From 959940dbc805037dfc6c7858865528cb3ebf0005 Mon Sep 17 00:00:00 2001 From: ejc12 Date: Mon, 17 Jan 2011 01:50:47 +0000 Subject: [PATCH] The upgrade-1.2.html is up2date with the content in upgrade-1.2.txt, so I will ask developers to edit upgrade-1.2.html --- doc/upgrade-1.2.txt | 242 -------------------------------------------- 1 file changed, 242 deletions(-) delete mode 100644 doc/upgrade-1.2.txt diff --git a/doc/upgrade-1.2.txt b/doc/upgrade-1.2.txt deleted file mode 100644 index 33b4b8c9..00000000 --- a/doc/upgrade-1.2.txt +++ /dev/null @@ -1,242 +0,0 @@ - -------------------------------------------------------------------------------- - -Upgrading VIVO - -Steps to Upgrade from Release 1 Version 1.1.1 to Release 1 Version 1.2 - -This file provides a short description of the steps involved in upgrading your -installation of VIVO from Release 1 Version 1.1.1 to Release 1 Version 1.2. -This and other documentation can be found at: - -http://vivoweb.org/support - -Installation: -If you need to do a fresh install, please consult the install.txt in this -directory. - -------------------------------------------------------------------------------- - -I. Before Performing the Upgrade -II. The Upgrade Process -III. Ontology Upgrade - A. Verify Ontology upgrade process - B. Ontology knowledge base manual review -IV. Theme Changes - -------------------------------------------------------------------------------- - -I. Before Performing the Upgrade - -Please read the bullet points below BEFORE beginning the upgrade. - -The upgrade process is similar to the original install process with the following -exceptions: - -* DO NOT reinstall MySQL or recreate the MySQL database. Please ensure that - you back-up the MySQL database. -* It is not necessary to add RDF data. -* First-time login of the administrator account after the upgrade process is - complete will use the password previously set, NOT the default password used - on the first login after the initial installation. -* The 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 Upgrade" - below for more information. - -------------------------------------------------------------------------------- - -II. The Upgrade Process - - -1. Ensure that backups are created of the Tomcat webapps directory, the - original source directory, the MySQL database, and the uploaded files - directory (images). - -2. Download the new distribution file and unpack it into a new source - directory. - -3. Create deploy.properties, using the same values as in your previous - installation. - -4. Apply any previous changes you have made to the new source directory. - - ************* Special notes regarding source files ******************** - - This process assumes any changes made to the application were made in - the source directory and deployed, and were not made directly within - the Tomcat webapps directory. - - 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. - - At a minimum it will be necessary to apply the Google Analytics Tracking - Code (GATC) to googleAnalytics.ftl in the theme: - - [new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl - - A 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 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: - https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI - - If you had used the vivo/contrib/FLShibboleth code in your previous release, - you should stop using it. Consult install.txt for instructions on - "Using an External Authentication System with VIVO". - - ************************************************************************ - -5. If you had modified web.xml to configure the Pellet Reasoner (as described - in the installation instructions), repeat that modification. - -6. Stop Apache Tomcat and run ant by typing: ant all - -7. Start "Apache Tomcat" and log in to VIVO. - -------------------------------------------------------------------------------- - -III. Ontology Changes - -A. 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 - 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 processing 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/changedData/removedData.n3 - An N3 file containing all the statements that were removed from the knowledge base. - -ontologies/update/changedData/addedData.n3 - An N3 file containing all the statements that were added to the knowledge base. - -B. Ontology knowledge base manual review - -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: - - 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. - - Class or Property deletion - All individuals in a deleted class will be removed. - - All statements using a deleted property will be changed - to use the nearest available superproperty. 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. - - Property addition - If a newly added property is the inverse of a previously - existing property, the inverse of any statements using the - pre-existing property will be asserted. - - Annotation property default values - If 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 default 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. - -------------------------------------------------------------------------------- - -IV. Theme Changes - -VIVO 1.1 introduces the first step in a transition from JavaServer Pages (JSPs) -to the FreeMarker template engine for generating web pages. As part of this -process, the JSP files that were used for theme customization in earlier -versions of VIVO have been replaced by a set of FreeMarker templates. -In the 1.1 install package, these files are located in -/vivo/themes/vivo-basic/templates and 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 VIVO 1.0, but used -the 1.0 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 1.0, follow the steps below -under sections "Templates," "Stylesheets," and "Site Icons" to upgrade your -theme to VIVO 1.1. - - 1. Templates - - a. Copy the directory /vivo/themes/vivo-basic/templates into your theme - directory /vivo/themes/. - - b. Follow step i or ii below, whichever is applicable to your theme. - - i. If you did not apply any customizations to the JSPs in your VIVO - 1.0 theme, then you do not need to apply any additional changes - to the VIVO 1.1 theme templates during the upgrade process. - - ii. 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 a new file to which you will 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. - - c. Remove the jsp directory from your themes directory. - - 2. Stylesheets - - 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 - 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 - use the vivo-basic 1.1 stylesheets as a starting point, and manually - merge your 1.0 style modifications in as needed. - - 3. Site Icons - - Copy the site icons from your 1.0 theme into the site_icons folder in - your 1.1 theme. \ No newline at end of file