{
  "status": "PASS",
  "module": "analysis/18_full_reanalysis/synthesis",
  "completed_at_utc": "2026-08-15T08:39:45.031492+00:00",
  "checks": [
    {
      "check": "five_upstream_hash_status_gates",
      "passed": true
    },
    {
      "check": "formal_recovery_inputs_exactly_E0_adjusted",
      "passed": true
    },
    {
      "check": "formal_recovery_input_paths_exclude_legacy_rawP",
      "passed": true
    },
    {
      "check": "integration_geometry_exact_30_metrics_x_1999",
      "passed": true
    },
    {
      "check": "integration_recovery_omnibus_six_rows_pq_NA",
      "passed": true
    },
    {
      "check": "integration_turning_18_rows_pq_NA",
      "passed": true
    },
    {
      "check": "integration_cross_SS_and_function_11level_macro",
      "passed": true
    },
    {
      "check": "candidate_exact_11_unique_combinations",
      "passed": true
    },
    {
      "check": "candidate_exact_tiers_8A_1B_2C",
      "passed": true
    },
    {
      "check": "candidate_selection_explicitly_posthoc_nonexhaustive",
      "passed": true
    },
    {
      "check": "candidate_recovery_rows_use_E0_adjusted_sources",
      "passed": true
    },
    {
      "check": "candidate_direct_recovery_rows_use_E0_adjusted_sources",
      "passed": true
    },
    {
      "check": "candidate_recovery_definition_names_estimand",
      "passed": true
    },
    {
      "check": "candidate_direct_progression_fields_present",
      "passed": true
    },
    {
      "check": "candidate_A_has_both_recovery_stages",
      "passed": true
    },
    {
      "check": "candidate_A_both_joint_q005",
      "passed": true
    },
    {
      "check": "candidate_A_rhythm_has_3of6_robust_cells",
      "passed": true
    },
    {
      "check": "rna_candidates_are_E8_only",
      "passed": true
    },
    {
      "check": "metabolite_annotations_marked_candidate",
      "passed": true
    },
    {
      "check": "direct_progress_four_layer_algebra",
      "passed": true
    },
    {
      "check": "sex_community_only_E6_E8",
      "passed": true
    },
    {
      "check": "rna_tissue_specific_direction",
      "passed": true
    },
    {
      "check": "scn_core_clock_no_mesor_two_edge_waveforms",
      "passed": true
    },
    {
      "check": "summary_exists",
      "passed": true
    },
    {
      "check": "three_figure_formats",
      "passed": true
    },
    {
      "check": "figure_png_decodes_pdf_svg_structurally_valid",
      "passed": true
    },
    {
      "check": "figure_text_inside_canvas_without_overlap",
      "passed": true
    },
    {
      "check": "manifest_output_hashes_reread_exact",
      "passed": true
    }
  ],
  "upstream_gate_rows": [
    {
      "module": "microbiome",
      "validation_path": "analysis/18_full_reanalysis/microbiome/outputs/validation.json",
      "validation_status": "PASS",
      "validation_sha256_expected": "ce35971c9b39457e30b0b34a4f9335b2bdf9b4e10bd689488d47dd7e1417ba8b",
      "validation_sha256_observed": "ce35971c9b39457e30b0b34a4f9335b2bdf9b4e10bd689488d47dd7e1417ba8b",
      "manifest_path": "analysis/18_full_reanalysis/microbiome/run_manifest.json",
      "manifest_status": "PASS",
      "manifest_sha256_expected": "78db9c320728c60ca77078a4f218ac7f8d355f97d53df1a9d51f8ab7b1ae9586",
      "manifest_sha256_observed": "78db9c320728c60ca77078a4f218ac7f8d355f97d53df1a9d51f8ab7b1ae9586",
      "validation_checks_present": true,
      "all_validation_checks_passed": true,
      "schema_validation_passed": null,
      "extra_locked_QA_hashes_passed": null,
      "independent_validation_path": null,
      "independent_validation_sha256_expected": null,
      "independent_validation_sha256_observed": null,
      "posthoc_comparison_path": null,
      "posthoc_comparison_sha256_expected": null,
      "posthoc_comparison_sha256_observed": null,
      "gate_passed": true
    },
    {
      "module": "metabolomics",
      "validation_path": "analysis/18_full_reanalysis/metabolomics/outputs/metabolomics_validation.json",
      "validation_status": "PASS",
      "validation_sha256_expected": "cab7d80d49cbd81f4b22c188437acc4b34d5aae1810df8e6ccfce8aea348f5e0",
      "validation_sha256_observed": "cab7d80d49cbd81f4b22c188437acc4b34d5aae1810df8e6ccfce8aea348f5e0",
      "manifest_path": "analysis/18_full_reanalysis/metabolomics/outputs/run_manifest.json",
      "manifest_status": "PASS",
      "manifest_sha256_expected": "467e9a998edb428d804d62e9009b1999085712b6aa9924267518d9ba224e9936",
      "manifest_sha256_observed": "467e9a998edb428d804d62e9009b1999085712b6aa9924267518d9ba224e9936",
      "validation_checks_present": false,
      "all_validation_checks_passed": null,
      "schema_validation_passed": true,
      "extra_locked_QA_hashes_passed": true,
      "independent_validation_path": "analysis/18_full_reanalysis/metabolomics/outputs/independent_validation.json",
