Updated documentation

NAMESPACE

@@ -3,6 +3,7 @@
 export(add_body)
 export(add_header)
 export(add_ont)
+export(add_ontology)
 export(add_user)
 export(add_user_roles)
 export(add_users)
@@ -14,6 +15,7 @@ export(create_admin)
 export(delete_concept)
 export(delete_ont)
 export(delete_users)
+export(fresh_install)
 export(populate_concept)
 export(populate_ont)
 export(secure_db)

man/add_ontology.Rd

@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ontology.R
+\name{add_ontology}
+\alias{add_ontology}
+\title{Add an ontology to i2b2}
+\usage{
+add_ontology(host = "localhost", admin, pass, name, scheme, description, ont,
+  modi)
+}
+\arguments{
+\item{host}{The host to connect to}
+
+\item{admin}{The admin account for the PostgreSQL database}
+
+\item{pass}{the password for the admin account}
+
+\item{name}{The name of the new ontology}
+
+\item{scheme}{The scheme to use for this ontology}
+
+\item{description}{The description of the scheme}
+
+\item{ont}{The ontology to insert}
+
+\item{modi}{The modifiers to insert}
+}
+\description{
+Add an ontology into i2b2
+Add the ontology table and entries in metadata
+Populate the ontology table
+Populate the concept and modifier dimensions in demodata
+}

man/create_admin.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/configure.R
+% Please edit documentation in R/system.R
 \name{create_admin}
 \alias{create_admin}
 \title{Create system and database admin accounts}

man/fresh_install.Rd

@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/fresh_install.R
+\name{fresh_install}
+\alias{fresh_install}
+\title{Make a fresh install from the base VM}
+\usage{
+fresh_install(admin, pass, domain_id, domain_name, project_id, project_name)
+}
+\arguments{
+\item{admin}{The admin account for the PostgreSQL database}
+
+\item{pass}{the password for the admin account}
+
+\item{domain_id}{The desired domain_id}
+
+\item{domain_name}{The desired domain_name}
+
+\item{project_id}{The desired project id}
+
+\item{project_name}{The desired project name}
+
+\item{host}{The host to connect to}
+}
+\description{
+Make a fresh install from the base VM
+}
+\details{
+Set the permissions,
+create the admin account for the system, database, and i2b2
+Set the domain and project
+Delete the default users
+Clear the metadata database, and the *_dimension tables in demodata
+}

man/secure_db.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/configure.R
+% Please edit documentation in R/system.R
 \name{secure_db}
 \alias{secure_db}
 \title{Secure the i2b2 databases}

man/set_domain.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/configure.R
+% Please edit documentation in R/pm.R
 \name{set_domain}
 \alias{set_domain}
 \title{Set the domain}

man/set_permissions.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/configure.R
+% Please edit documentation in R/system.R
 \name{set_permissions}
 \alias{set_permissions}
 \title{Set the permissions for the webclient and wildfly folders}

man/set_project.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/configure.R
+% Please edit documentation in R/pm.R
 \name{set_project}
 \alias{set_project}
 \title{Set the project}