revision 3067 merged from trunk

example.deploy.properties

@@ -0,0 +1,146 @@
+# -----------------------------------------------------------------------------
+#
+# VIVO deployment properties
+#
+# This file is provided as example.deploy.properties.
+#
+# Save a copy of this file as deploy.properties, and edit the properties as 
+# needed for your deployment.
+#
+# -----------------------------------------------------------------------------
+
+# 
+# This namespace will be used when generating URIs for objects created in the 
+# editor. Change it to reflect your own domain. For example, Cornell's 
+# namespace is http://vivo.cornell.edu/individual/
+#
+# Note: it is essential that this namespace end with a trailing slash.
+#
+Vitro.defaultNamespace = http://vivo.mydomain.edu/individual/
+
+#
+# Where is the Vitro core directory?
+# In most deployments, this is set to ./vitro-core (It is not uncommon for this 
+# setting to point elsewhere in development environments).
+#   Examples:
+#      vitro.core.dir = ./vitro-core
+#      vitro.core.dir = ../vitro
+#      vitro.core.dir = /usr/local/vitro/trunk
+vitro.core.dir = ./vitro-core
+
+#
+# The base install directory for your Tomcat server. The VIVO application 
+# will be deployed in the /webapps directory below this base. 
+#
+tomcat.home = /usr/local/tomcat
+
+#
+# The name of the VIVO application. This will be used as the name of the
+# subdirectory within your Tomcat server's /webapps directory. It also appears
+# in the URL for the application. For example, http://my.vivo.server/vivo
+#
+webapp.name = vivo
+
+# 
+# URL of Solr context used in local VIVO search. Should consist of
+# scheme + servername + port + contextpath + "solr"
+#
+vitro.local.solr.url = http://localhost:8080/vivosolr
+
+#
+# The location where the VIVO application will store the data that it creates.
+# This includes uploaded files (usually images) and the Lucene search index.
+#
+vitro.home.directory = /usr/local/vivo/data
+
+#
+# Email parameters which VIVO can use to send mail. If these are left empty, 
+# the "Contact Us" form will be disabled and users will not be notified of
+# changes to their accounts.
+#
+email.smtpHost = smtp.my.domain.edu
+email.replyTo = vivoAdmin@my.domain.edu
+
+#
+# The basic parameters for a database connection. Change the end of the 
+# URL to reflect your database name (if it is not "vitrodb"). Change the username 
+# and password to match the authorized database user you created.
+#
+VitroConnection.DataSource.url = jdbc:mysql://localhost/vitrodb
+VitroConnection.DataSource.username = vitrodbUsername
+VitroConnection.DataSource.password = vitrodbPassword
+
+#
+# The maximum number of active connections in the database connection pool.
+# Increase this value to support a greater number of concurrent page requests.
+#
+VitroConnection.DataSource.pool.maxActive = 40
+
+#
+# The maximum number of database connections that will be allowed
+# to remain idle in the connection pool.  Default is 25%
+# of the maximum number of active connections.
+#
+VitroConnection.DataSource.pool.maxIdle = 10
+
+#
+# Parameters to change in order to use VIVO with a database other than 
+# MySQL.
+#
+VitroConnection.DataSource.dbtype = MySQL
+VitroConnection.DataSource.driver = com.mysql.jdbc.Driver
+VitroConnection.DataSource.validationQuery = SELECT 1
+
+#
+# The email address of the root user for the VIVO application. The password 
+# for this user is initially set to "rootPassword", but you will be asked to 
+# change the password the first time you log in.
+#
+rootUser.emailAddress = root@myDomain.com
+
+#
+# How is a logged-in user associated with a particular Individual? One way is 
+# for the Individual to have a property whose value is the username of the user.
+# This value should be the URI for that property.
+#
+selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
+
+#
+# If an external authentication system like Shibboleth or CUWebAuth is to be
+# used, these properties say how the login button should be labeled, and which
+# HTTP header will contain the user ID from the authentication system. If such
+# a system is not to be used, leave these commented out. Consult the 
+# installation instructions for more details. 
+#
+#externalAuth.buttonText = Log in using BearCat Shibboleth
+#externalAuth.netIdHeaderName = remote_userID 
+
+#
+# The temporal graph visualization can require extensive machine resources.
+# This can have a particularly noticable impact on memory usage if
+# - The organization tree is deep,
+# - The number of grants and publications is large.
+# VIVO release 1.2 guards against this impact by disabling the temporal graph
+# visualization unless the "visualization.temporal" flag is set to "enabled".
+#
+# visualization.temporal = enabled 
+
+#
+# The temporal graph visualization is used to compare different organizations/people
+# within an organization on parameters like number of publications or grants.
+# By default, the app will attempt to make its best guess at the top level
+# organization in your instance. If you're unhappy with this selection, uncomment out
+# the property below and set it to the URI of the organization individual you want to
+# identify as the top level organization. It will be used as the default whenever the
+# temporal graph visualization is rendered without being passed an explicit org.
+# For example, to use "Ponce School of Medicine" as the top organization:
+# visualization.topLevelOrg = http://vivo.psm.edu/individual/n2862
+#
+# visualization.topLevelOrg = http://vivo.mydomain.edu/individual/topLevelOrgURI
+
+#
+# Default type(s) for Google Refine Reconciliation Service
+# The format for this property is id, name; id1, name1; id2, name2 etc.
+# See Service Metadata from this page http://code.google.com/p/google-refine/wiki/ReconciliationServiceApi
+# for more information.
+Vitro.reconcile.defaultTypeList = http://vivoweb.org/ontology/core#Role, core:Role; http://vivoweb.org/ontology/core#AcademicDegree, core:Academic Degree; http://purl.org/NET/c4dm/event.owl#Event, event:Event; http://vivoweb.org/ontology/core#Agreement, core:Agreement; http://vivoweb.org/ontology/core#Location, core:Location; http://xmlns.com/foaf/0.1/Organization, foaf:Organization; http://xmlns.com/foaf/0.1/Person, foaf:Person; http://vivoweb.org/ontology/core#InformationResource, core:Information Resource

