Specify project in demodata functions

R/demodata.R

@@ -26,7 +26,39 @@ clear_default_demodata <- function(host = "", admin = "", pass = "")
     "qt_query_instance",
     "qt_query_master",
     "visit_dimension") %>%
-  purrr::walk(~clear_table("i2b2demodata", .x, host, admin, pass))
+  purrr::walk(~clear_table(stringr::str_c("i2b2", project, "data"), .x, host, admin, pass))
+}
+
+#' Clear the demodata tables
+#'
+#' Clear the demodata tables
+#'
+#' @param project The name of the project
+#' @param host The host to connect to
+#' @param admin The admin account for the PostgreSQL database
+#' @param pass the password for the admin account
+#' @export
+clear_demodata <- function(project, host = "", admin = "", pass = "")
+{
+  c("code_lookup",
+    "concept_dimension",
+    "encounter_mapping",
+    "modifier_dimension",
+    "observation_fact",
+    "patient_dimension",
+    "patient_mapping",
+    "provider_dimension",
+    "qt_analysis_plugin",
+    "qt_analysis_plugin_result_type",
+    "qt_patient_enc_collection",
+    "qt_patient_set_collection",
+    "qt_pdo_query_master",
+    "qt_xml_result",
+    "qt_query_result_instance",
+    "qt_query_instance",
+    "qt_query_master",
+    "visit_dimension") %>%
+  purrr::walk(~clear_table(stringr::str_c("i2b2", project ,"data"), .x, host, admin, pass))
 }
 
 #' Delete modifiers
@@ -34,22 +66,23 @@ clear_default_demodata <- function(host = "", admin = "", pass = "")
 #' Delete modifiers from modifier_dimension
 #'
 #' @param scheme The scheme to delete from the concepts
+#' @param project The name of the project
 #' @param host The host to connect to
 #' @param admin The admin account for the PostgreSQL database
 #' @param pass the password for the admin account
 #' @export
-delete_modifier <- function(scheme, host = "", admin = "", pass = "")
+delete_modifier <- function(scheme, project, host = "", admin = "", pass = "")
 {
-  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = "i2b2demodata", user = admin, password = pass)
+  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = stringr::str_c("i2b2", project, "data"), user = admin, password = pass)
 
   RPostgreSQL::dbGetQuery(demodata, stringr::str_c("DELETE FROM modifier_dimension WHERE (modifier_cd LIKE '", scheme, ":%');"))
 
   RPostgreSQL::dbDisconnect(demodata)
 }
 
-list_modifier <- function(scheme, host = "", admin = "", pass = "")
+list_modifier <- function(scheme, project, host = "", admin = "", pass = "")
 {
-  dplyr::src_postgres("i2b2demodata", host = host, user = admin, pass = pass) %>%
+  dplyr::src_postgres(stringr::str_c("i2b2", project, "data"), host = host, user = admin, pass = pass) %>%
     dplyr::tbl("modifier_dimension") %>%
     dplyr::collect() %>%
     dplyr::filter(modifier_cd %>% stringr::str_detect(stringr::str_c(scheme, ":.*")))
@@ -60,13 +93,14 @@ list_modifier <- function(scheme, host = "", admin = "", pass = "")
 #' Delete concepts from concept_dimension
 #'
 #' @param scheme The scheme to delete from the concepts
+#' @param project The name of the project
 #' @param host The host to connect to
 #' @param admin The admin account for the PostgreSQL database
 #' @param pass the password for the admin account
 #' @export
-delete_concept <- function(scheme, host = "", admin = "", pass = "")
+delete_concept <- function(scheme, project, host = "", admin = "", pass = "")
 {
-  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = "i2b2demodata", user = admin, password = pass)
+  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = stringr::str_c("i2b2", project, "data"), user = admin, password = pass)
 
   RPostgreSQL::dbGetQuery(demodata, stringr::str_c("DELETE FROM concept_dimension WHERE (concept_cd LIKE '", scheme, ":%');"))
 
@@ -78,14 +112,15 @@ delete_concept <- function(scheme, host = "", admin = "", pass = "")
 #' List the concepts corresponding to a scheme
 #'
 #' @param scheme The scheme to get the concepts from
+#' @param project The name of the project
 #' @param host The host to connect to
 #' @param admin The admin account for the PostgreSQL database
 #' @param pass the password for the admin account
 #' @return A list of concepts
 #' @export
-list_concepts <- function(scheme, host = "", admin = "", pass = "")
+list_concepts <- function(scheme, project, host = "", admin = "", pass = "")
 {
-  dplyr::src_postgres("i2b2demodata", host = host, user = admin, pass = pass) %>%
+  dplyr::src_postgres(stringr::str_c("i2b2", project, "data"), host = host, user = admin, pass = pass) %>%
     dplyr::tbl("concept_dimension") %>%
     dplyr::collect() %>%
     dplyr::filter(concept_cd %>% stringr::str_detect(stringr::str_c(scheme, ":.*")))
@@ -103,13 +138,14 @@ list_concepts <- function(scheme, host = "", admin = "", pass = "")
 #' @param modi The modifiers to insert
 #' @param name The name of the new ontology
 #' @param scheme The scheme to use for this ontology
+#' @param project The name of the project
 #' @param host The host to connect to
 #' @param admin The admin account for the PostgreSQL database
 #' @param pass the password for the admin account
 #' @export
-populate_concept <- function(ont, modi, name, scheme, host = "", admin = "", pass = "")
+populate_concept <- function(ont, modi, name, scheme, project, host = "", admin = "", pass = "")
 {
-  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = "i2b2demodata", user = admin, password = pass)
+  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = stringr::str_c("i2b2", project, "data"), user = admin, password = pass)
 
