Merge pull request #171 from bhklab/feat/view-updateobject-guidance

feat: add guarded View shim for CoreSet/PharmacoSet

Author: mtran-code

.gitignore

@@ -24,3 +24,8 @@ local_data/**
 .VSCodeCounter/**
 *.o
 docs
+
+# build artifacts
+*.tar.gz
+*.Rcheck/
+*.BiocCheck/

DESCRIPTION

@@ -58,7 +58,7 @@ Imports:
 Depends: R (>= 3.6), CoreGx
 LinkingTo: Rcpp
 Roxygen: list(markdown = TRUE, r6=FALSE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 VignetteEngine: knitr::rmarkdown
 biocViews: GeneExpression, Pharmacogenetics, Pharmacogenomics, Software, Classification
@@ -102,6 +102,7 @@ Collate:
     'logLogisticRegression.R'
     'matthewCor.R'
     'mergePSets.R'
+    'methods-View.R'
     'methods-[.R'
     'methods-drugSensitivitySig.R'
     'methods-intersect.R'

NAMESPACE

@@ -12,6 +12,7 @@ export(.plotProjHill)
 export(PharmacoSet)
 export(PharmacoSet2)
 export(PharmacoSig)
+export(View)
 export(amcc)
 export(availablePSets)
 export(checkPsetStructure)
@@ -111,6 +112,8 @@ importClassesFrom(CoreGx,CoreSet)
 importClassesFrom(CoreGx,LongTable)
 importClassesFrom(CoreGx,TreatmentResponseExperiment)
 importClassesFrom(MultiAssayExperiment,MultiAssayExperiment)
+importClassesFrom(S4Vectors,DataFrame)
+importClassesFrom(S4Vectors,List)
 importFrom(Biobase,AnnotatedDataFrame)
 importFrom(BiocParallel,bplapply)
 importFrom(CoreGx,"sampleInfo<-")
@@ -143,6 +146,7 @@ importFrom(CoreGx,sampleNames)
 importFrom(CoreGx,subsetByFeature)
 importFrom(CoreGx,treatmentNames)
 importFrom(CoreGx,updateSampleId)
+importFrom(MultiAssayExperiment,MultiAssayExperiment)
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,SimpleList)
 importFrom(S4Vectors,metadata)
@@ -159,11 +163,22 @@ importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
 importFrom(boot,boot)
 importFrom(boot,boot.ci)
+importFrom(checkmate,assert)
+importFrom(checkmate,assertCharacter)
+importFrom(checkmate,assertClass)
+importFrom(checkmate,assertDataFrame)
 importFrom(checkmate,assertDataTable)
 importFrom(checkmate,assertInt)
+importFrom(checkmate,assertList)
 importFrom(checkmate,assertLogical)
 importFrom(checkmate,assertNumeric)
+importFrom(checkmate,assertSubset)
 importFrom(coop,pcor)
+importFrom(data.table,":=")
+importFrom(data.table,as.data.table)
+importFrom(data.table,data.table)
+importFrom(data.table,merge.data.table)
+importFrom(data.table,tstrsplit)
 importFrom(downloader,download)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,palette)
@@ -211,6 +226,8 @@ importFrom(utils,sessionInfo)
 importFrom(utils,setTxtProgressBar)
 importFrom(utils,txtProgressBar)
 importFrom(utils,write.table)
+importMethodsFrom(BiocGenerics,"annotation<-")
+importMethodsFrom(BiocGenerics,annotation)
 importMethodsFrom(CoreGx,"annotation<-")
 importMethodsFrom(CoreGx,"curation<-")
 importMethodsFrom(CoreGx,"datasetType<-")

R/methods-View.R

@@ -0,0 +1,52 @@
+#' Guarded View for CoreSet/PharmacoSet
+#'
+#' Emits the same compatibility error as `CoreGx::show()` and stops for
+#' outdated CoreSet-derived objects. Otherwise delegates to whatever
+#' `utils::View` is installed in `package:utils` (RStudio/Positron override
+#' or base).
+#'
+#' @param x Any R object, typically a data.frame-like or `CoreSet`-derived.
+#' @param title Optional title for the data viewer.
+#'
+#' @return Invisibly returns whatever the underlying viewer returns.
+#' @seealso [utils::View()]
+#'
+#' @examples
+#' if (interactive()) {
+#'   data("CCLEsmall", package = "PharmacoGx")
+#'   View(CCLEsmall)
+#' }
+#'
+#' @export
+View <- function(x, title = NULL) {
+  # Only intercept for CoreSet-derived objects; keep everything else untouched
+  if (methods::is(x, "CoreSet")) {
+    # Replicate CoreGx::show() outdated check (CoreGx/R/CoreSet-class.R:424-428)
+    hasSample <- methods::.hasSlot(x, "sample")
+    hasTreatment <- methods::.hasSlot(x, "treatment")
+    if (!(hasSample && hasTreatment)) {
+      # Hard stop with the same message as CoreGx::show()
+      stop(
+        CoreGx::.errorMsg(
+          "This ",
+          class(x)[1],
+          " object appears to be out of date! ",
+          "Please run object <- updateObject(object) to update ",
+          "the object for compatibility with the current release."
+        ),
+        call. = FALSE
+      )
+    }
+  }
+
+  # Ensure Positron/RStudio/base receive a scalar string title
+  if (missing(title) || is.null(title)) {
+    title2 <- base::deparse(substitute(x))
+  } else {
+    title2 <- base::as.character(title)[1]
+    if (is.na(title2)) title2 <- base::deparse(substitute(x))
+  }
+
+  # Delegate to whatever View is installed in package:utils
+  get("View", envir = as.environment("package:utils"))(x, title2)
+}