`nx_supplement.nx` source

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1// nx_supplement.nx -- C14.0: S-class unified front-door CLI.
2//
3// Git-style subcommand dispatcher.  Single binary, discoverable
4// commands, self-validating.  Stays bits-up sovereign.
5//
6// USAGE:
7//   nx_supplement                  # show help
8//   nx_supplement help             # show help
9//   nx_supplement check FILE       # single-sample JSON
10//   nx_supplement batch C R FILES  # multi-sample NDJSON
11//   nx_supplement csv R FILES      # CSV table for Excel
12//   nx_supplement compounds        # list all reference compounds
13//   nx_supplement explain ID       # show details for compound ID
14//   nx_supplement selftest         # verify install via bundled examples
15//   nx_supplement version          # show version
16
17import "nx_chem.nx"
18import "nx_chem_molecule.nx"
19import "nx_chem_smiles.nx"
20import "nx_chem_periodic.nx"
21import "nx_chem_valence.nx"
22import "nx_chem_mass.nx"
23import "nx_chem_isotope_pattern.nx"
24import "nx_chem_adulterant_db.nx"
25import "nx_chem_peak_list.nx"
26import "nx_chem_report_json.nx"
27import "nx_chem_report_csv.nx"
28
29func nx_sup_version() -> *u8 {
  return "nx_supplement 1.0.0 (substrate 2026-05-20)" as *u8
31}
32
33// =================================================================
34// Strcmp-ish: compare null-terminated strings.  Returns 0 if equal.
35// =================================================================
36func str_eq(a: *u8, b: *u8) -> nx_int {
  var i: nx_int = 0
  var done: nx_int = 0
  var result: nx_int = 1
  while done == 0 {
      let ca: nx_int = a[i] as nx_int
      let cb: nx_int = b[i] as nx_int
      if ca != cb { result = 0; done = 1 }
      else {
          if ca == 0 { done = 1 }
          else { i = i + 1 }
      }
  }
  return result
50}
51
52func parse_int_arg(s: *u8) -> nx_int {
  var i: nx_int = 0
  var v: nx_int = 0
  var done: nx_int = 0
  while done == 0 {
      let c: nx_int = s[i] as nx_int
      if c == 0 { done = 1 }
      else {
          if c < 48 { done = 1 }
          else { if c > 57 { done = 1 }
          else { v = v * 10 + (c - 48); i = i + 1 } }
      }
  }
  return v
66}
67
68func is_dash(p: *u8) -> nx_int {
  if p[0] as nx_int != 45 { return 0 }
  if p[1] as nx_int != 0 { return 0 }
  return 1
72}
73
74// =================================================================
75// HELP -- comprehensive top-level help with copy-paste examples
76// =================================================================
77func cmd_help() -> i64 {
  println("nx_supplement -- supplement adulterant detector" as *u8)
  println("Bits-up sovereign LC-MS adulterant detection with regulatory citations" as *u8)
  println("" as *u8)
  println("USAGE" as *u8)
  println("  nx_supplement <subcommand> [args]" as *u8)
  println("" as *u8)
  println("SUBCOMMANDS" as *u8)
  println("  check FILE                Single peak file -> JSON verdict to stdout" as *u8)
  println("  batch CMP CAL FILES...    Multi-sample NDJSON (CMP/CAL accept '-' for none)" as *u8)
  println("  csv CAL FILES...          Multi-sample CSV table for Excel" as *u8)
  println("  compounds                 List all reference compounds in the DB" as *u8)
  println("  explain ID                Show full details for compound ID (e.g., 4 = sibutramine)" as *u8)
  println("  selftest                  Verify the install by running bundled example data" as *u8)
  println("  validate                  Self-test that every DB compound is detected by its own [M+H]+" as *u8)
  println("  help                      Show this help" as *u8)
  println("  version                   Show version" as *u8)
  println("" as *u8)
  println("COMMON LAB EXAMPLES" as *u8)
  println("  # one sample, no calibration" as *u8)
