nx_labsci_gate.nx source

1// nx_labsci_gate.nx -- THE MISSING EVIDENCE ORGAN for the lab-science lane. 2// 3// WHY THIS EXISTS: the ecosystem carries a real chemistry/biochemistry stack (nx_peptide + _ext/_msms/ 4// _deconv/_denovo/_identify/_isotope, nx_supplement_screen, nx_thermal_process, nx_water_activity, 5// nx_shelf_life, nx_stability, nx_stability_rh, nx_icecream) exposed through nx_labsci_svc. 6// 7// The lane IS gated -- 43 gates / 497 assertions -- but by `_scratch/labsci_lane_gate.sh`: a shell 8// script, outside any deployable tree, hardcoding one laptop's absolute path (debt seq1352). So its 9// evidence can only be produced by hand, on one machine, into the AUTHORING root -- while the maturity 10// rollup reads the NAS root (181 logs there vs 1164 locally, debt seq1339). The domain is therefore 11// ungradeable not for want of measurement but because the witness cannot run where the reader looks. 12// 13// This organ is the sovereign, deployable replacement path: it builds and runs on the NAS, so the 14// evidence is PRODUCED where the ruler reads instead of copied there (a copied log is a stale claim). 15// 16// WHAT IT MEASURES: the library against PUBLISHED EXTERNAL REFERENCE VALUES, not against itself. 17// Self-agreement is not evidence -- these are standard MS calibration peptides and established 18// regulatory thresholds that were never inputs to our derivations: 19// Angiotensin II DRVYIHPF monoisotopic 1045.5345 Da 20// Bradykinin RPPGFSPFR monoisotopic 1059.5614 Da 21// Substance P RPKPQQFFGLM free acid 1347.7121 Da 22// HTST pasteurisation 72 C / 15 s = the legal PMO schedule 23// pH 4.6 = the C. botulinum high-acid regulatory line 24// Every positive has a NEGATIVE CONTROL so the gate can go RED. 25// 26// It writes knowledge/status/labsci_gate.log with a VERDICT= line, which is exactly the shape the 27// ecomat evkind-2 gate-liveness deriver (el_last_green) reads -- so admitting a `lab-science` domain 28// pointing here yields a MEASURED grade, never a stored assertion. 29// license_tier: ORIGINAL expect_exit: 0 30import "nx_syscalls.nx" 31import "nx_peptide.nx" 32import "nx_thermal_process.nx" 33import "nx_water_activity.nx" 34 35const LG_STDOUT: i64 = 1 36const LG_MODE: i64 = 420 37const LG_LOG: *u8 = "knowledge/status/labsci_gate.log" 38 39// Mass tolerance in q4 units (1e-4 Da). 100 = 0.01 Da -- tight enough that a wrong residue table or a 40// missing water of hydrolysis FAILS, loose enough to absorb fixed-point rounding. 41const LG_MASS_TOL_Q4: i64 = 100 42 43// Published monoisotopic masses x 10^4. 44const LG_ANGIOTENSIN2_Q4: i64 = 10455345 45const LG_BRADYKININ_Q4: i64 = 10595614 46// Substance P as the PLAIN sequence (free acid): sum of residue monoisotopic masses + H2O = 1347.7121. 47// NOT 1346.7281 -- that is the C-terminally AMIDATED physiological form, and amidation (OH -> NH2, 48// -0.9840 Da) is a modification the sequence alone does not declare. Feeding the amidated figure to a 49// sequence-only calculator is a ~1 Da category error; the first run of this gate caught exactly that, 50// and the library was right. Kept as a distinct constant so the distinction stays documented. 51const LG_SUBSTANCEP_Q4: i64 = 13477121 52 53// Monoisotopic proton, x 10^4 (1.007276 Da). 