|
- Specify a driver class name to use a database other than MySQL.
- Otherwise, leave this value unchanged.
+ Specify a driver class name to use a database other than MySQL.
+ Otherwise, leave this value unchanged.
This JAR file for this driver must be added to the the
webapp/lib directory within the vitro.core.dir specified above.
|
@@ -498,8 +497,7 @@
in order to serve Web requests quickly (the in-memory copy and the
underlying databaseare kept in synch as edits are performed).
- VIVO will
- require more memory than that allocated to Tomcat by default. With most
+ VIVO will 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.
@@ -517,16 +515,14 @@
data, 256m to 512m should be sufficient.
- If an OutOfMemoryError is
- encountered during VIVO execution, it can be remedied by increasing the
- heap parameters and restarting Tomcat.
+ If an OutOfMemoryError is encountered during VIVO execution, it can
+ be remedied by increasing the heap parameters and restarting Tomcat.
- Security limits: VIVO is a
- multithreaded web application that may require more threads than are
- permitted under your Linux installation's default configuration. Ensure
- that your installation can support the required number of threads
- by making the following edits to "/etc/security/limits.conf":
+ Security limits: VIVO is a multithreaded web application that may
+ require more threads than are permitted under your Linux installation's
+ default configuration. Ensure that your installation can support the
+ required number of threads by making the following edits to /etc/security/limits.conf:
apache hard nproc 400
@@ -534,18 +530,19 @@
VII. Start Tomcat
- Most Tomcat installations can be started by running "startup.sh" or
- "startup.bat" in Tomcat's bin directory. Point your browser to
- "http://localhost:8080/vivo/" to test the application. If Tomcat does not
- start up, or the VIVO application is not visible, check the
- catalina.out file in Tomcat's logs directory.
+ Most Tomcat installations can be started by running startup.sh
+ or startup.bat
+ in Tomcat's bin directory. Point your browser to
+ "http://localhost:8080/vivo/" to test the application. If Tomcat does not
+ start up, or the VIVO application is not visible, check the catalina.out
+ file in Tomcat's logs directory.
VIII. Log in and add RDF data
If the startup was successful, you will see a welcome message
informing you that you have successfully installed VIVO. Click the "Log in" link
- near the upper right corner. Log in with the initialAdminUser
- username you set up in Step IV. The initial password for the initialAdminUser
+ near the upper right corner. Log in with the initialAdminUser
+ username you set up in Step IV. The initial password for the initialAdminUser
account is "defaultAdmin" (without the quotes). On first login, you will be
prompted to select a new password and verify it a second time.
@@ -580,7 +577,7 @@
If you have configured your application to use the "Contact Us"
- feature in Step IV (Vitro.smtpHost), you will also need to add an email address
+ feature in Step IV (Vitro.smtpHost), you will also need to add an email address
to the VIVO application. This is the email that the contact form
submits to. It can be a list server or an individual's
email address.
@@ -588,12 +585,12 @@
Log in as a system administrator. Navigate to the
"Site Admin" table of contents (link in the right side of the header).
- Go to "Site Information" (under "Site Configuration"). In the
+ Go to "Site Information" (under "Site Configuration"). In the
"Site Information Editing Form," enter a functional email address in
the field "Contact Email Address." and submit the change.
- If you set theVitro.smtpHost
+ If you set theVitro.smtpHost
in Step IV and do NOT provide an email addressin this
step, your users will receive a java error in the interface.
@@ -610,14 +607,13 @@
Using the mod_jk connector allows for communication between Tomcat
- and the primary web server. The Quick
- Start HowTo
+ and the primary web server. The Quick Start HowTo
on the Apache site describes the minimum server configurations
for several popular web servers.
- After setting up the mod_jk connector above, you will need to
- modify the Tomcat's server.xml ([tomcat root]/conf/) to respond to
+ After setting up the mod_jk connector above, you will need to
+ modify the Tomcat's server.xml (located in [tomcat root]/conf/) to respond to
requests from Apache via the connector. Look for the
<connector> directive and add the following properties:
@@ -626,13 +622,15 @@
Note: the value for maxThreads (320) is equal to the value for MaxClients
- in the apache's "httpd.conf" file.
