+
This document provides a short description of the steps involved in upgrading your installation of VIVO from Release 1, Version 1.1 to Version 1.2. This and other documentation can be found on the support page @@ -41,95 +41,69 @@
- The VIVO 1.2 release incorporates major changes to the entire - application - theming and navigation changes that will be immediately - evident to any user, and underlying changes to the system architecture - that are less visible but address important questions of scalability - and extensibility. + The VIVO 1.2 release incorporates major changes throughout the + application - notably a new templating system to support more flexible + display and navigation, plus improvements to address scalability. The + 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.
-- A new installation of VIVO 1.2 will look strikingly different - the - User Interface team has designed a new visual theme that incorporates a - new navigation and browse structure as well as a much more modular - approach to page design. This theme is not only cosmetically different - but leverages entirely new page templates developed with the Freemarker - system, an open-source library for Java development that enables much - cleaner separation of application logic from the actual page design. - These changes extend the available configuration options controlling - VIVO's appearance and navigation options while also simplifying the - process of local customization and branding. + A new installation of VIVO 1.2 looks strikingly different, with a + new navigation and browse interface as well as a more modular page + design that is easier to customize and brand for your local + institution. Page displays now support inline navigation to streamline + viewing of expanded personal and organizational profiles, as well as + improved graphic layout and organization. New browsing controls on the + home page and each menu page include interactive visual controls to + provide an immediate overview of the size and range of content and + quick access down to the individual person, organization, research + feature, or event. VIVO's navigation has also been completely + overhauled. +
+
+ 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.
+
- For existing installations of VIVO, the upgrade will not immediately - transition to the new theme, navigation, or page templates. The current - default theme and "tabs" (top-level and secondary navigation controls) - will be left intact on upgrade and will still function as they do in - 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. + With version 1.2, VIVO has been converted to optionally use Jena's + SPARQL database (SDB) subsystem. SDB significantly reduces the baseline + memory footprint, allowing VIVO installations to scale well beyond what + has previously been possible.
-- In addition to changes in the top-level navigation, VIVO 1.2 - introduces a number of new browsing controls that will be made more - configurable and extensible in version 1.3 but which already offer - extensive functionality. + VIVO continues to expand visualization options including all-new + user-configurable temporal comparisons of publications and grants, + grouped by organization or by affiliated person. Visualizations of + 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.
+- A fresh installation of VIVO 1.2 will feature the new theme and - additional browsing options on other top-level navigation pages (Home, - People, Research, Organizations, and Events). Primary among the new - browsing options will be browsing by type, organized - hierarchically with the same upper-level class groups - 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. + VIVO 1.2 includes a new ontology module representing research + resources including biological specimens, human studies, instruments, + organisms, protocols, reagents, and research opportunities. This module + is aligned with the top-level ontology classes and properties from the + NIH-funded eagle-i Project.
+- Once a group has been selected, browsing can continue to the very - specific, at the level of individual people, organizations, events, or - publications via A ... Z listing featuring thumbnail pictures where - available. Sites will be able to configure which groups and which types - within a group are exposed in search results and for browsing. + 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.
-- Before this release, VIVO has used the Jena - (http://jena.sourceforge.net) - 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. -
-- 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. -
-- 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. -
-[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftlA sample
googleAnalytics.ftl
- 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
- 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
+ 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
@@ -587,299 +561,294 @@
- 4. If you had modified web.xml
- to configure the Pellet Reasoner (as described
- in the installation instructions), repeat that modification.
-
- 5. Stop Apache Tomcat and run ant by typing: ant all
-
- 6. Start Apache Tomcat and log in to VIVO. -
-
- After Apache Tomcat is started, these files should be reviewed to
- verify that the automated upgrade process was executed
- successfully. The ontology alignment process will create the
- following files in the Tomcat webapps/vivo/WEB-INF directory:
-
ontologies/update/logs/knowledgeBaseUpdate.log
- ontologies/update/logs/knowledgeBaseUpdate.error.log
- ontologies/update/changedData/removedData.n3
- ontologies/update/changedData/addedData.n3
- - Changes to the VIVO core ontology 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 process will make only the following - types of changes: -
-- Each uploaded file exists as an individual entity in VIVO. When the - browser requests an upload 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 the uploaded file, - is stored in the file entity. - That way, pages that contain many files can be displayed much more quickly. -
-- 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 - VIVO upload directory. You should review this file to ensure that - this upgrade worked properly. -
-upgrade/FileStorageAliasAdder-log.2011-00-00T00-00-00.txt
- 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
- corrective action needs to be taken.
