Merge branch 'maint-rel-1.6' into develop

build.xml

@@ -122,13 +122,16 @@
 	</target>
 
 	<!-- ================================= 
-          target: acceptance              
+          target: deployTestApp              
          ================================= -->
-	<target name="acceptance" description="--> Run the Selenium acceptance tests.">
+	<target name="deployTestApp" depends="deployProperties" description="description">
-		<ant dir="${vitro.core.dir}/utilities/testrunner" target="run" inheritall="false">
+		<property name="testApp.webapp.dir" value="${tomcat.home}/webapps/testApp" />
-			<property name="acceptance.dir" location="${basedir}/utilities/acceptance-tests" />
+		<property name="testApp.source.dir" value="utilities/acceptance-tests/testApp" />
-			<property name="acceptance.batch" value="${acceptance.batch}" />
+
-		</ant>
+		<mkdir dir="${testApp.webapp.dir}" />
+		<sync todir="${testApp.webapp.dir}" includeemptydirs="true">
+			<fileset dir="${testApp.source.dir}" />
+		</sync>
 	</target>
 
 </project>

productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/orcid.sparql

@@ -7,5 +7,6 @@ CONSTRUCT {
 } WHERE {
     ?s vivo:orcidId ?orcidString 
     FILTER(isLiteral(?orcidString))
+    FILTER (regex(str(?orcidString), "^[0-9][0-9][0-9][0-9]-[0-9][0-9][0-9][0-9]-[0-9][0-9][0-9][0-9]-[0-9][0-9][0-9]([0-9]|X)$"))
     BIND(IRI(concat("http://orcid.org/", str(?orcidString))) AS ?orcidURI)
 }

productMods/WEB-INF/ontologies/update/sparqlConstructs/deletions/orcidDel.sparql

@@ -6,4 +6,5 @@ CONSTRUCT {
 } WHERE {
     ?s vivo:orcidId ?orcidString 
     FILTER(isLiteral(?orcidString))
+    FILTER (regex(str(?orcidString), "^[0-9][0-9][0-9][0-9]-[0-9][0-9][0-9][0-9]-[0-9][0-9][0-9][0-9]-[0-9][0-9][0-9]([0-9]|X)$"))
 }

rdf/tbox/filegraph/object-properties.owl

@@ -1392,6 +1392,11 @@ there is a measurement process p that has specified output m, a measurement datu
     
 
 
+    <!-- http://vivoweb.org/ontology/core#conceptAssociatedWith -->
+
+    <owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/core#conceptAssociatedWith">
+    </owl:ObjectProperty>
+    
     <!-- http://vivoweb.org/ontology/core#hasAssociatedConcept -->
 
     <owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/core#hasAssociatedConcept">

