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Enable war deployment model (#197)

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* Add 'home' files into build war artifact

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

* Disable copying exploded war to Tomcat dir

- hardcode vivo.all.log file name
- must now set system property: -Dvivo-dir=/opt/vivo/home/

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

* Ensure build does not remove and re-add VIVO_HOME/rdf

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

* Remove unnecessary profile from installer/pom.xml

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

* Rename example config files to have 'default' prefix

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: app name (#2)

* Non-functional change to comment in example.applicationSetup.n3

Related to: https://jira.lyrasis.org/browse/VIVO-1741

* Update orcidConfirm.ftl (#199)

* remove example-settings.xml
* simplify war name and afford override during build
* default app name to vivo and pass into context.xml

Co-authored-by: Andrew Woods <awoods@duraspace.org>
Co-authored-by: L.O <53535673+lb-ov@users.noreply.github.com>

Co-authored-by: Andrew Woods <awoods@duraspace.org>
Co-authored-by: William Welling <wwelling@library.tamu.edu>
Co-authored-by: L.O <53535673+lb-ov@users.noreply.github.com>
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home/src/main/resources/config/example.runtime.properties
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# -----------------------------------------------------------------------------
#
# VIVO runtime properties
#
# This file is provided as example.runtime.properties.
#
# Save a copy of this file as runtime.properties in your VIVO home directory,
# and edit the properties as needed for your installation.
#
# 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
#
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
# BASIC PROPERTIES
# -----------------------------------------------------------------------------
#
# 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/
#
Vitro.defaultNamespace = http://vivo.mydomain.edu/individual/
#
# The email address of the root user for the VIVO 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.
#
rootUser.emailAddress = vivo_root@mydomain.edu
#
# Argon2 password hashing parameters for time, memory and parallelism required to
# compute a hash.
#
# A time cost defines the amount of computation realized and therefore the execution
# time, given in a number of iterations.
# A memory cost defines the memory usage, given in kibibytes
# A parallelism degree defines the number of parallel threads
# For determining the optimal values of the parameters for your setup please refer to
# the white paper section 9
# https://github.com/P-H-C/phc-winner-argon2/blob/master/argon2-specs.pdf
#
argon2.parallelism =1
argon2.memory = 1024
argon2.time = 1000
#
# NOTE: VitroConnection.DataSource.* properties are only used in conjuction with
# an SDB triple store.
#
# The basic parameters for a database connection. Change the end of the
# URL to reflect your database name (if it is not "vitrodb"). Change the username
# and password to match the authorized database user you created.
#
# VitroConnection.DataSource.url = jdbc:mysql://localhost/vitrodb
# VitroConnection.DataSource.username = vitrodbUsername
# VitroConnection.DataSource.password = vitrodbPassword
#
# Email parameters which VIVO can use to send mail. If these are left empty,
# the "Contact Us" form will be disabled and users will not be notified of
# changes to their accounts.
#
email.smtpHost = smtp.mydomain.edu
email.replyTo = vivoAdmin@mydomain.edu
#
# URL of Solr context used in local VIVO search. This will usually consist of:
# scheme + server_name + port + vivo_webapp_name + "solr"
# In the standard installation, the Solr context will be on the same server as VIVO,
# and in the same Tomcat instance. The path will be the VIVO webapp.name (specified
# in build.properties) + "solr"
# Example:
# vitro.local.solr.url = http://localhost:8080/vivosolr
#
vitro.local.solr.url = http://localhost:8080/vivosolr
# -----------------------------------------------------------------------------
# LINKING USER ACCOUNTS TO PROFILE PAGES
# -----------------------------------------------------------------------------
#
# How is a logged-in user associated with a particular Individual? One way is
# for the Individual to have a property whose value is the username of the user.
# This value should be the URI for that property.
#
selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
# -----------------------------------------------------------------------------
# USING AN EXTERNAL AUTHENTICATION SYSTEM
# -----------------------------------------------------------------------------
#
# If an external authentication system like Shibboleth or CUWebAuth is to be
# used, this property says which HTTP header will contain the user ID from
# the authentication system. If such a system is not to be used, leave this
# commented out. Consult the installation instructions for more details.
#
#externalAuth.netIdHeaderName = remote_userID
