Updated doc + checks

R/ontology.R

@@ -19,8 +19,6 @@ add_ontology <- function(name, scheme, ont, modi = NULL, include_code = T, host
   add_ont(name, scheme, host, admin, pass)
 
   populate_ont(ont, modi, name, scheme, include_code, host, admin, pass)
-
-  populate_concept(ont, modi, name, scheme, host, admin, pass)
 }
 
 #' Delete an ontology from i2b2
@@ -39,8 +37,4 @@ add_ontology <- function(name, scheme, ont, modi = NULL, include_code = T, host
 delete_ontology <- function(scheme, host = "", admin = "", pass = "")
 {
   delete_ont(scheme, host, admin, pass)
-
-  delete_concept(scheme, host, admin, pass)
-
-  delete_modifier(scheme, host, admin, pass)
 }

R/pm.R

@@ -91,7 +91,7 @@ add_project <- function(project_id, project_name, host = "", admin = "", pass =
 
 # crc-ds.xml
   xml2::read_html("/opt/wildfly-10.0.0.Final/standalone/deployments/crc-ds.xml") %>%
-    xml_nodes("datasources") -> crc
+    rvest::xml_nodes("datasources") -> crc
 
   datasource <- list()
   datasource$datasource$`connection-url` <- list(stringr::str_c("jdbc:postgresql://localhost:5432/i2b2", project_id, "data"))
@@ -107,11 +107,11 @@ add_project <- function(project_id, project_name, host = "", admin = "", pass =
   attr(datasource$datasource, "pool-name") <- stringr::str_c("QueryTool", project_id, "DS")
   attr(datasource$datasource, "enabled") <- "true"
   attr(datasource$datasource, "use-ccm") <- "false"
-  datasource %>% as_xml_document -> datasource
+  datasource %>% xml2::as_xml_document -> datasource
 
   crc %>% xml2::xml_add_child(datasource)
 
-  write_xml(crc, "/opt/wildfly-10.0.0.Final/standalone/deployments/crc-ds.xml")
+  xml2::write_xml(crc, "/opt/wildfly-10.0.0.Final/standalone/deployments/crc-ds.xml")
 }
 
 #' List projects
@@ -168,6 +168,6 @@ delete_project <- function(project_id, host = "", admin = "", pass = "")
   new <- list(datasources = datasources)
   attr(new$datasources, "xmlns") <- "http://www.jboss.org/ironjacamar/schema"
 
-  xml2::write_xml(new %>% as_xml_document, "/opt/wildfly-10.0.0.Final/standalone/deployments/crc-ds.xml")
+  xml2::write_xml(new %>% xml2::as_xml_document, "/opt/wildfly-10.0.0.Final/standalone/deployments/crc-ds.xml")
 }
 

R/system.R

@@ -76,6 +76,7 @@ create_admin <- function(admin = "i2b2admin", pass= NULL, pass_length = 8)
 #'
 #' @param service The service to manage (pg for short for postgresql-9.1)
 #' @param action The action to perform
+#' @param use_sudo Use sudo if not executed by root account (defaults to T)
 #' @export
 service <- function(service, action = c("start", "stop", "restart"), use_sudo = T)
 {

man/clear_demodata.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/demodata.R
+\name{clear_demodata}
+\alias{clear_demodata}
+\title{Clear the demodata tables}
+\usage{
+clear_demodata(project, host = "", admin = "", pass = "")
+}
+\arguments{
+\item{project}{The name of the project}
+
+\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 demodata tables
+}

man/service.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/system.R
+\name{service}
+\alias{service}
+\title{Manage services}
+\usage{
+service(service, action = c("start", "stop", "restart"), use_sudo = T)
+}
+\arguments{
+\item{service}{The service to manage (pg for short for postgresql-9.1)}
+
+\item{action}{The action to perform}
+
+\item{use_sudo}{Use sudo if not executed by root account (defaults to T)}
+}
+\description{
+Start/stop/restart services
+}