Updating from most recent release announcement draft. Still needs Nick's theme documentation.
This commit is contained in:
ejc12
parent
fad27accef
commit
5f3cd99335
1 changed files with 345 additions and 376 deletions
|
|
@ -26,7 +26,7 @@
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</toc>
|
</toc>
|
||||||
<p>
|
<p>
|
||||||
This document provides a short description of the steps involved in
|
This document provides a short description of the steps involved in
|
||||||
upgrading your installation of VIVO from Release 1, Version 1.1 to
|
upgrading your installation of VIVO from Release 1, Version 1.1 to
|
||||||
Version 1.2. This and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
|
Version 1.2. This and other documentation can be found on the <a href="http://vivoweb.org/support">support page</a>
|
||||||
|
|
@ -41,95 +41,69 @@
|
||||||
</p>
|
</p>
|
||||||
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2>
|
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2>
|
||||||
<p>
|
<p>
|
||||||
The VIVO 1.2 release incorporates major changes to the entire
|
The VIVO 1.2 release incorporates major changes throughout the
|
||||||
application - theming and navigation changes that will be immediately
|
application - notably a new templating system to support more flexible
|
||||||
evident to any user, and underlying changes to the system architecture
|
display and navigation, plus improvements to address scalability. The
|
||||||
that are less visible but address important questions of scalability
|
release also features two new visualization options: temporal graphing
|
||||||
and extensibility.
|
for organizations, and personal visualizations extended to cover grants
|
||||||
|
as well as publications. The VIVO Harvester library has also been
|
||||||
|
significantly improved and expanded in scope for its 1.0 release
|
||||||
|
through the VIVO SourceForge project at<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
|
||||||
</p>
|
</p>
|
||||||
<h3>Theming and Navigation</h3>
|
<h4>Templating system for page generation, navigation, and theming</h4>
|
||||||
<p>
|
<p>
|
||||||
A new installation of VIVO 1.2 will look strikingly different - the
|
A new installation of VIVO 1.2 looks strikingly different, with a
|
||||||
User Interface team has designed a new visual theme that incorporates a
|
new navigation and browse interface as well as a more modular page
|
||||||
new navigation and browse structure as well as a much more modular
|
design that is easier to customize and brand for your local
|
||||||
approach to page design. This theme is not only cosmetically different
|
institution. Page displays now support inline navigation to streamline
|
||||||
but leverages entirely new page templates developed with the Freemarker
|
viewing of expanded personal and organizational profiles, as well as
|
||||||
system, an open-source library for Java development that enables much
|
improved graphic layout and organization. New browsing controls on the
|
||||||
cleaner separation of application logic from the actual page design.
|
home page and each menu page include interactive visual controls to
|
||||||
These changes extend the available configuration options controlling
|
provide an immediate overview of the size and range of content and
|
||||||
VIVO's appearance and navigation options while also simplifying the
|
quick access down to the individual person, organization, research
|
||||||
process of local customization and branding.
|
feature, or event. VIVO's navigation has also been completely
|
||||||
|
overhauled.
|
||||||
|
</p>
|
||||||
|
<h4>Storage model</h4>
|
||||||
|
<p>
|
||||||
|
While server memory capacity has increased significantly in recent
|
||||||
|
years, VIVO's reliance on in-memory caching of RDF data had put limits
|
||||||
|
on the ultimate scalability of VIVO instances and potentially increased
|
||||||
|
the cost of servers required to support VIVO.
|
||||||
|
<br>
|
||||||
</p>
|
</p>
|
||||||
<p>
|
<p>
|
||||||
For existing installations of VIVO, the upgrade will not immediately
|
With version 1.2, VIVO has been converted to optionally use Jena's
|
||||||
transition to the new theme, navigation, or page templates. The current
|
SPARQL database (SDB) subsystem. SDB significantly reduces the baseline
|
||||||
default theme and "tabs" (top-level and secondary navigation controls)
|
memory footprint, allowing VIVO installations to scale well beyond what
|
||||||
will be left intact on upgrade and will still function as they do in
|
has previously been possible.
