litvinovg/vivo
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Added <code> tags to file names, directory locations, and variables consistently (hopefully).

Browse source
This commit is contained in:
ejc12 2011-01-16 00:00:10 +00:00
parent 05fbed9b6e
commit 32af04556f
1 changed files with 101 additions and 104 deletions
Download patch file Download diff file Expand all files Collapse all files

205
doc/install.html
View file

@ -12,20 +12,14 @@
<!-- Start of content --> <!-- Start of content -->
<div id="wrapper-content" role="main"> <div id="wrapper-content" role="main">
<h1>VIVO Release 1 V1.2 Installation Guide</h1> <h1>VIVO Release 1 V1.2 Installation Guide</h1>
<p> <small>
January 28, 2011 January 28, 2011
</p> </small>
<div style="background: #EEEEEE"> <div style="background: #EEEEEE">
<b>Missing pieces and fixes</b> <b>Missing pieces and fixes</b>
<ul> <ul>
<li> <li>
SDB - any checks? (BL/SM) Add release announcemnet
</li>
<li>
Theme changes, file locations, branding issues (NC/MB)
</li>
<li>
Fix styles on file, dir, parameters name styles
</li> </li>
<li> <li>
Link to upgrade pdf online at SF Link to upgrade pdf online at SF
@ -70,7 +64,7 @@
</p> </p>
<toc> <toc>
<h3>Steps to Installation</h3> <h3>Steps to Installation</h3>
<ol> <ol class="roman1">
<li> <li>
<a href="#required_software">Install required software</a> <a href="#required_software">Install required software</a>
</li> </li>
@ -133,19 +127,20 @@
</li> </li>
</ul> </ul>
<p> <p>
Be sure to setup the environment variables for "JAVA_HOME" and "ANT_HOME" Be sure to setup the environment variables for <code JAVA_HOME</code>
and <code>ANT_HOME</code>
and add the executables to your path per your operating system and and add the executables to your path per your operating system and
installation directions from the software support web sites. installation directions from the software support web sites.
</p> </p>
<h3 id="create_database">II. Create an empty MySQL database </h3> <h3 id="create_database">II. Create an empty MySQL database </h3>
<p> <p>
Decide on a database name, username, and password. Log into your Decide on a database name, username, and password. Log into your
MySQL server and create a new database in MySQL that uses UTF-8 MySQL server and create a new database in MySQL that uses <code>UTF-8
encoding. You will need&nbsp; these values for step IV when you encoding</code>. You will need these values for Step IV when you
configure the deployment properties. At the MySQL command line you can configure the deployment properties. At the MySQL command line you can
create the database and user with these commands&nbsp; substituting create the database and user with these commands substituting
your values for "dbname", "username", and "password". Most of the time, your values for <code>dbname</code>, <code>username</code>, and <code>password</code>. Most of the time,
the "hostname" will equal "localhost". the hostname will equal <code>localhost</code>.
</p> </p>
<pre> <pre>
CREATE DATABASE dbname CHARACTER SET utf8; CREATE DATABASE dbname CHARACTER SET utf8;
@ -164,29 +159,29 @@
<br> <br>
</h3> </h3>
<p> <p>
Download the VIVO application source as either rel-1.1.1.zip or Download the VIVO application source as either <code>rel-1.2.zip</code>
rel-1.1.1.gz file and unpack it on your web or <code>rel-1.2.gz</code>
server: file and unpack it on your web server:
<br/> <br/>
<a href="http://vivoweb.org/download">http://vivoweb.org/download</a> <a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
</p> </p>
<h3 id="deploy_properties">IV. Specify deployment properties </h3> <h3 id="deploy_properties">IV. Specify deployment properties </h3>
<p> <p>
At the top level of the unpacked distribution, copy the file At the top level of the unpacked distribution, copy the file <code>example.deploy.properties</code>
"example.deploy.properties" to a file named simply "deploy.properties". to a file named simply <code>deploy.properties</code>.
This file sets several properties used in compilation and deployment. This file sets several properties used in compilation and deployment.
</p> </p>
<p> <p>
<em>Windows:</em> <em>Windows:</em>
For those installing on Windows operating system, include the For those installing on Windows operating system, include the
windows drive and use the forward slash "/" and not the back slash "\" windows drive and use the forward slash "/" and not the back slash "\"
in the directory locations, e.g. "c:/tomcat". in the directory locations, e.g. <code>c:/tomcat</code>.
</p> </p>
<p> <p>
<em>External authentication:</em> <em>External authentication:</em>
If you want to use an external authentication system like Shibboleth or If you want to use an external authentication system like Shibboleth or
CUWebAuth, you will need to set two additional properties in this file. CUWebAuth, you will need to set two additional properties in this file.