+ in the apache's httpd.conf
+ file.
- Locate the <Host name="localhost"...> directive and update as
+ Locate the <Host name="localhost"...>
+ directive and update as
follows:
-
+
<Host name="localhost" appBase="webapps"
DeployOnStartup="false"
unpackWARs="true" autoDeploy="false"
@@ -666,9 +664,9 @@
By default, Pellet is fed only an incomplete view of
your ontology and only certain inferences are materialized. These
- include rdf:type, rdfs:subClassOf,owl:equivalentClass, and
+ include rdf:type, rdfs:subClassOf, owl:equivalentClass, and
owl:disjointWith. This mode is typically suitable for ontologies with a
- lot of instance data. If you would like to keep the default mode,
+ lot of instance data. If you would like to keep the default mode,
skip to the next step.
@@ -679,19 +677,17 @@
Then change the name of the listener class to
PelletReasonerSetupComplete. Because "complete" reasoning can be very
- resource intensive, there is also an option to materialize nearly
+ resource intensive, there is also an option to materialize nearly
all inferences except owl:sameAs and owl:differentFrom.
- This is enabled
- by specifying PelletReasonerSetupPseudocomplete. For ontologies with
- large numbers of individuals, this mode can offer enormous performance
+ This is enabled by specifying PelletReasonerSetupPseudocomplete. For ontologies
+ with large numbers of individuals, this mode can offer enormous performance
improvements over the "complete" mode.
- Finally, a class called
- PelletReasonerSetupPseudocompleteIgnoreDataproperties is provided to
- improve performance on ontologies with large literals where data
+ Finally, a class called PelletReasonerSetupPseudocompleteIgnoreDataproperties
+ is provided to improve performance on ontologies with large literals where data
property entailments are not needed.
@@ -721,10 +717,7 @@
external authentication system.
- For VIVO, this secured page is named:
-
- /loginExternalAuthReturn
-
+ For VIVO, this secured page is named: /loginExternalAuthReturn
When your instructions call for the location of the secured page, this is the
@@ -732,40 +725,49 @@
Configuring VIVO
- To enable external authentication, VIVO requires three values in the
- deploy.properties file.
+ To enable external authentication, VIVO requires three values in the deploy.properties
+ file.
-
- The name of the HTTP header that will hold the external user’s network ID
- When a user completes the authentication process, the Apache server will
- put the user’s network ID into one of the headers of the HTTP request.
- The instructions from your institution should tell you which header is
+
The name of the HTTP header that will hold the external user's network ID.
+ When a user completes the authentication process, the Apache server will
+ put the user's network ID into one of the headers of the HTTP request.
+ The instructions from your institution should tell you which header is
used for this purpose.
- You need to tell VIVO the name of that HTTP header. Insert a line like
- this in the deploy.properties file: externalAuth.netIdHeaderName = [the header name]
- For example: externalAuth.netIdHeaderName = remote_userID
+
+ You need to tell VIVO the name of that HTTP header. Insert a line like
+ this in the deploy.properties file:
externalAuth.netIdHeaderName = [the header name]
+ For example:
+
+ externalAuth.netIdHeaderName = remote_userID
-
- The text for the Login button
- To start the authentication process, the user will click on a button in
- the VIVO login form. You need to tell VIVO what text should appear in that
- button.
- Put a line like this in the deploy.properties file:
- externalAuth.buttonText = [the text for your login button]
- For example:
externalAuth.buttonText = Log in using BearCat Shibboleth
- The VIVO login form will display a button labelled “Log in using BearCat
- Shibboleth”.
+ The text for the Login button.
+ To start the authentication process, the user will click on a button in
+ the VIVO login form. You need to tell VIVO what text should appear in that
+ button.
+
+ Put a line like this in the deploy.properties file:
+ externalAuth.buttonText = [the text for your login button]
+ For example:
+
+ externalAuth.buttonText = Log in using BearCat Shibboleth
+ The VIVO login form will display a button labelled "Log in using BearCat
+ Shibboleth".