|
||||||
version 1.1.1, with the caveat that local modifications to the default
|
|
||||||
theme may conflict with internal application changes. We highly
|
|
||||||
recommend that current VIVO installations use the time between release
|
|
||||||
1.2 and the upcoming release of version 1.3 (targeted for June or July
|
|
||||||
2011) to migrate local theme branding and navigation to the new VIVO
|
|
||||||
template. Many legacy features such as the "tab" infrastructure have
|
|
||||||
been deprecated with version 1.2 and will no longer be supported as of
|
|
||||||
version 1.3.
|
|
||||||
</p>
|
</p>
|
||||||
<h3>Browsing</h3>
|
<h4>New visualizations</h4>
|
||||||
<p>
|
<p>
|
||||||
In addition to changes in the top-level navigation, VIVO 1.2
|
VIVO continues to expand visualization options including all-new
|
||||||
introduces a number of new browsing controls that will be made more
|
user-configurable temporal comparisons of publications and grants,
|
||||||
configurable and extensible in version 1.3 but which already offer
|
grouped by organization or by affiliated person. Visualizations of
|
||||||
extensive functionality.
|
networks of co-authors are now complemented by visualizations of
|
||||||
|
co-investigators on grants, with a similar interactivity and options
|
||||||
|
for export as images or data.
|
||||||
</p>
|
</p>
|
||||||
|
<h4>Ontology</h4>
|
||||||
<p>
|
<p>
|
||||||
A fresh installation of VIVO 1.2 will feature the new theme and
|
VIVO 1.2 includes a new ontology module representing research
|
||||||
additional browsing options on other top-level navigation pages (Home,
|
resources including biological specimens, human studies, instruments,
|
||||||
People, Research, Organizations, and Events). Primary among the new
|
organisms, protocols, reagents, and research opportunities. This module
|
||||||
browsing options will be browsing by <b>type</b>, organized
|
is aligned with the top-level ontology classes and properties from the
|
||||||
hierarchically with the same upper-level <b>class groups</b>
|
NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
|
||||||
currently
|
|
||||||
visible in search results - people, courses, activities, topics,
|
|
||||||
events, organizations, and publications. Class groups combine the
|
|
||||||
similar types such as people or organizations into groups for browsing
|
|
||||||
and searching, and are locally configurable using the VIVO ontology
|
|
||||||
editor.
|
|
||||||
</p>
|
</p>
|
||||||
|
<h3>Associated VIVO releases</h3>
|
||||||
|
<h4>VIVO Harvester</h4>
|
||||||
<p>
|
<p>
|
||||||
Once a group has been selected, browsing can continue to the very
|
The Harvester development team is releasing version 1.0 of the VIVO
|
||||||
specific, at the level of individual people, organizations, events, or
|
Harvester library, an extensible data ingest and updating framework
|
||||||
publications via A ... Z listing featuring thumbnail pictures where
|
with sample configurations for loading PubMed publication, grants, and
|
||||||
available. Sites will be able to configure which groups and which types
|
human resources data. The Harvester is available at<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
|
||||||
within a group are exposed in search results and for browsing.
|
|
||||||
</p>
|
</p>
|
||||||
<h3>Data Storage</h3>
|
<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
|
||||||
<p>
|
|
||||||
Before this release, VIVO has used the Jena
|
|
||||||
(<a href="http://jena.sourceforge.net/" rel="nofollow">http://jena.sourceforge.net</a>)
|
|
||||||
relational database (RDB)
|
|
||||||
subsystem for the storage of RDF data. The performance of this persistence layer
|
|
||||||
has never been fast enough for an interactivity at any significant scale, so
|
|
||||||
VIVO has also maintained a complete copy of data in memory. While server memory capacity
|
|
||||||
has increased significantly in recent years, this requirement has put
|
|
||||||
limits on the ultimate scalability of VIVO instances and also increased
|
|
||||||
the cost of servers required to support VIVO.
|
|
||||||
</p>
|
|
||||||
<p>
|
|
||||||
With version 1.2 VIVO uses the SPARQL database (SDB) subsystem of
|
|
||||||
Jena, specifically designed to support scalable storage and query of
|
|
||||||
RDF datasets while still using standard relational database technology.
|
|
||||||
This transition will significantly reduce the initial memory footprint
|
|
||||||
of a VIVO application, and while the application will still require
|
|
||||||
adequate processor and memory resources to generate pages from so many
|
|
||||||
individual RDF statements, the scalability of VIVO installations is
|
|
||||||
greatly improved.