   # Sanitize the ontology
   ont %>%
@@ -164,13 +200,14 @@ populate_concept <- function(ont, modi, name, scheme, host = "", admin = "", pas
 #' @param ont The ontology to insert
 #' @param name The name of the new ontology
 #' @param scheme The scheme to use for this ontology
+#' @param project The name of the project
 #' @param host The host to connect to
 #' @param admin The admin account for the PostgreSQL database
 #' @param pass the password for the admin account
 #' @export
-populate_provider <- function(ont, name, scheme, host = "", admin = "", pass = "")
+populate_provider <- function(ont, name, scheme, project, host = "", admin = "", pass = "")
 {
-  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = "i2b2demodata", user = admin, password = pass)
+  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = stringr::str_c("i2b2", project, "data"), user = admin, password = pass)
 
   # Sanitize the ontology
   ont <- ont %>% stringr::str_replace_all("'", "''")
@@ -211,7 +248,7 @@ populate_provider <- function(ont, name, scheme, host = "", admin = "", pass = "
 #' @export
 add_patients_demodata <- function(patients, project, host = "", admin = "", pass = "")
 {
-  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = "i2b2demodata", user = admin, password = pass)
+  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = stringr::str_c("i2b2", project, "data"), user = admin, password = pass)
 
 # Upsert patients mappings
   patients %>%
@@ -268,7 +305,7 @@ add_patients_demodata <- function(patients, project, host = "", admin = "", pass
 #' @export
 add_encounters <- function(encounters, project, patient_mapping = "", host = "", admin = "", pass = "")
 {
-  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = "i2b2demodata", user = admin, password = pass)
+  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = stringr::str_c("i2b2", project, "data"), user = admin, password = pass)
 
   encounters %>%
       dplyr::mutate(encounter_ide_source = "HIVE",
@@ -320,15 +357,16 @@ add_encounters <- function(encounters, project, patient_mapping = "", host = "",
 #' such as end_date, valtype_cd, tval_char, nval_num, valueflag_cd, units_cd, etc.
 #'
 #' @param observations A dataframe of observation facts
+#' @param project The name of the project
 #' @param patient_mapping The patient mapping table
 #' @param encounter_mapping The encounter mapping table
 #' @param host The host to connect to
 #' @param admin The admin account for the PostgreSQL database
 #' @param pass The password for the admin account
 #' @export
-add_observations <- function(observations, patient_mapping = "", encounter_mapping = "", host = "", admin = "", pass = "")
+add_observations <- function(observations, project, patient_mapping = "", encounter_mapping = "", host = "", admin = "", pass = "")
 {
-  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = "i2b2demodata", user = admin, password = pass)
+  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = stringr::str_c("i2b2", project, "data"), user = admin, password = pass)
 
   RPostgreSQL::dbGetQuery(demodata, "SELECT max(text_search_index) from observation_fact;") %>%
   .$max -> nextval
@@ -355,13 +393,14 @@ add_observations <- function(observations, patient_mapping = "", encounter_mappi
 #'
 #' Rebuild the indexes in i2b2demodata
 #'
+#' @param project The name of the project
 #' @param host The host to connect to
 #' @param admin The admin account for the PostgreSQL database
 #' @param pass The password for the admin account
 #' @export
-rebuild_indexes_demodata <- function(host = "", admin = "", pass = "")
+rebuild_indexes_demodata <- function(project, host = "", admin = "", pass = "")
 {
-  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = "i2b2demodata", user = admin, password = pass)
+  demodata <- RPostgreSQL::dbConnect(RPostgreSQL::PostgreSQL(), host = host, dbname = stringr::str_c("i2b2", project, "data"), user = admin, password = pass)
 
   RPostgreSQL::dbGetQuery(demodata, "REINDEX DATABASE i2b2demodata;")
   RPostgreSQL::dbDisconnect(demodata)

man/add_observations.Rd

@@ -4,12 +4,14 @@
 \alias{add_observations}
 \title{Add observations to the CRC cell}
 \usage{
-add_observations(observations, patient_mapping = "", encounter_mapping = "",
-  host = "", admin = "", pass = "")
+add_observations(observations, project, patient_mapping = "",
+  encounter_mapping = "", host = "", admin = "", pass = "")
 }
 \arguments{
 \item{observations}{A dataframe of observation facts}
 