      "independent_validation_sha256_expected": "46d01cc56b5584bd112632a963ffbf717b443f340301735a097cff7aa58b96a1",
      "independent_validation_sha256_observed": "46d01cc56b5584bd112632a963ffbf717b443f340301735a097cff7aa58b96a1",
      "posthoc_comparison_path": "analysis/18_full_reanalysis/metabolomics/outputs/posthoc_module12_comparison.json",
      "posthoc_comparison_sha256_expected": "2213f1b306657dd3b76d3ef5eeb0d31d091b3b53a4bd1319ff3dbd2314d2a81e",
      "posthoc_comparison_sha256_observed": "2213f1b306657dd3b76d3ef5eeb0d31d091b3b53a4bd1319ff3dbd2314d2a81e",
      "gate_passed": true
    },
    {
      "module": "rna_context",
      "validation_path": "analysis/18_full_reanalysis/rna_context/outputs/validation.json",
      "validation_status": "PASS",
      "validation_sha256_expected": "1244984ef025f4a2ba5a115e7afb9880aed7b87f8d6f3c2940bdec0f70122ece",
      "validation_sha256_observed": "1244984ef025f4a2ba5a115e7afb9880aed7b87f8d6f3c2940bdec0f70122ece",
      "manifest_path": "analysis/18_full_reanalysis/rna_context/outputs/run_manifest.json",
      "manifest_status": "PASS",
      "manifest_sha256_expected": "09a8cc8466663fdc07ee805a92e72dd3edbfcb562dd2f720922ebe0e5f0a06e0",
      "manifest_sha256_observed": "09a8cc8466663fdc07ee805a92e72dd3edbfcb562dd2f720922ebe0e5f0a06e0",
      "validation_checks_present": true,
      "all_validation_checks_passed": true,
      "schema_validation_passed": null,
      "extra_locked_QA_hashes_passed": null,
      "independent_validation_path": null,
      "independent_validation_sha256_expected": null,
      "independent_validation_sha256_observed": null,
      "posthoc_comparison_path": null,
      "posthoc_comparison_sha256_expected": null,
      "posthoc_comparison_sha256_observed": null,
      "gate_passed": true
    },
    {
      "module": "integration",
      "validation_path": "analysis/18_full_reanalysis/integration/outputs/validation.json",
      "validation_status": "PASS",
      "validation_sha256_expected": "b0b1563288f15cf3c20e65dffaa011a77b65c80867f496cd3786b32393ed7dc9",
      "validation_sha256_observed": "b0b1563288f15cf3c20e65dffaa011a77b65c80867f496cd3786b32393ed7dc9",
      "manifest_path": "analysis/18_full_reanalysis/integration/run_manifest.json",
      "manifest_status": "PASS",
      "manifest_sha256_expected": "c1abdce8520f26bd63d86d33c2f4efe8b933dafaca29d3be777e187b1e7a6690",
      "manifest_sha256_observed": "c1abdce8520f26bd63d86d33c2f4efe8b933dafaca29d3be777e187b1e7a6690",
      "validation_checks_present": true,
      "all_validation_checks_passed": true,
      "schema_validation_passed": null,
      "extra_locked_QA_hashes_passed": null,
      "independent_validation_path": null,
      "independent_validation_sha256_expected": null,
      "independent_validation_sha256_observed": null,
      "posthoc_comparison_path": null,
      "posthoc_comparison_sha256_expected": null,
      "posthoc_comparison_sha256_observed": null,
      "gate_passed": true
    },
    {
      "module": "recovery_e0_adjusted",
      "validation_path": "analysis/18_full_reanalysis/recovery_e0_adjusted/outputs/validation.json",
      "validation_status": "PASS",
      "validation_sha256_expected": "da7789985f4231266c341b5d4dd29140cd64e4ef0ea4fff7ecf62b8208fdd4b9",
      "validation_sha256_observed": "da7789985f4231266c341b5d4dd29140cd64e4ef0ea4fff7ecf62b8208fdd4b9",
      "manifest_path": "analysis/18_full_reanalysis/recovery_e0_adjusted/outputs/run_manifest.json",
      "manifest_status": "PASS",
      "manifest_sha256_expected": "6026398e0f39bba53688fad1134fc05766c72aa1e00a3428281d869914fae993",
      "manifest_sha256_observed": "6026398e0f39bba53688fad1134fc05766c72aa1e00a3428281d869914fae993",
      "validation_checks_present": true,
      "all_validation_checks_passed": true,
      "schema_validation_passed": true,
      "extra_locked_QA_hashes_passed": true,
      "independent_validation_path": "analysis/18_full_reanalysis/recovery_e0_adjusted/outputs/validation_independent.json",
      "independent_validation_sha256_expected": "c03244d2c64e81f83d07f2c01f6943fa7c7b733984dcfb6455889ea8acf82590",
      "independent_validation_sha256_observed": "c03244d2c64e81f83d07f2c01f6943fa7c7b733984dcfb6455889ea8acf82590",
      "posthoc_comparison_path": null,
      "posthoc_comparison_sha256_expected": null,
      "posthoc_comparison_sha256_observed": null,
      "gate_passed": true
    }
  ],
  "candidate_rows": 11,
  "candidate_tier_counts": {
    "A": 8,
    "C": 2,
    "B": 1
  },
  "direct_progress_rows": 4,
  "manifest_sha256": "306bade9a0733b01f4ca2e0ca0e9fac3ae7d992ab9ab7d7b5b8fdec49353a0fb",
  "manifest_written_before_final_validation": true,
  "environment": {
    "python": "3.9.6",
    "pandas": "2.3.3",
    "numpy": "2.0.2",
    "matplotlib": "3.9.4"
  }
}
