If you need to do a fresh install, please consult the VIVO Release 1 v1.2
- Installation Guide found on vivoweb.org
+ Installation Guide found on vivoweb.org
or the install.html file located in the doc
directory of the VIVO source code distribution. The installation
document also has a list of the required software and versions.
@@ -48,8 +48,8 @@
release also features two new visualization options: temporal graphing
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 athttp://sourceforge.net/projects/vivo.
+ significantly improved and expanded in scope for its 1.0 release
+ through the VIVO SourceForge project at http://sourceforge.net/projects/vivo.
@@ -101,8 +101,8 @@
The Harvester development team is releasing version 1.0 of the VIVO Harvester library, an extensible data ingest and updating framework - with sample configurations for loading PubMed publication, grants, and - human resources data. The Harvester is available athttp://sourceforge.net/projects/vivo. + with sample configurations for loading PubMed publication, grants, and + human resources data. The Harvester is available at http://sourceforge.net/projects/vivo.
VIVO 1.2 offers a choice of two triple store technologies: in-memory models backed by - Jena's legacy relational database store (RDB) and Jena's SPARQL database (SDB). RDB was + Jena's legacy relational database store (RDB), and Jena's SPARQL database (SDB). RDB was used by VIVO 1.1.1 and earlier. This mode offers fast response, but only by caching the entire RDF model in the server's main memory. The memory available to VIVO limits the number of RDF statements that may be stored. @@ -221,17 +221,17 @@
A VIVO 1.2 system that is upgraded from VIVO 1.1.1 must initially be run in RDB mode in order - receive required ontology updates. Attempting to run an upgraded system initially in SDB will + to receive required ontology updates. Attempting to run an upgraded system initially in SDB will result in a logged error message, and the application will not start. After the system starts up successfully the first time in RDB mode, it may then be switched to SDB, redeployed, and restarted. Upon restart, the data in the RDB store will be copied to the SDB store.
This copying process can take a number of hours to complete if the installation contains a large - amount of RDF data (roughly a million triples or more). See section - Set Up SDB Store in the Background (Optional) for instructions on how - to run this lengthy conversion process in the background while an RDB system is operating. - Doing this will reduce the time necessary to start VIVO the first time it is run in SDB mode. + amount of RDF data (roughly a million triples or more). See section Set Up SDB Store in the Background (Optional) + for instructions on how + to run this lengthy conversion process in the background while an RDB system is operating. + Doing this will reduce the time necessary to start VIVO the first time it is run in SDB mode.
@@ -260,7 +260,7 @@ 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 default namespace must have - certain structure and begin with the public web address of the VIVO + a certain structure and begin with the public 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 "http://vivo.example.edu/individual/" in order to support linked data. @@ -322,7 +322,7 @@
googleAnalytics.ftl
- in the theme:
- [new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl+ in the theme:
[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftlA sample
googleAnalytics.ftl
is included in the built-in theme. This file serves only as an example,
- and you must replace the tracking code shown with your institution's own
+ and you must replace the tracking code shown with your institution's own
tracking code. For additional information about the GATC for the NIH-funded
- VIVO implementation sites and a copy your institution's tracking code, see
- the
- VIVO Google Analytics wiki page.
+ VIVO implementation sites and a copy your institution's tracking code, see
+ the VIVO Google Analytics wiki page.
vivo/contrib/FLShibboleth
@@ -656,10 +660,9 @@
Each uploaded file exists as an individual in VIVO. When the browser - requests an uploaded file from VIVO, the data model is queried to find + requests an uploaded file from VIVO, the data model is queried to find out where the file is actually stored, so it can be downloaded to the browser.
- In VIVO release 1.2 this storage location, known as the "Alias URL" for + In VIVO 1.2 this storage location, known as the "Alias URL" for the uploaded file, is stored in the file individual. That way, pages that contain many files can be displayed much more quickly.
