diff --git a/doc/css/doc.css b/doc/css/doc.css index 051b3e7d5..447ebb585 100644 --- a/doc/css/doc.css +++ b/doc/css/doc.css @@ -28,7 +28,7 @@ body{ margin: 0 auto; } body{ - background: #f3f3f0 url(../images/header-background.png) center 0 no-repeat; + background: #fff url(../images/header-background.gif) center 0 repeat-x; } /* h1,h2,h3,h4,h5,h6 ------> */ h1 { diff --git a/doc/images/header-background.gif b/doc/images/header-background.gif new file mode 100644 index 000000000..5d18792c8 Binary files /dev/null and b/doc/images/header-background.gif differ diff --git a/doc/install.html b/doc/install.html index fe40a69b5..5294c55d7 100644 --- a/doc/install.html +++ b/doc/install.html @@ -334,21 +334,6 @@ http://vivo.mydomain.edu/individual/ - - - Directory where Vitro code is located. In most - deployments, this is set to ./vitro-core (It is not uncommon for this - setting to point elsewhere in development environments). - - - - - vitro.core.dir - - - ./vitro-core - - Directory where tomcat is installed. @@ -654,71 +639,12 @@ remote_userID - - - The temporal graph visualization can require - extensive machine resources. This can have a particularly noticable - impact on memory usage if - - VIVO V1.3 mitigates this problem by the way of a caching - mechanism and hence we can safely set this to be enabled by default. - - - - - 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-trunk.indiana.edu/individual/topLevelOrgURI - - An absolute file path, pointing to the root directory of the Harvester utility. You must include the final slash. - - - harvester.location - - - /usr/local/vivo/harvester/ - -

V. Compile and deploy

@@ -733,12 +659,12 @@

VI. Set Tomcat JVM parameters and security limits

- Currently, VIVO copies the contents of your RDF database into + VIVO copies small sections of your RDF database into memory in order to serve Web requests quickly (the in-memory copy and the underlying database are kept in synch as edits are performed).

- VIVO will require more memory than that allocated to Tomcat by + VIVO may require more memory than that allocated to Tomcat by default. With most installations of Tomcat, the "setenv.sh" or "setenv.bat" file in Tomcat's bin directory is a convenient place to set the memory parameters. If this file does not exist in Tomcat's @@ -746,14 +672,11 @@
For example:

- 
                    export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"
+ 
                    export CATALINA_OPTS="-Xms512m -Xmx512m -XX:MaxPermSize=128m"

- This sets Tomcat to allocate an initial heap of 2048 megabytes, a - maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024 - megabytes is a minimum practical heap size for production installations - storing data for large academic institutions, and additional heap space - is preferable. For testing with small sets of data, 256m to 512m should - be sufficient. + This sets Tomcat to allocate an initial heap of 512 megabytes, a + maximum heap of 512 megabytes, and a PermGen space of 128 megs. Lower + values may suffice, especially for small test installations.

If an OutOfMemoryError is encountered during VIVO execution, it can @@ -795,8 +718,8 @@ properties, data properties, and configure the display of data. Currently, any classes you wish to make visible on your website must be part of a class group, and there are a number of visibility and display - options available for each ontology entity. VIVO comes with a core VIVO - ontology, but you may also upload other ontologies from an RDF file. + options available for each ontology entity. Vitro comes with a minimal + ontology. You will likely want to upload additional ontologies from an RDF file.

Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note @@ -810,10 +733,7 @@ Clicking the "Index" tab in the navigation bar at the top right of the page will show a simple index of the knowledge base.

-

- See more documentation for configuring VIVO, ingesting data, and - manually adding data at http://vivoweb.org/support. -

+

IX. Set the Contact Email Address (if using "Contact Us" form)

@@ -875,7 +795,28 @@ directive and update as follows:

- 
	    
			<Host name="localhost" appBase="webapps"
	        
				DeployOnStartup="false"
	        
				unpackWARs="true" autoDeploy="false"
	        
				xmlValidation="false" xmlNamespaceAware="false">
	
		
				<Alias>example.com</Alias>
		
				<Context path=""
			
					docBase="/usr/local/tomcat/webapps/vivo"
			
					reloadable="true"
			
					cookies="true" >
			
					<Manager pathname="" />
			
					<Environment type="java.lang.String" override="false" 
				
						name="path.configuration" 
				
						value="deploy.properties"
			
					/>
		
				</Context>
		
				...
+ 
              <Host name="localhost" appBase="webapps"
+                       DeployOnStartup="false"
+                       unpackWARs="true" autoDeploy="false"
+                       xmlValidation="false" xmlNamespaceAware="false">
+                   
+                   <Alias>example.com</Alias>
+                   
+                   <Context path=""
+                           docBase="/usr/local/tomcat/webapps/vivo"
+                           reloadable="true"
+                           cookies="true" >
+                   
+                       <Manager pathname="" />
+                   
+                       <Environment type="java.lang.String" override="false"
+                               name="path.configuration"
+                               value="deploy.properties"
+                       />
+                   </Context>
+                  
+                   ...
+

XI. Using an External Authentication System with VIVO

@@ -954,11 +895,7 @@

  • Associating a User with a profile page.

    - If VIVO has an account for the user, the user will be given the - privileges assigned to that account. -

    -

    - In addition, VIVO will try to associate the user with a profile + VIVO will try to associate the user with a profile page, so the user may edit his own profile data. VIVO will search the data model for a person with a property that matches the User’s network ID (the value of the property must be either a String literal or an