productMods/edit/forms/addClinicalRoleToPerson.jsp

@@ -3,8 +3,6 @@
 <jsp:include page="addRoleToPersonTwoStage.jsp">    
 	<jsp:param name="roleActivityTypeLabel" value="clinical activity" />
 	<jsp:param name="roleType" value="http://vivoweb.org/ontology/core#ClinicalRole" />
-	<jsp:param name="roleToActivityPredicate" value="http://vivoweb.org/ontology/core#roleIn" />
-    <jsp:param name="activityToRolePredicate" value="http://vivoweb.org/ontology/core#relatedRole" />
 	<jsp:param name="roleActivityType_optionsType" value="HARDCODED_LITERALS" />
 	<jsp:param name="roleActivityType_objectClassUri" value="" /> 
 	<jsp:param name="roleActivityType_literalOptions" 

productMods/edit/forms/addHeadOfRoleToPerson.jsp

@@ -3,8 +3,6 @@
 <jsp:include page="addRoleToPersonTwoStage.jsp">    
 	<jsp:param name="roleActivityTypeLabel" value="head of" />
 	<jsp:param name="roleType" value="http://vivoweb.org/ontology/core#LeaderRole" />
-	<jsp:param name="roleToActivityPredicate" value="http://vivoweb.org/ontology/core#roleIn" />
-    <jsp:param name="activityToRolePredicate" value="http://vivoweb.org/ontology/core#relatedRole" />
 	<jsp:param name="roleActivityType_optionsType" value="HARDCODED_LITERALS" />
 	<jsp:param name="roleActivityType_objectClassUri" value="" />
 	 

productMods/edit/forms/addMemberRoleToPerson.jsp

@@ -3,8 +3,6 @@
 <jsp:include page="addRoleToPersonTwoStage.jsp">    
 	<jsp:param name="roleActivityTypeLabel" value="membership" />
 	<jsp:param name="roleType" value="http://vivoweb.org/ontology/core#MemberRole" />
-	<jsp:param name="roleToActivityPredicate" value="http://vivoweb.org/ontology/core#roleIn" />
-    <jsp:param name="activityToRolePredicate" value="http://vivoweb.org/ontology/core#relatedRole" />	
 	<jsp:param name="roleActivityType_optionsType" value="VCLASSGROUP" />
 	<jsp:param name="roleActivityType_objectClassUri" value="http://vivoweb.org/ontology#vitroClassGrouporganizations" /> 
 	<jsp:param name="roleActivityType_literalOptions" value="[ 'Select one' ]" />