-
- Associating a User with a profile page
- If VIVO has an account for the user, the user will be given the privileges
+
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 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.
- You need to tell VIVO what property should be used for matching. Insert
- a line like this in the deploy.properties file:selfEditing.idMatchingProperty = [the URI of the property]
+
+ In addition, 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.
+ You need to tell VIVO what property should be used for matching. Insert
+ a line like this in the deploy.properties file:
+
+ selfEditing.idMatchingProperty = [the URI of the property]
For example:selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
@@ -808,7 +810,8 @@
-
Point your browser to the home page of your website, and click the "Log in" link
- near the upper right corner. Log in with the initialAdminUser username you
+ near the upper right corner. Log in with the
initialAdminUser
+ username you
set up in Step IV. If this is your first time logging in, you will be
prompted to change the password.
@@ -824,7 +827,7 @@
the next step.
-
- Open a new web browser or browser tab to the page http://marbles.sourceforge.net/.
+ Open a new web browser or browser tab to the page http://marbles.sourceforge.net/.
In the pink box on that page enter the URI of the individual you created in the
previous step and click "open."
@@ -841,11 +844,11 @@
-
- The search box is on the right side, directly opposite the "Index" link.
- Type the word "Australia" into the box, and click on the "Search"
+ Type the word "Australia" into the search box, and click on the Search
button.You should see a page of results, with links to countries that
- border Australia, individuals that include Australia, and to
- Australia itself.
+ border Australia, individuals that include Australia, and to
+ Australia itself. To trigger the search index, you can log in as a site
+ administrator and go to "http://your-vivo-url/SearchIndex".
diff --git a/doc/install.txt b/doc/install.txt
deleted file mode 100644
index 2deeb1c3..00000000
--- a/doc/install.txt
+++ /dev/null
@@ -1,530 +0,0 @@
-
--------------------------------------------------------------------------------
-
-This document is a summary of the VIVO installation process. This and other documentation
-can be found at:
-
- http://vivoweb.org/support
-
-PLEASE NOTE!
-These instructions assume that you are performing a clean install,
-including emptying an existing database and removing a previous installation
-from the Tomcat webapps directory. Product functionality may not be as expected
-if you install over an existing installation of an earlier version.
-
-Upgrade:
-If you are going to upgrade an existing service, please consult the upgrade.txt
-in this directory.
-
-VIVO Developers:
-If you are working on the VIVO source code from Subversion, the instructions
-are slightly different. Please consult developers.txt in this directory.
-
--------------------------------------------------------------------------------
-
- * I. Install required software
- * II. Create an empty MySQL database
- * III. Download the VIVO Application Source
- * IV. Specify deployment properties
- * V. Compile and deploy
- * VI. Set Tomcat JVM parameters and security limits
- * VII. Start Tomcat
- * VIII. Log in and add RDF data
- * IX. Set the Contact Email Address (if using "Contact Us" form)
- * X. Setup Apache Tomcat Connector
- * XI. Configure Pellet Reasoner
- * XII. Using an External Authentication System with VIVO
- * XIII. Was the installation successful?
-
--------------------------------------------------------------------------------
-
-I. Install required software
-
-Before installing VIVO, make sure that the following software is installed on
-the desired machine:
-
- * Java (SE) 1.6 or higher [http://java.sun.com] (Not OpenJDK)
- * Apache Tomcat 6.x or higher [http://tomcat.apache.org]
- * Apache Ant 1.7 or higher [http://ant.apache.org]
- * MySQL 5.1 or higher [http://www.mysql.com]
-
-Be sure to setup the environment variables for "JAVA_HOME" and "ANT_HOME" and
-add the executables to your path per your operating system and installation
-directions from the software support web sites.
-
--------------------------------------------------------------------------------
-
-II. Create an empty MySQL database
-
-Decide on a database name, username, and password. Log into your MySQL server
-and create a new database in MySQL that uses UTF-8 encoding. You will need
-these values for step IV when you configure the deployment properties. At the
-MySQL command line you can create the database and user with these commands
-substituting your values for "dbname", "username", and "password". Most of the
-time, the "hostname" will equal "localhost".
