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NIHVIVO-3103 Convert VIVO references to appropriate Vitro references.

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j2blake 2011-11-16 17:30:30 +00:00
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@ -106,8 +106,6 @@
<p> <p>
In 2009, the National Institutes of Health (NIH) awarded a major grant to advance the development of VIVO. In 2009, the National Institutes of Health (NIH) awarded a major grant to advance the development of VIVO.
Much of the recent development on Vitro has been in support of that grant. Much of the recent development on Vitro has been in support of that grant.
</p>
<p>
However, Vitro retains its own identity, However, Vitro retains its own identity,
and still serves as the core of many projects and products. and still serves as the core of many projects and products.
Some of these are currently in use, and some are still in the planning stages. Some of these are currently in use, and some are still in the planning stages.
@ -167,9 +165,7 @@
<hr><!-- Page break --><!-- Installation process for Version 1.3 --><h2 id="installation">Installation process for Version 1.3</h2> <hr><!-- Page break --><!-- Installation process for Version 1.3 --><h2 id="installation">Installation process for Version 1.3</h2>
<p> <p>
This document is a summary of the VIVO installation process. This This document is a summary of the Vitro installation process.
and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
at <a href="http://vivoweb.org">VIVOweb.org</a>
</p> </p>
<toc> <toc>
<h3>Steps to Installation</h3> <h3>Steps to Installation</h3>
@ -208,19 +204,19 @@
</li> </li>
<li> <li>
<a href="#external_auth">Using an External Authentication <a href="#external_auth">Using an External Authentication
System with VIVO</a> System with Vitro</a>
</li> </li>
<li> <li>
<a href="#installation_check">Was the installation successful?</a> <a href="#installation_check">Was the installation successful?</a>
</li> </li>
<li> <li>
<a href="#termsofuse">Review the VIVO Terms of Use</a> <a href="#termsofuse">Review the Vitro Terms of Use</a>
</li> </li>
</ol> </ol>
</toc> </toc>
<h3 id="required_software">I. Install required software </h3> <h3 id="required_software">I. Install required software </h3>
<p> <p>
Before installing VIVO, make sure that the following software is Before installing Vitro, make sure that the following software is
installed on the desired machine: installed on the desired machine:
</p> </p>
<ul> <ul>
@ -237,6 +233,9 @@
<li> <li>
MySQL 5.1 or higher*, <a href="http://www.mysql.com">http://www.mysql.com</a> MySQL 5.1 or higher*, <a href="http://www.mysql.com">http://www.mysql.com</a>
</li> </li>
<li>
Apache Subversion 1.6.x or higher*, <a href="http://subversion.apache.org/">http://subversion.apache.org/</a>
</li>
</ul> </ul>
<p> <p>
Be sure to set up the environment variables for <code java_home="">JAVA_HOME</code> Be sure to set up the environment variables for <code java_home="">JAVA_HOME</code>
@ -245,12 +244,7 @@
your operating system and installation directions from the software your operating system and installation directions from the software
support websites. support websites.
</p> </p>
<p>
* Note that VIVO V1.2 or V1.3 will not run on older versions of MySQL that
may have worked with 1.1.1. Be sure to run VIVO 1.2 with MySQL 5.1 or
higher. Using unsupported versions may result in strange error messages
related to table formatting or other unexpected problems.
</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
@ -282,7 +276,7 @@
</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 VIVO distribution directory, copy the file <code>example.deploy.properties</code> In the <code>webapp</code> directory of the Vitro distribution, copy the file <code>example.deploy.properties</code>
to a file named simply <code>deploy.properties</code>. This file sets to a file named simply <code>deploy.properties</code>. This file sets
several properties used in compilation and deployment. several properties used in compilation and deployment.
</p> </p>
@ -297,8 +291,7 @@
If you want to use an external If you want to use an external
authentication system like Shibboleth or CUWebAuth, you will need to authentication system like Shibboleth or CUWebAuth, you will need to
set two additional properties in this file. See the section below set two additional properties in this file. See the section below
entitled <a href="#external_auth">Using an External Authentication entitled <a href="#external_auth">Using an External Authentication System with Vitro</a>.
System with VIVO</a>.
