Upgrade - Vivo

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17 Νοε 2013 (πριν από 3 χρόνια και 1 μήνα)

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1

Upgrading  NIH  VIVO
 to  Release  1.0
 


Steps to Upgrade from Release 1 Version 0.9 to Release 1 Version 1.0


This
document
provides a short description of the steps involved in upgrading
your installation of NIH VIVO from Release 1 Version 0.9 to Release 1 Ve
rsion
1.0.

This and other documentation

can be found at:


http://vivoweb.org/support

Table  of  Contents
 
Upgrading  NIH  VIVO  to  Release  1.0
 
1
 
I.  Before  Performing
 the  Upgrade
 
1
 
II.  The  Upgrade  Process
 
2
 
III.  Ontology  Changes
 
4
 
IV.  Special  Note  re:  Default  Namespace
 
5
 

I.  
Before  Performing  the  Up
grade
 

Please read the bullet points below BEFORE beginning the upgrade.


The upgrade process is similar to the original ins
tall process with the
following
exceptions:




DO NOT reinstall MySQL or recreate the MySQL database. Please
ensure that
y
ou back
up
the MySQL database.



It is not necessary to add RDF data or reconfigure the Apache HTTP
Server.



First
-
time login of the administrator account will use the password
previously set, NOT the password in deploy.properties.



Any image files that have been upl
oaded into the system will not be
disturbed by the upgrade.



T
he first time Apache Tomcat starts up after the upgrade, it will initiate
a process that modifies the knowledge base to align the data with the
revised ontology. See the section on "Ontology Chan
ges"

below for
more information.



2

 
II.  
The  
Upgrade  
Process
 

1.

Ensure that backups are created of the Tomcat webapps directory, the
original source directory, and the MySQL database.

2.

Download the new distribution file and unpack it into a new source
director
y.

3.

Create
deploy.properties
, using the same values as in your original
installation. Be aware that
deploy.properties
now requires an
additional property:
vitro.core.dir = ./vitro
-
core

The file example.deploy.properties
has been modified to show this.

4.

Apply
any changes you have made to the new source directory.


Note
: In many cases, simply copying the modified files from your original
source directory will not work since the files on which they are based have
changed. It will be necessary to inspect the new
source files and add any
changes to them at that time.

Note
: At a minimum it will be necessary to apply the Google Analytics
Tracking code to footer.jsp in the theme:

[new_source_directory]/themes
/[theme_dir]/jsp/footer.jsp

For additional information and
a copy your institution's tracking code, see the
Google Analytics wiki page.

https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI

Note
: Version 1 Release 0.9 contained two directories called "modifications"
and "ontology". These directori
es have been combined into a directory called
"productMods". If your site has made changes to the ontology ensure that
those changes are moved into the appropriate subdirectory of
"productMods".

Note:
This process assumes any changes made to the applicati
on were
made

in the source directory and deployed, and
were
not made directly within
the

Apache Tomcat
webapp
.


5.

If you had modified
web.xml
to
configure the Pellet Reasoner
(as
described

in the installation instructions), repeat that modification.

6.

Stop Ap
ache Tomcat and r
un ant deploy by typing: ant
deploy

7.

If you have setup the Apache Tomcat Connector using mod_jk and
modified your tomcat/conf/server.xml file, you will need to add 4 lines
to your context section, see examples below.



3



Context section befor
e:


<Context path=""



docBase="/usr/local/tomcat/webapps/vivo"



reloadable="true"



cookies="true" >


</Context>




Context section after:




<Context path=""



docBase="/usr/local/tomcat/webapps/vivo"



reloadable="true"



cookies="true" >



<Environmen
t type="java.lang.String" override="false"




name="path.configuration"




value="deploy.properties"



/>


</Context>



Also, if you have these 3 lines in your Apache virtual host
c
onfiguration,
please remove them!




<Location "/edit/forms">

den
y from all

<Location>


8.

Start Apache Tomcat
and login to VIVO.

9.

Rebuild the Lucene search index as described in step IX of

the install
process. This step will ensure that changes in the RDFdata to align
with the latest version of the core ontology

will be re
flected in the
search index.



4

 
III.  
Ontology  Changes
 

Changes to the VIVO core ont
ology may require corresponding
modifications
of the knowledge base instance data and local ontology

extensions.


When Apache Tomcat starts up following
the upgrade, it will
initiate
a
process to examine the knowledge base and apply necessary changes.

Not
all of the modifications that may be required can be automated,

so manual
review of the knowledge base is recommended after the

automated upgrade
process. The automated proc
ess will make only the following types of
changes:


Class or Property renaming

All references to the class (in the subject or object position) will

be updated to the new name. References to the property will be

updated to the new name.



C
lass or Property deletion

All individuals in a deleted class will be changed to
belong



to
the nearest available superclass (which may be owl:Thing).



All statements using a deleted property will be changed

to use the nearest available su
perproperty. If there is no available

superproperty then the statement will be deleted from the

knowledge base. Note that all removed and added data

is recorded in the files in the changedData directory.



Class or Property addition

If
a newly added class has a superclass and there are

individuals in that superclass, then a note will be

added to the log file suggesting review of those individuals to

see if they should be reasserted in the newly added class.



If a newly
added property has a superproperty and there are

statements using the superproperty, then a note will be added to

the log file suggesting review of those statements to see if they

should be reasserted using the newly added property.


Ann
otat
ion property default values

It a site has modified the value of a vitro annotation (such as

displayRankAnnot or displayLimitAnnot) so that it is

no longer using the default, then that setting will be left unchanged.

If a site is using the d
efault value of a vitro annotation, and the

default has been changed in the new version of the ontology, then

the new default value will be propagated to the knowledge base.




5


The ontology alignment process will create the following files in the

To
mcat
webapps/vivo/WEB
-
INF
directory:


ontologies/update/logs/knowledgeBaseUpdate.log

--

a log of a summary of updates that were made to the knowledge base and
notes about some recommended manual reviews. This file should end with

"Successfully finished pr
ocessing ontology changes".


ontologies/update/logs/knowledgeBaseUpdate.error.log

--

a log of errors that were encountered during the upgrade process. This file

should be empty if the upgrade was successful.


ontologies/update/
changed
Data/removedData.rdf

-

a file containing all the statements that were removed from the knowledge
base.


ontologies/update/
changed
Data/addedData.rdf

-
a file containing all the statements that w
ere added to the knowledge base.


After Apache Tomcat is started, these files shou
ld be reviewed to verify that

the automated upgrade process was executed successfully.

IV.  Special  Note  re:  Default  Namespace
 

We do
not
recommend changing the default namespace after you have
populated your VIVO knowledge base, since there is currently no
tool to
migrate existing data to reflect the new namespace. Note that your VIVO
installation will not support linked data access methods unless the
namespace corresponds to the base URL of your site, as outlined in section
IV of the VIVO installation doc
ument, so if you set up an additional server,
such as a test server, using your production data, the linked data
functionality will not work. If you have questions about your current
namespace setting or need to change it, please contact the VIVO team at
http://vivoweb.org/contact
.