54const LG_PROTON_Q4: i64 = 10073 55 56// PMO HTST: 72 C (milli-C) held 15 s (ms). pH in milli-units; 4.6 is the botulinum line. 57const LG_HTST_TEMP_MILLI_C: i64 = 72000 58const LG_HTST_HOLD_MS: i64 = 15000 59const LG_WEAK_TEMP_MILLI_C: i64 = 60000 60const LG_WEAK_HOLD_MS: i64 = 1000 61const LG_PH_HIGH_ACID_MILLI: i64 = 4000 62const LG_PH_LOW_ACID_MILLI: i64 = 5000 63 64func lg_puts(s: *u8) -> i64 { var n: i64 = 0; while s[n] != (0 as u8) { n = n + 1 } sys_write(LG_STDOUT, s, n); return 0 } 65func lg_num(fd: i64, v: i64) -> i64 { 66 var m: i64 = v 67 if m < 0 { m = 0 - m; sys_write(fd, "-" as *u8, 1) } 68 let t: *u8 = sys_mmap(28) 69 var k: i64 = 0 70 if m == 0 { t[0] = 48 as u8; k = 1 } 71 while m > 0 { t[k] = (48 + (m % 10)) as u8; m = m / 10; k = k + 1 } 72 let o: *u8 = sys_mmap(28) 73 var i: i64 = 0 74 while i < k { o[i] = t[k - 1 - i]; i = i + 1 } 75 sys_write(fd, o, k) 76 return 0 77} 78func lg_abs(v: i64) -> i64 { if v < 0 { return 0 - v } return v } 79 80// one check: report PASS/FAIL with the measured number so a RED is diagnosable, never just a count. 81func lg_check(ok: i64, label: *u8, got: i64, want: i64) -> i64 { 82 if ok == 1 { lg_puts(" PASS " as *u8) } else { lg_puts(" FAIL " as *u8) } 83 lg_puts(label) 84 lg_puts(" got=" as *u8); lg_num(LG_STDOUT, got) 85 lg_puts(" want=" as *u8); lg_num(LG_STDOUT, want) 86 lg_puts("\n" as *u8) 87 if ok == 1 { return 0 } 88 return 1 89} 90 91// mass within tolerance of the published value 92func lg_mass_ok(seq: *u8, want: i64, label: *u8) -> i64 { 93 let got: i64 = pep_mass_mono_q4(seq) 94 var ok: i64 = 0 95 if lg_abs(got - want) <= LG_MASS_TOL_Q4 { ok = 1 } 96 return lg_check(ok, label, got, want) 97} 98 99func main() -> i64 { 100 lg_puts("=== NISHI LAB-SCIENCE GATE -- chemistry measured vs PUBLISHED external references ===\n" as *u8) 101 var fails: i64 = 0 102 var checks: i64 = 0 103 104 lg_puts("-- peptide: monoisotopic mass vs standard MS calibration peptides --\n" as *u8) 105 fails = fails + lg_mass_ok("DRVYIHPF" as *u8, LG_ANGIOTENSIN2_Q4, "angiotensin-II mono q4" as *u8); checks = checks + 1 106 fails = fails + lg_mass_ok("RPPGFSPFR" as *u8, LG_BRADYKININ_Q4, "bradykinin mono q4" as *u8); checks = checks + 1 107 fails = fails + lg_mass_ok("RPKPQQFFGLM" as *u8, LG_SUBSTANCEP_Q4, "substance-P mono q4" as *u8); checks = checks + 1 108 109 lg_puts("-- peptide: structural invariants + validity neg-controls --\n" as *u8) 110 let l8: i64 = pep_len("DRVYIHPF" as *u8) 111 var ok: i64 = 0; if l8 == 8 { ok = 1 } 112 fails = fails + lg_check(ok, "angiotensin-II length" as *u8, l8, 8); checks = checks + 1 113 114 let v1: i64 = pep_seq_valid("DRVYIHPF" as *u8) 115 ok = 0; if v1 == 1 { ok = 1 } 116 fails = fails + lg_check(ok, "valid sequence accepted" as *u8, v1, 1); checks = checks + 1 117 118 // NEG-CONTROL: X is not a standard residue -- must be REFUSED, not silently approximated. 