</p> </p>
<table border='1' bordercolor="#CCCCCC" cellspacing="5"> <table border='1' bordercolor="#CCCCCC" cellspacing="5">
<tbody> <tbody>
@ -312,18 +305,18 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Default namespace: VIVO installations make their Default namespace: Vitro installations make their
RDF resources available for harvest using linked data. Requests for RDF RDF resources available for harvest using linked data. Requests for RDF
resource URIs redirect to HTML or RDF representations as specified by resource URIs redirect to HTML or RDF representations as specified by
the client. To make this possible, VIVO's default namespace must have a the client. To make this possible, Vitro's default namespace must have a
certain structure and begin with the public web address of the VIVO certain structure and begin with the public web address of the Vitro
installation. For example, if the web address of a VIVO installation is installation. For example, if the web address of a Vitro installation is
"http://vivo.example.edu/" the default namespace must be set to "http://vitro.example.edu/" the default namespace must be set to
"http://vivo.example.edu/individual/" in order to support linked data. "http://vitro.example.edu/individual/" in order to support linked data.
Similarly, if VIVO is installed at "http://www.example.edu/vivo" the Similarly, if Vitro is installed at "http://www.example.edu/vitro" the
default namespace must be set to default namespace must be set to
"http://www.example.edu/vivo/individual/"<h5>* The namespace must end with "individual/" (including the "http://www.example.edu/vitro/individual/"
trailing slash).</h5> <h5>* The namespace must end with "individual/" (including the trailing slash).</h5>
</td> </td>
</tr> </tr>
<tr class="odd_row"> <tr class="odd_row">
@ -331,7 +324,7 @@
Vitro.defaultNamespace Vitro.defaultNamespace
</td> </td>
<td> <td>
http://vivo.mydomain.edu/individual/ http://vitro.mydomain.edu/individual/
</td> </td>
</tr> </tr>
<tr> <tr>
@ -349,7 +342,7 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Name of your VIVO application. Name of your Vitro application.
</td> </td>
</tr> </tr>
<tr class="odd_row"> <tr class="odd_row">
@ -357,16 +350,16 @@
webapp.name webapp.name
</td> </td>
<td> <td>
vivo vitro
</td> </td>
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
URL of Solr context used in local VIVO search. URL of Solr context used in local Vitro search.
Should consist of:<pre> scheme + servername + port + vivo_webapp_name + "solr"</pre> Should consist of:<pre> scheme + servername + port + vitro_webapp_name + "solr"</pre>
In the standard installation, the Solr context will be on the same In the standard installation, the Solr context will be on the same
server as VIVO, and in the same Tomcat instance. The path will be the server as Vitro, and in the same Tomcat instance. The path will be the
VIVO webapp.name (specified above) + "solr" Vitro webapp.name (specified above) + "solr"
</td> </td>
</tr> </tr>
<tr class="odd_row"> <tr class="odd_row">
@ -374,7 +367,7 @@
vitro.local.solr.url vitro.local.solr.url
</td> </td>
<td> <td>
http://localhost:8080/vivosolr http://localhost:8080/vitrosolr
</td> </td>
</tr> </tr>
<tr> <tr>
@ -410,7 +403,7 @@
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Directory where the VIVO application will store Directory where the Vitro application will store
the data that it creates. This includes uploaded files (usually images) the data that it creates. This includes uploaded files (usually images)
and the Solr search index. Be sure this directory exists and is and the Solr search index. Be sure this directory exists and is
writable by the user who the Tomcat service is running as. writable by the user who the Tomcat service is running as.
@ -421,7 +414,7 @@
vitro.home.directory vitro.home.directory
</td> </td>
<td> <td>
/usr/local/vivo/data /usr/local/vitro/data
</td> </td>
</tr> </tr>
<tr> <tr>
@ -455,13 +448,13 @@
email.replyTo email.replyTo
</td> </td>
<td> <td>
vivoAdmin@my.domain.edu vitroAdmin@my.domain.edu
</td> </td>
</tr> </tr>
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify the JDBC URL of your database. Change Specify the JDBC URL of your database. Change
the end of the URL to reflect your database name (if it is not "vivo"). the end of the URL to reflect your database name (if it is not "vitro").
</td> </td>
</tr> </tr>
<tr class="odd_row"> <tr class="odd_row">
@ -469,7 +462,7 @@
VitroConnection.DataSource.url VitroConnection.DataSource.url
</td> </td>
<td> <td>
jdbc:mysql://localhost/vivo jdbc:mysql://localhost/vitro
</td> </td>
</tr> </tr>
<tr> <tr>
@ -582,12 +575,12 @@
<tr> <tr>
<td colspan="2"> <td colspan="2">
Specify the email address of the root user Specify the email address of the root user
account for the VIVO application. This user will have an initial account for the Vitro application. This user will have an initial
temporary password of 'rootPassword'. You will be prompted to create a temporary password of 'rootPassword'. You will be prompted to create a
new password on first login. new password on first login.
