updates to outdated URLs and branch names (#251)

updates to outdated URLs and branch names (typically master -> main)
vivo-project · Oct 6, 2021 · 1d6556f · 1d6556f
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,7 +1,7 @@
 **Thank you for submitting a pull request! Title this pull request with a brief description of what the pull request fixes/improves/changes. Please describe the pull request in detail using the template below.**
 * * *
 
-**[JIRA Issue](https://jira.duraspace.org/projects/VIVO)**: (please link to issue)
+**[JIRA Issue](https://jira.lyrasis.org/projects/VIVO)**: (please link to issue)
 
 * Other Relevant Links (Mailing list discussion, related pull requests, etc.)
 

diff --git a/.gitignore b/.gitignore
@@ -22,3 +22,6 @@ utilities/rdbmigration/.work
 **/bin/
 
 vivo-home/
+
+.fake
+.ionide
diff --git a/README.md b/README.md
@@ -14,12 +14,12 @@ desired information across disciplines.
 http://vivoweb.org/
 
 ### VIVO Project Wiki
-https://wiki.duraspace.org/display/VIVO/
+https://wiki.lyrasis.org/display/VIVO/
 
 ### Installation Instructions
 
 Installation instructions for the latest release can be found at this location on the wiki:  
-https://wiki.duraspace.org/display/VIVODOC112x/Installing+VIVO
+https://wiki.lyrasis.org/display/VIVODOC112x/Installing+VIVO
 
 ### Docker
 
@@ -92,7 +92,7 @@ development, implementation, and testing.
 
 ## Contributing Code
 If you would like to contribute code to the VIVO project, please open a ticket 
-in our [JIRA](https://jira.duraspace.org/projects/VIVO), and prepare a 
+in our [JIRA](https://jira.lyrasis.org/projects/VIVO), and prepare a 
 pull request that references your ticket.  Contributors welcome!
 
 ## Citing VIVO

diff --git a/home/pom.xml b/home/pom.xml
@@ -1,7 +1,4 @@
-<project
-    xmlns="http://maven.apache.org/POM/4.0.0"
-    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
@@ -72,4 +69,4 @@
             <type>tar.gz</type>
         </dependency>
     </dependencies>
-</project>
+</project>
diff --git a/home/src/main/resources/config/example.runtime.properties b/home/src/main/resources/config/example.runtime.properties
@@ -10,7 +10,7 @@
 # For more information on specific properties, see the configuration reference
 # or installation options section of the technical documentation for the
 # version of VIVO you are running:
-# https://wiki.duraspace.org/display/VIVO/VIVO+Technical+Documentation
+# https://wiki.lyrasis.org/display/VIVO/VIVO+Technical+Documentation
 #
 # -----------------------------------------------------------------------------
 

diff --git a/installer/pom.xml b/installer/pom.xml
@@ -272,7 +272,7 @@
         <repository>
             <id>vivo-dependencies</id>
             <name>VIVO Dependencies</name>
-            <url>https://raw.github.com/vivo-project/dependencies/master/</url>
+            <url>https://raw.github.com/vivo-project/dependencies/main/</url>
         </repository>
 
         <repository>

diff --git a/pom.xml b/pom.xml
@@ -1,5 +1,4 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
@@ -68,7 +67,7 @@
     </modules>
 
     <profiles>
-       <profile>
+        <profile>
             <id>Vitro-languages</id>
             <activation>
                 <file>
@@ -78,8 +77,8 @@
             <modules>
                 <module>../Vitro-languages</module>
             </modules>
-       </profile>
-       <profile>
+        </profile>
+        <profile>
             <id>VIVO-languages</id>
             <activation>
                 <file>
@@ -89,8 +88,8 @@
             <modules>
                 <module>../VIVO-languages</module>
             </modules>
-       </profile>
-       <profile>
+        </profile>
+        <profile>
             <id>vitro</id>
             <activation>
                 <file>
@@ -489,16 +488,19 @@
                     <failOnError>false</failOnError>
                 </configuration>
                 <reportSets>
-                    <reportSet><!-- by default, id = "default" -->
-                        <reports><!-- select non-aggregate reports -->
+                    <reportSet>
+                        <!-- by default, id = "default" -->
+                        <reports>
+                            <!-- select non-aggregate reports -->
                             <report>javadoc</report>
                             <report>test-javadoc</report>
                         </reports>
                     </reportSet>
-                    <reportSet><!-- aggregate reportSet, to define in poms 
+                    <reportSet>
+                        <!-- aggregate reportSet, to define in poms 
                             having modules -->
                         <id>aggregate</id>
-                        <inherited>false</inherited><!-- don't run aggregate 
+                        <inherited>false</inherited> <!-- don't run aggregate 
                             in child modules -->
                         <reports>
                             <report>aggregate</report>
@@ -530,7 +532,7 @@
         <repository>
             <id>vivo-dependencies</id>
             <name>VIVO Dependencies</name>
-            <url>https://raw.github.com/vivo-project/dependencies/master/</url>
+            <url>https://raw.github.com/vivo-project/dependencies/main/</url>
         </repository>
 
