# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#' Run the query to create the observation_period table.
#'
#' This function will call and run the sql file to create the observation_period tables. Requires that the function \code{chunkData} is run first.
#' @param connectionDetails An R object of type\cr\code{connectionDetails} created using the
#' function \code{createConnectionDetails} in the
#' \code{DatabaseConnector} package.
#' @param cdmDatabaseSchema The name of the database schema that contains the OMOP CDM
#' instance. Requires read permissions to this database. On SQL
#' Server, this should specifiy both the database and the schema,
#' so for example 'cdm_instance.dbo'.
#' @param sourceDatabaseSchema The name of the database schema that contains the raw data
#' instance. Requires read permissions to this database. On SQL
#' Server, this should specifiy both the database and the schema,
#' so for example 'raw_instance.dbo'.
#' @param oracleTempSchema For Oracle only: the name of the database schema where you want
#' all temporary tables to be managed. Requires create/insert
#' permissions to this database.
#' @param createWebmdObsPeriod Default is FALSE, set to TRUE if a second observation_period table should be created spanning only
#' the WebMD claims. Table name will be OBSERVATION_PERIOD_WEBMD.
#' @param iteraterNum The number of chunks of data the program should be looped over.
#'
#' @export
createObservationPeriodTable <- function(connectionDetails,
cdmDatabaseSchema,
sourceDatabaseSchema,
oracleTempSchema = NULL,
createWebmdObsPeriod = FALSE,
iteraterNum){
if(is.null(listHVIDChunks)){
return("Please run the chunkData function first to create the data chunks")
} else {
conn <- connect(connectionDetails)
tempTableNames <- paste0("#temp_obs_period_",1:iteraterNum)
sqlFile <- "ObservationPeriodTable.sql"
for(i in 1:iteraterNum){
print(paste0(i,":",iteraterNum," run Observation_Period for HVIDs starting with ", listHVIDChunks$HVID_CHUNK[i]))
sql <- SqlRender::loadRenderTranslateSql(sqlFilename = sqlFile,
packageName = "healthVerityBuildr",
dbms = connectionDetails$dbms,
oracleTempSchema = oracleTempSchema,
result_temp_table = tempTableNames[i],
cdm_schema = cdmDatabaseSchema,
source_schema = sourceDatabaseSchema,
HVID_CHUNK = listHVIDChunks$HVID_CHUNK[i],
n_substring = listHVIDChunks$NSUBSTRING[i])
DatabaseConnector::executeSql(conn, sql)
}
sql <- paste0("IF OBJECT_ID('@cdm_schema.OBSERVATION_PERIOD') IS NOT NULL DROP TABLE @cdm_schema.[OBSERVATION_PERIOD]\n
CREATE TABLE @cdm_schema.[OBSERVATION_PERIOD]\n
WITH (\n
CLUSTERED COLUMNSTORE INDEX,\n
DISTRIBUTION = HASH(PERSON_ID)\n
) AS\n
SELECT ROW_NUMBER () OVER (ORDER BY (SELECT NULL)) AS OBSERVATION_PERIOD_ID, * \nFROM (\n",
paste0(paste0(" SELECT * FROM ", tempTableNames), collapse = "\n UNION ALL\n"),
"\n) temp")
sql <- SqlRender::renderSql(sql = sql,
cdm_schema = cdmDatabaseSchema)$sql
sql <- SqlRender::translateSql(sql = sql,
targetDialect = connectionDetails$dbms)$sql
writeLines("Stack observation_period temp tables on top of each other")
DatabaseConnector::executeSql(conn, sql, progressBar = TRUE, reportOverallTime = TRUE)
if(createWebmdObsPeriod == TRUE){
tempTableNames <- paste0("#temp_op_webmd_",1:iteraterNum)
sqlFile <- "ObservationPeriodWebMDTable.sql"
for(i in 1:iteraterNum){
print(paste0(i,":",iteraterNum," run Observation_Period_WebMD for HVIDs starting with ", listHVIDChunks$HVID_CHUNK[i]))
sql <- SqlRender::loadRenderTranslateSql(sqlFilename = sqlFile,
packageName = "healthVerityBuildr",
dbms = connectionDetails$dbms,
oracleTempSchema = oracleTempSchema,
result_temp_table = tempTableNames[i],
cdm_schema = cdmDatabaseSchema,
source_schema = sourceDatabaseSchema,
HVID_CHUNK = listHVIDChunks$HVID_CHUNK[i],
n_substring = listHVIDChunks$NSUBSTRING[i])
DatabaseConnector::executeSql(conn, sql)
}
sql <- paste0("IF OBJECT_ID('@cdm_schema.OBSERVATION_PERIOD_WEBMD') IS NOT NULL DROP TABLE @cdm_schema.[OBSERVATION_PERIOD_WEBMD]\n
CREATE TABLE @cdm_schema.[OBSERVATION_PERIOD_WEBMD]\n
WITH (\n
CLUSTERED COLUMNSTORE INDEX,\n
DISTRIBUTION = HASH(PERSON_ID)\n
) AS\n
SELECT ROW_NUMBER () OVER (ORDER BY (SELECT NULL)) AS OBSERVATION_PERIOD_ID, * \nFROM (\n",
paste0(paste0(" SELECT * FROM ", tempTableNames), collapse = "\n UNION ALL\n"),
"\n) temp")
sql <- SqlRender::renderSql(sql = sql,
cdm_schema = cdmDatabaseSchema)$sql
sql <- SqlRender::translateSql(sql = sql,
targetDialect = connectionDetails$dbms)$sql
writeLines("Stack observation_period_webmd temp tables on top of each other")
DatabaseConnector::executeSql(conn, sql, progressBar = TRUE, reportOverallTime = TRUE)
}
sqlFile <- "BirthAfterObservation.sql"
sql <- SqlRender::loadRenderTranslateSql(sqlFilename = sqlFile,
packageName = "healthVerityBuildr",
dbms = connectionDetails$dbms,
oracleTempSchema = oracleTempSchema,
cdm_schema = cdmDatabaseSchema,
source_schema = sourceDatabaseSchema)
DatabaseConnector::executeSql(conn, sql, progressBar = TRUE, reportOverallTime = TRUE)
}
dbDisconnect(conn)
}
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