See the section below entitled "Using an External Authentication System with VIVO". See the section below entitled <a href="#external_auth">Using an External Authentication System with VIVO</a>.
</p> </p>
<table> <table>
<tr> <tr>
@ -202,14 +197,12 @@
Default namespace: VIVO installations make their RDF resources available Default namespace: VIVO installations make their RDF resources available
for harvest using linked data. Requests for RDF resource URIs redirect to HTML 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, 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 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 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 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, "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 if VIVO is installed at "http://www.example.edu/vivo" the default namespace must be
set to "http://www.example.edu/vivo/individual/" set to "http://www.example.edu/vivo/individual/" <h5>* The namespace must end with "individual/" (including the trailing slash).</h5>
<br/>
<strong>* The namespace must end with "individual/" (including the trailing slash).</strong>
</td> </td>
</tr> </tr>
<tr class="odd_row"> <tr class="odd_row">
@ -409,7 +402,7 @@
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify a driver class name to use a database other than MySQL. 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 This JAR file for this driver must be added to the the
webapp/lib directory within the vitro.core.dir specified above. webapp/lib directory within the vitro.core.dir specified above.
</td> </td>
@ -504,8 +497,7 @@
in order to serve Web requests quickly (the in-memory copy and the in order to serve Web requests quickly (the in-memory copy and the
underlying databaseare kept in synch as edits are performed). underlying databaseare kept in synch as edits are performed).
<p> <p>
VIVO will VIVO will require more memory than that allocated to Tomcat by default. With most
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 installations of Tomcat, the "setenv.sh" or "setenv.bat" file in Tomcat's
bin directory is a convenient place to set the memory parameters. bin directory is a convenient place to set the memory parameters.
<br/> <br/>
@ -523,16 +515,14 @@
data, 256m to 512m should be sufficient. data, 256m to 512m should be sufficient.
</p> </p>
<p> <p>
If an OutOfMemoryError is If an OutOfMemoryError is encountered during VIVO execution, it can
encountered during VIVO execution, it can be remedied by increasing the be remedied by increasing the heap parameters and restarting Tomcat.
heap parameters and restarting Tomcat.
</p> </p>
<p> <p>
Security limits: VIVO is a Security limits: VIVO is a multithreaded web application that may
multithreaded web application that may require more threads than are require more threads than are permitted under your Linux installation's
permitted under your Linux installation's default configuration. Ensure default configuration. Ensure that your installation can support the
that your installation can support the required number of threads required number of threads by making the following edits to <code>/etc/security/limits.conf</code>:
by making the following edits to "/etc/security/limits.conf":
</p> </p>
<pre> <pre>
apache hard nproc 400 apache hard nproc 400
@ -540,18 +530,19 @@
</pre> </pre>
<h3 id="start_tomcat">VII. Start Tomcat </h3> <h3 id="start_tomcat">VII. Start Tomcat </h3>
<p> <p>
Most Tomcat installations can be started by running "startup.sh" or Most Tomcat installations can be started by running <code>startup.sh</code>
"startup.bat" in Tomcat's bin directory. Point your browser to or <code>startup.bat</code>
"http://localhost:8080/vivo/" to test the application. If Tomcat does not in Tomcat's bin directory. Point your browser to
start up, or the VIVO application is not visible, check the "http://localhost:8080/vivo/" to test the application. If Tomcat does not
catalina.out file in Tomcat's logs directory. start up, or the VIVO application is not visible, check the <code>catalina.out</code>
file in Tomcat's logs directory.
</p> </p>
<h3 id="add_rdf">VIII. Log in and add RDF data </h3> <h3 id="add_rdf">VIII. Log in and add RDF data </h3>
<p> <p>
If the startup was successful, you will see a welcome message If the startup was successful, you will see a welcome message
informing you that you have successfully installed VIVO. Click the "Log in" link informing you that you have successfully installed VIVO. Click the "Log in" link
near the upper right corner. Log in with the <em>initialAdminUser</em> near the upper right corner. Log in with the <code>initialAdminUser</code>
username you set up in Step IV. The initial password for the <em>initialAdminUser</em> username you set up in Step IV. The initial password for the <code>initialAdminUser</code>
account is "defaultAdmin" (without the quotes). On first login, you will be account is "defaultAdmin" (without the quotes). On first login, you will be
prompted to select a new password and verify it a second time. prompted to select a new password and verify it a second time.