119 let v2: i64 = pep_seq_valid("DRVYIHPX" as *u8) 120 ok = 0; if v2 != 1 { ok = 1 } 121 fails = fails + lg_check(ok, "neg-ctrl non-standard residue refused" as *u8, v2, 0); checks = checks + 1 122 123 // average mass >= monoisotopic for any real peptide (isotope-weighted mean sits above the light peak) 124 let mono: i64 = pep_mass_mono_q4("DRVYIHPF" as *u8) 125 let avg: i64 = pep_mass_avg_q4("DRVYIHPF" as *u8) 126 ok = 0; if avg > mono { ok = 1 } 127 fails = fails + lg_check(ok, "average mass exceeds monoisotopic" as *u8, avg, mono); checks = checks + 1 128 129 // Charge-state arithmetic. [M+2H]2+ is NOT half of [M+H]+ -- it is M/2 + proton, while half of 130 // [M+H]+ is M/2 + proton/2, so they differ by half a proton BY CONSTRUCTION. The exact physical 131 // invariant is 2*mz2 - mz1 = one proton, which pins the charge-carrier mass itself. 132 let mz1: i64 = pep_mz_q4(mono, 1) 133 let mz2: i64 = pep_mz_q4(mono, 2) 134 let carrier: i64 = (2 * mz2) - mz1 135 ok = 0; if lg_abs(carrier - LG_PROTON_Q4) <= LG_MASS_TOL_Q4 { ok = 1 } 136 fails = fails + lg_check(ok, "2*[M+2H]2+ - [M+H]+ = proton" as *u8, carrier, LG_PROTON_Q4); checks = checks + 1 137 138 lg_puts("-- thermal: PMO pasteurisation schedule + neg-control --\n" as *u8) 139 let c1: i64 = tp_pasteurization_compliant(LG_HTST_TEMP_MILLI_C, LG_HTST_HOLD_MS, 0) 140 ok = 0; if c1 == 1 { ok = 1 } 141 fails = fails + lg_check(ok, "HTST 72C/15s compliant" as *u8, c1, 1); checks = checks + 1 142 143 // NEG-CONTROL: 60 C for 1 s is nowhere near lethal -- must NOT pass. 144 let c2: i64 = tp_pasteurization_compliant(LG_WEAK_TEMP_MILLI_C, LG_WEAK_HOLD_MS, 0) 145 ok = 0; if c2 != 1 { ok = 1 } 146 fails = fails + lg_check(ok, "neg-ctrl 60C/1s not compliant" as *u8, c2, 0); checks = checks + 1 147 148 // lethality must be monotone in hold time 149 let e1: i64 = tp_pasteurization_equiv_ms(LG_HTST_TEMP_MILLI_C, LG_HTST_HOLD_MS, 0) 150 let e2: i64 = tp_pasteurization_equiv_ms(LG_HTST_TEMP_MILLI_C, LG_HTST_HOLD_MS * 2, 0) 151 ok = 0; if e2 > e1 { ok = 1 } 152 fails = fails + lg_check(ok, "lethality monotone in hold time" as *u8, e2, e1); checks = checks + 1 153 154 lg_puts("-- acid barrier: the pH 4.6 C. botulinum regulatory line --\n" as *u8) 155 let a1: i64 = cs_is_high_acid(LG_PH_HIGH_ACID_MILLI) 156 ok = 0; if a1 == 1 { ok = 1 } 157 fails = fails + lg_check(ok, "pH 4.0 is high-acid" as *u8, a1, 1); checks = checks + 1 158 159 // NEG-CONTROL: pH 5.0 is above the line -- must NOT be called high-acid. 160 let a2: i64 = cs_is_high_acid(LG_PH_LOW_ACID_MILLI) 161 ok = 0; if a2 != 1 { ok = 1 } 162 fails = fails + lg_check(ok, "neg-ctrl pH 5.0 not high-acid" as *u8, a2, 0); checks = checks + 1 163 164 // ---- verdict + the evidence line the ecomat deriver reads ---- 165 let passed: i64 = checks - fails 166 var permil: i64 = 0 167 if checks > 0 { permil = (passed * 1000) / checks } 168 169 lg_puts("LABSCI-GATE checks=" as *u8); lg_num(LG_STDOUT, checks) 170 lg_puts(" passed=" as *u8); lg_num(LG_STDOUT, passed) 171 lg_puts(" permil=" as *u8); lg_num(LG_STDOUT, permil) 172 if fails == 0 { lg_puts(" VERDICT=GREEN\n" as *u8) } else { lg_puts(" VERDICT=RED\n" as *u8) } 173 174 let fd: i64 = sys_openat_append(LG_LOG, LG_MODE) 175 if fd >= 0 { 176 lg_num(fd, sys_now_realtime_sec()) 177 sys_write(fd, " nx_labsci_gate checks=" as *u8, 23) 178 lg_num(fd, checks) 179 sys_write(fd, " passed=" as *u8, 8) 180 lg_num(fd, passed) 181 sys_write(fd, " permil=" as *u8, 8) 182 lg_num(fd, permil) 183 if fails == 0 { sys_write(fd, " VERDICT=GREEN\n" as *u8, 15) } else { sys_write(fd, " VERDICT=RED\n" as *u8, 13) } 184 sys_close(fd) 185 } 186 187 if fails == 0 { sys_exit(0); return 0 } 188 sys_exit(1) 189 return 1 190}