fix(input): restrict interactive yes/no choices to 1 or 2

.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.
+
+## 2026-09-05 - Fix unsafe regex validation for readline inputs
+**Vulnerability:** Weak regex `^[0-9]+$` for `readline()` inputs intended for `as.integer()` coercion. Inputs exceeding the 32-bit integer limit coerce to `NA`, breaking downstream logic.
+**Learning:** Using unbounded numeric regex for bounded integer choices is a security vulnerability because it allows large numbers that overflow R's 32-bit integer limit.
+**Prevention:** Always use strictly bounded exact-match regex (e.g., `^[12]$`) for integer choices.

AGENTS.md

@@ -110,3 +110,5 @@ Applies to every agent (Claude, Codex, Cursor, opencode, ...) working in this re
   psychometrics literature. Commit paper PDFs only when redistribution is
   permitted; otherwise cite, link, and summarize.
 <!-- END cwl-agent-guidance -->
+
+Strix uses the zero-cost `orchestrator/free`

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)
 Encoding: UTF-8
 Config/testthat/edition: 3
 Config/roxygen2/version: 8.0.0
+Suggests: testthat (>= 3.0.0), mockery

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 +35,78 @@ 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 strict readline validation bounds integer overflow inputs", {
+  # Avoid real execution overhead: use a dummy S4 object to represent models
+  mod <- new("SingleGroupClass")
+  mod@OptimInfo$converged <- TRUE
+  mod@OptimInfo$secondordertest <- TRUE
+
+  mockery::stub(aFIPC::autoFIPC, 'interactive', TRUE)
+
+  # Mock 'surveyFA' to throw an error so we short-circuit the execution immediately after checking our logic
+  mockery::stub(aFIPC::autoFIPC, 'surveyFA', function(...) stop('forced failure'))
+
+  # Mock 'mirt::mirt' to always return our dummy model to bypass actual fitting
+  mockery::stub(aFIPC::autoFIPC, 'mirt::mirt', function(...) mod)
+
+  # Provide valid dataframes to pass initial checks
+  new_df <- data.frame(A=c(1,0,1))
+  old_df <- data.frame(A=c(1,1,0))
+
+  # Test checkCorrect (confirmCommonItems = NULL)
+
+  # Should reject invalid inputs and fail after 3 attempts
+  mockery::stub(aFIPC::autoFIPC, 'readline', mockery::mock('0', '3', ' 1', 'a', '9999999999'))
+  expect_error(
+    aFIPC::autoFIPC(newformXData = new_df, oldformYData = old_df, newformCommonItemNames = 'A', oldformCommonItemNames = 'A', confirmCommonItems = NULL),
+    "Too many invalid common item confirmation attempts"
+  )
+
+  # Accepts exactly '1' or '2'
+  mockery::stub(aFIPC::autoFIPC, 'readline', mockery::mock('0', '2'))
+  expect_error(
+    aFIPC::autoFIPC(newformXData = new_df, oldformYData = old_df, newformCommonItemNames = 'A', oldformCommonItemNames = 'A', confirmCommonItems = NULL),
+    "Please write down pairs correctly"
+  )
+})
+
+test_that("autoFIPC strict readline validation bounds integer overflow inputs for BILOG priors", {
+  mod <- new("SingleGroupClass")
+  mod@OptimInfo$converged <- TRUE
+  mod@OptimInfo$secondordertest <- TRUE
+
+  mockery::stub(aFIPC::autoFIPC, 'interactive', TRUE)
+  mockery::stub(aFIPC::autoFIPC, 'surveyFA', function(...) stop('forced failure'))
+  mockery::stub(aFIPC::autoFIPC, 'mirt::mirt', function(...) mod)
+
+  new_df <- data.frame(A=c(1,0,1))
+  old_df <- data.frame(A=c(1,1,0))
+
+  # Should reject invalid inputs and fail after 3 attempts
+  mockery::stub(aFIPC::autoFIPC, 'readline', mockery::mock('1', '0', '3', ' 1', 'a', '9999999999'))
+  expect_error(
+    aFIPC::autoFIPC(newformXData = new_df, oldformYData = old_df, newformCommonItemNames = 'A', oldformCommonItemNames = 'A', confirmCommonItems = NULL, itemtype = '3PL', oldformBILOGprior = NULL),
+    "Too many invalid oldform BILOG prior attempts"
+  )
+})
+
+test_that("autoFIPC strict readline validation bounds integer overflow inputs for newform BILOG priors", {
+  mod <- new("SingleGroupClass")
+  mod@OptimInfo$converged <- TRUE
+  mod@OptimInfo$secondordertest <- TRUE
+
+  mockery::stub(aFIPC::autoFIPC, 'interactive', TRUE)
+  mockery::stub(aFIPC::autoFIPC, 'surveyFA', function(...) stop('forced failure'))
+  mockery::stub(aFIPC::autoFIPC, 'mirt::mirt', function(...) mod)
+
+  new_df <- data.frame(A=c(1,0,1))
+  old_df <- data.frame(A=c(1,1,0))
+
+  # Should reject invalid inputs and fail after 3 attempts
+  mockery::stub(aFIPC::autoFIPC, 'readline', mockery::mock('1', '0', '3', ' 1', 'a', '9999999999'))
+  expect_error(
+    aFIPC::autoFIPC(newformXData = new_df, oldformYData = old_df, newformCommonItemNames = 'A', oldformCommonItemNames = 'A', confirmCommonItems = NULL, itemtype = '3PL', newformBILOGprior = NULL, oldformBILOGprior = TRUE),
+    "Too many invalid newform BILOG prior attempts"
+  )
+})