<p> <p>
NOTE: The root user account has access to all data and all NOTE: The root user account has access to all data and all
operations in VIVO. Data views may be surprising when logged in as the operations in Vitro. Data views may be surprising when logged in as the
root user. It is best to create a Site Admin account to use for every root user. It is best to create a Site Admin account to use for every
day administrative tasks. day administrative tasks.
</p> </p>
@ -598,7 +591,7 @@
rootUser.emailAddress rootUser.emailAddress
</td> </td>
<td> <td>
vivoAdmin@my.domain.edu vitroAdmin@my.domain.edu
</td> </td>
</tr> </tr>
<tr> <tr>
@ -615,7 +608,7 @@
selfEditing.idMatchingProperty selfEditing.idMatchingProperty
</td> </td>
<td> <td>
http://vivo.mydomain.edu/ns#networkId http://vitro.mydomain.edu/ns#networkId
</td> </td>
</tr> </tr>
<tr> <tr>
@ -649,22 +642,22 @@
</table> </table>
<h3 id="deploy">V. Compile and deploy</h3> <h3 id="deploy">V. Compile and deploy</h3>
<p> <p>
At the command line, from the top level of the VIVO distribution At the command line, from the top level of the Vitro distribution
directory, type: directory, type:
</p> </p>
<pre> ant all<br> </pre> <pre> ant all<br> </pre>
<p> <p>
to build VIVO and deploy to Tomcat's webapps directory. to build Vitro and deploy to Tomcat's webapps directory.
</p> </p>
<h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security <h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security
limits</h3> limits</h3>
<p> <p>
VIVO copies small sections of your RDF database into Vitro copies small sections of your RDF database into
memory in order to serve Web requests quickly (the in-memory copy and memory in order to serve Web requests quickly (the in-memory copy and
the underlying database are kept in synch as edits are performed). the underlying database are kept in synch as edits are performed).
</p> </p>
<p> <p>
VIVO may require more memory than that allocated to Tomcat by Vitro may require more memory than that allocated to Tomcat by
default. With most installations of Tomcat, the "setenv.sh" or default. With most installations of Tomcat, the "setenv.sh" or
"setenv.bat" file in Tomcat's bin directory is a convenient place to "setenv.bat" file in Tomcat's bin directory is a convenient place to
set the memory parameters. <em>If this file does not exist in Tomcat's set the memory parameters. <em>If this file does not exist in Tomcat's
@ -679,11 +672,11 @@
values may suffice, especially for small test installations. values may suffice, especially for small test installations.
</p> </p>
<p> <p>
If an OutOfMemoryError is encountered during VIVO execution, it can If an OutOfMemoryError is encountered during Vitro execution, it can
be remedied by increasing the heap parameters and restarting Tomcat. be remedied by increasing the heap parameters and restarting Tomcat.
</p> </p>
<p> <p>
Security limits: VIVO is a multithreaded web application that may Security limits: Vitro is a multithreaded web application that may
require more threads than are permitted under your Linux installation's require more threads than are permitted under your Linux installation's
default configuration. Ensure that your installation can support the default configuration. Ensure that your installation can support the
required number of threads by making the following edits to <code>/etc/security/limits.conf</code>: required number of threads by making the following edits to <code>/etc/security/limits.conf</code>:
@ -694,8 +687,8 @@
Most Tomcat installations can be started by running <code>startup.sh</code> Most Tomcat installations can be started by running <code>startup.sh</code>
or <code>startup.bat</code> or <code>startup.bat</code>
in Tomcat's bin directory. Point your in Tomcat's bin directory. Point your
browser to "http://localhost:8080/vivo/" to test the application. If browser to "http://localhost:8080/vitro/" to test the application. If
Tomcat does not start up, or the VIVO application is not visible, check Tomcat does not start up, or the Vitro application is not visible, check
the files in Tomcat's logs directory. Error messages are commonly found the files in Tomcat's logs directory. Error messages are commonly found
in <code>catalina.out</code> in <code>catalina.out</code>
or <code>localhost.log</code> or <code>localhost.log</code>
@ -703,7 +696,7 @@
<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 informing you that you have successfully installed Vitro. Click the "Log
in" link near the upper right corner. Log in with the <code>rootUser.emailAddress</code> in" link near the upper right corner. Log in with the <code>rootUser.emailAddress</code>
you set up in Step IV. The initial password for the root account is you set up in Step IV. The initial password for the root account is
"rootPassword" (without the quotes). On first login, you will be "rootPassword" (without the quotes). On first login, you will be
@ -739,7 +732,7 @@
<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 (<code>email.smtpHost</code>), you will also need to feature in Step IV (<code>email.smtpHost</code>), you will also need to
add an email address to the VIVO application.&nbsp; This is the email add an email address to the Vitro application.&nbsp; This is the email
to which the contact form will submit. It can be a list server or an to which the contact form will submit. It can be a list server or an
individual's email address. individual's email address.
