Added get_domain. Changed set_project with add_project and added

delete_project and list_projects

NAMESPACE

@@ -9,6 +9,7 @@ export(add_ont)
 export(add_ontology)
 export(add_patients_demodata)
 export(add_patients_imdata)
+export(add_project)
 export(add_user)
 export(add_user_roles)
 export(add_users)
@@ -24,12 +25,15 @@ export(delete_concept)
 export(delete_modifier)
 export(delete_ont)
 export(delete_ontology)
+export(delete_project)
 export(delete_users)
 export(fresh_install)
+export(get_domain)
 export(get_ont)
 export(import_data)
 export(list_concepts)
 export(list_ont)
+export(list_projects)
 export(list_schemes)
 export(list_user_roles)
 export(list_users)
@@ -41,5 +45,4 @@ export(secure_db)
 export(send_msg)
 export(set_domain)
 export(set_permissions)
-export(set_project)
 importFrom(dplyr,"%>%")

R/pm.R

@@ -4,17 +4,18 @@
 #'
 #' Set the domain id and domain name in the databases
 #' and set the domain name in the webclient'
-#' 
-#' @param admin Name of the database admin account
-#' @param pass Password of the database admin account
+#'
 #' @param domain_id The desired domain_id
 #' @param domain_name The desired domain_name
+#' @param host The host to connect to
+#' @param admin Name of the database admin account
+#' @param pass Password of the database admin account
 #' @export
-set_domain <- function(admin, pass, domain_id, domain_name)
+set_domain <- function(domain_id, domain_name, host = "", admin = "", pass = "")
 {
   # Connect to the db
-  hive <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = "127.0.0.1", dbname = "i2b2hive", user = admin, password = pass)
-  pm   <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = "127.0.0.1", dbname = "i2b2pm",   user = admin, password = pass)
+  hive <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = "i2b2hive", user = admin, password = pass)
+  pm   <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = "i2b2pm",   user = admin, password = pass)
 
   # Set the domain id to all cells in i2b2hive
   c("crc", "im", "ont", "work") %>%
@@ -36,35 +37,101 @@ set_domain <- function(admin, pass, domain_id, domain_name)
   RPostgreSQL::dbDisconnect(pm)
 }
 
-#' Set the project
-#'
-#' Set the project id, project path and project name of the instance
+#' Get the domain
 #'
-#' Set the project id, project path and project name in the databases
+#' Get the domain id of the instance
 #'
-#' @param host Address of the host, defaults to 127.0.0.1
+#' @param host The host to connect to
 #' @param admin Name of the database admin account
 #' @param pass Password of the database admin account
+#' @return The domain id and name
+#' @export
+get_domain <- function(host = "", admin = "", pass = "")
+{
+  dplyr::src_postgres("i2b2pm", host = host, user = admin, password = pass) %>%
+    dplyr::tbl("pm_hive_data") %>%
+    dplyr::collect()
+}
+
+#' Add a project
+#'
+#' Add a project with its id, path and name in the hive
+#'
+#' Also create a specific database for this project
+#'
 #' @param project_id The desired project id
 #' @param project_name The desired project name
+#' @param host Address of the host, defaults to 127.0.0.1
+#' @param admin Name of the database admin account
+#' @param pass Password of the database admin account
 #' @export
-set_project <- function(project_id, project_name, host = "", admin = "", pass = "")
+add_project <- function(project_id, project_name, host = "", admin = "", pass = "")
 {
+  # Get the current domain id
+  domain_id <- get_domain(host, admin, pass)$domain_id
+
   # Connect to the db
   hive <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host, dbname = "i2b2hive", user = admin, password = pass)
   pm   <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host, dbname = "i2b2pm",   user = admin, password = pass)
 
