From 80666aa0a07101e29fdd8b2d97f00c2540ad1c4b Mon Sep 17 00:00:00 2001 From: stellamit Date: Mon, 12 Dec 2011 17:15:39 +0000 Subject: [PATCH] merging changes from 1.4 branch --- doc/upgrade-1.4.html | 261 ++++++++---------- .../config/listViewConfig-relatedRole.xml | 7 +- src/org/vivoweb/webapp/util/ModelUtils.java | 1 + 3 files changed, 125 insertions(+), 144 deletions(-) diff --git a/doc/upgrade-1.4.html b/doc/upgrade-1.4.html index 6dcf14c3..137aeab3 100644 --- a/doc/upgrade-1.4.html +++ b/doc/upgrade-1.4.html @@ -16,19 +16,9 @@ December 9, 2011 - Upgrading from Release 1 V1.3 to Release 1 V1.4 - - -

- This document provides a short description of the steps involved in - upgrading your installation of VIVO from Version 1.3 to Version 1.4. + This document contains instructions on how to upgrade your + installation of VIVO from Version 1.3 to Version 1.4. This and other documentation can be found on the support page at VIVOweb.org

@@ -40,108 +30,102 @@ list of the required software and versions (there are no new hardware or software requirements for V1.4).

-

Release Announcement for V1.4

- -

TBD

-
- -

Upgrade process for V1.4

+

+ For a description of the release contents see the Release announcement for V1.4. +

+
+

Table of Contents

  1. - Before Performing the Upgrade -
    2. -
  2. - Noteworthy Changes + Upgrade process for V1.4
    -
      -
    1. - Template changes -
      2. -
    2. - Profile editing by Proxies -
      3. -
    3. - Change to Tomcat configuration -
      4. -
    -
    3. -
  3. - The Upgrade Process -
    4. -
  4. - Ontology Changes -
      -
    1. - Verify - Ontology upgrade process -
      2. -
    2. - Ontology - knowledge - base - manual review -
      3. +
        +
      1. + Before Performing the Upgrade +
        2. +
      2. + Noteworthy Changes +
        +
          +
        1. + Template changes +
          2. +
        2. + Profile editing by Proxies +
          3. +
        3. + Change to Tomcat configuration +
          4. +
        +
        3. +
      3. + The Upgrade Process +
        4. +
      4. + Knowledge Base Migration +
          +
        1. + Knowledge Base Migration Process +
          2. +
        2. + Knowledge Base Manual Review for Local Extensions +
          3. +
        +
      -
    3. Review the VIVO Terms of Use
      4. +
    4. + Next Steps +
    - +

    I. Before Performing the Upgrade

    -

    - Please ensure that backups are created of the: -

    +
    + Create backups of the:
    • Tomcat webapps directory
    • - Original source directory + Original source directory (TODO: I think we should specifically name the directory (I don't know what's intended) sjm)
    • MySQL database (mysqldump)

    - The upgrade process is similar to the original install process + The upgrade process is similar to the initial install process with - the following EXCEPTIONS: + the following exceptions:

    • - If you are still in RDB mode, it is required that you move - your - triple store to SDB while still at V1.2 (see Triple - Store - info below).  -
      -
      • -
    • - 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. + You do not need to reinstall MySQL or recreate the MySQL database. Please + backup your MySQL database as noted above.
    • First-time login of the root account after the upgrade - process is complete will use the password previously set, NOT the + process is complete will use the password previously set (not the default password used on the first login after the initial - installation. + 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 the Ontology Upgrade - below for more information. + The first time Apache Tomcat starts up after the upgrade, an automated + process will modify the knowledge base to align the + data with any ontology updates made for the new release. See the section on the Ontology Upgrade + below for more information. Note that

    II. Noteworthy Changes

    +

    (TOTO: I think this should contain only changes to the upgrade process itself. Changes to the source code that are too detailed for the release announcement could go in + an appendix (final section) to this document until such time as there is an granual release changes document.

    +

    i. Template changes

      @@ -176,9 +160,8 @@ source directory.

      - 2. Create a new deploy.properties using the same values as in - your - previous installation and set values for the new variables as described + 2. Create a new deploy.properties using the same settings as in + your previous installation and set values for the new variables as described below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask, vitro.home.directory, email.smptHost, email.replyTo, rootUser.emailAddress) @@ -649,12 +632,6 @@

    -

    - 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 from your VIVO source directory, run ant @@ -671,13 +648,12 @@ Go to the "Site Admin" page and click on "Rebuild Search Index" under the heading "Refresh Content".

