* reformated and retitled the notes to "Special notes about source files"
* restructured Stella's ontology section and Jim's file storage section to provide verification info earlier. Questions: * Stella and Chris - could you provide feedback if the changes I made address your improvement recommendations? * Jim - is it still the "localhost" log where the error for the file system storage shows up in Tomcat? * Rebecca - in B.2 of the theme changes, is it 'a' or 'b', then 'c' for regardless? Sorry if I'm being dense.
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@ -19,8 +19,12 @@ directory.
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I. Before Performing the Upgrade
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I. Before Performing the Upgrade
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II. The Upgrade Process
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II. The Upgrade Process
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III. Ontology Changes
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III. Ontology Upgrade
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IV. File Storage Changes
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A. Verify Ontology upgrade process
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B. Ontology knowledge base manual r
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IV. New File Storage System
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A. Verifying the File Storage upgrade
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B. File Storage changes
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V. Theme Changes
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V. Theme Changes
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-------------------------------------------------------------------------------
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-------------------------------------------------------------------------------
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@ -63,26 +67,32 @@ II. The Upgrade Process
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4. Apply any changes you have made to the new source directory.
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4. Apply any changes you have made to the new source directory.
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Note: In many cases, simply copying the modified files from your original
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************* Special notes regarding source files ********************
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This process assumes any changes made to the application were made in
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the source directory and deployed, and were not made directly within
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Apache Tomcat webapp.
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In many cases, simply copying the modified files from your original
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source directory will not work since the files on which they are based
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source directory will not work since the files on which they are based
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have changed. It will be necessary to inspect the new source files and
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have changed. It will be necessary to inspect the new source files and
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add any changes to them at that time.
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add any changes to them at that time.
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Note: At a minimum it will be necessary to apply the Google Analytics
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At a minimum it will be necessary to apply the Google Analytics Tracking
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Tracking Code to googleAnalytics.ftl in the theme:
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Code (GATC) to googleAnalytics.ftl in the theme:
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[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl
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[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl
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A sample googleAnalytics.ftl is included in the built-in theme. This file
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A sample googleAnalytics.ftl is included in the built-in theme. This file
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serves only as an example, and you must replace the tracking code shown
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serves only as an example, and you must replace the tracking code shown
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with your institution's own tracking code.
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with your institution's own tracking code.
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For additional information and a copy your institution's tracking code,
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For additional information about the GATC for the NIH-funded VIVO
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see the Google Analytics wiki page.
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implementation sites and a copy your institution's tracking code, see the
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VIVO Google Analytics wiki page:
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https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI
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https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI
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Note: This process assumes any changes made to the application were made in
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************************************************************************
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the source directory and deployed, and were not made directly within
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Apache Tomcat webapp.
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5. If you had modified web.xml to configure the Pellet Reasoner (as described
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5. If you had modified web.xml to configure the Pellet Reasoner (as described
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in the installation instructions), repeat that modification.
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in the installation instructions), repeat that modification.
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@ -124,6 +134,29 @@ II. The Upgrade Process
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III. Ontology Changes
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III. Ontology Changes
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A. Verify Ontology upgrade process
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After Apache Tomcat is started, these files should be reviewed to verify that
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the automated upgrade process was executed successfully. The ontology alignment
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process will create the following files in the Tomcat webapps/vivo/WEB-INF directory:
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ontologies/update/logs/knowledgeBaseUpdate.log
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a log of a summary of updates that were made to the knowledge base and notes
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about some recommended manual reviews. This file should end with
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"Successfully finished processing ontology changes".
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ontologies/update/logs/knowledgeBaseUpdate.error.log
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a log of errors that were encountered during the upgrade process. This file
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should be empty if the upgrade was successful.
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ontologies/update/changedData/removedData.n3
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an N3 file containing all the statements that were removed from the knowledge base.
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ontologies/update/changedData/addedData.n3
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an N3 file containing all the statements that were added to the knowledge base.
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B. Ontology knowledge base manual review
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Changes to the VIVO core ontology may require corresponding
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Changes to the VIVO core ontology may require corresponding
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modifications of the knowledge base instance data and local ontology
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modifications of the knowledge base instance data and local ontology
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extensions.
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extensions.
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@ -169,32 +202,41 @@ the following types of changes:
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default has been changed in the new version of the ontology, then
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default has been changed in the new version of the ontology, then
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the new default value will be propagated to the knowledge base.
