fix: constrain interactive confirmation choices to 1 or 2

.Rbuildignore

@@ -22,3 +22,4 @@
 ^\.jules(/.*)?$
 ^\.trivyignore\.yaml$
 ^trivy\.yaml$
+^\.semgrepignore$

.jules/sentinel.md

@@ -2,3 +2,8 @@
 **Vulnerability:** Unvalidated inputs passed to `if()` statements can cause process crashes (`condition has length > 1`) or unexpected coercion vulnerabilities.
 **Learning:** In R, optional boolean parameters that default to `NULL` should be validated using explicit runtime type validation (e.g., `if (!is.null(flag) && (!is.logical(flag) || length(flag) != 1 || is.na(flag)))`).
 **Prevention:** Always implement explicit runtime type validation for optional boolean parameters.
+
+## 2024-07-31 - Fix Denial of Service in readline integer coercions
+**Vulnerability:** Weak regex `^[0-9]+$` on interactive `readline()` user inputs allows abnormally large integers that will coerce to `NA` when evaluated via `as.integer()`. This can cause unhandled exceptions and infinite loops/crashes when the `NA` value is evaluated in downstream logic.
+**Learning:** In R, strings representing integers larger than `.Machine$integer.max` coerce to `NA`.
+**Prevention:** Use strictly bounded exact-match regex validations (e.g., `^[12]$`) for expected input formats to prevent coercion crashes and limit input lengths.

R/aFIPC.R

@@ -141,7 +141,7 @@ autoFIPC <-
       }
       for (attempt in seq_len(3)) {
         n <- readline(prompt = "Is it correct? (1: Yes 2: No) : ")
-        if (grepl("^[0-9]+$", n)) {
+        if (grepl("^[12]$", n)) {
           return(as.integer(n))
         }
       }
@@ -171,7 +171,7 @@ autoFIPC <-
               readline(
                 prompt = "Do you want to use default BILOG-MG priors for oldform Data? (1: Yes 2: No) : "
               )
-            if (grepl("^[0-9]+$", n)) {
+            if (grepl("^[12]$", n)) {
               return(as.integer(n))
             }
           }
@@ -390,7 +390,7 @@ autoFIPC <-
               readline(
                 prompt = "Do you want to use default BILOG-MG priors for newform Data? (1: Yes 2: No) : "
               )
-            if (grepl("^[0-9]+$", n)) {
+            if (grepl("^[12]$", n)) {
               return(as.integer(n))
             }
           }

tests/testthat/test-sentinel-validation.R

@@ -35,3 +35,72 @@ test_that("autoFIPC validates boolean flags for newformBILOGprior, oldformBILOGp
     "Security Error: confirmCommonItems must be a single non-NA logical value or NULL"
   )
 })
+
+test_that("autoFIPC handles interactive confirmCommonItems readline DoS inputs correctly", {
+  # Mock interactive() and readline() to simulate abnormally large integer input that used to coerce to NA
+  mockery::stub(aFIPC::autoFIPC, 'interactive', TRUE)
+  mockery::stub(aFIPC::autoFIPC, 'readline', mockery::mock('9999999999999999999', '9999999999999999999', '9999999999999999999'))
+
+  expect_error(
+    aFIPC::autoFIPC(
+      newformXData = data.frame(item1 = c(1,0,1)),
+      oldformYData = data.frame(item1 = c(1,1,0)),
+      newformCommonItemNames = c('item1'),
+      oldformCommonItemNames = c('item1'),
+      confirmCommonItems = NULL
+    ),
+    "Too many invalid common item confirmation attempts"
+  )
+})
+
+test_that("autoFIPC handles interactive oldformBILOGprior readline DoS inputs correctly", {
+  mockery::stub(aFIPC::autoFIPC, 'interactive', TRUE)
+  mockery::stub(aFIPC::autoFIPC, 'readline', mockery::mock('1', '9999999999999999999', '9999999999999999999', '9999999999999999999'))
+
+  expect_error(
+    aFIPC::autoFIPC(
+      newformXData = data.frame(item1 = c(1,0,1)),
+      oldformYData = data.frame(item1 = c(1,1,0)),
+      newformCommonItemNames = c('item1'),
+      oldformCommonItemNames = c('item1'),
+      confirmCommonItems = NULL,
+      itemtype = '3PL',
+      oldformBILOGprior = NULL
+    ),
+    "Too many invalid oldform BILOG prior attempts"
+  )
+})
+
+test_that("autoFIPC handles interactive newformBILOGprior readline DoS inputs correctly", {
+  mockery::stub(aFIPC::autoFIPC, 'interactive', TRUE)
+  mockery::stub(aFIPC::autoFIPC, 'readline', mockery::mock('1', '1', '9999999999999999999', '9999999999999999999', '9999999999999999999'))
+
+  # Stub out mirt::mirt but instead of failing with an error, return a proper S4 object Mock
+  mockClass <- setClass("MockClass", slots=c(OptimInfo="list"))
+
+  mock_mirt <- function(data, model, itemtype, ...) {
+    if (identical(data, data.frame(item1 = c(1,1,0)))) {
+      return(mockClass(OptimInfo=list(secondordertest=TRUE)))
+    }
+    stop('Should not reach here')
+  }
+
+  mockery::stub(aFIPC::autoFIPC, 'mirt::mirt', mock_mirt)
+
+  mockery::stub(aFIPC::autoFIPC, 'mirt::extract.mirt', function(...) data.frame(a1=1, d=0, g=0, u=1))
+  mockery::stub(aFIPC::autoFIPC, 'mirt::coef', function(...) list(item1=c(a1=1, d=0, g=0, u=1)))
+
+  expect_error(
+    aFIPC::autoFIPC(
+      newformXData = data.frame(item1 = c(1,0,1)),
+      oldformYData = data.frame(item1 = c(1,1,0)),
+      newformCommonItemNames = c('item1'),
+      oldformCommonItemNames = c('item1'),
+      confirmCommonItems = NULL,
+      itemtype = '3PL',
+      oldformBILOGprior = NULL,
+      newformBILOGprior = NULL
+    ),
+    "Too many invalid newform BILOG prior attempts"
+  )
+})