From f006431a5e4043f74d971586e0d528de5595d9d1 Mon Sep 17 00:00:00 2001 From: Clair Blacketer Date: Thu, 13 Jan 2022 13:59:03 -0500 Subject: [PATCH] Bug fixes and updates from Nov 2021 - Jan 2022 --- R/listSupportedVersions.R | 2 +- R/writeDDL.R | 8 +- docs/background.html | 128 +- docs/cdm30.html | 126 +- docs/cdm53.html | 138 +- docs/cdm531.html | 126 +- docs/cdm54.html | 261 +- docs/cdm54Changes.html | 126 +- docs/cdm60.html | 126 +- docs/cdmPrivacy.html | 128 +- docs/cdmRefreshProcess.html | 128 +- docs/contribute.html | 126 +- docs/dataModelConventions.html | 128 +- docs/download.html | 126 +- docs/drug_dose.html | 123 +- docs/ehrObsPeriods.html | 123 +- docs/faq.html | 121 +- docs/images/rexample1.png | Bin 79743 -> 0 bytes docs/images/rexample2.png | Bin 101935 -> 0 bytes docs/images/rexample3.png | Bin 45540 -> 0 bytes docs/index.html | 74 +- docs/indices-primary-foreign.html | 126 +- docs/oncology.html | 126 +- docs/queries.html | 121 +- docs/reviewProposals.html | 121 +- .../header-attrs.js | 0 docs/site_libs/jquery-1.11.3/jquery.min.js | 5 - docs/site_libs/jquery-3.6.0/jquery-3.6.0.js | 10881 ++++++++++++++++ .../jquery-3.6.0/jquery-3.6.0.min.js | 2 + .../jquery-3.6.0/jquery-3.6.0.min.map | 1 + docs/site_libs/navigation-1.1/codefolding.js | 19 +- docs/site_libs/tocify-1.9.1/jquery.tocify.js | 2 +- docs/sqlScripts.html | 131 +- docs/vocabulary.html | 126 +- extras/codeToRun.R | 12 +- .../5.3/bigquery/OMOPCDM_bigquery_5.3_ddl.sql | 12 +- .../5.3/netezza/OMOPCDM_netezza_5.3_ddl.sql | 12 +- .../ddl/5.3/oracle/OMOPCDM_oracle_5.3_ddl.sql | 12 +- inst/ddl/5.3/pdw/OMOPCDM_pdw_5.3_ddl.sql | 12 +- .../postgresql/OMOPCDM_postgresql_5.3_ddl.sql | 12 +- .../5.3/redshift/OMOPCDM_redshift_5.3_ddl.sql | 12 +- .../spark/OMOPCDM_spark_5.3_constraints.sql | 158 + inst/ddl/5.3/spark/OMOPCDM_spark_5.3_ddl.sql | 544 + .../5.3/spark/OMOPCDM_spark_5.3_indices.sql | 70 + .../spark/OMOPCDM_spark_5.3_primary_keys.sql | 26 + .../sql_server/OMOPCDM_sql_server_5.3_ddl.sql | 12 +- .../OMOPCDM_bigquery_5.4_constraints.sql | 2 - .../5.4/bigquery/OMOPCDM_bigquery_5.4_ddl.sql | 12 +- .../impala/OMOPCDM_impala_5.4_constraints.sql | 2 - .../ddl/5.4/impala/OMOPCDM_impala_5.4_ddl.sql | 16 +- .../OMOPCDM_netezza_5.4_constraints.sql | 2 - .../5.4/netezza/OMOPCDM_netezza_5.4_ddl.sql | 28 +- .../oracle/OMOPCDM_oracle_5.4_constraints.sql | 2 - .../ddl/5.4/oracle/OMOPCDM_oracle_5.4_ddl.sql | 28 +- .../5.4/pdw/OMOPCDM_pdw_5.4_constraints.sql | 2 - inst/ddl/5.4/pdw/OMOPCDM_pdw_5.4_ddl.sql | 28 +- .../OMOPCDM_postgresql_5.4_constraints.sql | 2 - .../postgresql/OMOPCDM_postgresql_5.4_ddl.sql | 28 +- .../OMOPCDM_redshift_5.4_constraints.sql | 2 - .../5.4/redshift/OMOPCDM_redshift_5.4_ddl.sql | 28 +- .../spark/OMOPCDM_spark_5.4_constraints.sql | 177 + inst/ddl/5.4/spark/OMOPCDM_spark_5.4_ddl.sql | 588 + .../5.4/spark/OMOPCDM_spark_5.4_indices.sql | 70 + .../spark/OMOPCDM_spark_5.4_primary_keys.sql | 28 + .../OMOPCDM_sql_server_5.4_constraints.sql | 2 - .../sql_server/OMOPCDM_sql_server_5.4_ddl.sql | 28 +- rmd/cdm54.Rmd | 23 +- rmd/cdmRPackage.rmd | 4 +- rmd/index.Rmd | 22 + 69 files changed, 13858 insertions(+), 1939 deletions(-) delete mode 100644 docs/images/rexample1.png delete mode 100644 docs/images/rexample2.png delete mode 100644 docs/images/rexample3.png rename docs/site_libs/{header-attrs-2.6 => header-attrs-2.11}/header-attrs.js (100%) delete mode 100644 docs/site_libs/jquery-1.11.3/jquery.min.js create mode 100644 docs/site_libs/jquery-3.6.0/jquery-3.6.0.js create mode 100644 docs/site_libs/jquery-3.6.0/jquery-3.6.0.min.js create mode 100644 docs/site_libs/jquery-3.6.0/jquery-3.6.0.min.map create mode 100644 inst/ddl/5.3/spark/OMOPCDM_spark_5.3_constraints.sql create mode 100644 inst/ddl/5.3/spark/OMOPCDM_spark_5.3_ddl.sql create mode 100644 inst/ddl/5.3/spark/OMOPCDM_spark_5.3_indices.sql create mode 100644 inst/ddl/5.3/spark/OMOPCDM_spark_5.3_primary_keys.sql create mode 100644 inst/ddl/5.4/spark/OMOPCDM_spark_5.4_constraints.sql create mode 100644 inst/ddl/5.4/spark/OMOPCDM_spark_5.4_ddl.sql create mode 100644 inst/ddl/5.4/spark/OMOPCDM_spark_5.4_indices.sql create mode 100644 inst/ddl/5.4/spark/OMOPCDM_spark_5.4_primary_keys.sql 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 @@ -background.utf8 +background.knit - - + + + @@ -40,11 +49,6 @@ - @@ -213,7 +173,6 @@ $(document).ready(function () { max-height: 500px; min-height: 44px; overflow-y: auto; - background: white; border: 1px solid #ddd; border-radius: 4px; } @@ -339,7 +298,7 @@ div.tocify { -
+ -