productMods/edit/forms/addOrganizerRoleToPerson.jsp

@@ -3,8 +3,6 @@
 <jsp:include page="addRoleToPersonTwoStage.jsp">    
 	<jsp:param name="roleActivityTypeLabel" value="organizer of" />
 	<jsp:param name="roleType" value="http://vivoweb.org/ontology/core#OrganizerRole" />	
-	<jsp:param name="roleToActivityPredicate" value="http://vivoweb.org/ontology/core#roleIn" />
-    <jsp:param name="activityToRolePredicate" value="http://vivoweb.org/ontology/core#relatedRole" />
 	<jsp:param name="roleActivityType_optionsType" value="HARDCODED_LITERALS" />
 	<jsp:param name="roleActivityType_objectClassUri" value="" /> 
 	<jsp:param name="roleActivityType_literalOptions" 

productMods/edit/forms/addOutreachRoleToPerson.jsp

@@ -3,8 +3,6 @@
 <jsp:include page="addRoleToPersonTwoStage.jsp">    
 	<jsp:param name="roleActivityTypeLabel" value="outreach & community service" />
 	<jsp:param name="roleType" value="http://vivoweb.org/ontology/core#OutreachProviderRole" />
-	<jsp:param name="roleToActivityPredicate" value="http://vivoweb.org/ontology/core#roleIn" />
-    <jsp:param name="activityToRolePredicate" value="http://vivoweb.org/ontology/core#relatedRole" />		
 	<jsp:param name="roleActivityType_optionsType" value="HARDCODED_LITERALS" />
 	<jsp:param name="roleActivityType_objectClassUri" value="" /> 
 	<jsp:param name="roleActivityType_literalOptions" 

productMods/edit/forms/addPresenterRoleToPerson.jsp

@@ -5,8 +5,6 @@
 	<jsp:param name="roleActivityTypeLabel" value="presentation" />
 	<jsp:param name="buttonLabel" value="presentation role" />
 	<jsp:param name="roleType" value="http://vivoweb.org/ontology/core#PresenterRole" />
-	<jsp:param name="roleToActivityPredicate" value="http://vivoweb.org/ontology/core#roleIn" />
-    <jsp:param name="activityToRolePredicate" value="http://vivoweb.org/ontology/core#relatedRole" />			
 	<jsp:param name="numDateFields" value="1" />
 	<jsp:param name="roleExamples" value="Moderator, Speaker, Panelist" />
 	<jsp:param name="roleActivityType_optionsType" value="HARDCODED_LITERALS" />

productMods/edit/forms/addResearcherRoleToPerson.jsp

@@ -3,8 +3,6 @@
 <jsp:include page="addRoleToPersonTwoStage.jsp">    
 	<jsp:param name="roleActivityTypeLabel" value="research activity" />
 	<jsp:param name="roleType" value="http://vivoweb.org/ontology/core#ResearcherRole" />
-	<jsp:param name="roleToActivityPredicate" value="http://vivoweb.org/ontology/core#roleIn" />
-    <jsp:param name="activityToRolePredicate" value="http://vivoweb.org/ontology/core#relatedRole" />		
 	<jsp:param name="roleActivityType_optionsType" value="HARDCODED_LITERALS" />
 	<jsp:param name="roleActivityType_objectClassUri" value="" /> 
 	<jsp:param name="roleActivityType_literalOptions" 

productMods/edit/forms/addRoleToPersonTwoStage.jsp

@@ -68,12 +68,14 @@ public static Log log = LogFactory.getLog("edu.cornell.mannlib.vitro.webapp.jsp.
 