|
|
||||||
</p>
|
|
||||||
<p>
|
|
||||||
The transition to retrieving all data via SPARQL queries also
|
|
||||||
enables additional features important for tracking data provenance and
|
|
||||||
access to data outside the immediate local VIVO instance. These
|
|
||||||
features will be more fully explored and developed for version 1.3.
|
|
||||||
</p>
|
|
||||||
<!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
|
|
||||||
<toc>
|
<toc>
|
||||||
<ol class="roman1">
|
<ol class="roman1">
|
||||||
<li>
|
<li>
|
||||||
|
|
@ -432,9 +406,9 @@
|
||||||
<tr>
|
<tr>
|
||||||
<td colspan="2">
|
<td colspan="2">
|
||||||
Change the dbtype setting to use a database
|
Change the dbtype setting to use a database
|
||||||
other than MySQL. Otherwise, leave this value unchanged. Possible
|
other than MySQL. Otherwise, leave this value unchanged. Possible
|
||||||
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
|
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
|
||||||
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
|
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
|
||||||
for additional information.
|
for additional information.
|
||||||
</td>
|
</td>
|
||||||
</tr>
|
</tr>
|
||||||
|
|
@ -566,11 +540,11 @@
|
||||||
in
|
in
|
||||||
the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
|
the theme:<pre>[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl</pre>
|
||||||
A sample <code>googleAnalytics.ftl</code>
|
A sample <code>googleAnalytics.ftl</code>
|
||||||
is included in the built-in
|
is included in the built-in
|
||||||
theme. This file serves only as an example, and you must replace the
|
theme. This file serves only as an example, and you must replace the
|
||||||
tracking code shown with your institution's own tracking code. For
|
tracking code shown with your institution's own tracking code. For
|
||||||
additional information about the GATC for the NIH-funded VIVO
|
additional information about the GATC for the NIH-funded VIVO
|
||||||
implementation sites and a copy your institution's tracking code, see
|
implementation sites and a copy your institution's tracking code, see
|
||||||
the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
|
the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
|
||||||
Google
|
Google
|
||||||
Analytics
|
Analytics
|
||||||
|
|
@ -587,299 +561,294 @@
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</blockquote>
|
</blockquote>
|
||||||
</p>
|
</p>
|
||||||
<p>
|
<p>
|
||||||
4. If you had modified <code>web.xml</code>
|
4. If you had modified <code>web.xml</code>
|
||||||
to configure the Pellet Reasoner (as described
|
to configure the Pellet Reasoner (as described
|
||||||
in the installation instructions), repeat that modification.
|
in the installation instructions), repeat that modification.
|
||||||
</p>
|
</p>
|
||||||
<p>
|
<p>
|
||||||
5. Stop Apache Tomcat and run ant by typing: <code>ant all</code>
|
5. Stop Apache Tomcat and run ant by typing: <code>ant all</code>
|
||||||
</p>
|
</p>
|
||||||
<p>
|
<p>
|
||||||
6. Start Apache Tomcat and log in to VIVO.
|
6. Start Apache Tomcat and log in to VIVO.
|
||||||
</p>
|
</p>
|
||||||
<h3 id="ontology">III. Ontology Changes</h3>
|
<h3 id="ontology">III. Ontology Changes</h3>
|
||||||
<h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4>
|
<h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4>
|
||||||
<p>
|
<p>
|
||||||
After Apache Tomcat is started, these files should be reviewed to
|
After Apache Tomcat is started, these files should be reviewed to
|
||||||
verify that the automated upgrade process was executed
|
verify that the automated upgrade process was executed
|
||||||
successfully. The ontology alignment process will create the
|
successfully. The ontology alignment process will create the
|
||||||
following files in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
|
following files in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
|
||||||
</p>
|
</p>
|
||||||
<dl>
|
<dl>
|
||||||
<dt>
|
<dt>
|
||||||
<code>ontologies/update/logs/knowledgeBaseUpdate.log</code>
|
<code>ontologies/update/logs/knowledgeBaseUpdate.log</code>
|
||||||
</dt>
|
</dt>
|
||||||
<dd>
|
<dd>
|
||||||
A log of a summary of updates that were made to the knowledge base and
|
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
|
notes about some recommended manual reviews. This file should end with
|
||||||
"Finished knowledge base migration".
