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If you want to install VIVO on a production server, or if you want to de= velop VIVO code, you should also read the section on Installation options.
Before installing VIVO, the following software should be installed on yo= ur computer:
Set up the environment variables for JAVA_HOME
and AN=
T_HOME
and add the executables to your path, as required. This step =
depends on the operating system you are using. Consult the installation dir=
ections from the software support websites.
The following browsers are supported for this release
You can test the software installation by typing these commands:
java -v= ersion mysql --version ant -version
Each of these command should print a response that tells you what versio= n is installed. If any of these commands prints an error message, or report= s an unexpected version number, you should review your installation.
Decide on a database name, username, and password.You will need these va= lues for this step, and again when you Specify runtime properties.
Log into your MySQL server and create a new database in MySQL that uses =
UTF-8
encoding. At the MySQL command line you can create the d=
atabase and user with these commands, substituting your values for db=
name
, username
, and password
. Most of the =
time, the hostname will be localhost
.
CREATE = DATABASE dbname CHARACTER SET utf8; GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';
Download the VIVO application source as either rel-1.8.zip
=
or rel-1.8.gz
file and unpack it on your web server: ht=
tp://vivoweb.org/download
At the top level of the VIVO distribution directory, rename the file These properties are used in compiling VIVO and deploying it to Tomcat. =
They will be incorporated into VIVO when it is compiled. If you want to cha=
nge these properties at a later date, you will need to stop Tomcat, repeat =
the Compile and depl=
oy step, and restart Tomcat. Windows: For those installing on a Windows operating system, in=
clude the windows drive, but use the forward slash "/" and not the back sla=
sh "\" in the directory locations, e.g. In the previous step, you defined the location of the VIVO home director=
y, by specifying At the command line, from the top level of the VIVO distribution directo=
ry, type: to build VIVO and deploy to Tomcat's webapps directory. The build script may run for as much as five minutes, and creates more t=
han 100 lines of output. The process includes several steps: If the output ends with a success message, the build was successful. Pro=
ceed to the next step. BUILD SUCCESSFUL Total time: 1 minute 49 seconds If the output ends with a failure message, the build has failed. Find th=
e cause of the failure, fix the problem, and run the script again. BUILD FAILED Total time: 35 seconds The output of the build may include warning messages. The Java compiler =
may warn of code that is outdated. Unit tests may produce warning messages,=
and some tests may be ignored if they do not produce consistent results. I=
f the output ends with a success message, these warnings may be ignored. 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 may require more memory than that allocated to Tomcat by default. W=
ith most installations of Tomcat, the This tells Tomcat to allocate an initial heap of 512 megabytes, a maximu=
m heap of 512 megabytes, and a PermGen space of 128 megs. Larger values may=
be required, especially for production installations in large enterprises.=
In general, VIVO runs more quickly if given more memory. If an VIVO is a multithreaded web application that may require more threads th=
an are permitted under your Linux installation's default configuration. Ens=
ure that your installation can support the required number of threads by ma=
king the following edits to In order for VIVO to correctly handle international characters, you must=
configure Tomcat to conform to the URI standard by accepting percent-encod=
ed UTF-8. Edit Tomcat's Some versions of Tomcat already include this attribute as the default.=
p>
Each of the webapps in the VIVO distribution (VIVO and Solr) includes a =
"context fragment" file, containing some of the deployment information for =
that webapp. Tomcat allows you to override these context fragments by adding Context =
elements to See the section entitled Running VIVO behind an Apache server for an examp=
le of overriding the VIVO context fragment. The build process in the&=
nbsp;Compile and deploy step created a file called This file specifies the c=
ode modules that VIVO selects when it runs. For most installations, there i=
s no need to edit this file. If you change this file a=
t a later date, you will need to restart Tomcat for the changes to take eff=
ect. You will not need to repeat the Compile and deploy step.=
The build process in the Compile and deploy step created a file called These properties are loaded when VIVO starts up. If you change these pro=
perties at a later date, you will need to restart Tomcat for the changes to=
take effect. You will not need to repeat the Compile and deploy step. Windows: For those installing on Windows operating system, incl=
ude the windows drive and use the forward slash "/" and not the back slash =
"\" in the directory locations, e.g. These properties define some fundamental aspects of your VIVO installati=
on. Most sites will need to modify all of these values. The default RDF namespace for this installati=
on. 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 d=
efault namespace must have a certain structure and begin with the public we=
b address of the VIVO installation. For example, if the web address of a VI=
VO installation is http://vivo.example.edu/ the default namespace mu=
st be set to "http://vivo.example.edu/individual/" in order to support link=
ed data. Similarly, if VIVO is installed at http://www.example.edu/vi=
vo the default namespace must be set to "http://www.example.edu/vivo/in=
dividual/" * The namespace must end with "individual/" (inclu=
ding the trailing slash). NOTE: The root user account has access to all =
data and all operations in VIVO. Data views may be surprising when logged i=
n as the root user. It is best to create a Site Admin account to use for ev=
ery day administrative tasks. Specify an SMTP host that the application wil=
l use for sending e-mail (Optional). If this is left blank, It is common practice to leave this field blank in test installatio=
ns, since it allows you to create user accounts based on fictional e-mail a=
ddresses. Specify an email address which will appear as=
the sender in e-mail notifications to users (Optional). If a user replies =
to the notification, this address will receive the reply. If a user's e-mai=
l address is invalid, this address will receive the error notice. If =
this is left blank, It is common practice to leave this field blank in test installatio=
ns, since it allows you to create user accounts based on fictional e-mail a=
ddresses. VIVO and its search index are actually two distinct web applications, an=
d the simple installation puts them both into the same instance of Tomcat. =
Even so, the VIVO webapp must be told how to reach the Solr webapp. URL of Solr context used in local VIVO search=
. Should consist of: In the standard installation, the Solr context =
will be on the same server as VIVO, and in the same Tomcat instance. The pa=
th will be the VIVO webapp.name (specified above) + "solr" The Most Tomcat installations can be started by running build.properties
. Edit t=
he file to suit your installation, as described in the following section.=
p>
c:/tomcat
.