-
-CREATE DATABASE dbname CHARACTER SET utf8;
-
-Grant access to a database user. For example:
-
-GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';
-
-Keep track of the database name, username, and password for Step IV.
-
--------------------------------------------------------------------------------
-
-III. Download the VIVO Application Source
-
-Download the VIVO application source as either rel-1.1.1.zip or rel-1.1.1.gz file
-and unpack it on your web server:
-
- http://vivoweb.org/download
-
--------------------------------------------------------------------------------
-
-IV. Specify deployment properties
-
-At the top level of the unpacked distribution, copy the file
-example.deploy.properties to a file named simply deploy.properties. This file
-sets several properties used in compilation and deployment.
-
-NOTE: For those installing on Windows operating system, include the windows
-drive and use the forward slash "/" and not the back slash "\" in the
-directory locations, e.g. "c:/tomcat".
-
- Default namespace: VIVO installations make their RDF resources available for harvest
- using linked data. Requests for RDF resource URIs redirect to HTML
- or RDF representations as specified by the client. To make this
- possible, VIVO's default namespace must have certain structure and
- begin with the public web address of the VIVO installation.
- For example, if the web address of a VIVO installation is
- http://vivo.example.edu/ the default namespace must be set to
- http://vivo.example.edu/individual/ in order to support linked data.
- Similarly, if VIVO is installed at http://www.example.edu/vivo the
- default namespace must be set to http://www.example.edu/vivo/individual/
- Note: The namespace must end with "individual/" (including the
- trailing slash).
-property name: Vitro.defaultNamespace
-example value: http://vivo.mydomain.edu/individual/
-
- Directory where Vitro code is located. In most deployments,
- this is set to ./vitro-core, but it commonly points elsewhere
- during development.
-property name: vitro.core.dir
-example value: ./vitro-core
-
- Directory where tomcat is installed
-property name: tomcat.home
-example value: /usr/local/tomcat
-
- Name of your VIVO application
-property name: webapp.name
-example value: vivo
-
- Directory where uploaded files will be stored. You must create
- this directory ahead of time.
-property name: upload.directory
-example value: /usr/local/vivo/data/uploads
-
- Directory where the Lucene search index will be built.
- Depending on your permissions and who Tomcat is running as,
- you may need to create this directory ahead of time.
-property name: LuceneSetup.indexDir
-example value: /usr/local/vivo/data/luceneIndex
-
- Specify an SMTP host that the form will use for sending
- e-mail (Optional). If this is left blank, the contact form
- will be hidden and disabled.
-property name: Vitro.smtpHost
-example value: smtp.servername.edu
-
- Specify the JDBC URL of your database. Change the end of the
- URL to reflect your database name (if it is not "vivo").
-property name: VitroConnection.DataSource.url
-example value: jdbc:mysql://localhost/vivo
-
- Change the username to match the authorized user you created in MySQL
-property name: VitroConnection.DataSource.username
-example value: username
-
- Change the password to match the password you created in MySQL
-property name: VitroConnection.DataSource.password
-example value: password
-
- Specify the Jena triple store technology to use. SDB is Jena's
- SPARQL database; this setting allows RDF data to scale beyond the
- limits of the JVM heap. Set to RDB to use the older Jena RDB
- store with in-memory caching.
-property name: VitroConnection.DataSource.tripleStoreType
-example value: SDB
-
- Specify the maximum number of active connections in the database
- connection pool to support the anticipated number of concurrent
- page requests. It is not necessary to adjust this value when
- using the RDB configuration.
-property name: VitroConnection.DataSource.pool.maxActive
-example value: 40
-
- Specify 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.
-property name: VitroConnection.DataSource.pool.maxIdle
-example value: 10
-
- Change the dbtype setting to use a database other than MySQL.
- Otherwise, leave this value unchanged.
- Possible values are DB2, derby, HSQLDB, H2, MySQL, Oracle,
- PostgreSQL, and SQLServer.
