Create vivo/home on application start-up (#192)

* Create vivo/home on application start-up

- Add logic for untarring vivo-home

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Require runtime.properties and applicationSetup.n3 be in 'config/' dir

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Support loading config files with or without 'default' prefix
* Prioritize without the prefix

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Add leading slash to location of vivo-home.tar resource path
* This allows for deployment in both Tomcat and Jetty

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Ensure VIVO_HOME is populated whether it is empty or not

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* Require common properties to be in JNDI

Properties include:
- vitro/home
- vitro/appName
- vitro/rootUserAddress
- vitro/defaultNamespace

Related to: https://jira.lyrasis.org/browse/VIVO-1443

* VIVO-1443: non destructive vivo home untarring (#2)

* Upgrade Jena version to 3.16.0 (#196)

Related to: https://jira.lyrasis.org/browse/VIVO-1943

* remove example-settings.xml
* update home directory untar non-destructive
* checksum digest to retain modified files
* compare checksum from digest with existing file
* overwrite files that have not changed
* add command to manually generate checksum digest
* simplify parsing checksum digest using pattern

Co-authored-by: Andrew Woods <awoods@lyrasis.org>
Co-authored-by: Andrew Woods <awoods@duraspace.org>

* not overwrite existing file if same as tar entry (#3)

* Upgrade Jena version to 3.16.0 (#196)

Related to: https://jira.lyrasis.org/browse/VIVO-1943

* remove example-settings.xml
* update home directory untar non-destructive
* checksum digest to retain modified files
* compare checksum from digest with existing file
* overwrite files that have not changed
* add command to manually generate checksum digest
* simplify parsing checksum digest using pattern
* do not overwrite file if same as already exists

Co-authored-by: Andrew Woods <awoods@lyrasis.org>
Co-authored-by: Andrew Woods <awoods@duraspace.org>

* Update log messages for clarity

Co-authored-by: Andrew Woods <awoods@duraspace.org>
Co-authored-by: William Welling <wwelling@library.tamu.edu>
Co-authored-by: Gross, Benjamin <benjamin.gross@clarivate.com>

installer/webapp/src/main/webResources/META-INF/context.xml

@@ -1,8 +1,51 @@
 <Context> <!-- useHttpOnly="false" -->
+
+   <!--
+     # The 'home' property specifies the location of Vitro HOME.
+     # The system user used to run the Vitro web application must have write access
+     # to the parent directory of the directory defined in this property, if Vitro HOME
+     # does not already exist.
+     # If this directory already exists, the system user used to run the Vitro web application
+     # must have write access to this directory.
+   -->
    <Environment
-        type="java.lang.String"
-        name="vitro/home"
-        value="${vitro-dir}" override="true"/>
+           type="java.lang.String"
+           name="vitro/home"
+           value="${vivo-dir}" override="true"/>
+
+   <!--
+     # The name of the application (possibly not used).
+   -->
+   <Environment
+           type="java.lang.String"
+           name="vitro/appName"
+           value="vivo" override="true"/>
+
+   <!--
+     # The email address of the root user for the Vitro application. The password
+     # for this user is initially set to "rootPassword", but you will be asked to
+     # change the password the first time you log in.
+   -->
+   <Environment
+           type="java.lang.String"
+           name="vitro/rootUserAddress"
+           value="vivo_root@mydomain.edu" override="true"/>
+
+   <!--
+     # This namespace will be used when generating URIs for objects created in the
+     # editor. In order to serve linked data, the default namespace must be composed
+     # as follows (optional elements in parentheses):
+     #
+     # scheme + server_name (+ port) (+ servlet_context) + "/individual/"
+     #
+     # For example, Cornell's default namespace is:
+     #
+     # http://vivo.cornell.edu/individual/
+   -->
+   <Environment
+           type="java.lang.String"
+           name="vitro/defaultNamespace"
+           value="http://vivo.mydomain.edu/individual/" override="true"/>
 
    <!-- Disable persist sessions on shut down.-->
    <Manager pathname="" />