|
"Finished knowledge base migration".
|
||||||
|
If this file contains any warnings they should be reviewed with
|
||||||
If this file contains any warnings they should be reviewed with
|
your implementation team representative to see whether any
|
||||||
your implementation team representative to see whether any
|
corrective action needs to be taken.
|
||||||
corrective action needs to be taken.
|
</dd>
|
||||||
</dd>
|
</dl>
|
||||||
</dl>
|
<dl>
|
||||||
<dl>
|
<dt>
|
||||||
<dt>
|
<code>ontologies/update/logs/knowledgeBaseUpdate.error.log</code>
|
||||||
<code>ontologies/update/logs/knowledgeBaseUpdate.error.log</code>
|
</dt>
|
||||||
</dt>
|
<dd>
|
||||||
<dd>
|
A log of errors that were encountered during the upgrade process. This
|
||||||
A log of errors that were encountered during the upgrade process. This
|
file should be empty if the upgrade was successful.
|
||||||
file should be empty if the upgrade was successful.
|
</dd>
|
||||||
</dd>
|
</dl>
|
||||||
</dl>
|
<dl>
|
||||||
<dl>
|
<dt>
|
||||||
<dt>
|
<code>ontologies/update/changedData/removedData.n3</code>
|
||||||
<code>ontologies/update/changedData/removedData.n3</code>
|
</dt>
|
||||||
</dt>
|
<dd>
|
||||||
<dd>
|
An N3 file containing all the statements that were removed from the
|
||||||
An N3 file containing all the statements that were removed from the
|
knowledge base.
|
||||||
knowledge base.
|
</dd>
|
||||||
</dd>
|
</dl>
|
||||||
</dl>
|
<dl>
|
||||||
<dl>
|
<dt>
|
||||||
<dt>
|
<code>ontologies/update/changedData/addedData.n3</code>
|
||||||
<code>ontologies/update/changedData/addedData.n3</code>
|
</dt>
|
||||||
</dt>
|
<dd>
|
||||||
<dd>
|
An N3 file containing all the statements that were added to the
|
||||||
An N3 file containing all the statements that were added to the
|
knowledge base.
|
||||||
knowledge base.
|
</dd>
|
||||||
</dd>
|
</dl>
|
||||||
</dl>
|
<h4 id="ontology_knowledge_base">ii. Ontology knowledge base manual review</h4>
|
||||||
<h4 id="ontology_knowledge_base">ii. Ontology knowledge base manual review</h4>
|
<p>
|
||||||
<p>
|
Changes to the VIVO core ontology may require corresponding
|
||||||
Changes to the VIVO core ontology may require corresponding
|
modifications of the knowledge base instance data and local ontology
|
||||||
modifications of the knowledge base instance data and local ontology
|
extensions.
|
||||||
extensions.
|
</p>
|
||||||
</p>
|
<p>
|
||||||
<p>
|
When Apache Tomcat starts up following the upgrade, it will initiate a
|
||||||
When Apache Tomcat starts up following the upgrade, it will initiate a
|
process to examine the knowledge base and apply necessary changes. Not
|
||||||
process to examine the knowledge base and apply necessary changes. Not
|
all of the modifications that may be required can be automated, so
|
||||||
all of the modifications that may be required can be automated, so
|
manual review of the knowledge base is recommended after the automated
|
||||||
manual review of the knowledge base is recommended after the automated
|
upgrade process. The automated process will make only the following
|
||||||
upgrade process. The automated process will make only the following
|
types of changes:
|
||||||
types of changes:
|
</p>
|
||||||
</p>
|
<dl>
|
||||||
<dl>
|
<dt>
|
||||||
<dt>
|
Class or Property renaming
|
||||||
Class or Property renaming
|
</dt>
|
||||||
</dt>
|
<dd>
|
||||||
<dd>
|
All references to the class (in the subject or object position) will be
|
||||||
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
|
||||||
updated to the new name. References to the property will be updated to
|
the new name.
|
||||||
the new name.