</p> </p>
@ -586,7 +577,7 @@
<h3 id="contact_email">IX. Set the Contact Email Address (if using "Contact Us" form)</h3> <h3 id="contact_email">IX. Set the Contact Email Address (if using "Contact Us" form)</h3>
<p> <p>
If you have configured your application to use the "Contact Us" If you have configured your application to use the "Contact Us"
feature in Step IV (<em>Vitro.smtpHost</em>), you will also need to add an email address feature in Step IV (<code>Vitro.smtpHost</code>), you will also need to add an email address
to the VIVO application.&nbsp; This is the email that the contact form to the VIVO application.&nbsp; This is the email that the contact form
submits to. It can be a list server or an individual's submits to. It can be a list server or an individual's
email address. email address.
@ -594,12 +585,12 @@
<p> <p>
Log in as a system administrator. Navigate to the Log in as a system administrator. Navigate to the
"Site Admin" table of contents (link in the right side of the header). "Site Admin" table of contents (link in the right side of the header).
Go to "Site Information" (under "Site Configuration").&nbsp; In the Go to "Site Information" (under "Site Configuration"). In the
"Site Information Editing Form," enter a functional email address in "Site Information Editing Form," enter a functional email address in
the field "Contact Email Address." and submit the change. the field "Contact Email Address." and submit the change.
</p> </p>
<p> <p>
If you set the<em>Vitro.smtpHost</em> If you set the<code>Vitro.smtpHost</code>
in Step IV and do NOT provide an email addressin this in Step IV and do NOT provide an email addressin this
step, your users will receive a java error in the interface. step, your users will receive a java error in the interface.
</p> </p>
@ -616,14 +607,13 @@
</p> </p>
<p> <p>
Using the mod_jk connector allows for communication between Tomcat Using the mod_jk connector allows for communication between Tomcat
and the primary web server. The <a href="http://tomcat.apache.org/connectors-doc/generic_howto/quick.html">Quick and the primary web server. The <a href="http://tomcat.apache.org/connectors-doc/generic_howto/quick.html">Quick Start HowTo</a>
Start HowTo</a>
on the Apache site describes the minimum server configurations on the Apache site describes the minimum server configurations
for several popular web servers. for several popular web servers.
</p> </p>
<p> <p>
After setting up the mod_jk connector above, you will need to After setting up the mod_jk connector above, you will need to
modify the Tomcat's server.xml ([tomcat root]/conf/) to respond to modify the Tomcat's server.xml (located in <code>[tomcat root]/conf/</code>) to respond to
requests from Apache via the connector. Look for the requests from Apache via the connector. Look for the
&lt;connector&gt; directive and add the following properties: &lt;connector&gt; directive and add the following properties:
</p> </p>
@ -632,13 +622,15 @@
</pre> </pre>
<p> <p>
Note: the value for maxThreads (320) is equal to the value for MaxClients Note: the value for maxThreads (320) is equal to the value for MaxClients
in the apache's "httpd.conf" file. in the apache's <code>httpd.conf</code>
file.
</p> </p>
<p> <p>
Locate the &lt;Host name="localhost"...&gt; directive and update as Locate the <code>&lt;Host name="localhost"...&gt;</code>
directive and update as
follows: follows:
</p> </p>
<!-- ELLY IS WORKING HERE. --><pre> <pre>
&lt;Host name="localhost" appBase="webapps" &lt;Host name="localhost" appBase="webapps"
DeployOnStartup="false" DeployOnStartup="false"
unpackWARs="true" autoDeploy="false" unpackWARs="true" autoDeploy="false"
@ -672,9 +664,9 @@
<p> <p>
By default, Pellet is fed only an incomplete view of By default, Pellet is fed only an incomplete view of
your ontology and only certain inferences are materialized. These your ontology and only certain inferences are materialized. These
include rdf:type,&nbsp; rdfs:subClassOf,owl:equivalentClass, and include rdf:type, rdfs:subClassOf, owl:equivalentClass, and
owl:disjointWith. This mode is typically suitable for ontologies with a owl:disjointWith. This mode is typically suitable for ontologies with a
lot of instance data.&nbsp; 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. skip to the next step.
</p> </p>
<p> <p>
@ -685,19 +677,17 @@
<p> <p>
Then change the name of the listener class to Then change the name of the listener class to
PelletReasonerSetupComplete. Because "complete" reasoning can be very PelletReasonerSetupComplete. Because "complete" reasoning can be very
resource intensive, there is also an&nbsp; option to materialize nearly resource intensive, there is also an option to materialize nearly
all inferences except owl:sameAs and owl:differentFrom. all inferences except owl:sameAs and owl:differentFrom.
</p> </p>
<p> <p>
This is enabled This is enabled by specifying PelletReasonerSetupPseudocomplete. For ontologies
by specifying PelletReasonerSetupPseudocomplete. For ontologies with with large numbers of individuals, this mode can offer enormous performance
large numbers of individuals, this mode can offer enormous performance
improvements over the "complete" mode. improvements over the "complete" mode.