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the new default value will be propagated to the knowledge base.
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The ontology alignment process will create the following files in the
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Tomcat webapps/vivo/WEB-INF directory:
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ontologies/update/logs/knowledgeBaseUpdate.log
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a log of a summary of updates that were made to the knowledge base and notes
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about some recommended manual reviews. This file should end with
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"Successfully finished processing ontology changes".
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ontologies/update/logs/knowledgeBaseUpdate.error.log
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a log of errors that were encountered during the upgrade process. This file
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should be empty if the upgrade was successful.
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ontologies/update/changedData/removedData.n3
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an N3 file containing all the statements that were removed from the knowledge base.
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ontologies/update/changedData/addedData.n3
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an N3 file containing all the statements that were added to the knowledge base.
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After Apache Tomcat is started, these files should be reviewed to verify that
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the automated upgrade process was executed successfully.
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-------------------------------------------------------------------------------
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-------------------------------------------------------------------------------
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IV. File Storage Changes
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IV. New File Storage System
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A. Verifying the File Storage upgrade
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If, for any reason, the File Storage upgrade process is not successful,
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VIVO will not start. Attempts to open VIVO in the browser will result in a
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404 error. Tomcat's "localhost" log file will contain an exception listing
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with more information.
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The File Storage upgrade process will create these files in the Vivo upload
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directory:
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upgrade/upgradeLog.2010-00-00T00-00-00.txt
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A log of the upgrade process. The actual filename includes a timestamp
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that tells when the upgrade executed. This file should be inspected
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for warnings or errors. The file should end with "File Storage update
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is complete."
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upgrade/translatedImages
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Contains the images that were translated to the new file storage system.
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upgrade/unreferencedImages
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Contains the images which were in the "images" directory, but were no
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longer referred to by any Individual.
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file_storage_root
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A directory where the uploaded images are stored. Within the root, the
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path to the image is derived from its unique ID and its filename.
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file_storage_namespaces.properties
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Contains the URL prefix used when serving the image files.
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B. File Storage changes
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Changes to the File Storage system in VIVO result in new properties to describe
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Changes to the File Storage system in VIVO result in new properties to describe
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the relationships involving files, and a new directory structure in which to
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the relationships involving files, and a new directory structure in which to
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@ -246,40 +288,11 @@ which makes the required changes:
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All image files are removed from their old locations in the upload
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All image files are removed from their old locations in the upload
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directory.
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directory.
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The File Storage upgrade process will create these files in the Vivo upload
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directory:
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upgrade/upgradeLog.2010-00-00T00-00-00.txt
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A log of the upgrade process. The actual filename includes a timestamp
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that tells when the upgrade executed. This file should be inspected
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for warnings or errors. The file should end with "File Storage update
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is complete."
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upgrade/translatedImages
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Contains the images that were translated to the new file storage system.
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upgrade/unreferencedImages
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Contains the images which were in the "images" directory, but were no
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longer referred to by any Individual.
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file_storage_root
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A directory where the uploaded images are stored. Within the root, the
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path to the image is derived from its unique ID and its filename.
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file_storage_namespaces.properties
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Contains the URL prefix used when serving the image files.
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If, for any reason, the File Storage upgrade process is not successful,
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VIVO will not start. Attempts to open VIVO in the browser will result in a
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404 error. Tomcat's "localhost" log file will contain an exception listing
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with more information.
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Once you are satisfied that the File Storage upgrade process is successful,
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Once you are satisfied that the File Storage upgrade process is successful,
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you may delete the "images" folder and the "upgrade" folder from the upload
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you may delete the "images" folder and the "upgrade" folder from the upload
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directory. You may also delete the WEB-INF/images directory from within
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directory. You may also delete the WEB-INF/images directory from within
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your Tomcat web application.
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your Tomcat web application.
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-------------------------------------------------------------------------------
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-------------------------------------------------------------------------------
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V. Theme Changes
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V. Theme Changes
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@ -345,10 +358,3 @@ to upgrade your theme to VIVO 1.1.
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style upgrades that your theme should pick up. Instead, you should
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style upgrades that your theme should pick up. Instead, you should
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use the vivo-basic 1.1 stylesheets as a starting point, and manually
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use the vivo-basic 1.1 stylesheets as a starting point, and manually
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merge your 1.0 style modifications in as needed.
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merge your 1.0 style modifications in as needed.
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