Merge pull request #499 from OHDSI/develop

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OHDSI · Oct 19, 2023 · bd4d98d · bd4d98d
2 parents e18c308 + 7845a00
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diff --git a/.github/workflows/R_CMD_check_Hades.yml b/.github/workflows/R_CMD_check_Hades.yml
@@ -29,21 +29,25 @@ jobs:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+      CDM5_ORACLE_CDM54_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM54_SCHEMA }}
       CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
       CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
       CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
       CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
       CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
+      CDM5_POSTGRESQL_CDM54_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM54_SCHEMA }}
       CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
       CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
       CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
       CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
       CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
+      CDM5_SQL_SERVER_CDM54_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM54_SCHEMA }}
       CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
       CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
       CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
       CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
       CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+      CDM5_REDSHIFT_CDM54_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM54_SCHEMA }}
       CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
       CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
       CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}

diff --git a/.github/workflows/R_CMD_check_main_weekly.yaml b/.github/workflows/R_CMD_check_main_weekly.yaml
@@ -21,21 +21,25 @@ jobs:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+      CDM5_ORACLE_CDM54_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM54_SCHEMA }}
       CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
       CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
       CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
       CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
       CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
+      CDM5_POSTGRESQL_CDM54_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM54_SCHEMA }}
       CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
       CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
       CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
       CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
       CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
+      CDM5_SQL_SERVER_CDM54_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM54_SCHEMA }}
       CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
       CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
       CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
       CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
       CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+      CDM5_REDSHIFT_CDM54_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM54_SCHEMA }}
       CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
       CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
       CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: DataQualityDashboard
 Type: Package
 Title: Execute and View Data Quality Checks on OMOP CDM Database
-Version: 2.4.0
-Date: 2023-07-26
+Version: 2.4.1
+Date: 2023-10-18
 Authors@R: c(
   person("Katy", "Sadowski", email = "[email protected]", role = c("aut", "cre")),
   person("Clair", "Blacketer", role = c("aut")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -18,6 +18,7 @@ importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,parse_json)
 importFrom(jsonlite,toJSON)
 importFrom(magrittr,"%>%")
+importFrom(readr,local_edition)
 importFrom(readr,read_csv)
 importFrom(rlang,.data)
 importFrom(stats,na.omit)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+DataQualityDashboard 2.4.1
+==========================
+This release includes: 
+
+- Minor documentation updates
+- A patch for an issue in one of DQD's transitive dependencies, `vroom`
+- Test suite upgrades to run remote DB tests against OMOP v5.4, and to add Redshift to remote DB tests
+
 DataQualityDashboard 2.4.0
 ==========================
 This release includes:

diff --git a/R/convertResultsCase.R b/R/convertResultsCase.R
@@ -30,6 +30,7 @@
 #' @importFrom SqlRender snakeCaseToCamelCase camelCaseToSnakeCase
 #' @importFrom dplyr rename_with
 #' @importFrom tools file_path_sans_ext
+#' @importFrom readr local_edition
 #'
 #' @export
 
@@ -47,6 +48,9 @@ convertJsonResultsFileCase <- function(
     stop("You must specify an output folder if writing to file.")
   }
 
+  # temporary patch to work around vroom 1.6.4 bug
+  readr::local_edition(1)
+
   results <- jsonlite::fromJSON(jsonFilePath)
 
   if ("numViolatedRows" %in% names(results$CheckResults) && targetCase == "camel") {

diff --git a/R/executeDqChecks.R b/R/executeDqChecks.R
@@ -16,7 +16,7 @@
 
 #' @title Execute DQ checks
 #'
-#' @description This function will connect to the database, generate the sql scripts, and run the data quality checks against the database.
+#' @description This function will connect to the database, generate the sql scripts, and run the data quality checks against the database. By default, results will be written to a json file as well as a database table.
 #'
 #' @param connectionDetails         A connectionDetails object for connecting to the CDM database
 #' @param cdmDatabaseSchema         The fully qualified database name of the CDM schema
@@ -54,7 +54,7 @@
 #' @importFrom utils packageVersion write.table
 #' @importFrom rlang .data
 #' @importFrom tidyselect all_of
-#' @importFrom readr read_csv
+#' @importFrom readr read_csv local_edition
 #' @importFrom dplyr mutate case_when
 #'
 #' @export
@@ -119,6 +119,9 @@ executeDqChecks <- function(connectionDetails,
     }
   }
 
+  # temporary patch to work around vroom 1.6.4 bug
+  readr::local_edition(1)
+
   # capture metadata -----------------------------------------------------------------------
   if (!sqlOnly) {
     connection <- DatabaseConnector::connect(connectionDetails = connectionDetails)

diff --git a/R/listChecks.R b/R/listChecks.R
@@ -24,10 +24,13 @@
 #' @param fieldCheckThresholdLoc    The location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied.
 #' @param conceptCheckThresholdLoc  The location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied.
 #'
-#' @importFrom readr read_csv
+#' @importFrom readr read_csv local_edition
 #'
 #' @export
 listDqChecks <- function(cdmVersion = "5.3", tableCheckThresholdLoc = "default", fieldCheckThresholdLoc = "default", conceptCheckThresholdLoc = "default") {
+  # temporary patch to work around vroom 1.6.4 bug
+  readr::local_edition(1)
+
   dqChecks <- {}
   dqChecks$checkDescriptions <-
     read_csv(system.file(

diff --git a/README.md b/README.md
@@ -73,6 +73,10 @@ System Requirements
 ===================
 Requires R (version 3.2.2 or higher). Requires [DatabaseConnector](https://github.com/OHDSI/DatabaseConnector) (version 2.0.2 or higher).
 
+A variety of database platforms are supported, as documented [here](https://ohdsi.github.io/Hades/supportedPlatforms.html). 
+
+Note that while data quality check threshold files are provided for OMOP CDM versions 5.2, 5.3, and 5.4, the package is currently only tested against versions 5.3 and 5.4.
+
 Installation
 =============
 1. See the instructions [here](https://ohdsi.github.io/Hades/rSetup.html) for configuring your R environment, including RTools and Java.

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/AddNewCheck.html b/docs/articles/AddNewCheck.html
diff --git a/docs/articles/CheckStatusDefinitions.html b/docs/articles/CheckStatusDefinitions.html
diff --git a/docs/articles/CheckTypeDescriptions.html b/docs/articles/CheckTypeDescriptions.html
diff --git a/docs/articles/DataQualityDashboard.html b/docs/articles/DataQualityDashboard.html
diff --git a/docs/articles/DqdForCohorts.html b/docs/articles/DqdForCohorts.html
diff --git a/docs/articles/SqlOnly.html b/docs/articles/SqlOnly.html
diff --git a/docs/articles/Thresholds.html b/docs/articles/Thresholds.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html