diff --git a/R/listSupportedVersions.R b/R/listSupportedVersions.R index 746368a..93c8cdf 100644 --- a/R/listSupportedVersions.R +++ b/R/listSupportedVersions.R @@ -12,6 +12,6 @@ listSupportedVersions <- function() { #' @export listSupportedDialects <- function() { - supportedDialects <- c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server") + supportedDialects <- c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark") return(supportedDialects) } diff --git a/R/writeDDL.R b/R/writeDDL.R index 9df7235..a5bc013 100644 --- a/R/writeDDL.R +++ b/R/writeDDL.R @@ -30,7 +30,7 @@ writeDdl <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") { # argument checks - stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) + stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark")) stopifnot(cdmVersion %in% listSupportedVersions()) stopifnot(is.character(cdmDatabaseSchema)) @@ -54,7 +54,7 @@ writeDdl <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema writePrimaryKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") { # argument checks - stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) + stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark")) stopifnot(cdmVersion %in% listSupportedVersions()) stopifnot(is.character(cdmDatabaseSchema)) @@ -78,7 +78,7 @@ writePrimaryKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabas writeForeignKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") { # argument checks - stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) + stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark")) stopifnot(cdmVersion %in% listSupportedVersions()) stopifnot(is.character(cdmDatabaseSchema)) @@ -102,7 +102,7 @@ writeForeignKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabas writeIndex <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") { # argument checks - stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) + stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark")) stopifnot(cdmVersion %in% listSupportedVersions()) stopifnot(is.character(cdmDatabaseSchema)) diff --git a/docs/background.html b/docs/background.html index d90cd4f..dd2e97f 100644 --- a/docs/background.html +++ b/docs/background.html @@ -11,15 +11,24 @@ -
Below is the specification document for the OMOP Common Data Model, v5.4. This is the latest version of the OMOP CDM. Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the forums or the github issue page.
+This is the specification document for the OMOP Common Data Model, v5.4. This is the latest version of the OMOP CDM. Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the forums or the github issue page.
+The table below details which OHDSI tools support CDM v5.4. There are two levels of support: legacy support means that the tool supports all tables and fields that were present in CDM v5.3 and feature support indicates that the tool supports any new tables and fields in CDM v5.4 that were not present in CDM v5.3. A green heart ๐ indicates that the support level for the listed tool is in place, has been tested, and released. A yellow heart ๐ indicates that the support level for the listed tool has been initiated but has not yet been tested and released.
Tool | +Description | +Legacy Support | +Feature Support | +
---|---|---|---|
CDM R package | +This package can be downloaded from https://github.com/OHDSI/CommonDataModel/. It functions to dynamically create the OMOP CDM documentation and DDL scripts to instantiate the CDM tables. | +๐ | +๐ | +
Data Quality Dashboard | +This package can be downloaded from https://github.com/OHDSI/DataQualityDashboard. It runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study. | +๐ | +๐ | +
Achilles | +This package can be downloaded from https://github.com/OHDSI/Achilles, performing a set of broad database characterizations agains an OMOP CDM instance. | +๐ | +๐ | +
ARES | +This package can be downloaded from https://github.com/OHDSI/Ares and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research. | +๐ | +๐ | +
ATLAS | +ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. Demo | +๐ | +๐ | +
Rabbit-In-A-Hat | +This package can be downloaded from https://github.com/OHDSI/WhiteRabbit and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit. | +๐ | +๐ | +
Feature Extraction | +This package can be downloaded from https://github.com/OHDSI/FeatureExtraction. It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. | +๐ | +๐* | +
Cohort Diagnostics | +This package can be downloaded from https://github.com/OHDSI/CohortDiagnostics and is used to critically evaluate cohort phenotypes. | +๐ | +๐ | +
* The Feature Extraction package supports all relevant new features in CDM v5.4. For example, it was decided that, from a methodological perspective, the EPISODE and EPISODE_EVENT tables should not be included to define cohort covariates because the events that make up episodes are already pulled in as potential covariates.
Looking to send us a pull request for a bug fix? Please see the readme on the main github page.
+
The table below details which OHDSI tools support CDM v5.4. There are two levels of support: legacy support means that the tool supports all tables and fields that were present in CDM v5.3 and feature support indicates that the tool supports any new tables and fields in CDM v5.4 that were not present in CDM v5.3. A green heart ๐ indicates that the support level for the listed tool is in place, has been tested, and released. A yellow heart ๐ indicates that the support level for the listed tool has been initiated but has not yet been tested and released.
Tool | +Description | +Legacy Support | +Feature Support | +
---|---|---|---|
CDM R package | +This package can be downloaded from https://github.com/OHDSI/CommonDataModel/. It functions to dynamically create the OMOP CDM documentation and DDL scripts to instantiate the CDM tables. | +๐ | +๐ | +
Data Quality Dashboard | +This package can be downloaded from https://github.com/OHDSI/DataQualityDashboard. It runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study. | +๐ | +๐ | +
Achilles | +This package can be downloaded from https://github.com/OHDSI/Achilles, performing a set of broad database characterizations agains an OMOP CDM instance. | +๐ | +๐ | +
ARES | +This package can be downloaded from https://github.com/OHDSI/Ares and is designed to display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research. | +๐ | +๐ | +
ATLAS | +ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data. Demo | +๐ | +๐ | +
Rabbit-In-A-Hat | +This package can be downloaded from https://github.com/OHDSI/WhiteRabbit and is an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit. | +๐ | +๐ | +
Feature Extraction | +This package can be downloaded from https://github.com/OHDSI/FeatureExtraction. It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. | +๐ | +๐* | +
Cohort Diagnostics | +This package can be downloaded from https://github.com/OHDSI/CohortDiagnostics and is used to critically evaluate cohort phenotypes. | +๐ | +๐ | +
* The Feature Extraction package supports all relevant new features in CDM v5.4. For example, it was decided that, from a methodological perspective, the EPISODE and EPISODE_EVENT tables should not be included to define cohort covariates because the events that make up episodes are already pulled in as potential covariates.
t |