Bug #5b: extend patient_id UPDATE to Tier 3 variants + apply pending-PR routines in orchestrator

Two changes:

1. Extend bug #5b's patient_id-NULL fix to the 10 multi-condition
   nrt_investigation variants (22000010-22000100) and the Tetanus
   variant (22000200). The original cherry-pick (bb7cec9) only set
   patient_id on the foundation Inv (20000100); the Tier 3 variants
   left it NULL, so the same DELETE-by-sentinel-PATIENT_UID cascade
   that blocks HEPATITIS_DATAMART would block any condition-datamart
   SP whose query path goes through F_PAGE_CASE -> D_PATIENT lookup.

2. New orchestrator step 2.5 apply_pending_pr_routines pulls each
   pending-PR routine (PRs #837, #839, #840) from its bug branch via
   `git show` and applies it to the freshly-reset DB before fixtures.
   Without this the orchestrator aborts at step 8 on
   ldf_answers_tetanus.sql (bug #7 early-RETURN guard fires on a SUB
   data_type ldf_uid, and bug #8 SUBSTRING fires on the tetanus
   datamart SP). Remove a branch from the list once its PR merges and
   the baseline image is refreshed.

End-to-end coverage uplift vs. coverage_tier_3.md baseline:
  HEPATITIS_DATAMART         0 -> 1    (5b)
  COVID_CASE_DATAMART        0 -> 1    (5b on 22000070)
  BMIRD_STREP_PNEUMO_DATAMART 0 -> 1   (5b on 22000100)
  F_PAGE_CASE                1 -> 6    (multi-condition + 5b)
  LDF_DIMENSIONAL_DATA       0 -> 5    (PR #839 bug-7)
  MORB_RPT_USER_COMMENT      0 -> 1    (PR #837 bug-3)

Still 0 (separate per-condition blockers, not 5b-related): HEPATITIS_CASE,
HEP100, F_STD_PAGE_CASE, STD_HIV_DATAMART, TB_DATAMART, VAR_DATAMART,
LDF_TETANUS, LDF_HEPATITIS — see coverage_hep_datamart_investigation.md
for per-condition diagnoses.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Author: nullflux

utilities/comparison-fixtures/fixtures/30_sp_coverage/ldf_answers_tetanus.sql

@@ -40,6 +40,11 @@ VALUES
      '2026-04-01T00:00:00', '2026-04-01T00:00:00', N'ACTIVE',
      '2026-04-01T00:00:00', '2026-04-01T00:00:00', N'O');
 
+-- RTR bug #5b: see multi_condition_investigations.sql for rationale.
+UPDATE dbo.nrt_investigation
+   SET patient_id = 20000000
+ WHERE public_health_case_uid = 22000200;
+
 EXEC dbo.sp_nrt_investigation_postprocessing @id_list = N'22000200', @debug = 0;
 
 -- Author nrt_ldf_data answer rows for the first 5 Tetanus LDFs.

utilities/comparison-fixtures/fixtures/30_sp_coverage/multi_condition_investigations.sql

@@ -120,6 +120,16 @@ VALUES
      '2026-04-01T00:00:00', '2026-04-01T00:00:00', N'ACTIVE',
      '2026-04-01T00:00:00', '2026-04-01T00:00:00', N'O');
 
+-- RTR bug #5b: point patient_id at the foundation nrt_patient.patient_uid
+-- so downstream Datamart SPs (sp_hepatitis_datamart_* etc. via F_PAGE_CASE)
+-- resolve to a real D_PATIENT row instead of falling back to the sentinel
+-- PATIENT_KEY=1 (PATIENT_UID=NULL) which the SPs then DELETE before INSERT.
+UPDATE dbo.nrt_investigation
+   SET patient_id = 20000000
+ WHERE public_health_case_uid IN
+       (22000010, 22000020, 22000030, 22000040, 22000050,
+        22000060, 22000070, 22000080, 22000090, 22000100);
+
 -- Run sp_nrt_investigation_postprocessing to flow these into INVESTIGATION.
 EXEC dbo.sp_nrt_investigation_postprocessing
     @id_list = N'22000010,22000020,22000030,22000040,22000050,22000060,22000070,22000080,22000090,22000100',

utilities/comparison-fixtures/scripts/merge_and_verify.sh

@@ -182,6 +182,59 @@ run_infrastructure_sps() {
   log "  RDB_DATE rows: $rdb_date_count, CONDITION rows: $cond_count"
 }
 
