730 2277668 first_pass.output
+#
+
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-event-1.5.owl
+productMods/WEB-INF/ontologies/update/oldAnnotations/vivo-core-1.5-annotations.rdf
+productMods/WEB-INF/ontologies/update/diff.tab.txt
+
+#
+# second_pass: excluded these nasty files. Ran against a clean distro, with VIVO and
+#          Vitro, but no .bin or .build
+#
+#    1798    5159  170092 second_pass.output
+#
+
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-foaf-1.5.owl
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-core-1.5.owl
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-bibo-1.5.owl
+productMods/WEB-INF/ontologies/update/oldVersion/scires-1.5.owl 
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcterms-1.5.owl
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcelements-1.5.owl
+
+#
+# Exclude old performance tests
+#
+utilities/LoadTesting/distros/release1.4/deploy.properties.template
+
+#
+# Exclude the migration code itself
+#
+productMods/WEB-INF/ontologies/update/**/*
+
+#
+# This is commented out.
+#
+src/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java 
+
+#
+# The URI is obsolete, but it has been replaced by another URI with the same localname.
+# http://purl.org/dc/terms/publisher	http://vivoweb.org/ontology/core#publisher
+# How to catch this?
+#
+

legacy/utilities/ISF-transition/obsoleteUris/vivo_known_exceptions_old.txt

@@ -0,0 +1,40 @@
+.GIF
+.as
+.class
+.fla
+.gif
+.gz
+.ico
+.jar
+.jpg
+.psd
+.png
+.swf
+.war
+.zip
+
+#
+# first_pass: no excluded files. everything was duplicated in the .bin directory, and
+#          probably in the .build directory also. Ran against the repository, so VIVO
+#          only.
+#
+#    7498   89730 2277668 first_pass.output
+#
+
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-event-1.5.owl
+productMods/WEB-INF/ontologies/update/oldAnnotations/vivo-core-1.5-annotations.rdf
+productMods/WEB-INF/ontologies/update/diff.tab.txt
+
+#
+# second_pass: excluded these nasty files. Ran against a clean distro, with VIVO and
+#          Vitro, but no .bin or .build
+#
+#    1798    5159  170092 second_pass.output
+#
+
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-foaf-1.5.owl
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-core-1.5.owl
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-bibo-1.5.owl
+productMods/WEB-INF/ontologies/update/oldVersion/scires-1.5.owl 
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcterms-1.5.owl
+productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcelements-1.5.owl