|
</dd>
|
||||||
</dd>
|
</dl>
|
||||||
</dl>
|
<dl>
|
||||||
<dl>
|
<dt>
|
||||||
<dt>
|
Class or Property deletion
|
||||||
Class or Property deletion
|
</dt>
|
||||||
</dt>
|
<dd>
|
||||||
<dd>
|
All individuals in a deleted class will be removed.
|
||||||
All individuals in a deleted class will be removed.
|
<br>
|
||||||
<br>
|
All statements using a deleted property will be changed to use the
|
||||||
All statements using a deleted property will be changed to use the
|
nearest available superproperty. If there is no available superproperty
|
||||||
nearest available superproperty. If there is no available superproperty
|
then the statement will be deleted from the knowledge base. Note that
|
||||||
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
|
||||||
all removed and added data is recorded in the files in the changedData
|
directory.
|
||||||
directory.
|
</dd>
|
||||||
</dd>
|
</dl>
|
||||||
</dl>
|
<dl>
|
||||||
<dl>
|
<dt>
|
||||||
<dt>
|
Property addition
|
||||||
Property addition
|
</dt>
|
||||||
</dt>
|
<dd>
|
||||||
<dd>
|
If a newly added property is the inverse of a previously existing
|
||||||
If a newly added property is the inverse of a previously existing
|
property, the inverse of any statements using the pre-existing property
|
||||||
property, the inverse of any statements using the pre-existing property
|
will be asserted.
|
||||||
will be asserted.
|
</dd>
|
||||||
</dd>
|
</dl>
|
||||||
</dl>
|
<dl>
|
||||||
<dl>
|
<dt>
|
||||||
<dt>
|
Annotation property default values
|
||||||
Annotation property default values
|
</dt>
|
||||||
</dt>
|
<dd>
|
||||||
<dd>
|
If a site has modified the value of a vitro annotation (such as
|
||||||
If a site has modified the value of a vitro annotation (such as
|
displayRankAnnot or displayLimitAnnot) so that it is no longer using
|
||||||
displayRankAnnot or displayLimitAnnot) so that it is no longer using
|
the default, then that setting will be left unchanged.
|
||||||
the default, then that setting will be left unchanged.
|
<br>
|
||||||
<br>
|
If a site is using the default value of a vitro annotation, and the
|
||||||
If a site is using the default value of a vitro annotation, and the
|
default has been changed in the new version of the ontology, then the
|
||||||
default has been changed in the new version of the ontology, then the
|
new default value will be propagated to the knowledge base.
|
||||||
new default value will be propagated to the knowledge base.
|
</dd>
|
||||||
</dd>
|
</dl>
|
||||||
</dl>
|
<h3 id="fileSystem">IV. File Storage System Upgrade</h3>
|
||||||
|
<h4 id="changes_to_storage">i. Changes to the File Storage System</h4>
|
||||||
<h3 id="fileSystem">IV. File Storage System Upgrade</h3>
|
<p>
|
||||||
<h4 id="changes_to_storage">i. Changes to the File Storage System</h4>
|
Each uploaded file exists as an individual entity in VIVO. When the
|
||||||
<p>
|
browser requests an upload file from VIVO, the data model is queried to
|
||||||
Each uploaded file exists as an individual entity in VIVO. When the
|
find out where the file is actually stored, so it can be downloaded to
|
||||||
browser requests an upload file from VIVO, the data model is queried to
|
the browser.
|
||||||
find out where the file is actually stored, so it can be downloaded to
|
</p>
|
||||||
the browser.
|
<p>
|
||||||
</p>
|
In VIVO release 1.2 this storage location,
|
||||||
<p>
|
known as the "Alias URL" for the uploaded file,
|
||||||
In VIVO release 1.2 this storage location,
|
is stored in the file entity.
|
||||||
known as the "Alias URL" for the uploaded file,
|
That way, pages that contain many files can be displayed much more quickly.
|
||||||
is stored in the file entity.
|
</p>
|
||||||
That way, pages that contain many files can be displayed much more quickly.
|
<p>
|
||||||
</p>
|
When Apache Tomcat starts up after the upgrade,
|
||||||
<p>
|
it will initiate a process to calculate the "Alias URL"
|
||||||
When Apache Tomcat starts up after the upgrade,
|
for each existing file and store it in the data model for fast access.