+# --------------------------------------------------------------------
+# Step 2.5 — Apply pending-PR routine fixes
+# --------------------------------------------------------------------
+#
+# The baseline docker image (DATABASE_VERSION=6.0.18.1) ships SP versions
+# that pre-date several RTR fixes under review. Until those PRs merge to
+# main and a new image is cut, pull each pending routine from its bug
+# branch via `git show` and apply it to the freshly-restored DB so Tier 3
+# fixtures and the datamart chain can execute cleanly.
+#
+# Remove a branch from this list once its PR merges and the baseline
+# image is refreshed.
+
+apply_pending_pr_routines() {
+  log "Step 2.5: apply pending-PR routine fixes"
+  local routines=(
+    # PR #837 (bug-3): morbidity user-comment join via NRT staging CSV
+    "aw/app-471/bug-3:liquibase-service/src/main/resources/db/005-rdb_modern/routines/016-sp_nrt_morbidity_report_postprocessing-001.sql"
+    # PR #839 (bug-7): sp_nrt_ldf_dimensional_data_postprocessing
+    "aw/app-471/bug-7:liquibase-service/src/main/resources/db/005-rdb_modern/routines/265-sp_nrt_ldf_dimensional_data_postprocessing-001.sql"
+    # PR #840 (bug-8): SUBSTRING guards across 6 per-condition LDF datamart SPs
+    "aw/app-471/bug-8:liquibase-service/src/main/resources/db/005-rdb_modern/routines/285-sp_ldf_bmird_datamart_postprocessing-001.sql"
+    "aw/app-471/bug-8:liquibase-service/src/main/resources/db/005-rdb_modern/routines/290-sp_ldf_foodborne_datamart_postprocessing-001.sql"
+    "aw/app-471/bug-8:liquibase-service/src/main/resources/db/005-rdb_modern/routines/295-sp_ldf_mumps_datamart_postprocessing-001.sql"
+    "aw/app-471/bug-8:liquibase-service/src/main/resources/db/005-rdb_modern/routines/300-sp_ldf_tetanus_datamart_postprocessing-001.sql"
+    "aw/app-471/bug-8:liquibase-service/src/main/resources/db/005-rdb_modern/routines/305-sp_ldf_vaccine_prevent_diseases_datamart_postprocessing-001.sql"
+    "aw/app-471/bug-8:liquibase-service/src/main/resources/db/005-rdb_modern/routines/320-sp_ldf_hepatitis_datamart_postprocessing-001.sql"
+  )
+
+  local tmp_dir
+  tmp_dir=$(mktemp -d)
+  trap "rm -rf '$tmp_dir'" RETURN
+
+  for spec in "${routines[@]}"; do
+    local branch="${spec%%:*}"
+    local path="${spec#*:}"
+    local fname
+    fname=$(basename "$path")
+    local outfile="$tmp_dir/$fname"
+
+    if ! git -C "$NEDSS_DR_ROOT" show "$branch:$path" > "$outfile" 2>/dev/null; then
+      log "  skip (branch '$branch' not present): $fname"
+      continue
+    fi
+
+    log "  apply: $branch -> $fname"
+    if ! $SQLCMD_BASE -d RDB_MODERN -i "$outfile" -b >/dev/null 2>&1; then
+      printf '\033[1;31m[merge ERROR]\033[0m failed to apply %s from %s\n' "$fname" "$branch" >&2
+      return 1
+    fi
+  done
+}
+
 # --------------------------------------------------------------------
 # Step 3 — Foundation
 # --------------------------------------------------------------------
@@ -579,6 +632,7 @@ main() {
   if [[ $SKIP_RESET -eq 0 ]]; then
     reset_baseline
     run_infrastructure_sps
+    apply_pending_pr_routines
   else
     log "Skipping baseline reset (--skip-reset)"
   fi