From 3d60cb50afb83a00ce2bff49d38e68fb00f44cd1 Mon Sep 17 00:00:00 2001 From: Anthony Sena Date: Wed, 7 Oct 2026 12:18:55 -0400 Subject: [PATCH 1/3] Release v1.1.0 preparation --- DESCRIPTION | 22 +++++++++++----------- NAMESPACE | 11 +++++------ R/CommonDataModel-package.R | 11 ++++++++--- R/utils.R | 8 -------- man/CommonDataModel-package.Rd | 20 ++++++++++++++++++++ 5 files changed, 44 insertions(+), 28 deletions(-) delete mode 100644 R/utils.R create mode 100644 man/CommonDataModel-package.Rd diff --git a/DESCRIPTION b/DESCRIPTION index 1a5c4f52..76fd99d5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: CommonDataModel Type: Package Title: OMOP CDM DDL and Documentation Generator -Version: 1.0.1 +Version: 1.1.0 Authors@R: person(given = "Clair", family = "Blacketer", role = c("aut", "cre"), @@ -12,20 +12,20 @@ License: Apache License 2.0 Encoding: UTF-8 LazyData: true Depends: + R (>= 4.1.0) +Imports: DatabaseConnector, SqlRender, - rJava -Imports: - rmarkdown, stringr, - DBI, - dplyr, readr Suggests: - knitr, - testthat (>= 3.0.0), - RSQLite, - withr + DBI, + dplyr, + knitr, + rmarkdown, + RSQLite, + testthat (>= 3.0.0), + withr NeedsCompilation: no -RoxygenNote: 7.3.3 Config/testthat/edition: 3 +Config/roxygen2/version: 8.1.0 diff --git a/NAMESPACE b/NAMESPACE index 9664e777..9d0fbc2a 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -14,9 +14,8 @@ export(writeDdl) export(writeForeignKeys) export(writeIndex) export(writePrimaryKeys) -import(DatabaseConnector) -import(SqlRender) -import(rJava) -importFrom(utils,download.file) -importFrom(utils,read.csv) -importFrom(utils,write.csv) +importFrom(utils, + download.file, + read.csv, + write.csv +) diff --git a/R/CommonDataModel-package.R b/R/CommonDataModel-package.R index 55354369..3b3c9510 100644 --- a/R/CommonDataModel-package.R +++ b/R/CommonDataModel-package.R @@ -1,4 +1,9 @@ -#' @import rJava -#' @import DatabaseConnector -#' @import SqlRender +#' @keywords internal +"_PACKAGE" + +## usethis namespace: start +## usethis namespace: end + +## mockable bindings: start +## mockable bindings: end NULL diff --git a/R/utils.R b/R/utils.R deleted file mode 100644 index 213b47fa..00000000 --- a/R/utils.R +++ /dev/null @@ -1,8 +0,0 @@ -# these packages are used in utilities or functions outside of check's vision -# this function ensures that check is satisfied and does not report the -# packages as imported but not imported from -checkSatisfier <- function() { - DBI::dbConnect - dplyr::sql - rmarkdown::draft -} diff --git a/man/CommonDataModel-package.Rd b/man/CommonDataModel-package.Rd new file mode 100644 index 00000000..ddc720d2 --- /dev/null +++ b/man/CommonDataModel-package.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/CommonDataModel-package.R +\docType{package} +\name{CommonDataModel-package} +\alias{CommonDataModel} +\alias{CommonDataModel-package} +\title{CommonDataModel: OMOP CDM DDL and Documentation Generator} +\description{ +Generates the scripts required to create an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) database and associated documentation for supported database platforms. Leverages the 'SqlRender' package to convert the Data Definition Language (DDL) script written in parameterized Structured Query Language (SQL) to the other supported dialects. +} +\author{ +\strong{Maintainer}: Clair Blacketer \email{mblacke@its.jnj.com} + +Authors: +\itemize{ + \item Clair Blacketer \email{mblacke@its.jnj.com} +} + +} +\keyword{internal} From f34355c032325b0267d4f6252a5f64a91c345c6a Mon Sep 17 00:00:00 2001 From: Anthony Sena Date: Wed, 7 Oct 2026 13:17:03 -0400 Subject: [PATCH 2/3] Add NEWS.md release info --- NEWS.