<commit_before># -----------------------------------------------------------------------------
#
# VIVO deployment properties
#
# This file is provided as example.deploy.properties.
#
# Save a copy of this file as deploy.properties, and edit the properties as 
# needed for your deployment.
#
# -----------------------------------------------------------------------------

# 
# This namespace will be used when generating URIs for objects created in the 
# editor. Change it to reflect your own domain. For example, Cornell's 
# namespace is http://vivo.cornell.edu/individual/
#
# Note: it is essential that this namespace end with a trailing slash.
#
Vitro.defaultNamespace = http://vivo.mydomain.edu/individual/

#
# Where is the Vitro core directory?
# In most deployments, this is set to ./vitro-core, but internal developers may
# prefer to set it to ../vitro
#   Examples:
#      vitro.core.dir = ./vitro-core
#      vitro.core.dir = ../vitro
#      vitro.core.dir = /usr/local/vitro/trunk
vitro.core.dir = ./vitro-core

#
# The base install directory for your Tomcat server. The VIVO application 
# will be deployed in the /webapps directory below this base. 
#
tomcat.home = /usr/local/tomcat

#
# The name of the VIVO application. This will be used as the name of the
# subdirectory within your Tomcat server's /webapps directory. It also appears
# in the URL for the application. For example, http://my.vivo.server/vivo
#
webapp.name = vivo

#
# The location where the VIVO application will store uploaded files 
# (usually images). You should arrange for these files to be backed up in some
# way.
#
upload.directory = /usr/local/vivo/data/uploads

#
# The location where the VIVO application will create its Lucene search 
# index. 
#
LuceneSetup.indexDir = /usr/local/vivo/data/luceneIndex

#
# SMTP host which the "Contact Us" form can use to send mail. If this is left 
# empty, the "Contact Us" form will be disabled.
#
Vitro.smtpHost =

#
# The basic parameters for a database connection. Change the end of the 
# URL to reflect your database name (if it is not "vitro"). Change the username 
# and password to match the authorized database user you created. Increase the
# maximum size of the database connection pool if you need to serve a greater
# number of concurrent page requests.
#
VitroConnection.DataSource.url = jdbc:mysql://localhost/vitrodb
VitroConnection.DataSource.username = vitrodbUsername
VitroConnection.DataSource.password = <PASSWORD>

#
# The Jena triple store technology to use.  SDB is Jena's SPARQL database;
# this setting allows RDF data to scale beyond the limits of the JVM heap.
# Set to RDB to use the older Jena RDB store with in-memory caching. 
#
VitroConnection.DataSource.tripleStoreType = SDB

#
# The maximum number of active connections in the database connection pool.
# Increase this value to support a greater number of concurrent page requests
# with SDB.  It is not necessary to adjust this value when using the
# RDB configuration.
#
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

#
# 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

#
# The name of your first admin user for the VIVO application. The password 
# for this user is initially set to "<PASSWORD>", but you will be asked to 
# change the password the first time you log in.
#
initialAdminUser = defaultAdmin

#
# 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 is the name of that property.
#
selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId

#
# If an external authentication system like Shibboleth or CUWebAuth is to be
# used, these properties say how the login button should be labeled, and which
# HTTP header will contain the user ID from the authentication system. If such
# as system is not to be used, leave these commented out. Consult the 
# installation instructions for more details. 
#
#externalAuth.buttonText = Log in using BearCat Shibboleth
#externalAuth.netIdHeaderName = remote_userID 

#
# 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.

# visualization.topLevelOrg = http://vivo.mydomain.edu/individual/topLevelOrgURI<commit_msg>Updated the text to match the install and upgrade docs for the deploy.properties settings: vitro.core.dir, upload.directory, luceneSetup.indexDir, selfEditing.idMatchingProperty, visualization.topLevelOrg.<commit_after># -----------------------------------------------------------------------------
#
# VIVO deployment properties
#
# This file is provided as example.deploy.properties.
#
# Save a copy of this file as deploy.properties, and edit the properties as 
# needed for your deployment.
#
# -----------------------------------------------------------------------------

# 
# This namespace will be used when generating URIs for objects created in the 
# editor. Change it to reflect your own domain. For example, Cornell's 
# namespace is http://vivo.cornell.edu/individual/
#
# Note: it is essential that this namespace end with a trailing slash.
#
Vitro.defaultNamespace = http://vivo.mydomain.edu/individual/

#
# Where is the Vitro core directory?
# In most deployments, this is set to ./vitro-core (It is not uncommon for this 
# setting to point elsewhere in development environments).
#   Examples:
#      vitro.core.dir = ./vitro-core
#      vitro.core.dir = ../vitro
#      vitro.core.dir = /usr/local/vitro/trunk
vitro.core.dir = ./vitro-core

#
# The base install directory for your Tomcat server. The VIVO application 
# will be deployed in the /webapps directory below this base. 
#
tomcat.home = /usr/local/tomcat

#
# The name of the VIVO application. This will be used as the name of the
# subdirectory within your Tomcat server's /webapps directory. It also appears
# in the URL for the application. For example, http://my.vivo.server/vivo
#
webapp.name = vivo

#
# The location where the VIVO application will store uploaded files 
# (usually images). Be sure this directory exists and is writable by the 
# user that the Tomcat service is running as. You should arrange for these 
# files to be backed up in some way. 
#
upload.directory = /usr/local/vivo/data/uploads

#
# The location where the VIVO application will create its Lucene search 
# index. Be sure this directory exists and is writable by the 
# user that the Tomcat service is running as.
#
LuceneSetup.indexDir = /usr/local/vivo/data/luceneIndex

#
# SMTP host which the "Contact Us" form can use to send mail. If this is left 
# empty, the "Contact Us" form will be disabled.
#
Vitro.smtpHost =

#
# The basic parameters for a database connection. Change the end of the 
# URL to reflect your database name (if it is not "vitro"). Change the username 
# and password to match the authorized database user you created. Increase the
# maximum size of the database connection pool if you need to serve a greater
# number of concurrent page requests.
#
VitroConnection.DataSource.url = jdbc:mysql://localhost/vitrodb
VitroConnection.DataSource.username = vitrodbUsername
VitroConnection.DataSource.password = <PASSWORD>

#
# The Jena triple store technology to use.  SDB is Jena's SPARQL database;
# this setting allows RDF data to scale beyond the limits of the JVM heap.
# Set to RDB to use the older Jena RDB store with in-memory caching. 
#
VitroConnection.DataSource.tripleStoreType = SDB

#
# The maximum number of active connections in the database connection pool.
# Increase this value to support a greater number of concurrent page requests
# with SDB.  It is not necessary to adjust this value when using the
# RDB configuration.
#
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

#
# 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

#
# The name of your first admin user for the VIVO application. The password 
# for this user is initially set to "<PASSWORD>", but you will be asked to 
# change the password the first time you log in.
#
initialAdminUser = defaultAdmin

#
# 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

#
# If an external authentication system like Shibboleth or CUWebAuth is to be
# used, these properties say how the login button should be labeled, and which
# HTTP header will contain the user ID from the authentication system. If such
# a system is not to be used, leave these commented out. Consult the 
# installation instructions for more details. 
#
#externalAuth.buttonText = Log in using BearCat Shibboleth
#externalAuth.netIdHeaderName = remote_userID 

#
# 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
{'fraction_non_alphanumeric': 0.09114296214626975, 'fraction_numerical': 0.0016538037486218302, 'mean_word_length': 3.588954468802698, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1042250', 'n_tokens_mistral': 2988, 'n_tokens_neox': 2844, 'n_words': 1374}