|
||||||
it will initiate a process to calculate the "Alias URL"
|
</p>
|
||||||
for each existing file and store it in the data model for fast access.
|
<h4 id="verify_file_upgrade">ii. Verify File Storage System upgrade process</h4>
|
||||||
</p>
|
<p>
|
||||||
<h4 id="verify_file_upgrade">ii. Verify File Storage System upgrade process</h4>
|
The File Storage upgrade process will create a log file in the
|
||||||
<p>
|
VIVO upload directory. You should review this file to ensure that
|
||||||
The File Storage upgrade process will create a log file in the
|
this upgrade worked properly.
|
||||||
VIVO upload directory. You should review this file to ensure that
|
</p>
|
||||||
this upgrade worked properly.
|
<dl>
|
||||||
</p>
|
<dt>
|
||||||
<dl>
|
<code>upgrade/FileStorageAliasAdder-log.2011-00-00T00-00-00.txt</code>
|
||||||
<dt>
|
</dt>
|
||||||
<code>upgrade/FileStorageAliasAdder-log.2011-00-00T00-00-00.txt</code>
|
<dd>
|
||||||
</dt>
|
A log of the upgrade process. The actual filename includes a timestamp
|
||||||
<dd>
|
that tells when the upgrade executed.
|
||||||
A log of the upgrade process. The actual filename includes a timestamp
|
This file should end with<code>Finished adding alias URLs to FileByteStreams.</code>
|
||||||
that tells when the upgrade executed.
|
If this file contains any warnings they should be reviewed with
|
||||||
This file should end with
|
your implementation team representative to see whether any
|
||||||
<code>Finished adding alias URLs to FileByteStreams.</code>
|
corrective action needs to be taken.
|
||||||
|
</dd>
|
||||||
If this file contains any warnings they should be reviewed with
|
</dl>
|
||||||
your implementation team representative to see whether any
|
<h3 id="theme">V. Theme Changes</h3>
|
||||||
corrective action needs to be taken.
|
<h4 style="color:red">Need Nick to help with this section</h4>
|
||||||
</dd>
|
<p>
|
||||||
</dl>
|
VIVO 1.2 comes with a new theme called "wilma" that uses the FreeMarker template
|
||||||
|
engine for generating web pages. The theme is located in /vivo/themes/wilma and
|
||||||
<h3 id="theme">V. Theme Changes</h3>
|
the FreeMarker files have an ftl (for FreeMarker Template Language) extension.
|
||||||
<h4 style="color:red">Need Nick to help with this section</h4>
|
</p>
|
||||||
<p>
|
<p>
|
||||||
VIVO 1.2 comes with a new theme called "wilma" that uses the FreeMarker template
|
Follow step A or B below, whichever is applicable to your site:
|
||||||
engine for generating web pages. The theme is located in /vivo/themes/wilma and
|
</p>
|
||||||
the FreeMarker files have an ftl (for FreeMarker Template Language) extension.
|
<p>
|
||||||
</p>
|
A. If you did not create a customized theme for your site in V1.0 or V1.1, but used
|
||||||
<p>
|
the vivo-basic theme in its original directory, you need not take any
|
||||||
Follow step A or B below, whichever is applicable to your site:
|
action in order to convert your site to the VIVO 1.1 theme.
|
||||||
</p>
|
</p>
|
||||||
<p>
|
<p>
|
||||||
A. If you did not create a customized theme for your site in V1.0 or V1.1, but used
|
B. If you created your own theme directory in VIVO 1.1, follow the steps below
|
||||||
the vivo-basic theme in its original directory, you need not take any
|
under sections "Templates," "Stylesheets," and "Site Icons" to upgrade your
|
||||||
action in order to convert your site to the VIVO 1.1 theme.
|
theme to VIVO 1.2.
|
||||||
</p>
|
</p>
|
||||||
<p>
|
<dl>
|
||||||
B. If you created your own theme directory in VIVO 1.1, follow the steps below
|
<dt>
|
||||||
under sections "Templates," "Stylesheets," and "Site Icons" to upgrade your
|
1. Templates
|
||||||
theme to VIVO 1.2.
