From bb468e774b73b77fa5063d2e47412086f469e4d0 Mon Sep 17 00:00:00 2001
From: Paul Hoffman <mojaveazure@users.noreply.github.com>
Date: Tue, 19 Oct 2021 14:35:14 -0400
Subject: [PATCH 1/3] Fix allowing duplicate keys Duplicate keys were being
 allowed when re-adding an object to a Seurat object Now, do better checking
 of duplicate keys

---
 R/seurat.R | 69 ++++++++++++++++++++++++++++++++++--------------------
 1 file changed, 43 insertions(+), 26 deletions(-)

diff --git a/R/seurat.R b/R/seurat.R
index 6d31c34b..e4e16add 100644
--- a/R/seurat.R
+++ b/R/seurat.R
@@ -1359,12 +1359,16 @@ Key.Seurat <- function(object, ...) {
     object = object,
     classes.keep = c('Assay', 'DimReduc', 'SpatialImage')
   )
-  return(sapply(
+  keys <- vapply(
     X = keyed.objects,
     FUN = function(x) {
       return(Key(object = object[[x]]))
-    }
-  ))
+    },
+    FUN.VALUE = character(length = 1L),
+    USE.NAMES = FALSE
+  )
+  names(x = keys) <- keyed.objects
+  return(keys)
 }
 
 #' @param reduction Name of reduction to pull feature loadings for
@@ -2812,30 +2816,43 @@ setMethod( # because R doesn't allow S3-style [[<- for S4 classes
         }
         Key(object = value) <- UpdateKey(key = Key(object = value))
         # Check for duplicate keys
-        object.keys <- sapply(
-          X = FilterObjects(object = x),
-          FUN = function(i) {
-            return(Key(object = x[[i]]))
-          }
-        )
-        if (Key(object = value) %in% object.keys && is.null(x = FindObject(object = x, name = i))) {
-          # Attempt to create a duplicate key based off the name of the object being added
-          new.keys <- c(paste0(tolower(x = i), c('_', paste0(RandomName(length = 2L), '_'))))
-          # Select new key to use
-          key.use <- min(which(x = !new.keys %in% object.keys))
-          new.key <- if (is.infinite(x = key.use)) {
-            RandomName(length = 17L)
+        object.keys <- Key(object = x)
+        vkey <- Key(object = value)
+        if (vkey %in% object.keys && !isTRUE(x = object.keys[i] == vkey)) {
+          new.key <- if (is.na(x = object.keys[i])) {
+            # Attempt to create a duplicate key based off the name of the object being added
+            new.keys <- paste0(
+              paste0(tolower(x = i), c('', RandomName(length = 2L))),
+              '_'
+            )
+            # Select new key to use
+            key.use <- min(which(x = !new.keys %in% object.keys))
+            new.key <- if (is.infinite(x = key.use)) {
+              RandomName(length = 17L)
+            } else {
+              new.keys[key.use]
+            }
+            warning(
+              "Cannot add objects with duplicate keys (offending key: ",
+              Key(object = value),
+              "), setting key to '",
+              new.key,
+              "'",
+              call. = FALSE
+            )
+            new.key
           } else {
-            new.keys[key.use]
+            # Use existing key
+            warning(
+              "Cannot add objects with duplicate keys (offending key: ",
+              Key(object = value),
+              ") setting key to original value '",
+              object.keys[i],
+              "'",
+              call. = FALSE
+            )
+            object.keys[i]
           }
-          warning(
-            "Cannot add objects with duplicate keys (offending key: ",
-            Key(object = value),
-            "), setting key to '",
-            new.key,
-            "'",
-            call. = FALSE
-          )
           # Set new key
           Key(object = value) <- new.key
         }
@@ -2843,7 +2860,7 @@ setMethod( # because R doesn't allow S3-style [[<- for S4 classes
       # For Assays, run CalcN
       if (inherits(x = value, what = 'Assay')) {
         if ((!i %in% Assays(object = x)) |
-            (i %in% Assays(object = x) && ! identical(
+            (i %in% Assays(object = x) && !identical(
               x = GetAssayData(object = x, assay = i, slot = "counts"),
               y = GetAssayData(object = value, slot = "counts"))
             )) {

From bc71384ee97560239b59e8deb17c4ca4c8519598 Mon Sep 17 00:00:00 2001
From: Paul Hoffman <mojaveazure@users.noreply.github.com>
Date: Tue, 19 Oct 2021 14:40:10 -0400
Subject: [PATCH 2/3] Bump develop version

---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3bd369f1..652e2d83 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SeuratObject
 Type: Package
 Title: Data Structures for Single Cell Data
-Version: 4.0.2.9000
-Date: 2021-09-07
+Version: 4.0.2.9001
+Date: 2021-10-19
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Andrew', family = 'Butler', email = 'abutler@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),

From 8c04519d4f0b66c4fa0dae08df60e4e2d377cd6e Mon Sep 17 00:00:00 2001
From: Paul Hoffman <mojaveazure@users.noreply.github.com>
Date: Tue, 19 Oct 2021 14:40:16 -0400
Subject: [PATCH 3/3] Update changelog

---
 NEWS.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 5a0db1ae..98800e08 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,8 @@
 
 ## Changed
 - Export utility functions (#22)
+- Bug fix in names with `Key.Seurat` (#26)
+- Improved duplicate key checking and resolution
 
 # SeuratObject 4.0.2