Regenerated documentation

NAMESPACE

@@ -1,7 +1,18 @@
 # Generated by roxygen2: do not edit by hand
 
+export(add_body)
+export(add_header)
+export(add_ont)
+export(add_user)
+export(add_user_roles)
+export(add_users)
+export(base_msg)
+export(clear_default_metadata)
 export(create_admin)
+export(delete_users)
+export(populate_ont)
 export(secure_db)
+export(send_msg)
 export(set_domain)
 export(set_permissions)
 export(set_project)

man/add_body.Rd

@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/i2b2_msg.R
+\name{add_body}
+\alias{add_body}
+\title{Add the body to the message}
+\usage{
+add_body(msg, service, ..., attrib = NULL)
+}
+\arguments{
+\item{msg}{The XML message to add the body to}
+
+\item{service}{The service to request in the body message}
+
+\item{...}{Optionnaly named tags to add inside the body, with their value}
+
+\item{attrib}{A list of XML attributes to add to the service tag}
+}
+\value{
+The XML message list object
+}
+\description{
+Add the body to the XML message
+}
+\details{
+Add the body to the XML message created by base_msg and passed through add_header
+base_msg can be piped into add_header and then into add_body to build a message
+}

man/add_header.Rd

@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/i2b2_msg.R
+\name{add_header}
+\alias{add_header}
+\title{Add the header to the message}
+\usage{
+add_header(msg, domain, 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}
+}
+\value{
+The XML message list object
+}
+\description{
+Add the header to the XML message
+}
+\details{
+Add the header to the XML base message created by base_msg
+base_msg can be piped into add_header
+}

man/add_ont.Rd

@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/metadata.R
+\name{add_ont}
+\alias{add_ont}
+\title{Add an ontology to metadata}
+\usage{
+add_ont(host = "localhost", admin, pass, name, scheme, description)
+}
+\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}
+}
+\description{
+Add an empty ontology space
+}
+\details{
+Add a new empty table to metadata, with indexes
+Add a new scheme to the schemes table
+Add the corresponding table_access entry for the new table
+}

man/add_user.Rd

@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/users.R
+\name{add_user}
+\alias{add_user}
+\title{Add an user}
+\usage{
+add_user(domain, admin, pass, id, name, email, password,
+  url = "http://localhost:9090/i2b2/services/PMService/getServices")
+}
+\arguments{
+\item{domain}{The name of the domain to interact with}
+
+\item{pass}{The password for the user}
+
+\item{id}{The id (no spaces, unique) of the new user}
+
+\item{name}{The full name of the new user}
+
+\item{email}{The email of the new user}
+
+\item{password}{The password for the new user}
+
+\item{url}{The URL of the i2b2 cell to communicate with}
+
+\item{username}{The username to connect with}
+}
+\value{
+The XML return message as an httr::content() object
+}
+\description{
+Add an i2b2 user to the instance
+}

man/add_user_roles.Rd

@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/users.R
+\name{add_user_roles}
+\alias{add_user_roles}
+\title{Add user roles}
+\usage{
+add_user_roles(domain, admin, pass, id, project, roles,
+  url = "http://localhost:9090/i2b2/services/PMService/getServices")
+}
+\arguments{
+\item{domain}{The name of the domain to interact with}
+
+\item{pass}{The password for the user}
+
+\item{id}{The id (no spaces, unique) of the new user}
+
+\item{project}{The project to add the user role to}
+
+\item{roles}{A character vector of roles to add}
+
+\item{url}{The URL of the i2b2 cell to communicate with}
+
+\item{username}{The username to connect with}
+}
+\value{
+The XML return message as an httr::content() object
+}
+\description{
+Add roles to an i2b2 user
+}

man/add_users.Rd

@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/users.R
+\name{add_users}
+\alias{add_users}
+\title{Add multiple users}
+\usage{
+add_users(domain, admin, pass, users,
+  url = "http://localhost:9090/i2b2/services/PMService/getServices")
+}
+\arguments{
+\item{domain}{The name of the domain to interact with}
+
+\item{pass}{The password for the user}
+
+\item{users}{The dataframe containing the users to add}
+
+\item{url}{The URL of the i2b2 cell to communicate with}
+
+\item{username}{The username to connect with}
+}
+\value{
+The XML return message as an httr::content() object
+}
+\description{
+Add users in bulk from a dataframe
+}
+\details{
+Add users in bulk from a dataframe containing the following columns:
+* id: The unique user id to add for each user
+* name: The name for each user
+* email: The email address for each user
+* password: The password for each user
+* role: The role to give the user
+
+Any role can be given from the ones defined
+(ADMIN, MANAGER, USER, DATA_PROT, DATA_DEID, DATA_LDS, DATA_AGG, DATA_OBFSC)
+ADMIN gives all roles for the project, and ADMIN role to project @
+MANAGER gives all roles down from DATA_DEID for the project
+USER gives USER and DATA_OBFSC roles for the project
+Any DATA_* role gives USER and roles down from the DATA_* role given to the project
+}