    -

    IV. 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: + 8. Review and save aside the knowledge base migration logs. + The knowledge base migration process described in the next section will generate logs. + These logs will be overwritten if you redeploy the VIVO application (but not if you restart tomcat), and since + they may be a useful reference if questions come up about your 1.4 VIVO data after deployment, you should save them aside. + The logs are created in the Tomcat webapps/vivo/WEB-INF directory:

    @@ -685,10 +661,9 @@
    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 "Finished knowledge base migration". 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. + base. This file should end with "Finished knowledge base migration". + 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.
    @@ -697,43 +672,25 @@
    A log of errors that were encountered during the upgrade - process. This file should be empty if the upgrade was successful. + process. This file should be empty if the upgrade was successful. If any errors are encountered + you will need to rerun the knowledge base migration.
    -
    -
    - 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. -
    -
    -

    ii. 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. + +

    +

    +

    IV. Knowledge Base Migration

    +

    i.Knowledge Base Migration Process

    +

    + For an description of changes to the VIVO ontology in version 1.4 see the sourceforge wiki page on ontology changes

    - When Apache Tomcat starts up following the upgrade, it will + Changes to the VIVO core ontology may require corresponding + modifications to the knowledge base instance data and ontology annotations. + When VIVO first 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: + changes. The knowledge base migration process will make the following types of changes:

    @@ -741,8 +698,7 @@
    All references to the class (in the subject or object - position) - will be updated to the new name. References to the property will be + position) will be updated to the new name. References to the property will be updated to the new name.
    @@ -760,16 +716,6 @@ 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 @@ -785,6 +731,38 @@ new default value will be propagated to the knowledge base.
    +
    +
    + Structural changes +
    +
    + Changes in the way individuals (intances of classes) are related to other individuals. +
    +
    +

    + In addition to the logs described in step 8 of the previous section, the knowledge base migration + process will log copies of all additions and deletions that were made to the knowledge base in the following files: +

    +
    +
    + webapps/vivo/WEB-INF/ontologies/update/changedData/removedData.n3 +
    +
    + An N3 file containing all the statements that were removed from the knowledge base. +
    +
    +
    +
    + webapps/vivo/WEB-INF/ontologies/update/changedData/addedData.n3 +
    +
    + An N3 file containing all the statements that were added to the knowledge base. +
    +
    +

    ii. Knowledge Base Manual Review for Local Extensions

    + Not all of the modifications that may be required are + automated. If you have local extensions to areas of the ontology that have changed, a manual review of the knowledge base is recommended after + the automated upgrade process.

    V. Review the VIVO Terms of Use

    VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name" @@ -795,9 +773,10 @@ Be sure to make the changes in your source files and deploy them to your tomcat so you don't lose your changes next time you deploy for another reason.

    -

    Next Step ...

    +

    Next Steps

    - Now that you have VIVO up and running, please go read the Site Administrator's Guide. + Now that you have VIVO up and running, please refer to the Site Administrator's Guide + for information about its operation.

    diff --git a/productMods/config/listViewConfig-relatedRole.xml b/productMods/config/listViewConfig-relatedRole.xml index d36e03d0..e3de6ddf 100644 --- a/productMods/config/listViewConfig-relatedRole.xml +++ b/productMods/config/listViewConfig-relatedRole.xml @@ -33,8 +33,9 @@ http://vivoweb.org/ontology/core#realizedRole and http://vivoweb.org/ontology/co OPTIONAL { ?subclass rdfs:label ?roleTypeLabel } ?roleProp rdfs:subPropertyOf core:roleOf ; rdfs:domain ?subclass . - ?role ?roleProp ?indivInRole - OPTIONAL { ?indivInRole rdfs:label ?indivLabel } + OPTIONAL { ?role ?roleProp ?indivInRole + OPTIONAL { ?indivInRole rdfs:label ?indivLabel } + } } OPTIONAL { ?role core:dateTimeInterval ?dateTimeInterval @@ -86,7 +87,7 @@ http://vivoweb.org/ontology/core#realizedRole and http://vivoweb.org/ontology/co ?role vitro:mostSpecificType ?subclass } UNION { ?subject ?property ?role . - ?role a ?subclass . + ?role vitro:mostSpecificType ?subclass . ?subclass rdfs:label ?roleTypeLabel } UNION { ?subject ?property ?role . diff --git a/src/org/vivoweb/webapp/util/ModelUtils.java b/src/org/vivoweb/webapp/util/ModelUtils.java index ab3f9aff..4277fded 100644 --- a/src/org/vivoweb/webapp/util/ModelUtils.java +++ b/src/org/vivoweb/webapp/util/ModelUtils.java @@ -56,6 +56,7 @@ public class ModelUtils { VClassDao vcd = wadf.getVClassDao(); List superClassURIs = vcd.getSuperClassURIs(classURI, false); + superClassURIs.add(classURI); Iterator iter = superClassURIs.iterator(); ObjectProperty op = new ObjectProperty();