# -----------------------------------------------------------------------------
# TUNING THE DATABASE CONNECTION POOL
# -----------------------------------------------------------------------------
#
# The maximum number of active connections in the database connection pool.
# Increase this value to support a greater number of concurrent page requests.
#
# VitroConnection.DataSource.pool.maxActive = 40
#
# The maximum number of database connections that will be allowed
# to remain idle in the connection pool. Default is 25%
# of the maximum number of active connections.
#
# VitroConnection.DataSource.pool.maxIdle = 10
# -----------------------------------------------------------------------------
# USING A DIFFERENT DATABASE
# -----------------------------------------------------------------------------
#
# Parameters to change in order to use VIVO with a database other than
# MySQL.
#
# VitroConnection.DataSource.dbtype = MySQL
# VitroConnection.DataSource.driver = com.mysql.jdbc.Driver
# VitroConnection.DataSource.validationQuery = SELECT 1
# Note: the above parameters allow you to change the relational database that
# is used as the back end for Jena SDB. If you want to use a triple store
# other than SDB, you will need to edit applicationSetup.n3. See the
# installation instructions for more details.
# -----------------------------------------------------------------------------
# ADDING OPENSOCIAL GADGETS TO VIVO
# -----------------------------------------------------------------------------
#
# For OpenSocial integration
# The base URL of the ORNG Shindig server. Usually, this is the same host and port
# number as VIVO itself, with a context path of "shindigorng".
#
#OpenSocial.shindigURL = http://localhost:8080/shindigorng
#
# For OpenSocial integration
# The host name and port number of the service that provides security tokens for VIVO and
# Shindig to share. For now, the host name must be the actual host, not "localhost" or "127.0.0.1"
# The port number must be 8777
#
#OpenSocial.tokenService = myhost.mydomain.edu:8777
#
# For OpenSocial integration
# The path to the key file that will be used when generating security tokens for VIVO and
# shindig to share.
#
#OpenSocial.tokenKeyFile = /usr/local/vivo/data/shindig/openssl/securitytokenkey.txt
#
# For OpenSocial integration
# Only set sandbox to True for dev/test environments. Comment out or set to False in production
#
#OpenSocial.sandbox = True
# -----------------------------------------------------------------------------
# ADDING LANGUAGES TO VIVO
# -----------------------------------------------------------------------------
#
# Show only the most appropriate data values based on the Accept-Language
# header supplied by the browser. Default is false if not set.
#
# RDFService.languageFilter = false
#
# Force VIVO to use a specific language or Locale instead of those
# specified by the browser. This affects RDF data retrieved from the model,
# if RDFService.languageFilter is true. This also affects the text of pages
# that have been modified to support multiple languages.
#
# languages.forceLocale = en_US
#
# A list of supported languages or Locales that the user may choose to
# use instead of the one specified by the browser. Selection images must
# be available in the i18n/images directory of the theme. This affects
# RDF data retrieved from the model, if RDFService.languageFilter is true.
# This also affects the text of pages that have been modified to support
# multiple languages.
#
# This should not be used with languages.forceLocale, which will override it.
#
# languages.selectableLocales = en_US, es_GO
# -----------------------------------------------------------------------------
# ORCID INTEGRATION
# -----------------------------------------------------------------------------
# orcid.clientId = 0000-0000-0000-000X
# orcid.clientPassword = 00000000-0000-0000-0000-000000000000
#
# The orcid.webappBaseUrl must end in a front slash (/)
# if it includes a path past the domain and (if required) port.
#
# orcid.webappBaseUrl = http://vivo.mydomain.edu/vivo/
# orcid.externalIdCommonName = VIVO Cornell Identifier
# 1.2, 2.0
# orcid.apiVersion = 2.0
# release, sandbox
# orcid.api = sandbox
# Specify the type of API access that you have - public or member
# public - only allows you to confirm ORCID IDs
# member - allows VIVO to write a link to the VIVO profile in the ORCID record
# If you only have a public API key, ensure that you have entered public here
#orcid.apiLevel = public
# -----------------------------------------------------------------------------
# OTHER OPTIONS
# -----------------------------------------------------------------------------
# Google Maps Key
# ---------------
# To use the Google Maps (e.g. Map of Science), you need to have a key for Google Maps
# See https://developers.google.com/maps/documentation/javascript/get-api-key
#
# When you have a key, uncomment the line below and add it here
#google.maps.key=
# AltMetric badges
# ----------------
# Options to embed AltMetric badges on information resource (e.g. journal article) pages
# See the AltMetric documentation for more imformation about each option: http://api.altmetric.com/embeds.html
# The embed code will use a DOI, or PubMed ID, if present
# Enable AltMetric badges
# Uncomment and set this to disabled if you don't want AltMetric badges
#resource.altmetric=disabled
# Display the badge to the left or right of the title (default = right)
# Options: left, right
#resource.altmetric.displayto=right
