Hotfix 3.2.5 (#1101)

* Alternative method of updating time id in andromeda objects (#1091) * Fix exported null concepts in included_source_concept result * Fix exported null concepts in included_source_concept result * Update Migration_3-v3_2_0_suport_cohort_subsets.sql (#1086) * fixed manual links * added manual for link download * Description and news * addeed readr::local_edition(1) to fix issue with vroom * Description and news * Java fix on linux platforms in shiny app * package maintenance * name source concept field * table_prefix missing in migration * Removed bad migrations
OHDSI · Dec 1, 2023 · 03c40ab · 03c40ab
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commit 03c40ab
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: CohortDiagnostics
 Type: Package
 Title: Diagnostics for OHDSI Cohorts
-Version: 3.2.4
-Date: 2022-12-19
+Version: 3.2.5
+Date: 2023-29-11
 Authors@R: c(
     person("Jamie", "Gilbert", email = "[email protected]", role = c("aut", "cre")),
     person("Gowtham", "Rao", role = c("aut")),
@@ -25,7 +25,7 @@ Depends:
 	R (>= 4.1.0)
 Imports:
   Andromeda (>= 0.6.0),
-  ResultModelManager,
+  ResultModelManager (>= 0.5.2),
   checkmate,
   clock,
   digest,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,15 @@
+CohortDiagnostics 3.2.5
+=======================
+Bug Fixes:
+
+1. fixed broken migrations using "ADD COLUMN "
+
+2. Fixed broken links in manaual
+
+3. Fixed issue with Andromeda calls in characterization on R 4.3.x
+
+4. Fix for Vroom issue on mac
+
 CohortDiagnostics 3.2.4
 =======================
 Bug Fix:

diff --git a/R/CohortCharacterizationDiagnostics.R b/R/CohortCharacterizationDiagnostics.R
@@ -111,8 +111,15 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
           "mean",
           "sd"
         )
-      if (length(is.na(covariates$timeId)) > 0) {
-        covariates[is.na(covariates$timeId), ]$timeId <- -1
+
+      tidNaCount <- covariates %>%
+        dplyr::filter(is.na(timeId)) %>%
+        dplyr::count() %>%
+        dplyr::pull()
+
+      if (tidNaCount > 0) {
+        covariates <- covariates %>%
+          dplyr::mutate(timeId = if_else(is.na(.data$timeId), -1, .data$timeId))
       }
     } else {
       covariates <- covariates %>%
@@ -153,8 +160,15 @@ getCohortCharacteristics <- function(connectionDetails = NULL,
           "mean",
           "sd"
         )
-      if (length(is.na(covariates$timeId)) > 0) {
-        covariates[is.na(covariates$timeId), ]$timeId <- -1
+
+      tidNaCount <- covariates %>%
+        dplyr::filter(is.na(timeId)) %>%
+        dplyr::count() %>%
+        dplyr::pull()
+
+      if (tidNaCount > 0) {
+        covariates <- covariates %>%
+          dplyr::mutate(timeId = if_else(is.na(.data$timeId), -1, .data$timeId))
       }
     } else {
       covariates <- covariates %>%

diff --git a/R/ConceptSets.R b/R/ConceptSets.R
@@ -615,6 +615,7 @@ runConceptSetDiagnostics <- function(connection,
     }
     if (nrow(subsetBreakdown) > 0) {
       start <- Sys.time()
+      readr::local_edition(1)
       domains <-
         readr::read_csv(
           system.file("csv", "domains.csv", package = utils::packageName()),

diff --git a/R/Incremental.R b/R/Incremental.R
@@ -29,6 +29,7 @@ isTaskRequired <-
            recordKeepingFile,
            verbose = TRUE) {
     if (file.exists(recordKeepingFile)) {
+      readr::local_edition(1)
       recordKeeping <- readr::read_csv(recordKeepingFile,
         col_types = readr::cols(),
         guess_max = min(1e7),
@@ -64,6 +65,7 @@ isTaskRequired <-
 getRequiredTasks <- function(..., checksum, recordKeepingFile) {
   tasks <- list(...)
   if (file.exists(recordKeepingFile) && length(tasks[[1]]) > 0) {
+    readr::local_edition(1)
     recordKeeping <- readr::read_csv(recordKeepingFile,
       col_types = readr::cols(),
       guess_max = min(1e7),
@@ -112,6 +114,7 @@ recordTasksDone <-
     }
 
     if (file.exists(recordKeepingFile)) {
+      readr::local_edition(1)
       # reading record keeping file into memory
       # prevent lazy loading to avoid lock on file
       recordKeeping <- readr::read_csv(
@@ -142,6 +145,7 @@ recordTasksDone <-
     newRow$checksum <- checksum
     newRow$timeStamp <- as.character(Sys.time())
     recordKeeping <- dplyr::bind_rows(recordKeeping, newRow)
+    readr::local_edition(1)
     readr::write_csv(x = recordKeeping, file = recordKeepingFile, na = "")
   }
 
