Merge branch 'develop' of https://github.com/vivo-project/VIVO into develop
This commit is contained in:
commit
ec5e81f75c
237 changed files with 8151 additions and 3172 deletions
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@ -10,6 +10,8 @@ class DirectoryWalker
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if FileTest.directory?(path)
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if File.basename(path).start_with?(".")
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Find.prune # Don't look any further into this directory.
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elsif @known_exceptions.skip?(path)
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Find.prune
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else
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next
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end
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@ -33,13 +35,13 @@ class DirectoryWalker
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def scan_line(path, line_number, line)
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@obsolete_uris.uris.each do |uri|
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next if @known_exceptions.skip?(path, line_number, uri)
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# next if @known_exceptions.skip?(path, line_number, uri)
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@report.add_event(Event.new(path, line_number, line, uri)) if line =~ Regexp.new("\\b#{Regexp.quote(uri)}\\b")
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end
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if @complete
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@obsolete_uris.localnames.each do |localname|
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term = ":#{localname}"
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next if @known_exceptions.skip?(path, line_number, term)
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# next if @known_exceptions.skip?(path, line_number, term)
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@report.add_event(Event.new(path, line_number, line, term)) if line =~ Regexp.new("#{Regexp.quote(term)}\\b")
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end
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end
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7
utilities/ISF-transition/obsoleteUris/doit
Executable file
7
utilities/ISF-transition/obsoleteUris/doit
Executable file
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@ -0,0 +1,7 @@
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ruby obsoleteUriChecker.rb /Users/jeb228/git/VIVO \
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../../../productMods/WEB-INF/ontologies/update/diff.tab.txt \
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vivo_known_exceptions.txt complete > scan_VIVO_maint_branch
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ruby obsoleteUriChecker.rb /Users/jeb228/git/Vitro \
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../../../productMods/WEB-INF/ontologies/update/diff.tab.txt \
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vivo_known_exceptions.txt complete > scan_Vitro_maint_branch
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2
utilities/ISF-transition/obsoleteUris/doit_old
Executable file
2
utilities/ISF-transition/obsoleteUris/doit_old
Executable file
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@ -0,0 +1,2 @@
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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
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@ -5,9 +5,15 @@ class Event
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attr_reader :string
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attr_reader :is_localname
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require 'pathname'
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# ------------------------------------------------------------------------------------
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private
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# ------------------------------------------------------------------------------------
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def relativize(root, path)
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Pathname.new(path).relative_path_from(Pathname.new(root)).to_s
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end
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# ------------------------------------------------------------------------------------
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public
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@ -21,7 +27,11 @@ class Event
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@is_localname = string[0] == ?:
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end
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def to_s()
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"#{@path} \n #{@line_number} #{@line} \n #{@string} #{@is_localname ? "Localname" : "URI"}"
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def to_s(directory_root = nil)
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if directory_root
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"#{relativize(directory_root, @path)} \n #{@line_number} #{@line} \n #{@string} #{@is_localname ? "Localname" : "URI"}"
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else
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"#{@path} \n #{@line_number} #{@line} \n #{@string} #{@is_localname ? "Localname" : "URI"}"
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end
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end
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end
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@ -1,5 +1,22 @@
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require 'pathname'
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class KnownExceptionsError < StandardError; end
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class GlobSkipper
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def initialize(root_path, glob)
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@root_path = root_path
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@glob = glob
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end
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def relativize(path)
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Pathname.new(path).relative_path_from(Pathname.new(@root_path)).to_s
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end
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def skip?(path, line, uri)
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return File.fnmatch(@glob, relativize(path))
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end
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end
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class ExtensionSkipper
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def initialize(extension)
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@extension = extension
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@ -44,10 +61,11 @@ class KnownExceptions
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line.strip!
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next if line.length == 0 || line[0..0] == '#' || line[0] == ?!