man/base_msg.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/i2b2_msg.R
+\name{base_msg}
+\alias{base_msg}
+\title{Create base XML message}
+\usage{
+base_msg()
+}
+\value{
+The base msg list object
+}
+\description{
+Create the base XML message
+}
+\details{
+Creates the base XML message as an R list
+}

man/clear_default_metadata.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/metadata.R
+\name{clear_default_metadata}
+\alias{clear_default_metadata}
+\title{Clear the default metadata tables}
+\usage{
+clear_default_metadata(host = "localhost", admin, pass)
+}
+\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}
+}
+\description{
+Clear the default metadata tables
+}
+\details{
+Drop the birn, custom_meta, i2b2 and icd10_icd9 tables
+Delete all schemes and table_access
+Insert the 'No scheme' scheme
+}

man/create_admin.Rd

@@ -4,10 +4,10 @@
 \alias{create_admin}
 \title{Create system and database admin accounts}
 \usage{
-create_admin(name = "i2b2admin", pass = NULL, pass_length = 8)
+create_admin(admin = "i2b2admin", pass = NULL, pass_length = 8)
 }
 \arguments{
-\item{name}{Name of the account}
+\item{admin}{Name of the admin account to create}
 
 \item{pass}{An arbitrary password if provided, i2b2admin by default}
 

man/delete_users.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/users.R
+\name{delete_users}
+\alias{delete_users}
+\title{Delete users}
+\usage{
+delete_users(host = "localhost", admin, pass, users)
+}
+\arguments{
+\item{host}{The host to connect to}
+
+\item{admin}{The admin account for the PostgreSQL database}
+
+\item{pass}{The password for the database admin}
+
+\item{users}{A character vector of user ids}
+}
+\description{
+Delete i2b2 users from the instance
+}

man/populate_ont.Rd

@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/metadata.R
+\name{populate_ont}
+\alias{populate_ont}
+\title{Populate an empty ontology table}
+\usage{
+populate_ont(host = "localhost", admin, pass, ont, name, scheme)
+}
+\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{ont}{The ontology to insert}
+
+\item{name}{The name of the new ontology}
+
+\item{scheme}{The scheme to use for this ontology}
+}
+\description{
+Populate an empty ontology table
+}
+\details{
+Populate an ontology table
+ont is a character vector containing all the leaves of the ontology
+with their respective path, in the form
+code_level1 label_level1/code_level2 label_level2/.../code_leaf label_leaf
+The function rebuilds the folders automatically
+}

man/secure_db.Rd

@@ -4,10 +4,10 @@
 \alias{secure_db}
 \title{Secure the i2b2 databases}
 \usage{
-secure_db(name, pass, pass_length = 8)
+secure_db(admin, pass, pass_length = 8)
 }
 \arguments{
-\item{name}{Name of the database admin account}
+\item{admin}{Name of the database admin account}
 
 \item{pass}{Password of the database admin account}
 
@@ -20,7 +20,7 @@ A vector for one statistic column
 Secure the i2b2 databases
 }
 \details{
-Connect to the database using the admin account credentials, provided as name and pass,
+Connect to the database using the admin account credentials, provided as admin and pass,
 generate pass_length long passwords for each database
 and update the cells config with the new passwords.
 }

man/send_msg.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/i2b2_msg.R
+\name{send_msg}
+\alias{send_msg}
+\title{Send the message}
+\usage{
+send_msg(msg, cellurl)
+}
+\arguments{
+\item{msg}{The XML message as an R list}
+
+\item{cellurl}{The URL of the i2b2 cell to communicate with}
+}
+\value{
+The XML return message as an httr::content() object
+}
+\description{
+Send the XML message to an i2b2 cell
+}
+\details{
+Send the XML message built by base_msg %>% add_header %>% add_body
+to the specified cellurl
+}

man/set_domain.Rd

@@ -4,10 +4,10 @@
 \alias{set_domain}
 \title{Set the domain}
 \usage{
-set_domain(name, pass, domain_id, domain_name)
+set_domain(admin, pass, domain_id, domain_name)
 }
 \arguments{
-\item{name}{Name of the database admin account}
+\item{admin}{Name of the database admin account}
 
 \item{pass}{Password of the database admin account}
 

man/set_project.Rd

@@ -4,12 +4,12 @@
 \alias{set_project}
 \title{Set the project}
 \usage{
-set_project(host = "127.0.0.1", name, pass, project_id, project_name)
+set_project(host = "localhost", admin, pass, project_id, project_name)
 }
 \arguments{
 \item{host}{Address of the host, defaults to 127.0.0.1}
 
-\item{name}{Name of the database admin account}
+\item{admin}{Name of the database admin account}
 
 \item{pass}{Password of the database admin account}