 <%--
   These are the parameters that MUST be set of this form:
-   role type
+     role type
-   predicate inverse          
+     predicate inverse          
-   role activity type label (should be singular)
+     role activity type label (should be singular)
-   super type of role types for roleActivityType select list generation
+     super type of role types for roleActivityType select list generation
-   roleToActivityPredicate 
+     
-   activityToRolePredicate
+  These are optional parameters:
+     roleToActivityPredicate (default value is http://vivoweb.org/ontology/core#roleIn)
+     activityToRolePredicate (default value is http://vivoweb.org/ontology/core#relatedRole) 
 --%>
 
 <c:set var="roleActivityTypeLabel">${param.roleActivityTypeLabel}</c:set>
@@ -83,8 +85,8 @@ public static Log log = LogFactory.getLog("edu.cornell.mannlib.vitro.webapp.jsp.
 <c:set var="roleActivityType_objectClassUri" >${param.roleActivityType_objectClassUri}</c:set> 
 <c:set var="roleActivityType_literalOptions" >${param.roleActivityType_literalOptions}</c:set>
 <c:set var="numDateFields">${! empty param.numDateFields ? param.numDateFields : 2 }</c:set>
-<c:set var="roleToActivityPredicate" scope="request">${param.roleToActivityPredicate}</c:set>
+<c:set var="roleToActivityPredicate" scope="request">${! empty param.roleToActivityPredicate ? param.roleToActivityPredicate : "http://vivoweb.org/ontology/core#roleIn"}</c:set>
-<c:set var="activityToRolePredicate">${param.activityToRolePredicate}</c:set>
+<c:set var="activityToRolePredicate">${! empty param.activityToRolePredicate ? param.activityToRolePredicate : "http://vivoweb.org/ontology/core#relatedRole"}</c:set>
 
 <%
     VitroRequest vreq = new VitroRequest(request);

productMods/edit/forms/addServiceProviderRoleToPerson.jsp

@@ -3,8 +3,6 @@
 <jsp:include page="addRoleToPersonTwoStage.jsp">    
 	<jsp:param name="roleActivityTypeLabel" value="service to the profession" />
 	<jsp:param name="roleType" value="http://vivoweb.org/ontology/core#ServiceProviderRole" />
-	<jsp:param name="roleToActivityPredicate" value="http://vivoweb.org/ontology/core#roleIn" />
-    <jsp:param name="activityToRolePredicate" value="http://vivoweb.org/ontology/core#relatedRole" />	
 	
 	<jsp:param name="roleActivityType_optionsType" value="HARDCODED_LITERALS" />
 	<jsp:param name="roleActivityType_objectClassUri" value="" /> 	

productMods/edit/forms/addTeacherRoleToPerson.jsp

@@ -3,8 +3,6 @@
 <jsp:include page="addRoleToPersonTwoStage.jsp">    
 	<jsp:param name="roleActivityTypeLabel" value="teaching activity" />
 	<jsp:param name="roleType" value="http://vivoweb.org/ontology/core#TeacherRole" />
-	<jsp:param name="roleToActivityPredicate" value="http://vivoweb.org/ontology/core#roleIn" />
-    <jsp:param name="activityToRolePredicate" value="http://vivoweb.org/ontology/core#relatedRole" />	
 	<jsp:param name="roleExamples" value="Instructor, Facilitator, Assistant" />
 	<jsp:param name="roleActivityType_optionsType" value="HARDCODED_LITERALS" />
 	<jsp:param name="roleActivityType_objectClassUri" value="" /> 

productMods/templates/freemarker/body/individual/individual-menu.ftl

@@ -1,21 +0,0 @@
-<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
-
-<#-- Default VIVO individual profile page template (extends individual.ftl in vitro) -->
-
-<#include "individual-setup.ftl">
-
-<#assign individualProductExtension>
-    <#-- Include for any class specific template additions -->
-    ${classSpecificExtension!}
-    
-    <#include "individual-overview.ftl">
-        </section> <!-- #individual-info -->
-    </section> <!-- #individual-intro -->
-</#assign>
-
-<#include "individual-menu-vitro.ftl">
-
-${stylesheets.add('<link rel="stylesheet" href="${urls.base}/css/individual/individual-vivo.css" />')}
-
-${headScripts.add('<script type="text/javascript" src="${urls.base}/js/jquery_plugins/jquery.truncator.js"></script>')}
-${scripts.add('<script type="text/javascript" src="${urls.base}/js/individual/individualUtils.js"></script>')}

productMods/templates/freemarker/body/partials/individual/individual-menu-properties.ftl

