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Address Issue 162 improve version support #174

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merged 3 commits into from
Dec 20, 2023
Merged

Address Issue 162 improve version support #174

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9321ea9
Update convenience functions for supported OMOP versions
burrowse Dec 15, 2023
13f1308
Update CreateCDMIndexAndConstraintScripts.r
burrowse Dec 20, 2023
965fb69
Correct PDW references
burrowse Dec 20, 2023
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181 changes: 46 additions & 135 deletions R/CreateCDMIndexAndConstraintScripts.r
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,11 @@
#' function \code{createConnectionDetails} in the
#' \code{DatabaseConnector} package.
#' @param cdmSchema The name of the CDM database schema. Requires read and write permissions to this database. On SQL
#' Server, this should specifiy both the database and the schema,
#' Server, this should specify both the database and the schema,
#' so for example 'cdm_instance.dbo'.
#' @param cdmVersion Your CDM version. Currently "5.3.1" and "6.0.0" are supported.
#' @param cdmVersion Your CDM version. Currently "5.3.1" and "5.4.0" are supported.
#' @param githubTag An optional github tag from which to pull the DDL script.
#' Currently "v5.3.1", "v5.3.1_fixes", "v6.0.0", and "v6.0.0_fixes" are supported. The default is NULL.
#' Currently "v5.3.1" and "v5.4.0" are supported. The default is NULL.
#'
#' @details This function creates SQL scripts for the indices and constraints on tables in a CDM by referring to the
#' correct SQL DDL script in the OHDSI CommonDataModel repo. The database platform is
Expand All @@ -29,13 +29,13 @@
{
supportedDbs <-
c("oracle", "postgresql", "pdw", "netezza", "sql server")
supportedVersions <- c("5.3.1", "6.0.0")
supportedVersions <- c("5.3.1", "5.4.0")
supportedTags <-
c("v5.3.1", "v6.0.0", "v5.3.1_fixes", "v6.0.0_fixes")
c("v5.3.1", "v5.4.0")
rdbms <- tolower(connectionDetails$dbms)

if (!(cdmVersion %in% supportedVersions)) {
stop("Unsupported CDM specified. Supported CDM versions are \"5.3.1\" and \"6.0.0\"")
stop("Unsupported CDM specified. Supported CDM versions are \"5.3.1\" and \"5.4.0\"")
}

if (!(rdbms %in% supportedDbs)) {
Expand All @@ -46,17 +46,17 @@

if (!is.null(githubTag) && !(githubTag %in% supportedTags)) {
stop(
"Unrecognized github tag. Supported values are \"v5.3.1\", \"v6.0.0\", \"v5.3.1_fixes\", and \"v6.0.0_fixes\""
"Unrecognized github tag. Supported values are \"v5.3.1\" and \"v5.4.0\""
)
}

if (cdmVersion == "5.3.1" &&
!(githubTag %in% c("v5.3.1", "v5.3.1_fixes"))) {
!(githubTag %in% c("v5.3.1"))) {

Check warning on line 54 in R/CreateCDMIndexAndConstraintScripts.r

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GitHub Actions / lintr-job 

file=R/CreateCDMIndexAndConstraintScripts.r,line=54,col=8,[indentation_linter] Indentation should be 10 spaces but is 8 spaces.
stop("cdmVersion and githubTag mismatch.")
}

if (cdmVersion == "6.0.0" &&
!(githubTag %in% c("v6.0.0", "v6.0.0_fixes"))) {
if (cdmVersion == "5.4.0" &&
!(githubTag %in% c("v5.4.0"))) {

Check warning on line 59 in R/CreateCDMIndexAndConstraintScripts.r

View workflow job for this annotation

GitHub Actions / lintr-job 

file=R/CreateCDMIndexAndConstraintScripts.r,line=59,col=8,[indentation_linter] Indentation should be 10 spaces but is 8 spaces.
stop("cdmVersion and githubTag mismatch.")
}