         <repository>
@@ -560,4 +562,4 @@
             <url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
         </repository>
     </distributionManagement>
-</project>
+</project>
diff --git a/rc_script.sh b/rc_script.sh
@@ -1,12 +1,12 @@
 #!/bin/bash
 # RC Script
 
-RC_VERSION=1.11.1
+RC_VERSION=1.12.0
 RC_NUM=1
 
-git checkout master
+git checkout main
 git pull
-git push origin master:rel-${RC_VERSION}-RC
+git push origin main:rel-${RC_VERSION}-RC
 
 
 git checkout rel-${RC_VERSION}-RC

diff --git a/update-versions.sh b/update-versions.sh
@@ -2,7 +2,7 @@
 
 if  [ -z "$1" ]
   then
-    echo 'New version number required eg. 1.9.0-rc1'
+    echo 'New version number required eg. 1.12.0-RC1'
     exit 1
 fi
 

diff --git a/webapp/src/main/webapp/config/listViewConfig-additionalEmail.xml b/webapp/src/main/webapp/config/listViewConfig-additionalEmail.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-adviseeIn.xml b/webapp/src/main/webapp/config/listViewConfig-adviseeIn.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-advisorIn.xml b/webapp/src/main/webapp/config/listViewConfig-advisorIn.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-authorInAuthorship.xml b/webapp/src/main/webapp/config/listViewConfig-authorInAuthorship.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-awardOrHonor.xml b/webapp/src/main/webapp/config/listViewConfig-awardOrHonor.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-awardOrHonorGiven.xml b/webapp/src/main/webapp/config/listViewConfig-awardOrHonorGiven.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-dateTimeInterval.xml b/webapp/src/main/webapp/config/listViewConfig-dateTimeInterval.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-dateTimeValue.xml b/webapp/src/main/webapp/config/listViewConfig-dateTimeValue.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-default.xml b/webapp/src/main/webapp/config/listViewConfig-default.xml
@@ -3,7 +3,7 @@
 
 <!-- VIVO-specific default list view config file for object properties
 
-     See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+     See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-degreeEarned.xml b/webapp/src/main/webapp/config/listViewConfig-degreeEarned.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-doi.xml b/webapp/src/main/webapp/config/listViewConfig-doi.xml
@@ -3,7 +3,7 @@
 
 <!-- VIVO-specific default list view config file for object properties
 
-     See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+     See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-editorship.xml b/webapp/src/main/webapp/config/listViewConfig-editorship.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-educationalTraining.xml b/webapp/src/main/webapp/config/listViewConfig-educationalTraining.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-fauxPropertyDefault.xml b/webapp/src/main/webapp/config/listViewConfig-fauxPropertyDefault.xml
@@ -3,7 +3,7 @@
 
 <!-- VIVO-specific default list view config file for object properties
 
-     See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+     See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-faxNumber.xml b/webapp/src/main/webapp/config/listViewConfig-faxNumber.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-fullName.xml b/webapp/src/main/webapp/config/listViewConfig-fullName.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-grantAdministeredBy.xml b/webapp/src/main/webapp/config/listViewConfig-grantAdministeredBy.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-hasAssociatedConcept.xml b/webapp/src/main/webapp/config/listViewConfig-hasAssociatedConcept.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-hasAttendeeRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasAttendeeRole.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-hasClinicalActivity.xml b/webapp/src/main/webapp/config/listViewConfig-hasClinicalActivity.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-hasCoPrincipalInvestigatorRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasCoPrincipalInvestigatorRole.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-hasEditorRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasEditorRole.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-hasInvestigatorRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasInvestigatorRole.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <list-view-config>
     <query-select>

diff --git a/webapp/src/main/webapp/config/listViewConfig-hasPresenterRole.xml b/webapp/src/main/webapp/config/listViewConfig-hasPresenterRole.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!-- $This file is distributed under the terms of the license in LICENSE$ -->
 
-<!-- See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
+<!-- See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
 
 <!-- Note: ?workshop is a generic name for any intervening event between a presentation and -->
 <!-- a conference, such as a workshop or session or exhibit.  tlw72 -->
-Original file line number
+Diff line change
@@ Expand Up / @@ -22,3 +22,6 @@ utilities/rdbmigration/.work @@
     **/bin/
     vivo-home/
+    .fake
+    .ionide