Updated documentation

NAMESPACE

@@ -6,7 +6,6 @@ export(add_encounters)
 export(add_header)
 export(add_observations)
 export(add_ont)
-export(add_ontology)
 export(add_patients_demodata)
 export(add_patients_imdata)
 export(add_project)
@@ -25,7 +24,6 @@ export(create_admin)
 export(delete_concept)
 export(delete_modifier)
 export(delete_ont)
-export(delete_ontology)
 export(delete_project)
 export(delete_users)
 export(fresh_install)

man/add_header.Rd

@@ -4,13 +4,11 @@
 \alias{add_header}
 \title{Add the header to the message}
 \usage{
-add_header(msg, domain, username, password)
+add_header(msg, username, password)
 }
 \arguments{
 \item{msg}{The XML message to add the header to}
 
-\item{domain}{The name of the domain to interact with}
-
 \item{username}{The username to connect with}
 
 \item{password}{The password for the user}

man/add_ontology.Rd

@@ -1,32 +0,0 @@
-% 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(name, scheme, ont, modi = NULL, include_code = T, host = "",
-  admin = "", pass = "")
-}
-\arguments{
-\item{name}{The name of the new ontology}
-
-\item{scheme}{The scheme to use for this ontology}
-
-\item{ont}{The ontology to insert}
-
-\item{modi}{The modifiers to insert}
-
-\item{include_code}{Whether to include the code in the label or not}
-
-\item{host}{The host to connect to}
-
-\item{admin}{The admin account for the PostgreSQL database}
-
-\item{pass}{the password for the admin account}
-}
-\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/add_user.Rd

@@ -4,12 +4,10 @@
 \alias{add_user}
 \title{Add an user}
 \usage{
-add_user(domain, admin, pass, id, name, email, password,
+add_user(admin, pass, id, name, email, password,
   url = "http://127.0.0.1:9090/i2b2/services/PMService/getServices")
 }
 \arguments{
-\item{domain}{The name of the domain to interact with}
-
 \item{admin}{The username to connect with}
 
 \item{pass}{The password for the user}

man/add_user_roles.Rd

@@ -4,12 +4,10 @@
 \alias{add_user_roles}
 \title{Add user roles}
 \usage{
-add_user_roles(domain, admin, pass, id, project, roles,
+add_user_roles(admin, pass, id, project, roles,
   url = "http://127.0.0.1:9090/i2b2/services/PMService/getServices")
 }
 \arguments{
-\item{domain}{The name of the domain to interact with}
-
 \item{admin}{The username to connect with}
 
 \item{pass}{The password for the user}

man/add_users.Rd

@@ -4,12 +4,10 @@
 \alias{add_users}
 \title{Add multiple users}
 \usage{
-add_users(domain, admin, pass, users,
+add_users(admin, pass, users,
   url = "http://127.0.0.1:9090/i2b2/services/PMService/getServices")
 }
 \arguments{
-\item{domain}{The name of the domain to interact with}
-
 \item{admin}{The username to connect with}
 
 \item{pass}{The password for the user}

man/delete_ontology.Rd

@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ontology.R
-\name{delete_ontology}
-\alias{delete_ontology}
-\title{Delete an ontology from i2b2}
-\usage{
-delete_ontology(scheme, host = "", admin = "", pass = "")
-}
-\arguments{
-\item{scheme}{The scheme to use for this ontology}
-
-\item{host}{The host to connect to}
-
-\item{admin}{The admin account for the PostgreSQL database}
-
-\item{pass}{the password for the admin account}
-}
-\description{
-Delete an existing ontology from metadata
-}
-\details{
-Delete the corresponding table
-Delete the scheme in schemes table
-Delete the entry in table_acess
-}

man/fresh_install.Rd

@@ -4,7 +4,7 @@
 \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)
+fresh_install(admin, pass, domain_id, domain_name)
 }
 \arguments{
 \item{admin}{The admin account for the PostgreSQL database}
@@ -14,10 +14,6 @@ fresh_install(admin, pass, domain_id, domain_name, project_id, project_name)
 \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}
 }
 \description{
 Make a fresh install from the base VM