|
</dt>
|
||||||
</p>
|
<dd>
|
||||||
<dl>
|
<dl>
|
||||||
<dt>
|
<dt>
|
||||||
1. Templates
|
a. Copy the directory <code>/vivo/themes/wilma/templates</code>
|
||||||
</dt>
|
into your theme directory <code>/vivo/themes/[your-theme-name]</code>.
|
||||||
<dd>
|
</dt>
|
||||||
<dl>
|
<dd>
|
||||||
<dt>
|
</dd>
|
||||||
a. Copy the directory <code>/vivo/themes/vivo-basic/templates</code>
|
<dt>
|
||||||
into your theme directory <code>/vivo/themes/[your-theme-name]</code>.
|
b. Follow step i or ii below, whichever is applicable to your theme.
|
||||||
</dt>
|
</dt>
|
||||||
<dd>
|
<dd>
|
||||||
</dd>
|
<ol class="roman2">
|
||||||
<dt>
|
<li>
|
||||||
b. Follow step i or ii below, whichever is applicable to your theme.
|
If you did not apply any customizations to the JSPs in your VIVO
|
||||||
</dt>
|
1.0 theme, then you do not need to apply any additional changes
|
||||||
<dd>
|
to the VIVO 1.1 theme templates during the upgrade process.
|
||||||
<ol class="roman2">
|
</li>
|
||||||
<li>
|
<li>
|
||||||
If you did not apply any customizations to the JSPs in your VIVO
|
<p>
|
||||||
1.0 theme, then you do not need to apply any additional changes
|
If you did apply customizations to the JSPs in your VIVO 1.0
|
||||||
to the VIVO 1.1 theme templates during the upgrade process.
|
theme,you will need to hand-replicate those modifications in the
|
||||||
</li>
|
new theme template files.
|
||||||
<li>
|
</p>
|
||||||
<p>
|
<p>
|
||||||
If you did apply customizations to the JSPs in your VIVO 1.0
|
The theme template content that was previously contained in
|
||||||
theme,you will need to hand-replicate those modifications in the
|
three JSP files is now contained in five FTL files. The
|
||||||
new theme template files.
|
correspondence between the 1.0 JSPs and the 1.1 FTLs is as
|
||||||
</p>
|
follows:
|
||||||
<p>
|
</p>
|
||||||
The theme template content that was previously contained in
|
<pre>
|
||||||
three JSP files is now contained in five FTL files. The
|
|
||||||
correspondence between the 1.0 JSPs and the 1.1 FTLs is as
|
|
||||||
follows:
|
|
||||||
</p>
|
|
||||||
<pre>
|
|
||||||
identity.jsp => identity.ftl
|
identity.jsp => identity.ftl
|
||||||
menu.jsp => menu.ftl and search.ftl
|
menu.jsp => menu.ftl and search.ftl
|
||||||
footer.jsp => footer.ftl and googleAnalytics.ftl
|
footer.jsp => footer.ftl and googleAnalytics.ftl
|
||||||
</pre>
|
</pre>
|
||||||
<p>
|
<p>
|
||||||
<code>googleAnalytics.ftl</code>
|
<code>googleAnalytics.ftl</code>
|
||||||
is the file to which you add your site's Google Analytics Tracking
|
is the file to which you add your site's Google Analytics Tracking
|
||||||
Code (see section II).
|
Code (see section II).
|
||||||
</p>
|
</p>
|
||||||
<p>
|
<p>
|
||||||
Because the FreeMarker Template Language uses many syntactic
|
Because the FreeMarker Template Language uses many syntactic
|
||||||
conventions that will be familiar to template authors from JSP
|
conventions that will be familiar to template authors from JSP
|
||||||
or other common templating systems, the translation of your JSP
|
or other common templating systems, the translation of your JSP
|
||||||
changes into the new FTLs should be relatively straightforward.
|
changes into the new FTLs should be relatively straightforward.
|
||||||
</p>
|
</p>
|
||||||
<p>
|
<p>
|
||||||
Consult the FreeMarker Template Author's Guide at <a href="http://freemarker.org/docs/dgui.html">http://freemarker.org/docs/dgui.html</a>
|
Consult the FreeMarker Template Author's Guide at <a href="http://freemarker.org/docs/dgui.html">http://freemarker.org/docs/dgui.html</a>
|
||||||
and the Reference at <a href="http://freemarker.org/docs/ref.html">http://freemarker.org/docs/ref.html</a>
|
and the Reference at <a href="http://freemarker.org/docs/ref.html">http://freemarker.org/docs/ref.html</a>
|
||||||
for complete documentation of the syntax and available built-in constructs. Template
|
for complete documentation of the syntax and available built-in constructs. Template
|
||||||
authors need not be concerned with the Programmer's Guide or Java API documentation.