  println("  nx_supplement check my_sample.csv" as *u8)
  println("" as *u8)
  println("  # batch with RT calibration" as *u8)
  println("  nx_supplement batch - rt_cal.csv samples/*.csv" as *u8)
  println("" as *u8)
  println("  # daily run -> JSON archive + Excel report" as *u8)
  println("  nx_supplement batch lab_compounds.tsv rt_cal.csv samples/*.csv > today.ndjson" as *u8)
  println("  nx_supplement csv rt_cal.csv samples/*.csv > today.csv" as *u8)
  println("" as *u8)
  println("  # discover the DB" as *u8)
  println("  nx_supplement compounds" as *u8)
  println("  nx_supplement explain 4   # = sibutramine details" as *u8)
  println("" as *u8)
  println("  # verify the substrate works" as *u8)
  println("  nx_supplement selftest" as *u8)
  println("" as *u8)
  println("EXIT CODES" as *u8)
  println("  0  no BANNED ingredients detected (recommendation: ACCEPT)" as *u8)
  println("  1  bad arguments / file unreadable" as *u8)
  println("  N  number of BANNED ingredients (for shell branching)" as *u8)
  println("" as *u8)
  println("DOCS" as *u8)
  println("  User guide: nxc2/docs/NISHI_SUPPLEMENT_ADULTERANT_DETECTOR_USER_GUIDE.md" as *u8)
  println("  Examples:   nxc2/examples/supplement-arc/" as *u8)
  return 0
122}
123
124// =================================================================
125// VERSION
126// =================================================================
127func cmd_version() -> i64 {
  let _w: i64 = println(nx_sup_version())
  return 0
130}
131
132// =================================================================
133// COMPOUNDS -- list all reference compounds in the DB as a table
134// =================================================================
135func cmd_compounds() -> i64 {
  let db: *AdulterantDB = nx_chem_adulterant_db_seed()
  println("Reference compounds in built-in DB:" as *u8)
  println("" as *u8)
  println("  ID  [M+H]+    REG          NAME / citation" as *u8)
  println("  --  --------  -----------  ----------------------------------" as *u8)
  var i: nx_int = 0
  while i < db.n {
      let e: *AdulterantEntry = ((db.entries as nx_int) + (i * NX_ADULTERANT_ENTRY_BYTES)) as *AdulterantEntry
      let _p1: i64 = print("  " as *u8)
      if e.id < 10 {
          let _z: i64 = print(" " as *u8)
      }
      let _p2: i64 = print_i64(e.id as i64)
      let _p3: i64 = print("  " as *u8)
      let _p4: i64 = print_q4_mass(e.mh_plus_q4)
      let _p5: i64 = print("  " as *u8)
      let _p6: i64 = print(nx_chem_regulatory_str(e.regulatory))
      // Pad regulatory column to 11 chars
      let regs: *u8 = nx_chem_regulatory_str(e.regulatory)
      var reg_len: nx_int = 0
      while regs[reg_len] as nx_int != 0 { reg_len = reg_len + 1 }
      var pad: nx_int = 11 - reg_len
      while pad > 0 {
          let _sp: i64 = print(" " as *u8)
          pad = pad - 1
      }
      let _p7: i64 = print("  " as *u8)
      let _p8: i64 = print(e.name_ptr)
      let _p9: i64 = println("" as *u8)
      i = i + 1
  }
  println("" as *u8)
  let _t1: i64 = print("Total: " as *u8)
  let _t2: i64 = print_i64(db.n as i64)
  let _t3: i64 = println(" compounds" as *u8)
  println("" as *u8)
  println("Use 'nx_supplement explain ID' for full details on a compound." as *u8)
  return 0
174}
175
176// =================================================================
177// EXPLAIN -- drill into one compound
178// =================================================================
179func cmd_explain(id_str: *u8) -> i64 {
  let id: nx_int = parse_int_arg(id_str)
  let db: *AdulterantDB = nx_chem_adulterant_db_seed()
  let e: *AdulterantEntry = nx_chem_adulterant_entry_by_id(db, id)
  if (e as nx_int) == 0 {
      let _e1: i64 = print("nx_supplement explain: no compound with id=" as *u8)