Expand All @@ -74,34 +74,16 @@
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1/Oracle/OMOP%20CDM%20oracle%20constraints.txt"
)
} else if (githubTag == "v5.3.1_fixes") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1_fixes/Oracle/OMOP%20CDM%20oracle%20v5_3_1%20primary%20keys.sql"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1_fixes/Oracle/OMOP%20CDM%20oracle%20v5_3_1%20constraints.sql"
)
}
} else if (cdmVersion == "6.0.0") {
if (is.null(githubTag) || githubTag == "v6.0.0") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0.0/Oracle/OMOP%20CDM%20oracle%20pk%20indexes.txt"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0.0/Oracle/OMOP%20CDM%20oracle%20constraints.txt"
)
} else if (githubTag == "v6.0.0_fixes") {
} else if (cdmVersion == "5.4.0") {
if (is.null(githubTag) || githubTag == "v5.4.0") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0_fixes/Oracle/OMOP%20CDM%20oracle%20pk%20indexes.txt"
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.4.0/inst/ddl/5.4/oracle/OMOPCDM_oracle_5.4_indices.sql"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0_fixes/Oracle/OMOP%20CDM%20oracle%20constraints.txt"
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.4.0/inst/ddl/5.4/oracle/OMOPCDM_oracle_5.4_constraints.sql"
)
}
}
Expand All @@ -116,34 +98,16 @@
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1/PostgreSQL/OMOP%20CDM%20postgresql%20constraints.txt"
)
} else if (githubTag == "v5.3.1_fixes") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1_fixes/PostgreSQL/OMOP%20CDM%20postgresql%20v5_3_1%20primary%20keys.sql"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1_fixes/PostgreSQL/OMOP%20CDM%20postgresql%20v5_3_1%20constraints.sql"
)
}
} else if (cdmVersion == "6.0.0") {
if (is.null(githubTag) || githubTag == "v6.0.0") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0.0/PostgreSQL/OMOP%20CDM%20postgresql%20pk%20indexes.txt"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0.0/PostgreSQL/OMOP%20CDM%20postgresql%20constraints.txt"
)
} else if (githubTag == "v6.0.0_fixes") {
} else if (cdmVersion == "5.4.0") {
if (is.null(githubTag) || githubTag == "v5.4.0") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0_fixes/PostgreSQL/OMOP%20CDM%20postgresql%20pk%20indexes.txt"
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.4.0/inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_indices.sql"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0_fixes/PostgreSQL/OMOP%20CDM%20postgresql%20constraints.txt"
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.4.0/inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_constraints.sql"
)
}
}
Expand All @@ -158,34 +122,16 @@
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1/ParallelDataWarehouse/OMOP%20CDM%20pdw%20constraints.txt"
)
} else if (githubTag == "v5.3.1_fixes") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1_fixes/ParallelDataWarehouse/OMOP%20CDM%20pdw%20v5_3_1%20indices.sql"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1_fixes/ParallelDataWarehouse/OMOP%20CDM%20pdw%20v5_3_1%20constraints.sql"
)
}
} else if (cdmVersion == "6.0.0") {
if (is.null(githubTag) || githubTag == "v6.0.0") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0.0/ParallelDataWarehouse/OMOP%20CDM%20pdw%20pk%20indexes.txt"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0.0/ParallelDataWarehouse/OMOP%20CDM%20pdw%20constraints.txt"
)
} else if (githubTag == "v6.0.0_fixes") {
} else if (cdmVersion == "5.4.0") {
if (is.null(githubTag) || githubTag == "v5.4.0") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0_fixes/ParallelDataWarehouse/OMOP%20CDM%20pdw%20pk%20indexes.txt"
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.4.0/inst/ddl/5.4/pdw/OMOPCDM_pdw_5.4_indices.sql"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0_fixes/ParallelDataWarehouse/OMOP%20CDM%20pdw%20constraints.txt"
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.4.0/inst/ddl/5.4/pdw/OMOPCDM_pdw_5.4_constraints.sql"
)
}
}
Expand All @@ -196,22 +142,12 @@
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1/Netezza/OMOP%20CDM%20netezza%20primary%20keys.txt"
)
} else if (githubTag == "v5.3.1_fixes") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1_fixes/Netezza/OMOP%20CDM%20netezza%20v5_3_1%20primary%20keys.sql"
)
}
} else if (cdmVersion == "6.0.0") {
if (is.null(githubTag) || githubTag == "v6.0.0") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0.0/Netezza/OMOP%20CDM%20netezza%20primary%20keys.txt"
)
} else if (githubTag == "v6.0.0_fixes") {
} else if (cdmVersion == "5.4.0") {
if (is.null(githubTag) || githubTag == "v5.4.0") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0_fixes/Netezza/OMOP%20CDM%20netezza%20primary%20keys.txt"
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.4.0/inst/ddl/5.4/netezza/OMOPCDM_netezza_5.4_primary_keys.sql"
)
}
}
Expand All @@ -226,34 +162,16 @@
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1/Sql%20Server/OMOP%20CDM%20sql%20server%20constraints.txt"
)
} else if (githubTag == "v5.3.1_fixes") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1_fixes/Sql%20Server/OMOP%20CDM%20sql%20server%20v5_3_1%20primary%20keys.sql"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.3.1_fixes/Sql%20Server/OMOP%20CDM%20sql%20server%20v5_3_1%20constraints.sql"
)
}
} else if (cdmVersion == "6.0.0") {
if (is.null(githubTag) || githubTag == "v6.0.0") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0.0/Sql%20Server/OMOP%20CDM%20sql%20server%20pk%20indexes.txt"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0.0/Sql%20Server/OMOP%20CDM%20sql%20server%20constraints.txt"
)
} else if (githubTag == "v6.0.0_fixes") {
} else if (cdmVersion == "5.4.0") {
if (is.null(githubTag) || githubTag == "v5.4.0") {
webResponseInd <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0_fixes/Sql%20Server/OMOP%20CDM%20sql%20server%20pk%20indexes.txt"
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.4.0/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_indices.sql"
)
webResponseCon <-
httr::GET(
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v6.0_fixes/Sql%20Server/OMOP%20CDM%20sql%20server%20constraints.txt"
"https://raw.githubusercontent.com/OHDSI/CommonDataModel/v5.4.0/inst/ddl/5.4/sql_server/OMOPCDM_sql_server_5.4_primary_keys.sql"
)
}
}
Expand All @@ -267,30 +185,23 @@
indexDDL <- toupper(indexDDL)
constraintDDL <- toupper(constraintDDL)