@@ -171,6 +175,7 @@ writeToCsv.default <- function(data, fileName, incremental = FALSE, ...) {
     } else {
       ParallelLogger::logDebug("creating ", fileName)
     }
+    readr::local_edition(1)
     readr::write_excel_csv(
       x = data,
       file = fileName,
@@ -194,11 +199,13 @@ writeToCsv.tbl_Andromeda <-
       tempName <- paste0(fileName, "2")
 
       processChunk <- function(chunk, pos) {
+        readr::local_edition(1)
         chunk <- chunk %>%
           dplyr::filter(!.data$cohort_id %in% cohortIds)
         readr::write_csv(chunk, tempName, append = (pos != 1))
       }
 
+      readr::local_edition(1)
       readr::read_csv_chunked(
         file = fileName,
         callback = processChunk,
@@ -246,6 +253,7 @@ writeToCsv.tbl_Andromeda <-
         if (first) {
           colnames(batch) <- SqlRender::camelCaseToSnakeCase(colnames(batch))
         }
+        readr::local_edition(1)
         readr::write_csv(batch, fileName, append = !first)
       }
       Andromeda::batchApply(data, writeToFile)
@@ -259,6 +267,7 @@ saveIncremental <- function(data, fileName, ...) {
     }
   }
   if (file.exists(fileName)) {
+    readr::local_edition(1)
     previousData <- readr::read_csv(fileName,
       col_types = readr::cols(),
       guess_max = min(1e7),

diff --git a/R/Private.R b/R/Private.R
@@ -92,6 +92,7 @@ enforceMinCellValue <-
 #' Throws an error if the input file does not have the correct encoding.
 #'
 checkInputFileEncoding <- function(fileName) {
+  readr::local_edition(1)
   encoding <- readr::guess_encoding(file = fileName, n_max = min(1e7))
 
   if (!encoding$encoding[1] %in% c("UTF-8", "ASCII")) {
@@ -318,6 +319,7 @@ timeExecution <- function(exportFolder,
                           start = NA,
                           execTime = NA,
                           expr = NULL) {
+  readr::local_edition(1)
   executionTimePath <- file.path(exportFolder, "executionTimes.csv")
   if (is.na(start)) {
     start <- Sys.time()

diff --git a/R/ResultsDataModel.R b/R/ResultsDataModel.R
@@ -22,6 +22,7 @@
 #'
 #' @export
 getResultsDataModelSpecifications <- function() {
+  readr::local_edition(1)
   pathToCsv <-
     system.file("settings", "resultsDataModelSpecification.csv", package = utils::packageName())
   resultsDataModelSpecifications <-

diff --git a/README.md b/README.md
@@ -53,10 +53,10 @@ Documentation can be found on the [package website](https://ohdsi.github.io/Coho
 
 PDF versions of the documentation are also available:
 
-* Package manual: [CohortDiagnostics manual](https://raw.githubusercontent.com/OHDSI/CohortDiagnostics/master/extras/CohortDiagnostics.pdf)
-* Vignette: [What is Cohort Diagnostics](https://raw.githubusercontent.com/OHDSI/CohortDiagnostics/master/inst/doc/WhatIsCohortDiagnostics.pdf)
-* Vignette: [Running Cohort Diagnostics](https://raw.githubusercontent.com/OHDSI/CohortDiagnostics/master/inst/doc/RunningCohortDiagnostics.pdf)
-* Vignette: [Viewing Results Using Diagnostics Explorer](https://raw.githubusercontent.com/OHDSI/CohortDiagnostics/master/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf)
+* Package manual: [CohortDiagnostics manual](https://raw.githubusercontent.com/OHDSI/CohortDiagnostics/main/extras/CohortDiagnostics.pdf)
+* Vignette: [What is Cohort Diagnostics](https://raw.githubusercontent.com/OHDSI/CohortDiagnostics/main/inst/doc/WhatIsCohortDiagnostics.pdf)
+* Vignette: [Running Cohort Diagnostics](https://raw.githubusercontent.com/OHDSI/CohortDiagnostics/main/inst/doc/RunningCohortDiagnostics.pdf)
+* Vignette: [Viewing Results Using Diagnostics Explorer](https://raw.githubusercontent.com/OHDSI/CohortDiagnostics/main/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf)
 
 
 Support

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/CreatingAStudyPackage.html b/docs/articles/CreatingAStudyPackage.html
diff --git a/docs/articles/DatabaseModeInDiagnosticsExplorer.html b/docs/articles/DatabaseModeInDiagnosticsExplorer.html
diff --git a/docs/articles/RunningCohortDiagnostics.html b/docs/articles/RunningCohortDiagnostics.html
diff --git a/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html b/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html
diff --git a/docs/articles/WhatIsCohortDiagnostics.html b/docs/articles/WhatIsCohortDiagnostics.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -7,5 +7,5 @@ articles:
   RunningCohortDiagnostics: RunningCohortDiagnostics.html
   ViewingResultsUsingDiagnosticsExplorer: ViewingResultsUsingDiagnosticsExplorer.html
   WhatIsCohortDiagnostics: WhatIsCohortDiagnostics.html
-last_built: 2023-09-19T21:26Z
+last_built: 2023-11-30T21:46Z
 
diff --git a/docs/reference/CohortDiagnostics-package.html b/docs/reference/CohortDiagnostics-package.html