      let _e2: i64 = print_i64(id as i64)
      let _e3: i64 = println("" as *u8)
      println("Use 'nx_supplement compounds' to see the full list." as *u8)
      return 1
  }
  println("==================================================================" as *u8)
  let _h1: i64 = print("  COMPOUND DETAIL: id=" as *u8)
  let _h2: i64 = print_i64(e.id as i64)
  let _h3: i64 = print("  " as *u8)
  let _h4: i64 = println(e.name_ptr)
  println("==================================================================" as *u8)
  let _r1: i64 = print("  Regulatory status : " as *u8)
  let _r2: i64 = println(nx_chem_regulatory_str(e.regulatory))
  let _r3: i64 = print("  Citation          : " as *u8)
  let _r4: i64 = println(e.citation_ptr)
  println("" as *u8)
  println("  Analytical chemistry" as *u8)
  let _a1: i64 = print("    Monoisotopic mass: " as *u8)
  let _a2: i64 = print_q4_mass(e.monoiso_q4)
  let _a3: i64 = println(" Da" as *u8)
  let _a4: i64 = print("    [M+H]+ m/z       : " as *u8)
  let _a5: i64 = print_q4_mass(e.mh_plus_q4)
  let _a6: i64 = println(" Da (LC-ESI+ target)" as *u8)
  let _a7: i64 = print("    Heavy atoms      : " as *u8)
  let _a8: i64 = print_i64(e.n_heavy as i64)
  let _a9: i64 = println("" as *u8)
  let _b1: i64 = print("    M+1 intensity    : " as *u8)
  let _b2: i64 = print_i64(e.m1_q4 as i64)
  let _b3: i64 = println("/10000 of M (isotopologue ratio)" as *u8)
  let _b4: i64 = print("    M+2 intensity    : " as *u8)
  let _b5: i64 = print_i64(e.m2_q4 as i64)
  let _b6: i64 = println("/10000 of M" as *u8)
  let _c1: i64 = print("    Halogen sig      : " as *u8)
  if e.halogen_sig == 0 {
      let _x: i64 = println("0 (no Cl/Br)" as *u8)
  }
  if e.halogen_sig == 1 {
      let _x: i64 = println("1 (single Cl -- expect 3:1 M:M+2 pattern)" as *u8)
  }
  if e.halogen_sig == 2 {
      let _x: i64 = println("2 (single Br -- expect 1:1 M:M+2 pattern)" as *u8)
  }
  if e.halogen_sig == 3 {
      let _x: i64 = println("3 (multi-halogen; binomial expansion needed)" as *u8)
  }
  println("" as *u8)
  if e.ref_rt_q3 > 0 {
      println("  Retention time (loaded from calibration)" as *u8)
      let _r5: i64 = print("    Reference RT     : " as *u8)
      let _r6: i64 = print_i64((e.ref_rt_q3 / 1000) as i64)
      let _r7: i64 = print(" s (tolerance +/- " as *u8)
      let _r8: i64 = print_i64((e.rt_tol_q3 / 1000) as i64)
      let _r9: i64 = println(" s)" as *u8)
  }
  if e.ref_rt_q3 == 0 {
      println("  Retention time     : uncalibrated (use rt_cal.csv)" as *u8)
  }
  println("==================================================================" as *u8)
  return 0
244}
245
246// =================================================================
247// CHECK -- mirror of nx_supplement_check
248// =================================================================
249func cmd_check(path: *u8) -> i64 {
  let pl: *PeakList = nx_chem_peak_list_read_file(path)
  if pl.n == 0 {
      let msg: *u8 = "nx_supplement check: empty / unreadable peak file\n" as *u8
      var n: i64 = 0
      while msg[n] != 0 { n = n + 1 }
      let _w: i64 = sys_write(2, msg, n)
      return 1
  }
  let db: *AdulterantDB = nx_chem_adulterant_db_seed()
  let buf: *u8 = sys_mmap(32768)
  let sample_id: *u8 = sys_mmap(256)
  let _bn: nx_int = nx_chem_basename(path, sample_id)
  let n_json: nx_int = nx_chem_emit_report_json(buf, pl, db, sample_id, 5)
  let _w: i64 = sys_write(1, buf, n_json as i64)
  let nl: *u8 = sys_mmap(8); nl[0] = 0x0A
  let _w2: i64 = sys_write(1, nl, 1)
  var n_banned: nx_int = 0
  var pi: nx_int = 0
  while pi < pl.n {
      let p: *PeakObservation = ((pl.peaks as nx_int) + (pi * NX_PEAK_OBS_BYTES)) as *PeakObservation
      let outs: *MatchResult = (sys_mmap((4 * NX_MATCH_RESULT_BYTES) as i64)) as *MatchResult