- - 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 - the FreeMarker files have an ftl (for FreeMarker Template Language) extension. -
-- Follow step A or B below, whichever is applicable to your site: -
-- A. If you did not create a customized theme for your site in V1.0 or V1.1, but used - the vivo-basic theme in its original directory, you need not take any - action in order to convert your site to the VIVO 1.1 theme. -
-- B. If you created your own theme directory in VIVO 1.1, follow the steps below - under sections "Templates," "Stylesheets," and "Site Icons" to upgrade your - theme to VIVO 1.2. -
-/vivo/themes/vivo-basic/templates
- into your theme directory /vivo/themes/[your-theme-name].
- - If you did apply customizations to the JSPs in your VIVO 1.0 - theme,you will need to hand-replicate those modifications in the - new theme template files. -
-- The theme template content that was previously contained in - 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: -
-+ ++ 4. If you had modified
+web.xml+ to configure the Pellet Reasoner (as described + in the installation instructions), repeat that modification. ++ 5. Stop Apache Tomcat and run ant by typing:
+ant all++ 6. Start Apache Tomcat and log in to VIVO. +
+III. Ontology Changes
+i. Verify Ontology upgrade process
++ After Apache Tomcat is started, these files should be reviewed to + verify that the automated upgrade process was executed + successfully. The ontology alignment process will create the + following files in the Tomcat
+webapps/vivo/WEB-INF directory: +
ontologies/update/logs/knowledgeBaseUpdate.log
+ ontologies/update/logs/knowledgeBaseUpdate.error.log
+ ontologies/update/changedData/removedData.n3
+ ontologies/update/changedData/addedData.n3
+ + Changes to the VIVO core ontology 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 process will make only the following + types of changes: +
++ Each uploaded file exists as an individual entity in VIVO. When the + browser requests an upload 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 the uploaded file, + is stored in the file entity. + That way, pages that contain many files can be displayed much more quickly. +
++ 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 + VIVO upload directory. You should review this file to ensure that + this upgrade worked properly. +
+upgrade/FileStorageAliasAdder-log.2011-00-00T00-00-00.txt
+ 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
+ corrective action needs to be taken.
+ + 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 + the FreeMarker files have an ftl (for FreeMarker Template Language) extension. +
++ Follow step A or B below, whichever is applicable to your site: +
++ A. If you did not create a customized theme for your site in V1.0 or V1.1, but used + the vivo-basic theme in its original directory, you need not take any + action in order to convert your site to the VIVO 1.1 theme. +
++ B. If you created your own theme directory in VIVO 1.1, follow the steps below + under sections "Templates," "Stylesheets," and "Site Icons" to upgrade your + theme to VIVO 1.2. +
+/vivo/themes/wilma/templates
+ into your theme directory /vivo/themes/[your-theme-name].
+ + If you did apply customizations to the JSPs in your VIVO 1.0 + theme,you will need to hand-replicate those modifications in the + new theme template files. +
++ The theme template content that was previously contained in + 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: +
+
identity.jsp => identity.ftl
menu.jsp => menu.ftl and search.ftl
footer.jsp => footer.ftl and googleAnalytics.ftl
-
- googleAnalytics.ftl
- is the file to which you add your site's Google Analytics Tracking
- Code (see section II).
-
- Because the FreeMarker Template Language uses many syntactic - conventions that will be familiar to template authors from JSP - or other common templating systems, the translation of your JSP - changes into the new FTLs should be relatively straightforward. -
-- Consult the FreeMarker Template Author's Guide at http://freemarker.org/docs/dgui.html - and the Reference at http://freemarker.org/docs/ref.html - 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. -
-- - ©2011 - All Rights Reserved | Terms of Use - - | Powered by VIVO -
- -
+ googleAnalytics.ftl
+ is the file to which you add your site's Google Analytics Tracking
+ Code (see section II).
+
+ Because the FreeMarker Template Language uses many syntactic + conventions that will be familiar to template authors from JSP + or other common templating systems, the translation of your JSP + changes into the new FTLs should be relatively straightforward. +
++ Consult the FreeMarker Template Author's Guide at http://freemarker.org/docs/dgui.html + and the Reference at http://freemarker.org/docs/ref.html + 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. +
++ + ©2011 + All Rights Reserved | Terms of Use + + | Powered by VIVO +
+ +