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if line =~ /^\.[^\/]*$/
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skippers << ExtensionSkipper.new(line)
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elsif line =~ /^(\S+)\s*$/
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skippers << PathSkipper.new(@root_path, $1)
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# if line =~ /^\.[^\/]*$/
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# skippers << ExtensionSkipper.new(line)
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if line =~ /^(\S+)\s*$/
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# skippers << PathSkipper.new(@root_path, $1)
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skippers << GlobSkipper.new(@root_path, $1)
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elsif line =~ /^(\S+)\s*(\d+)\s*$/
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skippers << LineSkipper.new(@root_path, $1, $2.to_i)
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else
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@ -71,7 +89,7 @@ class KnownExceptions
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if line_number == -1
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next if skipper.is_a?(LineSkipper)
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else
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next if skipper.is_a?(ExtensionSkipper) || skipper.is_a?(PathSkipper)
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next if skipper.is_a?(ExtensionSkipper) || skipper.is_a?(PathSkipper) || skipper.is_a?(GlobSkipper)
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end
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if skipper.skip?(file, line_number, string)
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@ -80,8 +80,8 @@ class ObsoleteUriChecker
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# ------------------------------------------------------------------------------------
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def initialize(args)
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@report = Report.new(args)
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@directory_root, @obsolete_uris, @known_exceptions, @complete = parse_arguments(args)
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@report = Report.new(args, @directory_root)
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rescue UsageError => e
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puts "\n----------------\nUsage error\n----------------\n\n#{e}\n\n----------------\n\n"
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exit
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@ -3,6 +3,10 @@ class Report
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private
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# ------------------------------------------------------------------------------------
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def relativize(path)
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Pathname.new(path).relative_path_from(Pathname.new(@directory_root)).to_s
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end
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def state_arguments()
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puts
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puts "-----------------------------------------------------------------"
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@ -29,9 +33,8 @@ class Report
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hash[event.path] = hash[event.path] << event
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end
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# puts "FLAT: #{hash.to_a.flatten}"
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hash.sort.each do |path, events|
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puts "#{path}"
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puts "#{relativize(path)}"
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events.sort{|a, b| a.line_number <=> b.line_number }.each do |e|
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trimmed =
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if e.line.size <= 100
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@ -46,18 +49,13 @@ class Report
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end
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end
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def list_events()
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@events.each do |event|
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puts "Event: #{event}"
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end
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end
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# ------------------------------------------------------------------------------------
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public
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# ------------------------------------------------------------------------------------
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def initialize(args)
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def initialize(args, directory_root)
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@args = args;
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@directory_root = directory_root
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@file_count = 0
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@extensions_count = Hash.new(0)
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@events = []
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@ -75,7 +73,6 @@ class Report
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def report()
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state_arguments()
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file_summary()
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# list_events()
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collate_and_list_events()
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end
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end
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@ -1,17 +1,23 @@
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.GIF
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.as
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.class
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.fla
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.gif
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.gz
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.ico
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.jar
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.jpg
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.psd
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.png
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.swf
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.war
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.zip
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bin
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utilities/ISF-transition/obsoleteUris
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*.GIF
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*.as
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*.class
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*.fla
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*.gif
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*.gz
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*.ico
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*.jar
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*.jpg
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*.psd
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*.png
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*.swf
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*.war
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*.zip
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**/.*
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#
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# first_pass: no excluded files. everything was duplicated in the .bin directory, and
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@ -39,3 +45,25 @@ productMods/WEB-INF/ontologies/update/oldVersion/vivo-bibo-1.5.owl
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productMods/WEB-INF/ontologies/update/oldVersion/scires-1.5.owl
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productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcterms-1.5.owl
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productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcelements-1.5.owl
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#
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# Exclude old performance tests
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#
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utilities/LoadTesting/distros/release1.4/deploy.properties.template
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#
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# Exclude the migration code itself
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#
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productMods/WEB-INF/ontologies/update/**/*
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#
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# This is commented out.
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#
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src/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java
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#
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# The URI is obsolete, but it has been replaced by another URI with the same localname.
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# http://purl.org/dc/terms/publisher http://vivoweb.org/ontology/core#publisher
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# How to catch this?
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#
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@ -0,0 +1,41 @@
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.GIF
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.as
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.class
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.fla
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.gif
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.gz
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.ico
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.jar
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.jpg
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.psd
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.png
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.swf
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.war
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.zip
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#
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# first_pass: no excluded files. everything was duplicated in the .bin directory, and
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# probably in the .build directory also. Ran against the repository, so VIVO
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# only.