@@ -1,40 +0,0 @@
-<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
-
-<#-- Template for property listing on individual profile page -->
-
-<#import "lib-properties.ftl" as p>
-<#list propertyGroups.all as group>
-   
-     <#assign groupName = group.getName(nameForOtherGroup)>
-    <section class="property-group" role="region">
-        <nav class="scroll-up" role="navigation">
-            <a href="#branding">
-                <img src="${urls.images}/individual/scroll-up.gif" alt="scroll to property group menus" />
-            </a>
-        </nav>
-        
-        <#-- Display the group heading --> 
-        <#if groupName?has_content>
-            <h2 id="${groupName}">${groupName?capitalize}</h2>
-        </#if>
-        
-        <#-- List the properties in the group -->
-        <#list group.properties as property>
-            <article class="property" role="article">
-                <#-- Property display name -->
-                <h3 id="${property.localName}">${property.name} <@p.addLink property editable /> <@p.verboseDisplay property /></h3>               
-                <#-- List the statements for each property -->
-                <ul class="property-list" role="list">
-                	
-                    <#-- data property -->
-                    <#if property.type == "data">
-                        <@p.dataPropertyList property editable />
-                    <#-- object property -->
-                    <#else>
-                        <@p.objectProperty property editable property.template />
-                    </#if>
-                </ul>
-            </article> <!-- end property -->
-        </#list>
-    </section> <!-- end property-group -->
-</#list>

productMods/templates/freemarker/body/partials/individual/individual-menu-vitro.ftl

@@ -1,21 +0,0 @@
-<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
-
-<#-- Default individual profile page template -->
-<#--@dumpAll /-->
-
-<#assign nameForOtherGroup = "other"> <#-- used by both individual-propertyGroupMenu.ftl and individual-properties.ftl -->
-
-<#-- Menu Ontology properties -->
-<#include "individual-menu-properties.ftl">
-
-${stylesheets.add('<link rel="stylesheet" href="${urls.base}/css/individual/individual.css" />')}
-
-${headScripts.add('<script type="text/javascript" src="${urls.base}/js/jquery_plugins/getURLParam.js"></script>',
-                  '<script type="text/javascript" src="${urls.base}/js/jquery_plugins/colorAnimations.js"></script>',
-                  '<script type="text/javascript" src="${urls.base}/js/jquery_plugins/jquery.form.js"></script>',
-                  '<script type="text/javascript" src="${urls.base}/js/jquery_plugins/qtip/jquery.qtip-1.0.0-rc3.min.js"></script>',
-                  '<script type="text/javascript" src="${urls.base}/js/tiny_mce/tiny_mce.js"></script>',
-                  '<script type="text/javascript" src="${urls.base}/js/controls.js"></script>',
-                  '<script type="text/javascript" src="${urls.base}/js/toggle.js"></script>')}
-
-${scripts.add('<script type="text/javascript" src="${urls.base}/js/imageUpload/imageUploadUtils.js"></script>')}

productMods/templates/freemarker/body/partials/individual/propStatement-hasEditReviewRole.ftl

@@ -16,7 +16,11 @@
 <#macro showRole statement>
     <#local linkedIndividual>
         <#if statement.infoResource??>
-            <a href="${profileUrl(statement.infoResource)}">${statement.infoResourceLabel!statement.infoResourceName}</a>
+            <#if statement.activity??>
+                <a href="${profileUrl(statement.infoResource)}">${statement.infoResourceLabel!statement.infoResourceName}</a> <a href="${profileUrl(statement.activity)}">${statement.activityLabel!statement.activityName}</a>
+            <#else>
+                <a href="${profileUrl(statement.infoResource)}">${statement.infoResourceLabel!statement.infoResourceName}</a>
+            </#if>
         <#elseif statement.activity??>
             <a href="${profileUrl(statement.activity)}">${statement.activityLabel!statement.activityName}</a>
         <#else>