Address Issue 162 improve version support (#174)

* Update functions for supported OMOP versions
OHDSI · Dec 20, 2023 · f669358 · f669358
1 parent 0d128c0
commit f669358
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Showing 6 changed files with 68 additions and 157 deletions.
diff --git a/R/CreateCDMIndexAndConstraintScripts.r b/R/CreateCDMIndexAndConstraintScripts.r
@@ -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
@@ -29,13 +29,13 @@ CreateCDMIndexAndConstraintScripts <-
   {
     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)) {
@@ -46,17 +46,17 @@ CreateCDMIndexAndConstraintScripts <-
 
     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"))) {
       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"))) {
       stop("cdmVersion and githubTag mismatch.")
     }
 
@@ -74,34 +74,16 @@ CreateCDMIndexAndConstraintScripts <-
             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"
             )
         }
       }
@@ -116,34 +98,16 @@ CreateCDMIndexAndConstraintScripts <-
             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"
             )
         }
       }
@@ -158,34 +122,16 @@ CreateCDMIndexAndConstraintScripts <-
             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"
             )
         }
       }
@@ -196,22 +142,12 @@ CreateCDMIndexAndConstraintScripts <-
             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"
             )
         }
       }
@@ -226,34 +162,16 @@ CreateCDMIndexAndConstraintScripts <-
             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"
             )
         }
       }
@@ -267,30 +185,23 @@ CreateCDMIndexAndConstraintScripts <-
     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")) {

diff --git a/R/backupCDM.r b/R/backupCDM.r
@@ -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
 
@@ -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(

diff --git a/R/createPrunedTables.r b/R/createPrunedTables.r
@@ -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
 
@@ -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"),

diff --git a/R/getEventConceptId.r b/R/getEventConceptId.r
@@ -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
 
@@ -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"),

diff --git a/R/pruneCDM.r b/R/pruneCDM.r
@@ -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