- Refer to http://openjena.org/wiki/SDB/Databases_Supported
- for additional information.
-property name: VitroConnection.DataSource.dbtype
-example value: MySQL
-
- Specify a driver class name to use a database other than MySQL.
- Otherwise, leave this value unchanged.
- This JAR file for this driver must be added to the the
- webapp/lib directory within the vitro.core.dir specified above.
-property name: VitroConnection.DataSource.driver
-example value: com.mysql.jdbc.Driver
-
- Change the validation query used to test database connections
- only if necessary to use a database other than MySQL.
- Otherwise, leave this value unchanged.
-property name: VitroConnection.DataSource.validationQuery
-example value: SELECT 1
-
- Specify the name of your first admin user for the VIVO application.
- This user will have an initial temporary password of 'defaultAdmin'.
- You will be prompted to create a new password on first login.
-property name: initialAdminUser
-example value: defaultAdmin
-
- The name of a property that can be used to associate an Individual
- with a user account. When a user logs in with a name that matches
- the value of this property, the user will be authorized to edit
- that Individual.
-property name: selfEditing.idMatchingProperty
-example value: http://vivo.mydomain.edu/ns#networkId
-
-NOTE: If you want to use an external authentication system like Shibboleth or
-CUWebAuth, you will need to set two additional properties in this file. See
-the section below entitled "Using an External Authentication System with VIVO".
-
- Temporal Graph Visualization is used to compare different
- organizations/people within an organization on different parameters
- like number of publications, grants. This parameter will be used
- as a default in case a URI is not provided. It will be also used
- whenever this visualization is to be rendered for top level organization.
- In absence of this parameter a SPARQL query will be fired which will
- attempt to provide a top level organization.The name of a property
- that can be used to associate an Individual with a user account.
- When a user logs in with a name that matches the value of this property,
- the user will be authorized to edit that Individual.
-property name: visualization.topLevelOrg
-example value: http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
-
-NOTE: If you want to use an external authentication system like Shibboleth or
-CUWebAuth, you will need to set two additional properties in this file. See
-the section below entitled "Using an External Authentication System with VIVO".
-
--------------------------------------------------------------------------------
-
-V. Compile and deploy
-
-At the command line, from the top level of the unpacked distribution directory,
-type:
-
-ant all
-
-to build VIVO and deploy to Tomcat's webapps directory.
-
--------------------------------------------------------------------------------
-
-VI. Set Tomcat JVM parameters and security limits
-
-Currently, VIVO copies the contents 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 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.
-
-For example:
-
-export CATALINA_OPTS="-Xms1024m -Xmx1024m -XX:MaxPermSize=64m"
-
-This sets Tomcat to allocate an initial heap of 1024 megabytes, a maximum heap
-of 1024 megabytes, and a PermGen space of 64 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.
-
-If an OutOfMemoryError is encountered during VIVO execution, it can be remedied
-by increasing the heap parameters and restarting Tomcat.
-
-Security limits: VIVO is a multithreaded web application that may require more threads than are
-permitted under your Linux installation's default configuration. Ensure that
-your installation can support the required number of threads by making the
-following edits to /etc/security/limits.conf:
-
- apache hard nproc 400
- tomcat6 hard nproc 1500
-
--------------------------------------------------------------------------------
-
-VII. Start Tomcat
-
-Most Tomcat installations can be started by running startup.sh or startup.bat
-in Tomcat's bin directory. Point your browser to http://localhost:8080/vivo/
-to test the application.
-
-If Tomcat does not start up, or the VIVO application is not visible, check the
-catalina.out file in Tomcat's logs directory.
-
--------------------------------------------------------------------------------
-
-VIII. Log in and add RDF data
-
-If the startup was successful, you will see a welcome message informing you
-that you have successfully installed VIVO. Click the "Log in" link near the
-upper right corner. Log in with the initialAdminUser username you set up in
-Step IV. The initial password for initialAdminUser is defaultAdmin. On first
-login, you will be prompted to select a new password and verify it a second
-time.