</p> </p>
<p> <p>
Finally, a class called Finally, a class called PelletReasonerSetupPseudocompleteIgnoreDataproperties
PelletReasonerSetupPseudocompleteIgnoreDataproperties is provided to is provided to improve performance on ontologies with large literals where data
improve performance on ontologies with large literals where data
property entailments are not needed. property entailments are not needed.
</p> </p>
</p> </p>
@ -727,10 +717,7 @@
external authentication system. external authentication system.
</p> </p>
<p> <p>
For VIVO, this secured page is named: For VIVO, this secured page is named: <code>/loginExternalAuthReturn</code>
<code>
/loginExternalAuthReturn
</code>
</p> </p>
<p> <p>
When your instructions call for the location of the secured page, this is the When your instructions call for the location of the secured page, this is the
@ -738,40 +725,49 @@
</p> </p>
<h4>Configuring VIVO</h4> <h4>Configuring VIVO</h4>
<p> <p>
To enable external authentication, VIVO requires three values in the To enable external authentication, VIVO requires three values in the <code>deploy.properties</code>
deploy.properties file. file.
</p> </p>
<ul> <ul>
<li> <li>
The name of the HTTP header that will hold the external user’s network ID <h5>The name of the HTTP header that will hold the external user's network ID.</h5>
When a user completes the authentication process, the Apache server will 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. 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 instructions from your institution should tell you which header is
used for this purpose. used for this purpose.
You need to tell VIVO the name of that HTTP header. Insert a line like <p>
this in the deploy.properties file: <pre>externalAuth.netIdHeaderName = [the header name]</pre> You need to tell VIVO the name of that HTTP header. Insert a line like
For example: <pre>externalAuth.netIdHeaderName = remote_userID</pre> this in the deploy.properties file: <pre>externalAuth.netIdHeaderName = [the header name]</pre>
For example:
</p>
<pre>externalAuth.netIdHeaderName = remote_userID</pre>
</li> </li>
<li> <li>
The text for the Login button <h5>The text for the Login button.</h5>
To start the authentication process, the user will click on a button in 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 the VIVO login form. You need to tell VIVO what text should appear in that
button. button.
Put a line like this in the deploy.properties file: <p>
externalAuth.buttonText = [the text for your login button] Put a line like this in the deploy.properties file:
For example: <pre>externalAuth.buttonText = Log in using BearCat Shibboleth</pre> externalAuth.buttonText = [the text for your login button]
The VIVO login form will display a button labelled “Log in using BearCat For example:
Shibboleth”. </p>
<pre>externalAuth.buttonText = Log in using BearCat Shibboleth</pre>
The VIVO login form will display a button labelled "Log in using BearCat
Shibboleth".
</li> </li>
<li> <li>
Associating a User with a profile page <h5>Associating a User with a profile page</h5>
If VIVO has an account for the user, the user will be given the privileges If VIVO has an account for the user, the user will be given the privileges
assigned to that account. assigned to that account.
In addition, VIVO will try to associate the user with a profile page, so <p>
the user may edit his own profile data. VIVO will search the data model In addition, VIVO will try to associate the user with a profile page, so
for a person with a property that matches the User’s network ID. the user may edit his own profile data. VIVO will search the data model
You need to tell VIVO what property should be used for matching. Insert for a person with a property that matches the User’s network ID.
a line like this in the deploy.properties file:<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre> You need to tell VIVO what property should be used for matching. Insert
a line like this in the deploy.properties file:
</p>
<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
For example:<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre> For example:<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre>
</li> </li>
</ul> </ul>
@ -814,7 +810,8 @@
<ul> <ul>
<li> <li>
Point your browser to the home page of your website, and click the "Log in" link 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 <code>initialAdminUser</code>
username you
set up in Step IV. If this is your first time logging in, you will be set up in Step IV. If this is your first time logging in, you will be
prompted to change the password. prompted to change the password.
</li> </li>
@ -830,7 +827,7 @@
the next step. the next step.
</li> </li>
<li> <li>
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 <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>.
In the pink box on that page enter the URI of the individual you created in the In the pink box on that page enter the URI of the individual you created in the
previous step and click "open." previous step and click "open."
</li> </li>
@ -847,11 +844,11 @@
</p> </p>
<ul> <ul>
<li> <li>
The search box is on the right side, directly opposite the "Index" link. Type the word "Australia" into the search box, and click on the Search
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 button.You should see a page of results, with links to countries that
border Australia, individuals that include Australia, and to border Australia, individuals that include Australia, and to
Australia itself. Australia itself. To trigger the search index, you can log in as a site
administrator and go to "http://your-vivo-url/SearchIndex".
</li> </li>
</ul> </ul>
</div> </div>