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Fix exportToSQLite errors caused by old table name and parameter order (
#159) * Fix exportToSQLite errors caused by old table name and parameter order * Add the rest of the tables to exportToSqlite() * Add cdm version support for 5.3 and 5.4 to exportToSQLite --------- Co-authored-by: Evanette Burrows <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,87 +1,87 @@ | ||
| #' @title Export a CDM (Vocabulary and Event tables) into a SQLite Database. | ||
| #' | ||
| #' @description This function fetches (pruned) table data into R dataframes and writes them to a SQLite DB. (Eunomia support) | ||
| #' | ||
| #' @param connectionDetails An R object of type\cr\code{connectionDetails} created using the | ||
| #' function \code{createConnectionDetails} in the | ||
| #' \code{DatabaseConnector} package. | ||
| #' | ||
| #' @param cdmSchema The name of the database schema that contains the CDM. | ||
| #' Requires read and write permissions to this database. On SQL | ||
| #' Server, this should specifiy both the database and the schema, | ||
| #' so for example 'cdm_instance.dbo'. | ||
| #' | ||
| #' @param SQLiteDbName The name of the SQLite Database File. | ||
| #' | ||
| #'@export | ||
|
|
||
| exportToSQLite <- | ||
| function(connectionDetails, | ||
| cdmSchema, | ||
| SQLiteDbName = "cdm.sqlite") | ||
| { | ||
| conn <- DatabaseConnector::connect(connectionDetails) | ||
| sqliteCD <- | ||
| DatabaseConnector::createConnectionDetails(dbms = "sqlite", server = SQLiteDbName) | ||
| sqliteCon <- DatabaseConnector::connect(sqliteCD) | ||
|
|
||
| eventTable <- c( | ||
| "care_site", | ||
| "cdm_source", | ||
| "cohort", | ||
| "cohort_attribute", | ||
| "condition_era", | ||
| "condition_occurrence", | ||
| "cost", | ||
| "death", | ||
| "device_exposure", | ||
| "dose_era", | ||
| "drug_era", | ||
| "drug_exposure", | ||
| "fact_relationship", | ||
| "location", | ||
| "measurement", | ||
| "metadata", | ||
| "note", | ||
| "note_nlp", | ||
| "observation", | ||
| "observation_period", | ||
| "payer_plan_period", | ||
| "person", | ||
| "procedure_occurrence", | ||
| "provider", | ||
| "specimen", | ||
| "visit_detail", | ||
| "visit_occurrence" | ||
| ) | ||
|
|
||
| vocabTable <- c( | ||
| "concept", | ||
| "concept_ancestor", | ||
| "concept_class", | ||
| "concept_relationship", | ||
| "concept_synonym", | ||
| "domain", | ||
| "drug_strength", | ||
| "relationship", | ||
| "source_to_concept_map", | ||
| "vocabulary" | ||
| ) | ||
|
|
||
| for (tableName in c(eventTable, vocabTable)) { | ||
| sqlQuery <- | ||
| paste0("select * from ", paste0(cdmSchema, ".", tableName), ";") | ||
| translatedSql <- | ||
| SqlRender::translate(sqlQuery, targetDialect = connectionDetails$dbms) | ||
| writeLines(paste0("Fetching: ", tableName)) | ||
| tableData <- DatabaseConnector::querySql(conn, translatedSql) | ||
| DatabaseConnector::insertTable( | ||
| connection = sqliteCon, | ||
| tableName = toupper(tableName), | ||
| data = tableData | ||
| ) | ||
| } | ||
|
|
||
| DatabaseConnector::disconnect(conn) | ||
| DatabaseConnector::disconnect(sqliteCon) | ||
| } | ||
| #' @title Export a CDM (Vocabulary and Event tables) into a SQLite Database. | ||
| #' | ||
| #' @description This function fetches (pruned) table data into R dataframes and writes them to a SQLite DB. (Eunomia support) | ||
| #' | ||
| #' @param connectionDetails An R object of type\cr\code{connectionDetails} created using the | ||
| #' function \code{createConnectionDetails} in the | ||
| #' \code{DatabaseConnector} package. | ||
| #' | ||
| #' @param cdmSchema The name of the database schema that contains the CDM. | ||
| #' Requires read and write permissions to this database. On SQL | ||
| #' Server, this should specifiy both the database and the schema, | ||
| #' so for example 'cdm_instance.dbo'. | ||
| #' | ||
| #' @param SQLiteDbName The name of the SQLite Database File. | ||
| #' | ||
| #'@export | ||
|
|
||
| exportToSQLite <- | ||
| function(connectionDetails, | ||
| cdmSchema, | ||
| SQLiteDbName = "cdm.sqlite") | ||
| { | ||
| conn <- DatabaseConnector::connect(connectionDetails) | ||
| sqliteCD <- | ||
| DatabaseConnector::createConnectionDetails(dbms = "sqlite", server = SQLiteDbName) | ||
| sqliteCon <- DatabaseConnector::connect(sqliteCD) | ||
|
|
||
| eventTable <- c( | ||
| "care_site", | ||
| "cdm_source", | ||
| "cohort", | ||
| "cohort_attribute", | ||
| "condition_era", | ||
| "condition_occurrence", | ||
| "cost", | ||
| "death", | ||
| "device_exposure", | ||
| "dose_era", | ||
| "drug_era", | ||
| "drug_exposure", | ||
| "fact_relationship", | ||
| "location", | ||
| "measurement", | ||
| "metadata", | ||
| "note", | ||
| "note_nlp", | ||
| "observation", | ||
| "observation_period", | ||
| "payer_plan_period", | ||
| "person", | ||
| "procedure_occurrence", | ||
| "provider", | ||
| "specimen", | ||
| "visit_detail", | ||
| "visit_occurrence" | ||
| ) | ||
|
|
||
| vocabTable <- c( | ||
| "concept", | ||
| "concept_ancestor", | ||
| "concept_class", | ||
| "concept_relationship", | ||
| "concept_synonym", | ||
| "domain", | ||
| "drug_strength", | ||
| "relationship", | ||
| "source_to_concept_map", | ||
| "vocabulary" | ||
| ) | ||
|
|
||
| for (tableName in c(eventTable, vocabTable)) { | ||
| sqlQuery <- | ||
| paste0("select * from ", paste0(cdmSchema, ".", tableName), ";") | ||
| translatedSql <- | ||
| SqlRender::translate(sqlQuery, targetDialect = connectionDetails$dbms) | ||
| writeLines(paste0("Fetching: ", tableName)) | ||
| tableData <- DatabaseConnector::querySql(conn, translatedSql) | ||
| DatabaseConnector::insertTable( | ||
| connection = sqliteCon, | ||
| tableName = toupper(tableName), | ||
| data = tableData | ||
| ) | ||
| } | ||
|
|
||
| DatabaseConnector::disconnect(conn) | ||
| DatabaseConnector::disconnect(sqliteCon) | ||
| } |