fix(release): fail early on invalid qualification inputs

R/utils.R

@@ -94,6 +94,28 @@ cancerppir_elapsed_label <- function(
   )
 }
 
+##############################################################################
+cancerppir_log_has_completion_marker <- function(log_lines) {
+  log_lines <- as.character(log_lines)
+  log_lines <- log_lines[!is.na(log_lines)]
+
+  if (!length(log_lines)) {
+    return(FALSE)
+  }
+
+  any(
+    grepl(
+      paste0(
+        "^\\[CancerPPIr\\]",
+        "(?: \\[\\+[0-9]+:[0-9]{2}:[0-9]{2}\\])?",
+        " Done\\.$"
+      ),
+      log_lines,
+      perl = TRUE
+    )
+  )
+}
+
 ##############################################################################
 msg <- function(...) {
   message(

docs/reference/contracts/release-validation.md

@@ -4,7 +4,9 @@
 
 The release qualification is the single production qualification gate for a
 CancerPPIr release candidate. It runs repository preflight checks, one complete
-unit-test suite, and one seven-case production regression.
+unit-test suite, and one seven-case production regression. Before any tests or
+production cases start, all seven inputs must pass the strict scientific input
+contract.
 
 ## Command
 
@@ -46,6 +48,10 @@ The qualification requires all static release, documentation, publication
 readiness, reproducible-environment, repository-quality, and CLI checks to pass
 before the seven-case run begins.
 
+The input-contract preflight validates all seven files together and fails before
+unit tests or case execution if any file is incomplete, malformed, ambiguous, or
+contains duplicate gene symbols.
+
 ## Release evidence
 
 The output root contains:
@@ -54,6 +60,7 @@ The output root contains:
 - `release_case_summary.csv`
 - `release_validation.csv`
 - `release_preflight_validation.csv`
+- `release_input_contract.log`
 - `release_unit_tests.log`
 - `release_multicase.log`
 

scripts/run_release_qualification.R

@@ -256,6 +256,7 @@ required_project_files <- file.path(
   c(
     "R/load_all.R",
     "scripts/run_unit_tests.R",
+    "scripts/validate_input_contract.R",
     "scripts/validate_multicase_outputs.R",
     "scripts/validate_release_contract.R",
     "scripts/validate_documentation_contract.R",
@@ -401,6 +402,11 @@ unit_test_log_temporary <- tempfile(
   fileext = ".log"
 )
 
+input_contract_log_temporary <- tempfile(
+  pattern = "release_input_contract_",
+  fileext = ".log"
+)
+
 multicase_log_temporary <- tempfile(
   pattern = "release_multicase_",
   fileext = ".log"
@@ -409,13 +415,61 @@ multicase_log_temporary <- tempfile(
 on.exit(
   unlink(
     c(
+      input_contract_log_temporary,
       unit_test_log_temporary,
       multicase_log_temporary
     )
   ),
   add = TRUE
 )
 
+message(
+  "[CancerPPIr release] Validating the strict input contract for all seven cases."
+)
+
+input_contract_arguments <- c(
+  shQuote(
+    file.path(
+      project_root,
+      "scripts",
+      "validate_input_contract.R"
+    )
+  ),
+  vapply(
+    file.path(input_root, case_map$input_file),
+    shQuote,
+    FUN.VALUE = character(1)
+  )
+)
+
+input_contract_status <- system2(
+  command = rscript_command,
+  args = input_contract_arguments,
+  stdout = input_contract_log_temporary,
+  stderr = input_contract_log_temporary,
+  wait = TRUE
+)
+
+if (
+  is.null(input_contract_status) ||
+    is.na(input_contract_status) ||
+    input_contract_status != 0L
+) {
+  stop(
+    paste0(
+      "Seven-case input-contract preflight failed with exit status ",
+      input_contract_status,
+      ".\n\nLog tail:\n",
+      tail_log(input_contract_log_temporary)
+    ),
+    call. = FALSE
+  )
+}
+
+message(
+  "[CancerPPIr release] Seven-case input-contract preflight: PASS."
+)
+
 if (run_tests) {
   message(
     "[CancerPPIr release] Running the complete unit-test suite once."
@@ -695,6 +749,17 @@ output_root <- normalizePath(
   mustWork = TRUE
 )
 
+invisible(
+  file.copy(
+    input_contract_log_temporary,
+    file.path(
+      output_root,
+      "release_input_contract.log"
+    ),
+    overwrite = TRUE
+  )
+)
+
 invisible(
   file.copy(
     unit_test_log_temporary,
@@ -1381,6 +1446,7 @@ rownames(case_summary) <- NULL
 
 summary_table <- data.frame(
   metric = c(
+    "input_contract",
     "unit_tests",
     "static_release_checks",
     "documentation_checks",
@@ -1390,6 +1456,7 @@ summary_table <- data.frame(
     "execution_mode"
   ),
   value = c(
+    "PASS",
     if (run_tests) "PASS" else "SKIPPED",
     as.character(
       nrow(static_validation)

scripts/validate_multicase_technical_exports.R

@@ -1127,12 +1127,8 @@ for (case_index in seq_len(
     encoding = "UTF-8"
   )
 
-  pipeline_done <- any(
-    grepl(
-      "[CancerPPIr] Done.",
-      log_lines,
-      fixed = TRUE
-    )
+  pipeline_done <- cancerppir_log_has_completion_marker(
+    log_lines
   )
 
   internal_validation <- expected_evidence$validation

tests/testthat/test-release-edge-cases.R

@@ -195,6 +195,47 @@ testthat::test_that(
   }
 )
 
+testthat::test_that(
+  "release qualification validates inputs before tests or cases",
+  {
+    project_root <- Sys.getenv("CANCERPPIR_PROJECT_ROOT")
+    testthat::expect_true(nzchar(project_root))
+
+    release_text <- paste(
+      readLines(
+        file.path(
+          project_root,
+          "scripts",
+          "run_release_qualification.R"
+        ),
+        warn = FALSE,
+        encoding = "UTF-8"
+      ),
+      collapse = "\n"
+    )
+
+    input_position <- regexpr(
+      "Validating the strict input contract for all seven cases.",
+      release_text,
+      fixed = TRUE
+    )[[1L]]
+
+    unit_position <- regexpr(
+      "Running the complete unit-test suite once.",
+      release_text,
+      fixed = TRUE
+    )[[1L]]
+
+    testthat::expect_gt(input_position, 0L)
+    testthat::expect_gt(unit_position, input_position)
+    testthat::expect_match(
+      release_text,
+      "validate_input_contract.R",
+      fixed = TRUE
+    )
+  }
+)
+
 testthat::test_that(
   "release edge case: zero p-values remain finite and parser-safe in GraphML",
   {

tests/testthat/test-utils.R

@@ -162,6 +162,24 @@ testthat::test_that("ranking and text helpers retain qualified behavior", {
   testthat::expect_identical("value" %||% "fallback", "value")
 })
 
+testthat::test_that("pipeline completion markers support legacy and timed logs", {
+  testthat::expect_true(
+    cancerppir_log_has_completion_marker("[CancerPPIr] Done.")
+  )
+
+  testthat::expect_true(
+    cancerppir_log_has_completion_marker(
+      "[CancerPPIr] [+00:03:15] Done."
+    )
+  )
+
+  testthat::expect_false(
+    cancerppir_log_has_completion_marker(
+      "[CancerPPIr] [+00:03:15] Not done."
+    )
+  )
+})
+
 testthat::test_that("candidate score requires five complete finite components", {
   degree <- c(1, 2, 4)
   betweenness <- c(0.1, 0.2, 0.5)