-
-After verifying your new password, you will be presented with a menu of
-editing options. Here you can create OWL classes, object 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 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. Under the "Advanced Data Tools" click "Add/Remove RDF Data."
-Note that Vitro currently works best with OWL-DL ontologies and has only limited
-support for pure RDF data. You can enter a URL pointing to the RDF data you
-wish to load or upload a file on your local machine. Ensure that the "add RDF"
-radio button is selected. You will also likely want to check "create
-classgroups automatically." Clicking the "Index" tab in the navigation bar at
-the top left 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)
-
-If you have configured your application to use the "Contact Us" feature in Step
-IV (Vitro.smtpHost), you will also need to add an email address to the VIVO
-application. This is the email that the contact form submits to. It can be a
-list server or an individual's email address.
-
-Log in as a system administrator. Navigate to the "Site Admin" table of contents
-(link in the right side of the header). Go to "Site Information" (under "Site
-Configuration"). In the "Site Information Editing Form," enter a functional
-email address in the field "Contact Email Address." and submit the change.
-
-If you set the Vitro.smtpHost in Step IV and do NOT provide an email address
-in this step, your users will receive a java error in the interface.
-
--------------------------------------------------------------------------------
-
-X. Set up Apache Tomcat Connector
-
-It is recommended that a Tomcat Connector such as mod_jk be used to ensure that
-the site address does not include the port number (e.g. 8080) and an additional
-reference to the Tomcat context name (e.g. /vivo).
-
-For example - http://example.com instead of http://example.com:8080/vivo
-
-Using the mod_jk connector allows for communication between Tomcat and the
-primary web server. The "Quick Start HowTo" on the Apache site
-http://tomcat.apache.org/connectors-doc/generic_howto/quick.html describes
-the minimum server configurations for several popular web servers.
-
-After setting up the mod_jk connector above, you will need to modify the Tomcat's
-server.xml ([tomcat root]/conf/) to respond to requests from Apache via the connector.
-
-Look for the directive and add the following properties:
-
- connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"
-
-Note: the value for maxThreads (320) is equal to the value for MaxClients in the
-httpd.conf file.
-
-Locate the directive and update as follows:
-
-
- example.com
-
-
-
-
-
--------------------------------------------------------------------------------
-
-XI. Configure Pellet Reasoner
-
-VIVO uses the Pellet engine to perform reasoning, which runs in the
-background at startup and also when the knowledge base is edited. VIVO
-continues serving pages while the reasoner continues working; when the
-reasoner finishes, the new inferences appear. Inferred statements are cached
-in a database graph so that they are available immediately when VIVO is restarted.
-
-By default, Pellet is fed only an incomplete view of your ontology and only
-certain inferences are materialized. These include rdf:type,
-rdfs:subClassOf,owl:equivalentClass, and owl:disjointWith. This mode is
-typically suitable for ontologies with a lot of instance data. If you would
-like to keep the default mode, skip to the next step.
-
-To enable "complete" OWL inference (materialize all significant entailed
-statements), open "vitro-core/webapp/config/web.xml" and search for
-PelletReasonerSetup.
-
-Then change the name of the listener class to PelletReasonerSetupComplete.
-Because "complete" reasoning can be very resource intensive, there is also an
-option to materialize nearly all inferences except owl:sameAs and
-owl:differentFrom.
-
-This is enabled by specifying PelletReasonerSetupPseudocomplete. For ontologies
-with large numbers of individuals, this mode can offer enormous performance
-improvements over the "complete" mode.
-
-Finally, a class called PelletReasonerSetupPseudocompleteIgnoreDataproperties
-is provided to improve performance on ontologies with large literals where data
-property entailments are not needed.
-
--------------------------------------------------------------------------------
-
-XII. Using an External Authentication System with VIVO
-
-VIVO can be configured to work with an external authentication system like
-Shibboleth or CUWebAuth.
-
-VIVO must be accessible only through an Apache HTTP server. The Apache server
-will be configured to invoke the external authentication system. When the user
-completes the authentication, the Apache server will pass a network ID to VIVO,
-to identify the user.