</p> </p>
@ -761,17 +754,16 @@
It is recommended that a Tomcat Connector such as mod_jk be used to 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. 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. 8080) and an additional reference to the Tomcat context name (e.g.
/vivo). /vitro).
</p> </p>
<p> <p>
This will make VIVO available at "http://example.com" instead of This will make Vitro available at "http://example.com" instead of
"http://example.com:8080/vivo" "http://example.com:8080/vitro"
</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 Start HowTo</a>
HowTo</a>
on the Apache site describes the minimum server on the Apache site describes the minimum server
configurations for several popular web servers. configurations for several popular web servers.
</p> </p>
@ -803,7 +795,7 @@
&lt;Alias&gt;example.com&lt;/Alias&gt; &lt;Alias&gt;example.com&lt;/Alias&gt;
&lt;Context path="" &lt;Context path=""
docBase="/usr/local/tomcat/webapps/vivo" docBase="/usr/local/tomcat/webapps/vitro"
reloadable="true" reloadable="true"
cookies="true" &gt; cookies="true" &gt;
@ -818,22 +810,22 @@
... ...
</pre> </pre>
<h3 id="external_auth">XI. Using an External Authentication System <h3 id="external_auth">XI. Using an External Authentication System
with VIVO </h3> with Vitro </h3>
<p> <p>
</p> </p>
<p> <p>
VIVO can be configured to work with an external authentication Vitro can be configured to work with an external authentication
system like Shibboleth or CUWebAuth. system like Shibboleth or CUWebAuth.
</p> </p>
<p> <p>
VIVO must be accessible only through an Apache HTTP server. The Vitro must be accessible only through an Apache HTTP server. The
Apache server will be configured to invoke the external authentication Apache server will be configured to invoke the external authentication
system. When the user completes the authentication, the Apache server system. When the user completes the authentication, the Apache server
will pass a network ID to VIVO, to identify the user. will pass a network ID to Vitro, to identify the user.
</p> </p>
<p> <p>
If VIVO has an account for that user, the user will be logged in If Vitro 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 with the privileges of that account. In the absence of an account, Vitro
will try to find a page associated with the user. If such a page is 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. found, the user can log in to edit his own profile information.
</p> </p>
@ -841,19 +833,19 @@
<p> <p>
Your institution will provide you with instructions for setting up Your institution will provide you with instructions for setting up
the external authentication system. The Apache server must be the external authentication system. The Apache server must be
configured to secure a page in VIVO. When a user reaches this secured configured to secure a page in Vitro. When a user reaches this secured
page, the Apache server will invoke the external authentication system. page, the Apache server will invoke the external authentication system.
</p> </p>
<p> <p>
For VIVO, this secured page is named: <code>/loginExternalAuthReturn</code> For Vitro, this secured page is named: <code>/loginExternalAuthReturn</code>
</p> </p>
<p> <p>
When your instructions call for the location of the secured page, When your instructions call for the location of the secured page,
this is the value you should use. this is the value you should use.
</p> </p>
<h4>Configuring VIVO</h4> <h4>Configuring Vitro</h4>
<p> <p>
To enable external authentication, VIVO requires three values in To enable external authentication, Vitro requires three values in
the <code>deploy.properties</code> the <code>deploy.properties</code>
file. file.
</p> </p>
@ -868,7 +860,7 @@
which header is used for this purpose. which header is used for this purpose.