@@ -770,7 +772,7 @@ When Apache Tomcat starts up after the upgrade, it will initiate a process to calculate the "Alias URL" for each existing file and store it in the data model for fast access. - +The File Storage upgrade process will create a log file in the @@ -784,32 +786,26 @@
Finished adding alias URLs to FileByteStreams.
-
- If this file contains any warnings they should be reviewed with
- your implementation team representative to see whether any
+ This file should end withFinished adding alias URLs to FileByteStreams.
+ If this file contains any warnings they should be reviewed with
+ your implementation team representative to see whether any
corrective action needs to be taken.
- VIVO 1.2 includes a new default theme called wilma (located in - /vivo/themes/wilma) which fully supports all 1.2 features. For details on how to - create your own theme using wilma as a starting point, please review the - - Site Administrator's Guide. + VIVO 1.2 includes a new default theme called wilma + (located in + /vivo/themes/wilma) which fully supports all 1.2 features. For details on how to + create your own theme using wilma as a starting point, please review the Site Administrator's Guide.
-- The vivo-basic theme has been deprecated with the 1.2 release and is not - recommended for production instances. -
+The vivo-basic theme has been deprecated with the 1.2 release and is not + recommended for production instances.
Since vivo-basic was the default theme for all previous releases, it is - included as part of VIVO 1.2 to help with the transition of upgrading + included as part of VIVO 1.2 to help with the transition of upgrading existing installations to the latest code, but all vivo-basic development has ceased and it will not be distributed in future releases.
@@ -819,15 +815,21 @@ following:-
- new primary menu for site navigation (replaces tabs)
-- home page with class group browse and visual graph
-- menu pages with class group and individual browse
+- + new primary menu for site navigation (replaces tabs) +
+- + home page with class group browse and visual graph +
+- + menu pages with class group and individual browse +
The 1.2 release continues the transition from JavaServer Pages (.jsp) to - Freemarker templates (.ftl) for generating web pages. While there are still + Freemarker templates (.ftl) for generating web pages. While there are still JSP files in action behind the scenes, as of 1.2 all theme templates are of the Freemarker variety and are located in the "templates" directory within a theme. @@ -837,19 +839,45 @@ the vivo-basic theme in its original directory, you need not take any action in order to remain using the vivo-basic theme in 1.2.
-If you did make changes to the vivo-basic theme, you will need to reapply those changes. - We recommend you apply these changes to the wilma theme.
++ If you did make changes to the vivo-basic theme, you will need to reapply those changes. + We recommend you apply these changes to the wilma theme. +
- Please note: The vivo-basic theme has been deprecated and is - not recommended for production instances. + Please note: + The vivo-basic theme has been deprecated and is not recommended for production instances.-
+
For details on the new structure of themes in 1.2 and further information - regarding the development of your own custom theme, please review the - - Site Administrator's Guide. This document will focus on updating an existing + regarding the development of your own custom theme, please review the Site Administrator's Guide. This document will focus on updating an existing pre 1.2 theme.
++ If your VIVO installation is running in RDB mode, and you'd like to convert + to SDB, you can start the conversion process in the background while the RDB + system is running. This will reduce the delay in initial startup after the + application is redeployed with deploy.properties set for SDB. Note that it + is important not to edit any data anywhere in the application while this + background conversion is running. +
++ To start the SDB conversion, log in as a system + administrator and request /sdbsetup (For example, if your VIVO is installed + at http://vivo.myuniversity.edu/ you would type + http://vivo.myuniversity.edu/sdbsetup into your browser). +
++ Click the button that appears on this page. +
++ During the course of the SDB setup, which may take several hours on a + large database, subsequent requests to /sdbsetup will display a + message that the operation is still in progress. When a request for this + page shows a message that the SDB setup has completed successfully, shut down + Tomcat, set deploy.properties to SDB mode, redeploy, and restart Tomcat. + VIVO will now be running from the SDB store. +