|
authors need not be concerned with the Programmer's Guide or Java API documentation.
|
||||||
</p>
|
</p>
|
||||||
</li>
|
</li>
|
||||||
</ol>
|
</ol>
|
||||||
</dd>
|
</dd>
|
||||||
<dt>
|
<dt>
|
||||||
c. Remove the jsp directory from your themes directory.
|
c. Remove the jsp directory from your themes directory.
|
||||||
</dt>
|
</dt>
|
||||||
<dd>
|
<dd>
|
||||||
</dd>
|
</dd>
|
||||||
</dl>
|
</dl>
|
||||||
</dd>
|
</dd>
|
||||||
<dt>
|
<dt>
|
||||||
2. Stylesheets
|
2. Stylesheets
|
||||||
</dt>
|
</dt>
|
||||||
<dd>
|
<dd>
|
||||||
VIVO 1.1 includes changes to vivo-basic stylesheets. If you modified
|
VIVO 1.1 includes changes to vivo-basic stylesheets. If you modified
|
||||||
styles in your VIVO 1.0 theme, you will not be able to simply copy the
|
styles in your VIVO 1.0 theme, you will not be able to simply copy the
|
||||||
1.0 stylesheets into your 1.1 theme, because you will then lose 1.1
|
1.0 stylesheets into your 1.1 theme, because you will then lose 1.1
|
||||||
style upgrades that your theme should pick up. Instead, you should
|
style upgrades that your theme should pick up. Instead, you should
|
||||||
use the vivo-basic 1.1 stylesheets as a starting point, and manually
|
use the vivo-basic 1.1 stylesheets as a starting point, and manually
|
||||||
merge your 1.0 style modifications in as needed.
|
merge your 1.0 style modifications in as needed.
|
||||||
</dd>
|
</dd>
|
||||||
<dt>
|
<dt>
|
||||||
3. Site Icons
|
3. Site Icons
|
||||||
</dt>
|
</dt>
|
||||||
<dd>
|
<dd>
|
||||||
Copy the site icons from your 1.1 theme into the site_icons folder in
|
Copy the site icons from your 1.1 theme into the site_icons folder in
|
||||||
your 1.2 theme.
|
your 1.2 theme.
|
||||||
</dd>
|
</dd>
|
||||||
</dl>
|
</dl>
|
||||||
</div>
|
</div>
|
||||||
<!-- end of content -->
|
<!-- end of content -->
|
||||||
<div role="contentinfo">
|
<div role="contentinfo">
|
||||||
<p class="copyright">
|
<p class="copyright">
|
||||||
<small>
|
<small>
|
||||||
©2011
|
©2011
|
||||||
All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a>
|
All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a>
|
||||||
</small>
|
</small>
|
||||||
| Powered by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
|
| Powered by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
|
||||||
</p>
|
</p>
|
||||||
<nav role="navigation">
|
<nav role="navigation">
|
||||||
<ul id="footer-nav" role="list">
|
<ul id="footer-nav" role="list">
|
||||||
<li role="listitem">
|
<li role="listitem">
|
||||||
<a href="http://vivoweb.org/about">About</a>
|
<a href="http://vivoweb.org/about">About</a>
|
||||||
</li>
|
</li>
|
||||||
<li role="listitem">
|
<li role="listitem">
|
||||||
<a href="http://vivoweb.org/contact">Contact Us</a>
|
<a href="http://vivoweb.org/contact">Contact Us</a>
|
||||||
</li>
|
</li>
|
||||||
<li role="listitem">
|
<li role="listitem">
|
||||||
<a href="http://www.vivoweb.org/support" target="blank">Support</a>
|
<a href="http://www.vivoweb.org/support" target="blank">Support</a>
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</nav>
|
</nav>
|
||||||
</div>
|
</div>
|
||||||
</body>
|
</body>
|
||||||
</html>
|
</html>
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue