|
Specify a driver class name to use a database other than MySQL.
- Otherwise, leave this value unchanged.
+ 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.
|
@@ -504,8 +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.
@@ -523,16 +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
@@ -540,18 +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.
@@ -586,7 +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.
@@ -594,12 +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.
@@ -616,14 +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:
@@ -632,13 +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"
@@ -672,9 +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.
@@ -685,19 +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.
@@ -727,10 +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
@@ -738,40 +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
@@ -814,7 +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.
@@ -830,7 +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."
@@ -847,11 +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".