utilities/acceptance-tests/suites/LinkedOpenData/TestLinkedOpenData.html

@@ -1,115 +0,0 @@
-<!-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
-
-<script src="js/jquery.js"></script>
-
-<script>
-function TestLOD() {
-	self = this;
-	
-	this.setup = setupButtons;
-	
-	this.uri = "lodFacultyMember";
-	
-	function setupButtons() {
-	    document.getElementById("RDFXML_button").onclick = function() {
-			requestWithAcceptHeader(self.uri, "application/rdf+xml");
-	    }
-	    document.getElementById("N3_button").onclick = function() {
-			requestWithAcceptHeader(self.uri, "text/n3");
-	    }
-	    document.getElementById("TTL_button").onclick = function() {
-			requestWithAcceptHeader(self.uri, "text/turtle");
-	    }
-	    document.getElementById("JSONLD_button").onclick = function() {
-			requestWithAcceptHeader(self.uri, "application/json");
-	    }
-	    
-	    document.getElementById("BOGUS_URI_button").onclick = function() {
-			requestWithAcceptHeader(self.uri + "XX", "application/rdf+xml");
-	    }
-	    document.getElementById("BOGUS_ACCEPT_button").onclick = function() {
-			requestWithAcceptHeader(self.uri, "image/png");
-	    }
-	    document.getElementById("BOGUS_FORMAT_button").onclick = function() {
-			requestWithFormat(self.uri, "bogus");
-	    }
-	    document.getElementById("BOGUS_EXTENSION_button").onclick = function() {
-			requestWithExtension(self.uri, "bogus");
-	    }
-
-	    document.getElementById("CLEAR_button").onclick = clearResult
-	}
-	
-	function requestWithAcceptHeader(uri, mimetype) {
-	    $.ajax({
-	        url: "individual/" + uri,
-	        headers: {Accept: mimetype}, 
-	        dataType: "text",
-	        complete: displayResult
-	    });
-	}
-	
-	function requestWithFormat(uri, format) {
-	    $.ajax({
-	        url: "individual/" + uri + "?format=" + format,
-	        dataType: "text",
-	        complete: displayResult
-	    });
-	}
-	
-	function requestWithExtension(uri, extension) {
-	    $.ajax({
-	        url: "individual/" + uri + "/" + uri + "." + extension,
-	        dataType: "text",
-	        complete: displayResult
-	    });
-	}
-	
-	function displayResult(xhr, status) {
-	    $("#responseCode").text(xhr.status);
-	   	$("#mimeType").text(getMimeType(xhr));
-	   	$("#responseText").text(xhr.responseText);
-	}
-	
-	function clearResult() {
-	    $("#responseCode").text("000");
-	   	$("#mimeType").text("No type");
-	   	$("#responseText").text("No text");
-	}
-	
-	function getMimeType(xhr) {
-		var header = xhr.getResponseHeader("Content-Type");
-		var where = header.indexOf(";");
-		if (where == -1) {
-			return header;
-		} else {
-			return header.substring(0, where);
-		}
-	}
-}
-
-$(document).ready(function() {   
-	new TestLOD().setup();	
-}); 
-</script>
-
-<h1>Test the Linked Open Data requests</h1>
-
-<h3>Try various accept headers</h3>
-<input type="submit" value="get RDFXML" id="RDFXML_button">
-<input type="submit" value="get N3" id="N3_button">
-<input type="submit" value="get TTL" id="TTL_button">
-<input type="submit" value="get JSONLD" id="JSONLD_button">
-
-<h3>Try non-existent URI with RDFXML accept header</h3>
-<input type="submit" value="get BOGUS Individual" id="BOGUS_URI_button">
-<input type="submit" value="use BOGUS Accept header" id="BOGUS_ACCEPT_button">
-<input type="submit" value="use BOGUS format" id="BOGUS_FORMAT_button">
-<input type="submit" value="use BOGUS extension" id="BOGUS_EXTENSION_button">
-
-<h3>Response data</h3>
-<input type="submit" value="CLEAR response" id="CLEAR_button">
-<div>Response code is <b><span id="responseCode">000</span></b></div>
-<div>MIME type is <b><span id="mimeType">No type</span></b></div>
-<div>Text is:</div>
-<div id="responseText" style="font-size:small;">No text</div>

utilities/acceptance-tests/suites/SparqlUpdateApi/EnableSparqlUpdateApi.n3

@@ -1,8 +1,6 @@
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix auth: <http://vitro.mannlib.cornell.edu/ns/vitro/authorization#> .
 @prefix simplePermission: <java:edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission#> .
-@prefix displayByRole: <java:edu.cornell.mannlib.vitro.webapp.auth.permissions.DisplayByRolePermission#> .
-@prefix editByRole: <java:edu.cornell.mannlib.vitro.webapp.auth.permissions.EditByRolePermission#> .
 
 auth:ADMIN 
   	auth:hasPermission simplePermission:UseSparqlUpdateApi ;    