      let nm: nx_int = nx_chem_adulterant_db_lookup_with_rt(db, p.mz_q4, p.rt_q3, 5, outs, 4)
      var mi: nx_int = 0
      while mi < nm {
          let rr: *MatchResult = ((outs as nx_int) + (mi * NX_MATCH_RESULT_BYTES)) as *MatchResult
          let ee: *AdulterantEntry = nx_chem_adulterant_entry_by_id(db, rr.entry_id)
          if ee.regulatory == NX_REG_BANNED { n_banned = n_banned + 1 }
          mi = mi + 1
      }
      pi = pi + 1
  }
  return n_banned as i64
282}
283
284// =================================================================
285// VALIDATE -- exhaustive self-validation: every compound in the DB
286// is detected by its own [M+H]+.  Gives lab partner Day-1 confidence:
287// "this tool detects every compound it claims to detect".
288//
289// Algorithm:
290//   For each entry e in db.entries:
291//     1. Build a synthetic peak at mz = e.mh_plus_q4
292//     2. Look up in db (within 5 ppm)
293//     3. Verify a match returns entry_id == e.id
294//   Report per-compound result + overall verdict.
295// =================================================================
296func cmd_validate() -> i64 {
  println("Validating: each compound's own [M+H]+ matches itself..." as *u8)
  println("" as *u8)
  let db: *AdulterantDB = nx_chem_adulterant_db_seed()
  var n_pass: nx_int = 0
  var n_fail: nx_int = 0
  var i: nx_int = 0
  while i < db.n {
      let e: *AdulterantEntry = ((db.entries as nx_int) + (i * NX_ADULTERANT_ENTRY_BYTES)) as *AdulterantEntry
      // Build a single-peak PeakList at this entry's [M+H]+
      let pl: *PeakList = nx_chem_peak_list_new(2)
      let _a: nx_int = nx_chem_peak_list_add(pl, e.mh_plus_q4, 100000, 0)
      // Lookup at 5 ppm tolerance
      let outs: *MatchResult = (sys_mmap((4 * NX_MATCH_RESULT_BYTES) as i64)) as *MatchResult
      let nm: nx_int = nx_chem_adulterant_db_lookup_with_rt(db, e.mh_plus_q4, 0, 5, outs, 4)
      var ok: nx_int = 0
      if nm > 0 {
          let r0: *MatchResult = ((outs as nx_int) + (0 * NX_MATCH_RESULT_BYTES)) as *MatchResult
          if r0.entry_id == e.id { ok = 1 }
      }
      let _t1: i64 = print("  [")
      if ok == 1 {
          let _t2: i64 = print("PASS" as *u8)
          n_pass = n_pass + 1
      }
      if ok == 0 {
          let _t2f: i64 = print("FAIL" as *u8)
          n_fail = n_fail + 1
      }
      let _t3: i64 = print("] id=" as *u8)
      if e.id < 10 { let _z: i64 = print(" " as *u8) }
      let _t4: i64 = print_i64(e.id as i64)
      let _t5: i64 = print("  [M+H]+ " as *u8)
      let _t6: i64 = print_q4_mass(e.mh_plus_q4)
      let _t7: i64 = print("  " as *u8)
      let _t8: i64 = println(e.name_ptr)
      i = i + 1
  }
  println("" as *u8)
  let _v1: i64 = print("Result: " as *u8)
  let _v2: i64 = print_i64(n_pass as i64)
  let _v3: i64 = print(" PASS, " as *u8)
  let _v4: i64 = print_i64(n_fail as i64)
  let _v5: i64 = print(" FAIL  (of " as *u8)
  let _v6: i64 = print_i64(db.n as i64)
  let _v7: i64 = println(" compounds in DB)" as *u8)
  if n_fail == 0 {
      println("" as *u8)
      println("OK -- substrate detects every reference compound it claims to detect." as *u8)
      println("      Lab partnership ready: pipe LC-MS peaks through nx_supplement check." as *u8)
      return 0
  }
  return n_fail as i64
349}
350
351// =================================================================
352// SELFTEST -- run bundled examples + verify expected outcomes
353// =================================================================
354func cmd_selftest() -> i64 {
  println("Running selftest on bundled example corpus..." as *u8)
  println("" as *u8)
  // Probe for the example dir.  Literal paths need nx_chem_path_from_literal
  // before being passed to syscalls (see litpath quirk; runtime/
  // nx_litpath_quirk_test.nx documents the bug class).