Property name
vitro.core.dir
Description
The directory where Vitro source code is located=
. In the simple installation, this is set to
./vitro-core
Default value
NONE
Example value
./vitro-core
Property name
tomcat.home
Description
The directory where tomcat is installed.
Default value
NONE
Example value
/usr/local/tomcat
Property name
webapp.name
Description
The name of your VIVO application. This is not a=
name that will be displayed to the user. This name appears in the URL used=
to access VIVO, and in the path to the VIVO directory within Tomcat.
Default value
NONE
Example value
vivo
Property name
vitro.home
Description
The directory where VIVO will store the data tha=
t it creates. This includes uploaded files (usually images) and the Solr se=
arch index. Be sure this directory exists and is writable by the Tomcat ser=
vice.
Default value
NONE
Example value
/usr/local/vivo/home
<=
/td>
Compile and deploy
vitro.home
in the build.properties file. If that directory does not exist, create it now.
ant all=
Did it work?
Running VIVO
Configure Tomcat
Set JVM parameters
setenv.sh
or seten=
v.bat
file in Tomcat's bin
directory is a convenient pl=
ace to set the memory parameters. If this file does not exist in Tomcat=
's bin directory, you can create it.
For example:export =
CATALINA_OPTS=3D"-Xms512m -Xmx512m -XX:MaxPermSize=3D128m"
OutOfMemoryError
occurs during VIVO execution, increa=
se the heap parameters and restart Tomcat.Set security limits
/etc/security/limits.conf
:apache=
=09hard=09nproc=09400
tomcat6=09hard=09nproc=091500
Set URI encoding
conf/server.xml
and add the following attribu=
te to each of the Connector elements: URIEncoding=3D"UTF-8".<Ser=
ver ...>
<Service ...>
<Connector ... URIEncoding=3D"UTF-8"/>
...
</Connector>
</Service>
</Server>
Take car=
e when creating Context elements
server.xml
. If you decide to do this, be sure that=
your new Context element includes the necessary deployment parameters from=
the overridden context fragment.Configure the VIVO application
Modular application setup
example.applic=
ationSetup.n3
in the config
sub-directory of your =
VIVO home directory (specified by vitro.home
in the buil=
d.properties
file). Rename or copy this file to applicationSet=
up.n3
.Specify runtime pro=
perties
example.run=
time.properties
in your VIVO home directory (specified by vitr=
o.home
in the build.properties
file). Rename or copy th=
is file to runtime.properties
and edit the file to suit your i=
nstallation, as described below.c:/tomcat
.Basic properties
Property name
Vitro.defaultNamespace
Description
Default value
NONE
Example value
http://=
vivo.mydomain.edu/individual/
Property name
rootUser.emailAddress
Description
Specify the email address of the root user=
account for the VIVO application. This user will have an initial temporary=
password of
rootPassword
. You will be prompted to create a ne=
w password on first login.
Default value
NONE
Example value
vivoAdmin@my.domain=
.edu
Property name
VitroConnection.DataSource.url
Description
Specify the JDBC URL of your database. Cha=
nge the end of the URL to reflect your database name (if it is not "vivo").=
Default value
NONE
Example value
jdbc:mysql://=
localhost/vivo
Property name
VitroConnection.DataSource.username
Description
Change the username to match the authorize=
d user you created in MySQL.
Default value
NONE
Example value
username
Property name
VitroConnection.DataSource.password
Description
Change the password to match the password =
you created in MySQL.
