diff --git a/R/mongo.R b/R/mongo.R
index 2aff9fe..b3b7659 100644
--- a/R/mongo.R
+++ b/R/mongo.R
@@ -57,6 +57,8 @@ delete_pub <- function(pub_con, model_con, pub_id, verbose = TRUE) {
   pub_con$remove(pub_find)
 }
 
+#' Get a vector of pub_ids that do not exist in the set of currently maintained
+#' pub ids
 get_nonexistent_pubs <- function(pub_con, verbose = TRUE) {
   pub_find <- list(
     "_id" = list(
@@ -64,14 +66,14 @@ get_nonexistent_pubs <- function(pub_con, verbose = TRUE) {
     )
   ) |> jsonlite::toJSON()
 
-  nonexistent_pubs <- pub_con$find(pub_find)
+  nonexistent_pubs <- pub_con$find(pub_find, fields = '{}')
 
   if(verbose) {
     print(paste("Found", nrow(nonexistent_pubs), "nonexistent publications"))
   }
 
   if(nrow(nonexistent_pubs) > 0) {
-    return(nonexistent_pubs$pub_id)
+    return(nonexistent_pubs$`_id`)
   } else {
     return(NULL)
   }
@@ -110,7 +112,7 @@ write_update_commit <- function(update_con) {
 #'
 #' This is the main function for updating the database. It proceeds in five
 #' phases, meant to remove old/"hangnail" publications and models.
-#'  1. Delete all nonexistent publications from db (i.e., in publications
+#'  1. Delete all nonexistent publications from db (i.e., publications
 #'     no longer in directory) and their models
 #'  2. Determine which publications have been modified since last commit
 #'  3. Generate JSON for modified publications+models, retain newly generated
diff --git a/tests/testthat/test-mongo.R b/tests/testthat/test-mongo.R
index 811ad34..2a2f600 100644
--- a/tests/testthat/test-mongo.R
+++ b/tests/testthat/test-mongo.R
@@ -2,6 +2,7 @@
 test_pub_path <- system.file("testdata/test_publications/a_e/barrett_1978.R", package = "models")
 source(test_pub_path)
 test_pub <- barrett_1978
+pub_parsed <- publication_to_json(test_pub)
 
 is_github_action <- function() {
   return(tolower(Sys.getenv("GITHUB_ACTIONS")) == "true")
@@ -36,9 +37,22 @@ with_mocked_database <- function(code, ...) {
   force(code(pub_conn, model_conn, ...))
 }
 
+with_mocked_update_conn <- function(code) {
+  update_conn <- mongolite::mongo(
+    collection = "update",
+    db = "test",
+    url = Sys.getenv("MONGODB_URL_DEV")
+  )
+
+  on.exit({
+    update_conn$drop()
+  })
+
+  force(code(update_conn))
+}
+
 test_that("upsert_publication inserts a document when it does not exist", {
   with_mocked_database(function(pub_conn, model_conn) {
-    pub_parsed <- publication_to_json(test_pub)
 
     upsert_publication(
       pub_conn, model_conn, pub_parsed$pub_json, pub_parsed$models_json,
@@ -56,3 +70,75 @@ test_that("upsert_publication inserts a document when it does not exist", {
     expect_equal(models_res$`_id`, "cc2078aa")
   })
 })
+
+test_that("upsert_publication updates a document when it does exist", {
+  with_mocked_database(function(pub_conn, model_conn) {
+    # insert
+    upsert_publication(
+      pub_conn, model_conn, pub_parsed$pub_json, pub_parsed$models_json,
+      verbose = FALSE
+    )
+
+    pub_parsed$pub_json$citation$bibtype <- jsonlite::unbox("Article")
+
+    # update
+    upsert_publication(
+      pub_conn, model_conn, pub_parsed$pub_json, pub_parsed$models_json,
+      verbose = FALSE
+    )
+
+    pub_res <- pub_conn$find('{}')
+
+    expect_equal(pub_res$citation$bibtype, "Article")
+  })
+})
+
+test_that("delete_pubs deletes the publication and its member models", {
+  with_mocked_database(function(pub_conn, model_conn) {
+    upsert_publication(
+      pub_conn, model_conn, pub_parsed$pub_json, pub_parsed$models_json,
+      verbose = FALSE
+    )
+
+    delete_pubs(pub_conn, model_conn, "barrett_1978", verbose = FALSE)
+
+    pub_res <- pub_conn$find('{}')
+    model_res <- model_conn$find('{}')
+
+    expect_equal(nrow(pub_res), 0)
+    expect_equal(nrow(model_res), 0)
+  })
+})
+
+test_that("get_nonexistent_pubs returns correct set of pub_ids", {
+  with_mocked_database(function(pub_conn, model_conn) {
+    nonexist_ids_first <- get_nonexistent_pubs(pub_conn)
+    expect_true(is.null(nonexist_ids_first))
+
+    pub_conn$insert('{"_id": "nonexist_1987"}')
+    nonexist_ids <- get_nonexistent_pubs(pub_conn)
+
+    expect_equal(nonexist_ids, "nonexist_1987")
+  })
+})
+
+test_that("get_last_update_commit gets most recent commit", {
+  with_mocked_update_conn(function(update_conn) {
+    update_conn$insert('{"datetime": 1727726535, "commit_id": "bbbbbbb"}')
+    update_conn$insert('{"datetime": 1727726735,  "commit_id": "aaaaaaa"}')
+
+    last_commit <- get_last_update_commit(update_conn)
+
+    expect_equal(last_commit, "aaaaaaa")
+  })
+})
+
+test_that("write_update_commit writes an update", {
+  with_mocked_update_conn(function(update_conn) {
+    write_update_commit(update_conn)
+
+    update_res <- update_conn$find('{}')
+
+    expect_equal(nrow(update_res), 1)
+  })
+})
\ No newline at end of file