utilities/acceptance-tests/testApp/TestLinkedOpenData.html

@@ -0,0 +1,188 @@
+<!-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
+
+<script src="js/jquery.js"></script>
+
+<script>
+function TestLOD() {
+	self = this;
+	
+	this.setup = setupButtons;
+	
+	this.uri = "lodFacultyMember";
+	
+	function setupButtons() {
+	    
+	    <!-- Extension buttons -->
+	    
+	    document.getElementById("RDFXML_EXTENSION_button").onclick = function() {
+			requestWithExtension(self.uri, "rdf");
+	    }
+	    document.getElementById("N3_EXTENSION_button").onclick = function() {
+			requestWithExtension(self.uri, "n3");
+	    }
+	    document.getElementById("TTL_EXTENSION_button").onclick = function() {
+			requestWithExtension(self.uri, "ttl");
+	    }
+	    document.getElementById("JSONLD_EXTENSION_button").onclick = function() {
+			requestWithExtension(self.uri, "jsonld");
+	    }
+	    
+	    <!-- Format buttons -->
+	    
+	    document.getElementById("RDFXML_FORMAT_button").onclick = function() {
+			requestWithFormat(self.uri, "rdfxml");
+	    }
+	    document.getElementById("N3_FORMAT_button").onclick = function() {
+			requestWithFormat(self.uri, "n3");
+	    }
+	    document.getElementById("TTL_FORMAT_button").onclick = function() {
+			requestWithFormat(self.uri, "ttl");
+	    }
+	    document.getElementById("JSONLD_FORMAT_button").onclick = function() {
+			requestWithFormat(self.uri, "jsonld");
+	    }
+	    
+	    <!-- Accept header buttons -->
+	    
+	    document.getElementById("RDFXML_HEADER_button").onclick = function() {
+			requestWithAcceptHeader(self.uri, "application/rdf+xml");
+	    }
+	    document.getElementById("N3_HEADER_button").onclick = function() {
+			requestWithAcceptHeader(self.uri, "text/n3");
+	    }
+	    document.getElementById("TTL_HEADER_button").onclick = function() {
+			requestWithAcceptHeader(self.uri, "text/turtle");
+	    }
+	    document.getElementById("JSONLD_HEADER_button").onclick = function() {
+			requestWithAcceptHeader(self.uri, "application/json");
+	    }
+	    
+	    <!-- Failure buttons -->
+	    
+	    document.getElementById("BOGUS_URI_button").onclick = function() {
+			requestWithAcceptHeader(self.uri + "XX", "application/rdf+xml");
+	    }
+	    document.getElementById("BOGUS_ACCEPT_button").onclick = function() {
+			requestWithAcceptHeader(self.uri, "image/png");
+	    }
+	    document.getElementById("BOGUS_FORMAT_button").onclick = function() {
+			requestWithFormat(self.uri, "bogus");
+	    }
+	    document.getElementById("BOGUS_EXTENSION_button").onclick = function() {
+			requestWithExtension(self.uri, "bogus");
+	    }
+
+	    document.getElementById("CLEAR_REQUEST_button").onclick = clearRequest
+	    document.getElementById("CLEAR_RESPONSE_button").onclick = clearResult
+	}
+	
+	function requestWithAcceptHeader(uri, mimetype) {
+		var parms = {
+	        url: "/vivo/individual/" + uri,
+	        headers: {Accept: mimetype}, 
+	        dataType: "text",
+	        complete: displayResult
+	    };
+	    displayRequest(parms);
+	    $.ajax(parms);
+	}
+	
+	function requestWithFormat(uri, format) {
+		var parms = {
+	        url: "/vivo/individual/" + uri + "?format=" + format,
+	        dataType: "text",
+	        complete: displayResult
+	    };
+	    displayRequest(parms);
+	    $.ajax(parms);
+	}
+	