# Badge type to display (default = donut)
# Options: See AltMetric documentation - recommended settings: donut, medium-donut
#resource.altmetric.badge-type=donut
# Hide the badge if there are no mentions (default = true)
# Options: true, false
#resource.altmetric.hide-no-mentions=true
# Display more details about the score when you hover over the badge (default = right)
# Options, right, left, up, down
#resource.altmetric.badge-popover=right
# Dsiplay extended details alongside the badge (default = none)
#resource.altmetric.badge-details=right
# Plum prints
# ----------------
# Options to embed Plum prints on information resource (e.g. journal article) pages
# The embed code will use a DOI, PubMed ID, ISBN, or OCLC number, if present
# Enable Plum prints
# Uncomment and set this to disabled if you don't want Plum prints
#resource.plum-print=disabled
# Display the badge to the left or right of the title (default = right)
# Options: left, right
#resource.plum-print.displayto=right
# Hide the print if there are no metrics (default = true)
# Options: true, false
#resource.plum-print.hide-when-empty=true
# Display more details about the score when you hover over the print (default = right)
# Options: right, left, top, bottom, hidden
#resource.plum-print.popover=right
# Size of the print (default = medium)
# Options: tiny, small, medium, large
#resource.plum-print.size=medium
#
# When the following flag is set to enabled, the VIVO home page displays a
# global map highlighting the geographical focus of foaf:person individuals.
#
#homePage.geoFocusMaps=enabled
#
# VIVO supports the simultaneous use of a full foaf:Person profile page view
# and a "quick" page view that emphasizes the individual's webpage presence.
# Implementing this feature requires an installation to develop a web service
# that captures images of web pages or to use an existing service outside of VIVO.
#
#multiViews.profilePageTypes=enabled
#
# Tell VIVO to generate HTTP headers on its responses to facilitate caching the
# profile pages that it creates.
#
# Developers will likely want to leave caching disabled, since a change to a
# Freemarker template or to a Java class would not cause the page to be
# considered stale.
#
http.createCacheHeaders = true
#
# Absolute path on the server of the Harvester root directory.
# You must include the final slash.
#
# Setting a value for harvester.location indicates that the Harvester is installed at
# this path. This will enable the Harvester functions in the Ingest Tools page.
#
# harvester.location = /usr/local/vivo/harvester/
#
# The temporal graph visualization is used to compare different organizations/people
# within an organization on parameters like number of publications or grants.
# By default, the app will attempt to make its best guess at the top level
# organization in your instance. If you're unhappy with this selection, uncomment out
# the property below and set it to the URI of the organization individual you want to
# identify as the top level organization. It will be used as the default whenever the
# temporal graph visualization is rendered without being passed an explicit org.
# For example, to use "Ponce School of Medicine" as the top organization:
# visualization.topLevelOrg = http://vivo.psm.edu/individual/n2862
#
# visualization.topLevelOrg = http://vivo.mydomain.edu/individual/topLevelOrgURI
#
# The temporal graph visualization can require extensive machine resources.
# This can have a particularly noticeable impact on memory usage if
# - The organization tree is deep,
# - The number of grants and publications is large.
# VIVO 1.3 release mitigates this problem by the way of a caching mechanism &
# hence we can safely set this to be enabled by default.
#
visualization.temporal = enabled
#
# Types of individual for which we can create proxy editors.
# If this is omitted, defaults to http://www.w3.org/2002/07/owl#Thing
#
proxy.eligibleTypeList = http://xmlns.com/foaf/0.1/Person, http://xmlns.com/foaf/0.1/Organization
#
# Default type(s) for Google Refine Reconciliation Service
# The format for this property is id, name; id1, name1; id2, name2 etc.
# For more information, see Service Metadata from this page:
# https://github.com/OpenRefine/OpenRefine/wiki/Reconciliation-Service-Api
#
Vitro.reconcile.defaultTypeList = http://vivoweb.org/ontology/core#Role, core:Role; \
http://vivoweb.org/ontology/core#AcademicDegree, core:Academic Degree; \
http://purl.org/NET/c4dm/event.owl#Event, event:Event; \
http://vivoweb.org/ontology/core#Location, core:Location; \
http://xmlns.com/foaf/0.1/Organization, foaf:Organization; \
http://xmlns.com/foaf/0.1/Person, foaf:Person; \
http://purl.obolibrary.org/obo/IAO_0000030, obo:IAO_0000030
# Configure the support for claiming by DOI or PMID
# This is a list of all the providers that are active for claiming articles from
# Options: doi, pmid
# which search Crossref and PubMed, respectively
# If you do not wish to use the claiming interface, set this property to nothing (empty)
createAndLink.providers = doi, pmid
# Triple pattern fragments is a very fast, very simple means for querying a triple store.
# The triple pattern fragments API in VIVO puts little load on the server, providing a simple means for getting data from the triple store. The API has a web interface for manual use, can be used from the command line via curl, and can be used by programs.
#
# tpf.activeFlag = true