   # Set the project id to all cells in i2b2hive
+  RPostgreSQL::dbGetQuery(hive, stringr::str_c("INSERT INTO im_db_lookup (c_domain_id, c_project_path, c_owner_id, c_db_fullschema, c_db_datasource, c_db_servertype, c_db_nicename) VALUES ('", domain_id, "', '", project_id, "/', '@', 'public', 'java:/IMDemoDS', 'POSTGRESQL', 'IM');"))
+  RPostgreSQL::dbGetQuery(hive, stringr::str_c("INSERT INTO ont_db_lookup (c_domain_id, c_project_path, c_owner_id, c_db_fullschema, c_db_datasource, c_db_servertype, c_db_nicename) VALUES ('", domain_id, "', '", project_id, "/', '@', 'public', 'java:/OntologyDemoDS', 'POSTGRESQL', 'Metadata');"))
+  RPostgreSQL::dbGetQuery(hive, stringr::str_c("INSERT INTO work_db_lookup (c_domain_id, c_project_path, c_owner_id, c_db_fullschema, c_db_datasource, c_db_servertype, c_db_nicename) VALUES ('", domain_id, "', '", project_id, "/', '@', 'public', 'java:/WorkplaceDemoDS', 'POSTGRESQL', 'Workplace');"))
+  RPostgreSQL::dbGetQuery(hive, stringr::str_c("INSERT INTO crc_db_lookup (c_domain_id, c_project_path, c_owner_id, c_db_fullschema, c_db_datasource, c_db_servertype, c_db_nicename) VALUES ('", domain_id, "', '/", project_id, "/', '@', 'public', 'java:/QueryTool", project_id, "DS', 'POSTGRESQL', '", project_name,"');"))
+
+  # Set the project id and name in pm_hive_data
+  RPostgreSQL::dbGetQuery(pm, stringr::str_c("INSERT INTO pm_project_data (project_id, project_name, project_wiki, project_path) VALUES ('", project_id, "', '", project_name, "', 'http://www.i2b2.org', '/", project_id, "');"))
+
+  RPostgreSQL::dbGetQuery(hive, stringr::str_c("CREATE DATABASE i2b2", project_id, "data WITH TEMPLATE i2b2demodata owner i2b2demodata;"))
+
+  # Disconnect the db
+  RPostgreSQL::dbDisconnect(hive)
+  RPostgreSQL::dbDisconnect(pm)
+}
+
+#' List projects
+#'
+#' List available projects in the hive
+#'
+#' @param host Address of the host, defaults to 127.0.0.1
+#' @param admin Name of the database admin account
+#' @param pass Password of the database admin account
+#' @return The list of projects
+#' @export
+list_projects <- function(host = "", admin = "", pass = "")
+{
+  dplyr::src_postgres(dbname = "i2b2pm", host = host, user = admin, password = pass) %>%
+    dplyr::tbl("pm_project_data") %>%
+    dplyr::collect()
+}
+
+
+#' Delete a project
+#'
+#' Delete a project from the hive
+#'
+#' @param project_id The project to delete
+#' @param host Address of the host, defaults to 127.0.0.1
+#' @param admin Name of the database admin account
+#' @param pass Password of the database admin account
+#' @export
+delete_project <- function(project_id, host = "", admin = "", pass = "")
+{
+  # Connect to the db
+  hive <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = "i2b2hive", user = admin, password = pass)
+  pm <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host, dbname = "i2b2pm", user = admin, password = pass)
+
   c("im", "ont", "work") %>%
-    purrr::walk(~RPostgreSQL::dbGetQuery(hive, stringr::str_c("UPDATE ", .x, "_db_lookup SET c_project_path = '", project_id, "/';")))
+    purrr::walk(~RPostgreSQL::dbGetQuery(hive, stringr::str_c("DELETE FROM ", .x, "_db_lookup WHERE c_project_path = '", project_id, "/';")))
+  RPostgreSQL::dbGetQuery(hive, stringr::str_c("DELETE FROM crc_db_lookup WHERE c_project_path = '/", project_id, "/';"))
 
-  RPostgreSQL::dbGetQuery(hive, stringr::str_c("UPDATE crc_db_lookup SET c_project_path = '/", project_id, "/';"))
+  RPostgreSQL::dbGetQuery(pm, stringr::str_c("DELETE FROM pm_project_data WHERE project_id = '", project_id, "';"))
 
-  # Set the project id and name in pm_hive_data
-  RPostgreSQL::dbGetQuery(pm, stringr::str_c("UPDATE pm_project_data SET project_id = '", project_id, "', project_name = '", project_name, "', project_path = '/", project_id, "';"))
-  RPostgreSQL::dbGetQuery(pm, stringr::str_c("UPDATE pm_project_user_roles SET project_id = '", project_id, "' WHERE (project_id = 'Demo');"))
+  RPostgreSQL::dbGetQuery(pm, stringr::str_c("DROP DATABASE i2b2", project_id, "demodata;"))
 
   # Disconnect the db
   RPostgreSQL::dbDisconnect(hive)
   RPostgreSQL::dbDisconnect(pm)
 }
+

man/set_domain.Rd

@@ -4,16 +4,18 @@
 \alias{set_domain}
 \title{Set the domain}
 \usage{
-set_domain(admin, pass, domain_id, domain_name)
+set_domain(domain_id, domain_name, host = "", admin = "", pass = "")
 }
 \arguments{
-\item{admin}{Name of the database admin account}
-
-\item{pass}{Password of the database admin account}
-
 \item{domain_id}{The desired domain_id}
 
 \item{domain_name}{The desired domain_name}
+
+\item{host}{The host to connect to}
+
+\item{admin}{Name of the database admin account}
+
+\item{pass}{Password of the database admin account}
 }
 \description{
 Set the domain id and domain name of the instance

man/set_project.Rd

@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pm.R
-\name{set_project}
-\alias{set_project}
-\title{Set the project}
-\usage{
-set_project(host = "127.0.0.1", admin, pass, project_id, project_name)
-}
-\arguments{
-\item{host}{Address of the host, defaults to 127.0.0.1}
-
-\item{admin}{Name of the database admin account}
-
-\item{pass}{Password of the database admin account}
-
-\item{project_id}{The desired project id}
-
-\item{project_name}{The desired project name}
-}
-\description{
-Set the project id, project path and project name of the instance
-}
-\details{
-Set the project id, project path and project name in the databases
-}