+\item{project}{The name of the project}
+
 \item{patient_mapping}{The patient mapping table}
 
 \item{encounter_mapping}{The encounter mapping table}
@@ -31,6 +33,6 @@ The observations dataframe must contain the following columns:
 - concept_cd: the concept to insert
 - provider_id: the provider
 - modifier_cd: optionnal modifier for the concept
-Other observation fact columns can optionnaly be included, 
+Other observation fact columns can optionnaly be included,
 such as end_date, valtype_cd, tval_char, nval_num, valueflag_cd, units_cd, etc.
 }

man/delete_concept.Rd

@@ -4,11 +4,13 @@
 \alias{delete_concept}
 \title{Delete concepts}
 \usage{
-delete_concept(scheme, host = "", admin = "", pass = "")
+delete_concept(scheme, project, host = "", admin = "", pass = "")
 }
 \arguments{
 \item{scheme}{The scheme to delete from the concepts}
 
+\item{project}{The name of the project}
+
 \item{host}{The host to connect to}
 
 \item{admin}{The admin account for the PostgreSQL database}

man/delete_modifier.Rd

@@ -4,11 +4,13 @@
 \alias{delete_modifier}
 \title{Delete modifiers}
 \usage{
-delete_modifier(scheme, host = "", admin = "", pass = "")
+delete_modifier(scheme, project, host = "", admin = "", pass = "")
 }
 \arguments{
 \item{scheme}{The scheme to delete from the concepts}
 
+\item{project}{The name of the project}
+
 \item{host}{The host to connect to}
 
 \item{admin}{The admin account for the PostgreSQL database}

man/import_data.Rd

@@ -28,7 +28,7 @@ The data dataframe must contain the following columns:
 - concept_cd: the concept to insert
 - provider_id: the provider
 - modifier_cd: optionnal modifier for the concept
-Other observation fact columns can optionnaly be included, 
+Other observation fact columns can optionnaly be included,
 such as end_date, valtype_cd, tval_char, nval_num, valueflag_cd, units_cd, etc.
 
 The function creates and updates the corresponding patients and encounters,

man/list_concepts.Rd

@@ -4,11 +4,13 @@
 \alias{list_concepts}
 \title{List concepts}
 \usage{
-list_concepts(scheme, host = "", admin = "", pass = "")
+list_concepts(scheme, project, host = "", admin = "", pass = "")
 }
 \arguments{
 \item{scheme}{The scheme to get the concepts from}
 
+\item{project}{The name of the project}
+
 \item{host}{The host to connect to}
 
 \item{admin}{The admin account for the PostgreSQL database}

man/list_projects.Rd

@@ -7,7 +7,7 @@
 list_projects(host = "", admin = "", pass = "")
 }
 \arguments{
-\item{host}{Address of the host, defaults to 127.0.0.1}
+\item{host}{Address of the hostdefaults to 127.0.0.1}
 
 \item{admin}{Name of the database admin account}
 

man/populate_concept.Rd

@@ -4,7 +4,7 @@
 \alias{populate_concept}
 \title{Populate the concept_dimension}
 \usage{
-populate_concept(ont, modi, name, scheme, host = "", admin = "",
+populate_concept(ont, modi, name, scheme, project, host = "", admin = "",
   pass = "")
 }
 \arguments{
@@ -16,6 +16,8 @@ populate_concept(ont, modi, name, scheme, host = "", admin = "",
 
 \item{scheme}{The scheme to use for this ontology}
 
+\item{project}{The name of the project}
+
 \item{host}{The host to connect to}
 
 \item{admin}{The admin account for the PostgreSQL database}

man/populate_provider.Rd

@@ -4,7 +4,8 @@
 \alias{populate_provider}
 \title{Populate the provider_dimension}
 \usage{
-populate_provider(ont, name, scheme, host = "", admin = "", pass = "")
+populate_provider(ont, name, scheme, project, host = "", admin = "",
+  pass = "")
 }
 \arguments{
 \item{ont}{The ontology to insert}
@@ -13,6 +14,8 @@ populate_provider(ont, name, scheme, host = "", admin = "", pass = "")
 
 \item{scheme}{The scheme to use for this ontology}
 
+\item{project}{The name of the project}
+
 \item{host}{The host to connect to}
 
 \item{admin}{The admin account for the PostgreSQL database}

man/rebuild_indexes_demodata.Rd

@@ -4,9 +4,11 @@
 \alias{rebuild_indexes_demodata}
 \title{Rebuild the indexes}
 \usage{
-rebuild_indexes_demodata(host = "", admin = "", pass = "")
+rebuild_indexes_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}