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Merge branch 'maint-rel-1.6' of https://github.com/vivo-project/VIVO into maint-rel-1.6

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This commit is contained in:
hudajkhan 2013-11-01 10:22:00 -04:00
commit c1c7a5ab31
10 changed files with 132 additions and 26 deletions
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2
productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-3.sparql
View file

@ -7,7 +7,7 @@ PREFIX owl: <http://www.w3.org/2002/07/owl#>
CONSTRUCT {
?s arg:ARG_2000028 _:vcard .
_:vcard arg:ARG_2000029 ?s .
_:vcard a v:Individual .
_:vcard a v:Kind .
} WHERE {
?s vivo:webpage ?webpage
FILTER NOT EXISTS { ?s a foaf:Agent }

12
rdf/tbox/filegraph/classes-additional.owl
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@ -194,12 +194,6 @@
<owl:allValuesFrom rdf:resource="http://www.w3.org/2000/01/rdf-schema#Literal"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/ontology/bibo/numPages"/>
<owl:allValuesFrom rdf:resource="http://www.w3.org/2000/01/rdf-schema#Literal"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://vivoweb.org/ontology/core#publisher"/>
@ -313,6 +307,12 @@
<owl:allValuesFrom rdf:resource="http://purl.org/ontology/bibo/DocumentPart"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.org/ontology/bibo/numPages"/>
<owl:allValuesFrom rdf:resource="http://www.w3.org/2000/01/rdf-schema#Literal"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>

13
rdf/tbox/filegraph/object-properties3.owl
View file

@ -213,7 +213,8 @@
<!-- http://purl.org/ontology/bibo/reproducedIn -->
<owl:ObjectProperty rdf:about="http://purl.org/ontology/bibo/reproducedIn">
<rdfs:range rdf:resource="http://purl.org/ontology/bibo/Document"/>
<rdfs:domain rdf:resource="http://purl.org/ontology/bibo/Document"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
</owl:ObjectProperty>
@ -447,9 +448,19 @@
<owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/core#hasSubjectArea">
<rdfs:subPropertyOf rdf:resource="http://vivoweb.org/ontology/core#hasAssociatedConcept"/>
<owl:inverseOf rdf:resource="http://vivoweb.org/ontology/core#subjectAreaOf"/>
</owl:ObjectProperty>
<!-- http://vivoweb.org/ontology/core#hasSubjectArea -->
<owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/core#subjectAreaOf">
<rdfs:subPropertyOf rdf:resource="http://vivoweb.org/ontology/core#conceptAssociatedWith"/>
</owl:ObjectProperty>
<!-- http://vivoweb.org/ontology/core#hasSuccessorOrganization -->

17
rdf/tbox/firsttime/initialTBoxAnnotations.n3
View file

@ -583,6 +583,23 @@ vivo:researchAreaOf
vitro:selectFromExistingAnnot
"true"^^xsd:boolean .
vivo:subjectAreaOf
rdfs:label "subject area of"@en-US ;
vitro:displayLimitAnnot
"5"^^xsd:int ;
vitro:displayRankAnnot
"10"^^xsd:int ;
vitro:hiddenFromDisplayBelowRoleLevelAnnot
<http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
vitro:inPropertyGroupAnnot
<http://vivoweb.org/ontology#vitroPropertyGroupoverview> ;
vitro:offerCreateNewOptionAnnot
"true"^^xsd:boolean ;
vitro:prohibitedFromUpdateBelowRoleLevelAnnot
<http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
vitro:selectFromExistingAnnot
"true"^^xsd:boolean .
geo:populationTotal
rdfs:label "total population"@en-US ;
vitro:hiddenFromDisplayBelowRoleLevelAnnot

7
utilities/ISF-transition/obsoleteUris/doit2 Executable file
View file

@ -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

12
utilities/ISF-transition/obsoleteUris/event.rb
View file

@ -5,10 +5,16 @@ 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()
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

28
utilities/ISF-transition/obsoleteUris/known_exceptions.rb
View file

@ -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)

2
utilities/ISF-transition/obsoleteUris/obsoleteUriChecker.rb
View file

@ -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

17
utilities/ISF-transition/obsoleteUris/report.rb
View file

@ -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

46
utilities/ISF-transition/obsoleteUris/vivo_known_exceptions_2.txt Normal file
View file

@ -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