+	function requestWithExtension(uri, extension) {
+		var parms = {
+	        url: "/vivo/individual/" + uri + "/" + uri + "." + extension,
+	        dataType: "text",
+	        complete: displayResult
+	    };
+	    displayRequest(parms);
+	    $.ajax(parms);
+	}
+
+    function displayRequest(parms) {
+        clearRequest();
+        $("#requestUrl").text(parms.url);
+        if (parms.headers) {
+            $("#acceptHeader").text(parms.headers.Accept);
+        }
+    }
+    	
+	function displayResult(xhr, status) {
+	    clearResult();
+	    $("#responseCode").text(xhr.status);
+	   	$("#mimeType").text(getMimeType(xhr));
+	   	$("#responseText").text(xhr.responseText);
+	}
+	
+	function clearRequest() {
+	    $("#requestUrl").text("No URL");
+	   	$("#acceptHeader").text("No header");
+	}
+	
+	function clearResult() {
+	    $("#responseCode").text("000");
+	   	$("#mimeType").text("No type");
+	   	$("#responseText").text("No text");
+	}
+	
+	function getMimeType(xhr) {
+		var header = xhr.getResponseHeader("Content-Type");
+		var where = header.indexOf(";");
+		if (where == -1) {
+			return header;
+		} else {
+			return header.substring(0, where);
+		}
+	}
+}
+
+$(document).ready(function() {   
+	new TestLOD().setup();	
+}); 
+</script>
+
+<h1>Test the Linked Open Data requests</h1>
+
+<h3>Request by extension</h3>
+<input type="submit" value="get RDFXML by extension" id="RDFXML_EXTENSION_button">
+<input type="submit" value="get N3 by extension" id="N3_EXTENSION_button">
+<input type="submit" value="get TTL by extension" id="TTL_EXTENSION_button">
+<input type="submit" value="get JSONLD by extension" id="JSONLD_EXTENSION_button">
+
+<h3>Request by format parameters</h3>
+<input type="submit" value="get RDFXML by format parameter" id="RDFXML_FORMAT_button">
+<input type="submit" value="get N3 by format parameter" id="N3_FORMAT_button">
+<input type="submit" value="get TTL by format parameter" id="TTL_FORMAT_button">
+<input type="submit" value="get JSONLD by format parameter" id="JSONLD_FORMAT_button">
+
+<h3>Request by accept headers</h3>
+<input type="submit" value="get RDFXML by accept header" id="RDFXML_HEADER_button">
+<input type="submit" value="get N3 by accept header" id="N3_HEADER_button">
+<input type="submit" value="get TTL by accept header" id="TTL_HEADER_button">
+<input type="submit" value="get JSONLD by accept header" id="JSONLD_HEADER_button">
+
+<h3>An assortment of failures</h3>
+<input type="submit" value="get BOGUS Individual" id="BOGUS_URI_button">
+<input type="submit" value="use BOGUS Accept header" id="BOGUS_ACCEPT_button">
+<input type="submit" value="use BOGUS format" id="BOGUS_FORMAT_button">
+<input type="submit" value="use BOGUS extension" id="BOGUS_EXTENSION_button">
+
+<h2>Request data</h2>
+<input type="submit" value="CLEAR request" id="CLEAR_REQUEST_button">
+<div>Request URL is <b><span id="requestUrl">No URL</span></b></div>
+<div>Accept header is <b><span id="acceptHeader">No header</span></b></div>
+
+<h2>Response data</h2>
+<input type="submit" value="CLEAR response" id="CLEAR_RESPONSE_button">
+<div>Response code is <b><span id="responseCode">000</span></b></div>
+<div>MIME type is <b><span id="mimeType">No type</span></b></div>
+<div>Text is:</div>
+<div><pre id="responseText" style="font-size:small;">No text</pre></div>