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#
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# 7498 89730 2277668 first_pass.output
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#
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test/edu/cornell/mannlib/vitro/webapp/search/solr/NIHVIVO3853_DataSet1.rdf
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productMods/WEB-INF/ontologies/update/oldVersion/vivo-event-1.5.owl
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productMods/WEB-INF/ontologies/update/oldAnnotations/vivo-core-1.5-annotations.rdf
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productMods/WEB-INF/ontologies/update/diff.tab.txt
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#
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# second_pass: excluded these nasty files. Ran against a clean distro, with VIVO and
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# Vitro, but no .bin or .build
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#
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# 1798 5159 170092 second_pass.output
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#
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productMods/WEB-INF/ontologies/update/oldVersion/vivo-foaf-1.5.owl
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productMods/WEB-INF/ontologies/update/oldVersion/vivo-core-1.5.owl
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productMods/WEB-INF/ontologies/update/oldVersion/vivo-bibo-1.5.owl
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productMods/WEB-INF/ontologies/update/oldVersion/scires-1.5.owl
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productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcterms-1.5.owl
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productMods/WEB-INF/ontologies/update/oldVersion/vivo-dcelements-1.5.owl
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@ -12,11 +12,22 @@ directory, for possible inspection later.
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require File.expand_path('subscripts/common', File.dirname(__FILE__))
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require 'date'
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require "#{File.dirname(__FILE__)}/subscripts/loadParms"
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def figure_time_stamp()
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return DateTime.now.strftime("%Y-%m-%d_%H-%M-%S")
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end
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def add_read_me()
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puts "Add a comment for the README.txt file"
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comment = STDIN.gets.strip
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return if comment.empty?
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File.open('README.txt', "w") do |file|
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file.puts comment
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end
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end
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@tomcat_logs_dir = version_file('tomcatLogs')
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if (! File.directory?(@tomcat_logs_dir))
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Dir.mkdir(@tomcat_logs_dir)
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@ -29,5 +40,5 @@ end
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Dir.chdir(@this_logs_dir) do |path|
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system("cp #{@home}/tomcat/logs/* .")
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add_read_me()
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end
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|
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@ -52,9 +52,10 @@ mydomain:facultyDepartmentDG
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display:query """
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX vivo: <http://vivoweb.org/ontology/core#>
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PREFIX obo: <http://purl.obolibrary.org/obo/>
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SELECT ?deptName
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WHERE {
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?individualUri vivo:hasMemberRole ?membership .
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?individualUri obo:RO_0000053 ?membership .
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?membership vivo:roleContributesTo ?deptUri .
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?deptUri
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a vivo:AcademicDepartment ;
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|
@ -98,11 +99,11 @@ mydomain:departmentLocationDG
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display:saveToVar "locations" ;
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display:query """
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX vivo: <http://vivoweb.org/ontology/core#>
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PREFIX obo: <http://purl.obolibrary.org/obo/>
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SELECT ?label
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WHERE
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{
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?location vivo:geographicLocationOf ?individualUri ;
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?location obo:RO_0001015 ?individualUri ;
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rdfs:label ?label .
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}
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LIMIT 20
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|
@ -113,12 +114,13 @@ mydomain:departmentHeadDG
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|||
display:saveToVar "deptHead" ;
|
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display:query """
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||||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX obo: <http://purl.obolibrary.org/obo/>
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PREFIX vivo: <http://vivoweb.org/ontology/core#>
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SELECT ?label
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WHERE
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{
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?individualUri vivo:contributingRole ?role .
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?role vivo:leaderRoleOf ?head .
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||||
?role obo:RO_0000052 ?head .
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?head rdfs:label ?label .
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}
|
||||
LIMIT 1
|
||||
|
|
2
utilities/languageSupport/i18nChecker/check
Executable file
2
utilities/languageSupport/i18nChecker/check
Executable file
|
@ -0,0 +1,2 @@
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|||
ruby i18nChecker.rb '/Library/Tomcat/webapps/vivo/i18n/*.properties' complete
|
||||
ruby i18nChecker.rb '/Library/Tomcat/webapps/vivo/themes/wilma/i18n/*.properties' complete
|
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Reference in a new issue