if (githubTag == "v5.3.1_fixes") {
indexDDL <-
SqlRender::render(sql = indexDDL, CDMDATABASESCHEMA = cdmSchema)
constraintDDL <-
SqlRender::render(sql = constraintDDL, CDMDATABASESCHEMA = cdmSchema)
} else {
indexDDL <- gsub(" ON ", " ON @CDM_SCHEMA.", indexDDL)
indexDDL <-
gsub("ALTER TABLE", "ALTER TABLE @CDM_SCHEMA.", indexDDL)
indexDDL <- gsub("@CDM_SCHEMA. ", "@CDM_SCHEMA.", indexDDL)
indexDDL <-
SqlRender::render(indexDDL, CDM_SCHEMA = cdmSchema)
indexDDL <-
SqlRender::translate(indexDDL, targetDialect = rdbms)

constraintDDL <-
gsub("ALTER TABLE", "ALTER TABLE @CDM_SCHEMA.", constraintDDL)
constraintDDL <-
gsub("@CDM_SCHEMA. ", "@CDM_SCHEMA.", constraintDDL)
constraintDDL <-
SqlRender::render(constraintDDL, CDM_SCHEMA = cdmSchema)
constraintDDL <-
SqlRender::translate(constraintDDL, targetDialect = rdbms)
}
indexDDL <- gsub(" ON ", " ON @CDM_SCHEMA.", indexDDL)
indexDDL <-
gsub("ALTER TABLE", "ALTER TABLE @CDM_SCHEMA.", indexDDL)
indexDDL <- gsub("@CDM_SCHEMA. ", "@CDM_SCHEMA.", indexDDL)
indexDDL <-
SqlRender::render(indexDDL, CDM_SCHEMA = cdmSchema)
indexDDL <-
SqlRender::translate(indexDDL, targetDialect = rdbms)

constraintDDL <-
gsub("ALTER TABLE", "ALTER TABLE @CDM_SCHEMA.", constraintDDL)
constraintDDL <-
gsub("@CDM_SCHEMA. ", "@CDM_SCHEMA.", constraintDDL)
constraintDDL <-
SqlRender::render(constraintDDL, CDM_SCHEMA = cdmSchema)
constraintDDL <-
SqlRender::translate(constraintDDL, targetDialect = rdbms)