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/NEWS.md b/NEWS.md index 7b693552..160c3ab5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +CommonDataModel v5.5.0 +====================== + +Provides suport for the OMOP Common Data Model v5.5 - announcement and release notes are found here: https://forums.ohdsi.org/t/omop-cdm-v5-5-release/25881 + + CommonDataModel v5.4.2 ====================== From d7624132d94e4e1a6aaaf7b2a3d9c62fb811fca8 Mon Sep 17 00:00:00 2001 From: Anthony Sena Date: Wed, 7 Oct 2026 13:26:46 -0400 Subject: [PATCH 3/3] Update SiteMaintenance to use Quarto to render site docs. Updated site docs. --- docs/background.html | 53 ++- docs/cdm30.html | 36 +- docs/cdm53.html | 36 +- docs/cdm531.html | 36 +- docs/cdm53Changes.html | 53 ++- docs/cdm54.html | 36 +- docs/cdm54Changes.html | 53 ++- docs/cdm54ToolingSupport.html | 53 ++- docs/cdm54erd.html | 53 ++- docs/cdm55.html | 36 +- docs/cdm55Changes.html | 53 ++- docs/cdm60.html | 241 ++++++++------ docs/cdmDecisionTree/cdmDecisionTree.html | 53 ++- docs/cdmDecisionTree/contactVocab.html | 53 ++- docs/cdmDecisionTree/leaveAsIs.html | 53 ++- docs/cdmDecisionTree/localChange.html | 53 ++- docs/cdmDecisionTree/networkUseCase.html | 53 ++- docs/cdmDecisionTree/useCaseN.html | 53 ++- docs/cdmDecisionTree/useCaseY.html | 53 ++- docs/cdmDecisionTree/vocabN.html | 53 ++- docs/cdmDecisionTree/vocabRequest.html | 53 ++- docs/cdmDecisionTree/vocabY.html | 53 ++- docs/cdmPrivacy.html | 53 ++- docs/cdmRPackage.html | 57 ++-- docs/cdmRefreshProcess.html | 53 ++- docs/cdmRequestProcess.html | 53 ++- docs/contribute.html | 53 ++- docs/customConcepts.html | 53 ++- docs/dataModelConventions.html | 53 ++- docs/download.html | 53 ++- docs/drug_dose.html | 53 ++- docs/ehrObsPeriods.html | 53 ++- docs/faq.html | 53 ++- docs/index.html | 53 ++- docs/indices-primary-foreign.html | 53 ++- docs/queries.html | 57 ++-- docs/reviewProposals.html | 53 ++- docs/search.json | 176 +++++++++- ...p-172ba59bd5e0b52282274ba0c0cc16fc.min.css | 12 + ...k-8b348f4b4b74a528bf910da1e8c5139e.min.css | 12 + docs/site_libs/bootstrap/bootstrap-icons.css | 34 +- docs/site_libs/bootstrap/bootstrap-icons.woff | Bin 176200 -> 180288 bytes ...hting-64a204ab8560d761af7679ceaba22944.css | 236 +++++++++++++ ...-dark-b85bc7c33db8c58e0ec93c3465666fed.css | 219 +++++++++++++ docs/site_libs/quarto-nav/quarto-nav.js | 5 +- .../quarto-search/autocomplete.umd.js | 4 +- docs/site_libs/quarto-search/quarto-search.js | 309 ++++++++++++++---- docs/sitemap.xml | 80 ++--- docs/sqlScripts.html | 81 +++-- docs/typesOfAdditions.html | 53 ++- docs/vocabulary.html | 53 ++- extras/SiteMaintenance.R | 33 +- 52 files changed, 2513 insertions(+), 866 deletions(-) create mode 100644 docs/site_libs/bootstrap/bootstrap-172ba59bd5e0b52282274ba0c0cc16fc.min.css create mode 100644 docs/site_libs/bootstrap/bootstrap-dark-8b348f4b4b74a528bf910da1e8c5139e.min.css create mode 100644 docs/site_libs/quarto-html/quarto-syntax-highlighting-64a204ab8560d761af7679ceaba22944.css create mode 100644 docs/site_libs/quarto-html/quarto-syntax-highlighting-dark-b85bc7c33db8c58e0ec93c3465666fed.css diff --git a/docs/background.html b/docs/background.html index 28d5aa02..b3aac375 100644 --- a/docs/background.html +++ b/docs/background.html @@ -2,17 +2,23 @@ - + OMOP CDM Background – OMOP Common Data Model