Merge pull request #54 from OHDSI/develop

Release 0.5.7
OHDSI · May 2, 2024 · 1cff4f0 · 1cff4f0
2 parents 5810069 + 665b71a
commit 1cff4f0
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -32,4 +32,6 @@ deploy.sh
 compare_versions
 ^doc$
 ^Meta$
-LICENSE
+LICENSE
+.git
+..Rcheck
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ResultModelManager
-Title: Result Model Manager (RMM) for OHDSI packages
-Version: 0.5.6
+Title: Result Model Manager
+Version: 0.5.7
 Authors@R:
     person("Jamie", "Gilbert", , "[email protected]", role = c("aut", "cre"))
 Description: Database data model management utilities for OHDSI packages.

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# ResultModelManager 0.5.7
+
+Bug fixes:
+
+1. Added type conversion checking on upload of data where columns are characters but interpreted as numeric from reading
+inserted data
 
 # ResultModelManager 0.5.6
 

diff --git a/R/ConnectionHandler.R b/R/ConnectionHandler.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CemConnector
 #

diff --git a/R/DataMigrationManager.R b/R/DataMigrationManager.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #

diff --git a/R/DataModel.R b/R/DataModel.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of OHdsiSharing
 #
@@ -309,7 +309,7 @@ uploadChunk <- function(chunk, pos, env, specifications, resultsFolder, connecti
   # Ensure dates are formatted properly
   toDate <- specifications %>%
     dplyr::filter(
-      tableName == env$tableName &
+      .data$tableName == env$tableName &
         tolower(.data$dataType) == "date"
     ) %>%
     dplyr::select("columnName") %>%
@@ -322,7 +322,7 @@ uploadChunk <- function(chunk, pos, env, specifications, resultsFolder, connecti
 
   toTimestamp <- specifications %>%
     dplyr::filter(
-      tableName == env$tableName &
+      .data$tableName == env$tableName &
         grepl("timestamp", tolower(.data$dataType))
     ) %>%
     dplyr::select("columnName") %>%
@@ -347,6 +347,10 @@ uploadChunk <- function(chunk, pos, env, specifications, resultsFolder, connecti
 
   # Check if inserting data would violate primary key constraints:
   if (!is.null(env$primaryKeyValuesInDb)) {
+    chunk <- formatChunk(
+      pkValuesInDb = env$primaryKeyValuesInDb,
+      chunk = chunk
+    )
     primaryKeyValuesInChunk <- unique(chunk[env$primaryKey])
     duplicates <-
       dplyr::inner_join(env$primaryKeyValuesInDb,
@@ -791,3 +795,35 @@ loadResultsDataModelSpecifications <- function(filePath) {
   assertSpecificationColumns(colnames(spec))
   return(spec)
 }
+
+
+#' This helper function will convert the data in the
+#' primary key values in the `chunk` which is read from
+#' the csv file to the format of the primary key data
+#' retrieved from the database (`pkValuesInDb`). The assumption made
+#' by this function is that the `pkValuesInDb` reflect the proper data
+#' types while `chunk` is the best guess from the readr
+#' package. In the future, if we adopt strongly-types data.frames
+#' this will no longer be necessary.
+#'
+#' Another assumption of this function is that we're only attempting to
+#' recast to a character data type and not try to handle different type
+#' conversions.
+formatChunk <- function(pkValuesInDb, chunk) {
+  for (columnName in names(pkValuesInDb)) {
+    if (class(pkValuesInDb[[columnName]]) != class(chunk[[columnName]])) {
+      if (class(pkValuesInDb[[columnName]]) == "character") {
+        chunk <- chunk |> dplyr::mutate_at(columnName, as.character)
+      } else {
+        errorMsg <- paste0(
+          columnName,
+          " is of type ",
+          class(pkValuesInDb[[columnName]]),
+          " which cannot be converted between data frames pkValuesInDb and chunk"
+        )
+        stop(errorMsg)
+      }
+    }
+  }
+  return(chunk)
+}
diff --git a/R/PooledConnectionHandler.R b/R/PooledConnectionHandler.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #

diff --git a/R/QueryNamespace.R b/R/QueryNamespace.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #

diff --git a/R/ResultExportManager.R b/R/ResultExportManager.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #

diff --git a/R/ResultModelManager.R b/R/ResultModelManager.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #

diff --git a/R/SchemaGenerator.R b/R/SchemaGenerator.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #

diff --git a/R/Utils.R b/R/Utils.R
@@ -1,4 +1,4 @@
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of CohortDiagnostics
 #

diff --git a/README.md b/README.md
@@ -1,9 +1,9 @@
 ResultModelManager
 ==================
 [![Build Status](https://github.com/OHDSI/ResultModelManager/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/ResultModelManager/actions?query=workflow%3AR-CMD-check)
-[![codecov.io](https://codecov.io/github/OHDSI/ResultModelManager/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/ResultModelManager?branch=main)
+[![codecov.io](https://app.codecov.io/github/OHDSI/ResultModelManager/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/ResultModelManager?branch=main)
 
-ResultModelManager (RMM) [HADES](https://ohdsi.github.io/Hades).
+ResultModelManager (RMM) [HADES](https://ohdsi.github.io/Hades/).
 
 Introduction
 ============

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/CreatingMigrations.html b/docs/articles/CreatingMigrations.html
diff --git a/docs/articles/ExampleProject.html b/docs/articles/ExampleProject.html
diff --git a/docs/articles/PackageDesign.html b/docs/articles/PackageDesign.html
diff --git a/docs/articles/UploadFunctionality.html b/docs/articles/UploadFunctionality.html
diff --git a/docs/articles/UsingAnExportManager.html b/docs/articles/UsingAnExportManager.html
diff --git a/docs/articles/UsingConnectionHandlers.html b/docs/articles/UsingConnectionHandlers.html
-Original file line number
+Diff line change
@@ Expand Up / @@ -32,4 +32,6 @@ deploy.sh @@
     compare_versions
     ^doc$
     ^Meta$
-    LICENSE
+    LICENSE
+    .git
+    ..Rcheck