# Save the translated sql ddl to be run at a later time
if (!dir.exists("output")) {
Expand Down
10 changes: 5 additions & 5 deletions R/backupCDM.r
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@
#' \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,
#' Server, this should specify both the database and the schema,
#' so for example 'cdm_instance.dbo'.
#' @param cdmVersion The version of your CDM. Currently "5.3.1" and "6.0.1".
#' @param cdmVersion The version of your CDM. Currently "5.3.1" and "5.4.0".
#'
#'@export

Expand All @@ -18,10 +18,10 @@ backupCDM <- function(connectionDetails, cdmSchema, cdmVersion)
{
if (cdmVersion == "5.3.1")
sqlFilePath <- "cdm_version/v531"
else if (cdmVersion == "6.0.0")
sqlFilePath <- "cdm_version/v600"
else if (cdmVersion == "5.4.0")
sqlFilePath <- "cdm_version/v540"
else
stop("Unsupported CDM specified. Supported CDM versions are \"5.3.1\" and \"6.0.0\"")
stop("Unsupported CDM specified. Supported CDM versions are \"5.3.1\" and \"5.4.0\"")


sql <- SqlRender::loadRenderTranslateSql(
Expand Down
10 changes: 5 additions & 5 deletions R/createPrunedTables.r
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@
#'
#' @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,
#' Server, this should specify both the database and the schema,
#' so for example 'cdm_instance.dbo'.
#' @param eventConceptId A vector of concept_ids returned from \code{getEventConceptId}.
#' @param cdmVersion The version of your CDM. Currently "5.3.1" and "6.0.0".
#' @param cdmVersion The version of your CDM. Currently "5.3.1" and "5.4.0".
#'
#'@export

Expand All @@ -25,10 +25,10 @@ createPrunedTables <-
{
if (cdmVersion == "5.3.1")
sqlFilePath <- "cdm_version/v531"
else if (cdmVersion == "6.0.0")
sqlFilePath <- "cdm_version/v600"
else if (cdmVersion == "5.4.0")
sqlFilePath <- "cdm_version/v540"
else
stop("Unsupported CDM specified. Supported CDM versions are \"5.3.1\" and \"6.0.0\"")
stop("Unsupported CDM specified. Supported CDM versions are \"5.3.1\" and \"5.4.0\"")

sql <- SqlRender::loadRenderTranslateSql(
sqlFileName = paste0(sqlFilePath, "/create_pruned_tables.sql"),
Expand Down
10 changes: 5 additions & 5 deletions R/getEventConceptId.r
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@
#'
#' @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,
#' Server, this should specify both the database and the schema,
#' so for example 'cdm_instance.dbo'.
#' @param cdmVersion The version of your CDM. Currently "5.3.1" and "6.0.0".
#' @param cdmVersion The version of your CDM. Currently "5.3.1" and "5.4.0".
#'
#'@export

Expand All @@ -19,10 +19,10 @@ getEventConceptId <-
{
if (cdmVersion == "5.3.1")
sqlFilePath <- "cdm_version/v531"
else if (cdmVersion == "6.0.0")
sqlFilePath <- "cdm_version/v600"
else if (cdmVersion == "5.4.0")
sqlFilePath <- "cdm_version/v540"
else
stop("Unsupported CDM specified. Supported CDM versions are \"5.3.1\" and \"6.0.0\"")
stop("Unsupported CDM specified. Supported CDM versions are \"5.3.1\" and \"5.4.0\"")

sql <- SqlRender::loadRenderTranslateSql(
sqlFileName = paste0(sqlFilePath, "/get_event_concept_id.sql"),
Expand Down
4 changes: 2 additions & 2 deletions R/pruneCDM.r
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@
#' \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,
#' Server, this should specify both the database and the schema,
#' so for example 'cdm_instance.dbo'.
#' @param cdmVersion The version of your CDM. Currently "5.3.1" and "6.0.0".
#' @param cdmVersion The version of your CDM. Currently "5.3.1" and "5.4.0".
#'
#'@export

Expand Down
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