utilities/release1.6.1-scripts/addPublishTriplesToInitialTBoxAnnotations.rb

@@ -0,0 +1,76 @@
+=begin
+go through the lines of the file.
+
+If you find a line that matches
+vitro:hiddenFromDisplayBelowRoleLevelAnnot
+and followed by a line that matches 
+<http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
+--where "public" may be any string
+Insert 2 lines after the second one, replacing Display by Publish on the first, and duplicating the second.
+
+If you find a line that contains 
+vitro:hiddenFromDisplayBelowRoleLevelAnnot
+and does not match it, or is not followed by a line that matches 
+<http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
+Issue a warning and continue.
+
+=end
+
+FILE_PATH = "../../rdf/tbox/firsttime/initialTBoxAnnotations.n3"
+DISPLAY_URI = "vitro:hiddenFromDisplayBelowRoleLevelAnnot"
+DISPLAY_LOCALNAME = "hiddenFromDisplayBelowRoleLevelAnnot"
+
+def read_the_file()
+  @lines = File.readlines(FILE_PATH);
+end
+
+def scan_the_lines()
+  @lines.each_index do |i|
+    @line1 = @lines[i]
+    @line2 = @lines[i+1]
+    @index = i
+    if linesContainMatch()
+      replicateProperty()
+    else
+      checkForMismatch()
+    end
+  end
+end
+
+def linesContainMatch()
+  return false unless @line1.strip() == DISPLAY_URI
+  return false unless @line2
+  return false unless m = @line2.match(/<http:\/\/vitro\.mannlib\.cornell\.edu\/ns\/vitro\/role#(.*)>/)
+  @role = m[1]
+end
+
+def replicateProperty()
+  newline1 = @line1.gsub(/Display/, "Publish")
+  newline2 = @line2.gsub(/#.*>/, "##{@role}>")
+  @lines.insert(@index + 2, newline1, newline2)
+end
+
+def checkForMismatch()
+  return false unless @line1.strip() == DISPLAY_URI
+  if !@line2
+    puts "Found display property at end of file"
+    return
+  end
+  if !@line2.match(/^\s*<http:\/\/vitro\.mannlib\.cornell\.edu\/ns\/vitro\/role#(.*)>\s*;\s*$/)
+    puts "Found bogus clutter in the second line (#{@index}) '#{@line2}'"
+    return
+  end
+end
+
+def write_the_file()
+  f = File.new(FILE_PATH+"-modified", "w") 
+  @lines.each() do |line|
+    f.write(line)
+  end
+  f.close()
+end
+
+read_the_file()
+scan_the_lines()
+write_the_file()
+

utilities/release1.6.1-scripts/addPublishTriplesTovivo-tbox2.rb

@@ -0,0 +1,78 @@
+=begin
+go through the lines of the file.
+
+If you find a line that matches
+vitro:hiddenFromDisplayBelowRoleLevelAnnot
+and followed by a line that matches 
+<http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
+--where "public" may be any string
+Insert 2 lines after the second one, replacing Display by Publish on the first, and duplicating the second.
+
+If you find a line that contains 
+vitro:hiddenFromDisplayBelowRoleLevelAnnot
+and does not match it, or is not followed by a line that matches 
+<http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
+Issue a warning and continue.
+
+<http://vitro.mannlib.cornell.edu/ns/vitro/0.7#hiddenFromDisplayBelowRoleLevelAnnot>
+        <http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
+
+=end
+
+FILE_PATH = "/Users/jeb228/Documents/EclipseStuff/vivoWorkspace/vivoCornell/productMods/bjl23/ingest/weill/grants/submodels/vivo-tbox2.ttl"
+DISPLAY_URI = "<http://vitro.mannlib.cornell.edu/ns/vitro/0.7#hiddenFromDisplayBelowRoleLevelAnnot>"
+
+def read_the_file()
+  @lines = File.readlines(FILE_PATH);
+end
+
+def scan_the_lines()
+  @lines.each_index do |i|
+    @line1 = @lines[i]
+    @line2 = @lines[i+1]
+    @index = i
+    if linesContainMatch()
+      replicateProperty()
+    else
+      checkForMismatch()
+    end
+  end
+end
+
+def linesContainMatch()
+  return false unless @line1.strip() == DISPLAY_URI
+  return false unless @line2
+  return false unless m = @line2.match(/<http:\/\/vitro\.mannlib\.cornell\.edu\/ns\/vitro\/role#(.*)>/)
+  @role = m[1]
+end
+
+def replicateProperty()
+  newline1 = @line1.gsub(/Display/, "Publish")
+  newline2 = @line2.gsub(/#.*>/, "##{@role}>")
+  @lines.insert(@index + 2, newline1, newline2)
+end
+
+def checkForMismatch()
+  return false unless @line1.strip() == DISPLAY_URI
+  if !@line2
+    puts "Found display property at end of file"
+    return
+  end
+  if !@line2.match(/^\s*<http:\/\/vitro\.mannlib\.cornell\.edu\/ns\/vitro\/role#(.*)>\s*;\s*$/)
+    puts "Found bogus clutter in the second line (#{@index}) '#{@line2}'"
+    return
+  end
+end
+
+def write_the_file()
+  f = File.new(FILE_PATH+"-modified", "w") 
+  @lines.each() do |line|
+    f.write(line)
+  end
+  f.close()
+end
+
+read_the_file()
+scan_the_lines()
+write_the_file()
+