🛡️ Sentinel: [CRITICAL] Fix integer coercion vulnerability from weak regex

.Rbuildignore

@@ -22,3 +22,6 @@
 ^\.jules(/.*)?$
 ^\.trivyignore\.yaml$
 ^trivy\.yaml$
+^\.semgrepignore$
+^test_dummy\.R$
+^test_validation\.R$

.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.
+
+## 2024-07-28 - Fix integer coercion vulnerability from weak regex
+**Vulnerability:** Weak regex ^[0-9]+$ allows large integer inputs in readline that coerce to NA, crashing the process in subsequent if conditions.
+**Learning:** Coercing large string numbers via as.integer() results in NA. We must strictly bound inputs for interactive prompts to valid options only.
+**Prevention:** Use exactly-bounded regex like ^[12]$ when validating prompt options before coercion.

DESCRIPTION

@@ -10,7 +10,7 @@ Description: Automates fixed item parameter linking for test linking under
     the item response theory paradigm using mirt package estimates.
 License: GPL-3 | file LICENSE
 Imports: mirt, methods
-Suggests: testthat (>= 3.0.0)
+Suggests: testthat (>= 3.0.0), mockery
 Encoding: UTF-8
 Config/testthat/edition: 3
 Config/roxygen2/version: 8.0.0

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 integer validation bounds work for interactive prompts", {
+  library(mockery)
+
+  # Mock interactive() to return TRUE so we enter the readline loop
+  mock_interactive <- mock(TRUE, cycle = TRUE)
+  stub(aFIPC::autoFIPC, 'interactive', mock_interactive)
+
+  # Stub checkCorrect readline with '3' which is invalid, it should fail
+  mock_readline <- mock("3", "3", "3", cycle = TRUE)
+  stub(aFIPC::autoFIPC, 'readline', mock_readline)
+
+  expect_error(
+    aFIPC::autoFIPC(
+      newformXData = data.frame(A=c(1,0,1)),
+      oldformYData = data.frame(A=c(0,1,0)),
+      newformCommonItemNames = c('A'),
+      oldformCommonItemNames = c('A'),
+      confirmCommonItems = NULL # explicit NULL ensures we hit checkCorrect prompt
+    ),
+    "Too many invalid common item confirmation attempts"
+  )
+})
+
+test_that("autoFIPC integer validation bounds work for oldform and newform BILOG prior prompts", {
+  library(mockery)
+
+  mock_interactive <- mock(TRUE, cycle = TRUE)
+  stub(aFIPC::autoFIPC, 'interactive', mock_interactive)
+
+  mock_readline <- mock("3", "3", "3", cycle = TRUE)
+  stub(aFIPC::autoFIPC, 'readline', mock_readline)
+
+  # Need at least 4 items for mirt to fit the model initially without crashing before hitting newform prompt
+  df <- data.frame(A=c(1,0,1,0,1), B=c(0,1,0,1,0), C=c(1,1,0,0,1), D=c(0,0,1,1,0), E=c(1,0,1,0,1))
+
+  expect_error(
+    aFIPC::autoFIPC(
+      newformXData = df,
+      oldformYData = df,
+      newformCommonItemNames = c('A'),
+      oldformCommonItemNames = c('A'),
+      confirmCommonItems = TRUE,
+      itemtype = '3PL',
+      oldformBILOGprior = NULL,
+      newformBILOGprior = TRUE,
+      checkIPD = FALSE
+    ),
+    "Too many invalid oldform BILOG prior attempts"
+  )
+
+  # Stub oldform model directly so it bypasses fitting and goes to newform BILOG prompt
+  mock_oldformModel <- mirt::mirt(df, 1, itemtype='2PL', verbose=FALSE)
+
+  expect_error(
+    aFIPC::autoFIPC(
+      newformXData = df,
+      oldformYData = mock_oldformModel,
+      newformCommonItemNames = c('A'),
+      oldformCommonItemNames = c('A'),
+      confirmCommonItems = TRUE,
+      itemtype = '3PL',
+      oldformBILOGprior = TRUE,
+      newformBILOGprior = NULL,
+      checkIPD = FALSE
+    ),
+    "Too many invalid newform BILOG prior attempts"
+  )
+})