Default value
NONE
Example value
password
Property name
email.smtpHost
Description
Default value
NONE
Example value
smtp.servername.edu
=
td>
Property name
email.replyTo
Description
Default value
NONE
Example value
vivoAdmin@my.domain=
.edu
Connecting to=
the Solr search index
Property name
vitro.local.solr.url
Description
scheme + servername + port + vivo_webapp_=
name + "solr"
Default value
NONE
Example value
http://localhost:80=
80/vivosolr
Additional properties=
h3>
runtime.properties
file can accept many additional prop=
erties, but they aren't necessary for this simple installation. If you choo=
se any of the Ins=
tallation options, you will probably need to set some of those properti=
es.Start Tomcat
startup.sh
startup.bat
in Tomcat's bin
directory. Sta=
rt Tomcat and direct your browser to http://localhost:8080/viv=
o
to test the application. Note that Tomcat may require several =
minutes to start VIVO.
On start up VIVO will run some diagnostic tests. If a problem is detecte=
d the normal VIVO pages will redirect to a startup status page describing t=
he problem. You can stop Tomcat, attempt to fix the problem and proceed fro=
m the Compile and deploy<=
/a> step. If the problem is not serious, the startup status page may offer =
a continue
link which will allow you to use VIVO in spite of t=
he problems.
If the startup was successful, you will see the VIVO home page.
If Tomcat does not start up, or the VIVO application is not visible, che=
ck the files in Tomcat's logs directory. Error messages are commonly found =
in [tomcat]/logs/catalina.out
, [to=
mcat]/logs/vivo.all.log
or [tomcat]/log=
s/localhost.log
Remember that Tomcat must have permission to read and write its own file= s, and the files in the VIVO home directory. This may mean that you must us= e a particular script or a particular user account to start Tomcat.
Direct your browser to the VIVO home page. Click the "Log in" link near =
the upper right corner. Log in with the rootUser.emailAddress
=
that you set in the runtime.properties
file. The initial passw=
ord for the root account is rootPassword
. When you first log i=
n, VIVO will require you to change the password. When login is complete, th=
e search index is checked and, if it is empty, a full index build will be t=
riggered in the background, in order to ensure complete functionality acros=
s the site.
After logging in, you will be presented with a menu of editing options. = Here you can create OWL classes, object properties, data properties, and co= nfigure the display of data. Currently, any classes you wish to make visibl= e on your website must be part of a class group and any individual must hav= e an = rdfs:label. There are a number of visibility and display options availa= ble for classes and properites. VIVO comes with a core VIVO ontology, but y= ou may also upload other ontologies from an RDF file.
Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note that V= itro currently works best with OWL-DL ontologies and has only limited suppo= rt for pure RDF data. You can enter a URL pointing to the RDF data you wish= to load or upload from a file on your local machine. Ensure that the "add = RDF" radio button is selected. You will also likely want to check "create c= lassgroups automatically."
Clicking the "Index" tab in the navigation bar at the top right of the p= age will show a simple index of the knowledge base.
See more documentation for configuring VIVO, ingesting data, and manuall= y adding data at http://vivoweb.org/support.
If you have configured your application to use the "Contact Us" feature =
(email.smtpHost
is set in the runtime.properties
=
file), you will also need to add an email address to the VIVO application.&=
nbsp; This is the email to which the contact form will submit. 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 email.smtpHost
in the runtime.properti=
es
file, and do NOT provide an email address in this step, your user=
s will see an error message instead of the expected contact form.
VIVO comes with a "Terms of Use" statement linked from the footer. The "= Site Name" you assign in the "Site Information" form under the Site= Admin area will be inserted into the "Terms of Use" statement. If= you want to edit the text content more than just the "Site Name", the file= can be found here:
[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/term= sOfUse.ftl
Your "Terms of Use" statement is also referenced in the Linked Open Data= (RDF) that your site produces, so you should be sure that it accurately re= flects the way that your data may be used.
Be sure to make the changes in your source files and deploy them to your= tomcat so you don't lose your changes next time you deploy for another rea= son.
If you have completed the previous steps, you have good indications that= the installation was successful.
The startup status will indicate if the basic configuration of the syste= m was successful. If there were any serious errors, you will see the status= screen and will not be allowed to continue with VIVO. If there are warning= s, you will see the status screen when you first access VIVO, but after tha= t you may use VIVO without hinderance. In this case, you can review the sta= rtup status from siteAdmin -> Startup status.
Here is a simple test to see whether the ontology files were loaded:
Here is a test to see whether your system is configured to serve linked = data:
rootUser.email=
Address
you set in runtime.properties
. If this is =
your first time logging in, you will be prompted to change the password.
Finally, test the search index.
Q: I'm running VIVO in To= mcat on a Macintosh computer. When I start VIVO, a strange icon appears in = the dock. What's up with that?
A: The image processing c=
ode in VIVO uses javax.imageio.ImageIO
, which in turn uses cod=
e in the java.awt
package. By default, this package will open =
a work area on your screen, producing this icon even though no visible wind=
ow is created.
You can prevent this by e=
diting Tomcat's bin/setenv.sh
file, and adding the java.=
awt.headless
option. For example,
export = CATALINA_OPTS=3D"-Xms512m -Xmx512m -XX:MaxPermSize=3D128m -Djava.awt.headle= ss=3Dtrue"