</p> </p>
<p> <p>
You need to tell VIVO the name of that HTTP header. Insert a You need to tell Vitro the name of that HTTP header. Insert a
line like this in the deploy.properties file: line like this in the deploy.properties file:
</p> </p>
<pre>externalAuth.netIdHeaderName = [the header name]</pre> <pre>externalAuth.netIdHeaderName = [the header name]</pre>
@ -880,7 +872,7 @@
<li> <li>
<h5>The text for the Login button.</h5> <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 the Vitro login form. You need to tell Vitro what text should appear in
that button. that button.
<p> <p>
Put a line like this in the deploy.properties file: Put a line like this in the deploy.properties file:
@ -888,25 +880,25 @@
</p> </p>
<pre>externalAuth.buttonText = Log in using BearCat Shibboleth</pre> <pre>externalAuth.buttonText = Log in using BearCat Shibboleth</pre>
<p> <p>
The VIVO login form will display a button labelled "Log in The Vitro login form will display a button labelled "Log in
using BearCat Shibboleth". using BearCat Shibboleth".
</p> </p>
</li> </li>
<li> <li>
<h5>Associating a User with a profile page.</h5> <h5>Associating a User with a profile page.</h5>
<p> <p>
VIVO will try to associate the user with a profile Vitro will try to associate the user with a profile
page, so the user may edit his own profile data. VIVO will search the page, so the user may edit his own profile data. Vitro will search the
data model for a person with a property that matches the User’s network 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 ID (the value of the property must be either a String literal or an
untyped literal). You need to tell VIVO what property should be used untyped literal). You need to tell Vitro what property should be used
for matching. Insert a line like this in the deploy.properties file: for matching. Insert a line like this in the deploy.properties file:
</p> </p>
<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre> <pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
<p> <p>
For example: For example:
</p> </p>
<pre>selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId</pre> <pre>selfEditing.idMatchingProperty = http://vitro.mydomain.edu/ns#networkId</pre>
</li> </li>
</ul> </ul>
<h3 id="installation_check">XII. Was the installation successful? </h3> <h3 id="installation_check">XII. Was the installation successful? </h3>
@ -935,7 +927,7 @@
"Geographic Location." The index is built in a background thread, so on "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 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 periodically to see whether the index will be populated. This may take
some time: with VIVO installed on a modest laptop computer, loading the some time: with Vitro installed on a modest laptop computer, loading the
ontology files and building the index took more than 5 minutes from the ontology files and building the index took more than 5 minutes from the
time that Tomcat was started. time that Tomcat was started.
</li> </li>
@ -991,23 +983,35 @@
Type the word "Australia" into the search box, and click on the 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 Search button.You should see a page of results, with links to countries
that border Australia, individuals that include Australia, and to that border Australia, individuals that include Australia, and to
Australia itself. To trigger the search index, you can log in as a site Australia itself. If the search is not successful, try rebuilding the search index:
administrator and go to "http://your-vivo-url/SearchIndex". log in as a site
administrator and go to "http://your-vitro-url/SearchIndex".
</li> </li>
</ul> </ul>
<h3 id="termsofuse">XIII. Review the VIVO Terms of Use</h3> <h3 id="termsofuse">XIII. Review the Vitro Terms of Use</h3>
<p> <p>
VIVO comes with a "Terms of Use" statement linked from the footer. Vitro comes with a "Terms of Use" statement linked from the footer.
The "Site Name" you assign in the "Site Information" form under the <strong>Site Admin</strong> The "Site Name" you assign in the "Site Information" form under the <strong>Site Admin</strong>
area will be inserted into the "Terms of Use" area will be inserted into the "Terms of Use"
statement. If you want to edit the text content more than just the statement. If you want to edit the text content more than just the
"Site Name", the file can be found here:<pre>[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl</pre> "Site Name", the file can be found here:<pre>[vitro_source_dir]/webapp/web/templates/freemarker/body/termsOfUse.ftl</pre>
Be sure to make the changes in your source files and deploy them to your 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 reason. tomcat so you don't lose your changes next time you deploy for another reason.
</p> </p>
<h3>Next Step ...</h3> <h3>Next Step ...</h3>
<p> <p>
Now that you have VIVO up and running, please go read the <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">Site Administrator's Guide</a>. There is no further documentation specifically for Vitro.
However, you may find helpful information in the
<a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">
VIVO Site Administrator's Guide</a>.
</p>
<p>
For instant access to Vitro developers visit the VIVO IRC Channel:
<pre> Network: irc.freenode.net
Channel: #VIVO
WebInterface: http://webchat.freenode.net/</pre>
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@ -1016,22 +1020,7 @@
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