-
-If VIVO has an account for that user, the user will be logged in with the
-privileges of that account. In the absence of an account, VIVO will try to find
-a page associated with the user. If such a page is found, the user can log in
-to edit his own profile information.
-
----- Configuring the Apache server:
-
-Your institution will provide you with instructions for setting up the external
-authentication system. The Apache server must be configured to secure a page in
-VIVO. When a user reaches this secured page, the Apache server will invoke the
-external authentication system.
-
-For VIVO, this secured page is named:
- /loginExternalAuthReturn
-When your instructions call for the location of the secured page, this is the
-value you should use.
-
----- Configuring VIVO:
-
-To enable external authentication, VIVO requires three values in the
-deploy.properties file.
-
-* The name of the HTTP header that will hold the external user’s network ID
-
- When a user completes the authentication process, the Apache server will
- put the user’s network ID into one of the headers of the HTTP request.
- The instructions from your institution should tell you which header is
- used for this purpose.
-
- You need to tell VIVO the name of that HTTP header. Insert a line like
- this in the deploy.properties file:
- externalAuth.netIdHeaderName = [the header name]
- For example:
- externalAuth.netIdHeaderName = remote_userID
-
-* The text for the Login button
-
- To start the authentication process, the user will click on a button in
- the VIVO login form. You need to tell VIVO what text should appear in that
- button.
-
- Put a line like this in the deploy.properties file:
- externalAuth.buttonText = [the text for your login button]
- For example:
- externalAuth.buttonText = Log in using BearCat Shibboleth
-
- The VIVO login form will display a button labelled “Log in using BearCat
- Shibboleth”.
-
-* 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 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.
-
- You need to tell VIVO what property should be used for matching. Insert
- a line like this in the deploy.properties file:
- selfEditing.idMatchingProperty = [the URI of the property]
- For example:
- selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
-
--------------------------------------------------------------------------------
-
-XIII. Was the installation successful?
-
-If you have completed the previous steps, you have good indications that the
-installation was successful.
-
-* Step VII showed that Tomcat recognized the webapp, and that the webapp was
- able to present the initial page.
-* Step VIII verified that you can log in to the administrator account.
-
-Here is a simple test to see whether the ontology files were loaded:
-* Click on the "Index" link on the upper left, below the logo. You should see
- a "locations" section, with links for "Country" and "Geographic Location."
- The index is built in a background thread, so on your first login, you may
- see an empty index instead. Refresh the page periodically to see whether
- the index will be populated. This may take some time: with VIVO installed
- on a modest laptop computer, loading the ontology files and building the
- index took more than 5 minutes from the time that Tomcat was started.
-* Click on the "Country" link. You should see an alphabetical list of the
- countries of the world.
-
-Here is a test to see whether your system is configured to serve linked data:
-* Point your browser to the home page of your website, and click the "Log in" link
- near the upper right corner. Log in with the initialAdminUser username you
- set up in Step IV. If this is your first time logging in, you will be
- prompted to change the password.
-* After you have successfully logged in, click "site admin" in the upper right
- corner. In the drop down under "Data Input" select "Faculty Member(core)"
- and click the "Add individual of this class" button.
-* Enter the name "test individual" under the field "Individual Name," scroll to
- the bottom, and click "Create New Record." You will be taken to the "Individual
- Control Panel." Make note of the value of the field "URI" it will be used in
- the next step.
-* Open a new web browser or browser tab to the page http://marbles.sourceforge.net/.
- In the pink box on that page enter the URI of the individual you created in the
- previous step and click "open."
-* In the resulting page search for the URI of the "test individual." You should
- find it towards the bottom of the page next to a red dot followed by "redirect
- (303)." This indicates that you are successfully serving linked RDF data.
- If the URI of the "test individual" is followed by "failed (400)" you are not
- successfully serving linked data.
-
-Finally, test the search index.
-* The search box is on the right side, directly opposite the "Index" link.
- Type the word "Australia" into the box, and click on the "Search"
- button.You should see a page of results, with links to countries that
- border Australia, individuals that include Australia, and to
- Australia itself.