diff --git a/rdf/tbox/filegraph/classes-additional.owl b/rdf/tbox/filegraph/classes-additional.owl index 70b15bee..4e57d6f7 100644 --- a/rdf/tbox/filegraph/classes-additional.owl +++ b/rdf/tbox/filegraph/classes-additional.owl @@ -194,12 +194,6 @@ - - - - - - @@ -313,6 +307,12 @@ + + + + + + diff --git a/rdf/tbox/filegraph/object-properties3.owl b/rdf/tbox/filegraph/object-properties3.owl index c763feae..9016bea2 100644 --- a/rdf/tbox/filegraph/object-properties3.owl +++ b/rdf/tbox/filegraph/object-properties3.owl @@ -213,7 +213,8 @@ - + + diff --git a/utilities/ISF-transition/obsoleteUris/doit2 b/utilities/ISF-transition/obsoleteUris/doit2 new file mode 100755 index 00000000..2f8a8b33 --- /dev/null +++ b/utilities/ISF-transition/obsoleteUris/doit2 @@ -0,0 +1,7 @@ +ruby obsoleteUriChecker.rb /Users/jeb228/git/VIVO \ + ../../../productMods/WEB-INF/ontologies/update/diff.tab.txt \ + vivo_known_exceptions_2.txt complete > scan_VIVO_maint_branch +ruby obsoleteUriChecker.rb /Users/jeb228/git/Vitro \ + ../../../productMods/WEB-INF/ontologies/update/diff.tab.txt \ + vivo_known_exceptions_2.txt complete > scan_Vitro_maint_branch + diff --git a/utilities/ISF-transition/obsoleteUris/event.rb b/utilities/ISF-transition/obsoleteUris/event.rb index 00f1a598..b35de06c 100644 --- a/utilities/ISF-transition/obsoleteUris/event.rb +++ b/utilities/ISF-transition/obsoleteUris/event.rb @@ -5,9 +5,15 @@ class Event 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 @@ -21,7 +27,11 @@ class Event @is_localname = string[0] == ?: end - def to_s() - "#{@path} \n #{@line_number} #{@line} \n #{@string} #{@is_localname ? "Localname" : "URI"}" + 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 diff --git a/utilities/ISF-transition/obsoleteUris/known_exceptions.rb b/utilities/ISF-transition/obsoleteUris/known_exceptions.rb index 871782ee..745b0a1e 100644 --- a/utilities/ISF-transition/obsoleteUris/known_exceptions.rb +++ b/utilities/ISF-transition/obsoleteUris/known_exceptions.rb @@ -1,5 +1,22 @@ +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 @@ -44,10 +61,11 @@ class KnownExceptions line.strip! next if line.length == 0 || line[0..0] == '#' || line[0] == ?! - if line =~ /^\.[^\/]*$/ - skippers << ExtensionSkipper.new(line) - elsif line =~ /^(\S+)\s*$/ - skippers << PathSkipper.new(@root_path, $1) +# if line =~ /^\.[^\/]*$/ +# 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 @@ -71,7 +89,7 @@ class KnownExceptions if line_number == -1 next if skipper.is_a?(LineSkipper) else - next if skipper.is_a?(ExtensionSkipper) || skipper.is_a?(PathSkipper) + next if skipper.is_a?(ExtensionSkipper) || skipper.is_a?(PathSkipper) || skipper.is_a?(GlobSkipper) end if skipper.skip?(file, line_number, string) diff --git a/utilities/ISF-transition/obsoleteUris/obsoleteUriChecker.rb b/utilities/ISF-transition/obsoleteUris/obsoleteUriChecker.rb index 27463d8b..70a87211 100644 --- a/utilities/ISF-transition/obsoleteUris/obsoleteUriChecker.rb +++ b/utilities/ISF-transition/obsoleteUris/obsoleteUriChecker.rb @@ -80,8 +80,8 @@ class ObsoleteUriChecker # ------------------------------------------------------------------------------------ def initialize(args) - @report = Report.new(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 diff --git a/utilities/ISF-transition/obsoleteUris/report.rb b/utilities/ISF-transition/obsoleteUris/report.rb index 0bdef5eb..a964422e 100644 --- a/utilities/ISF-transition/obsoleteUris/report.rb +++ b/utilities/ISF-transition/obsoleteUris/report.rb @@ -3,6 +3,10 @@ class Report private # ------------------------------------------------------------------------------------ + def relativize(path) + Pathname.new(path).relative_path_from(Pathname.new(@directory_root)).to_s + end + def state_arguments() puts puts "-----------------------------------------------------------------" @@ -29,9 +33,8 @@ class Report hash[event.path] = hash[event.path] << event end -# puts "FLAT: #{hash.to_a.flatten}" hash.sort.each do |path, events| - puts "#{path}" + puts "#{relativize(path)}" events.sort{|a, b| a.line_number <=> b.line_number }.each do |e| trimmed = if e.line.size <= 100 @@ -46,18 +49,13 @@ class Report end end - def list_events() - @events.each do |event| - puts "Event: #{event}" - end - end - # ------------------------------------------------------------------------------------ public # ------------------------------------------------------------------------------------ - def initialize(args) + def initialize(args, directory_root) @args = args; + @directory_root = directory_root @file_count = 0 @extensions_count = Hash.new(0) @events = [] @@ -75,7 +73,6 @@ class Report def report() state_arguments() file_summary() -# list_events() collate_and_list_events() end end diff --git a/utilities/ISF-transition/obsoleteUris/vivo_known_exceptions_2.txt b/utilities/ISF-transition/obsoleteUris/vivo_known_exceptions_2.txt new file mode 100644 index 00000000..8d1d4e7e --- /dev/null +++ b/utilities/ISF-transition/obsoleteUris/vivo_known_exceptions_2.txt @@ -0,0 +1,46 @@ +.* +bin + +*.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 +# + +test/edu/cornell/mannlib/vitro/webapp/search/solr/NIHVIVO3853_DataSet1.rdf +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