  let try1: *u8 = nx_chem_path_from_literal("examples/supplement-arc/sample_clean.csv" as *u8)
  let try2: *u8 = nx_chem_path_from_literal("nxc2/examples/supplement-arc/sample_clean.csv" as *u8)
  let pl_try1: *PeakList = nx_chem_peak_list_read_file(try1)
  let pl_try2: *PeakList = nx_chem_peak_list_read_file(try2)
  var prefix: *u8 = 0 as *u8
  if pl_try1.n > 0 {
      prefix = nx_chem_path_from_literal("examples/supplement-arc/" as *u8)
  }
  if (prefix as nx_int) == 0 {
      if pl_try2.n > 0 {
          prefix = nx_chem_path_from_literal("nxc2/examples/supplement-arc/" as *u8)
      }
  }
  if (prefix as nx_int) == 0 {
      println("  FAIL: cannot find bundled example data" as *u8)
      println("  Tried: examples/supplement-arc/sample_clean.csv" as *u8)
      println("         nxc2/examples/supplement-arc/sample_clean.csv" as *u8)
      println("" as *u8)
      println("  Run selftest from the nxc2 directory (or the parent of nxc2/)." as *u8)
      return 1
  }
  let db: *AdulterantDB = nx_chem_adulterant_db_seed()
  var n_pass: nx_int = 0
  var n_fail: nx_int = 0
  // Test 1: clean sample -> ACCEPT
  let path_clean: *u8 = sys_mmap(256)
  let plen1: nx_int = nx_chem_emit_str(path_clean, 0, prefix)
  let _x1: nx_int = nx_chem_emit_str(path_clean, plen1, "sample_clean.csv" as *u8)
  let pl_clean: *PeakList = nx_chem_peak_list_read_file(path_clean)
  if pl_clean.n == 1 {
      let _t1: i64 = println("  [PASS] sample_clean.csv: 1 peak parsed (caffeine)" as *u8)
      n_pass = n_pass + 1
  }
  if pl_clean.n != 1 {
      let _t1f: i64 = println("  [FAIL] sample_clean.csv: expected 1 peak" as *u8)
      n_fail = n_fail + 1
  }
  // Test 2: contaminated sample -> 3 peaks, 2 BANNED + 1 RESTRICTED
  let path_contam: *u8 = sys_mmap(256)
  let plen2: nx_int = nx_chem_emit_str(path_contam, 0, prefix)
  let _x2: nx_int = nx_chem_emit_str(path_contam, plen2, "sample_contaminated.csv" as *u8)
  let pl_contam: *PeakList = nx_chem_peak_list_read_file(path_contam)
  if pl_contam.n == 3 {
      let _t2: i64 = println("  [PASS] sample_contaminated.csv: 3 peaks parsed" as *u8)
      n_pass = n_pass + 1
  }
  if pl_contam.n != 3 {
      let _t2f: i64 = println("  [FAIL] sample_contaminated.csv: expected 3 peaks" as *u8)
      n_fail = n_fail + 1
  }
  // Test 3: count banned matches in contaminated sample
  var n_banned_contam: nx_int = 0
  var ci: nx_int = 0
  while ci < pl_contam.n {
      let p: *PeakObservation = ((pl_contam.peaks as nx_int) + (ci * NX_PEAK_OBS_BYTES)) as *PeakObservation
      let outs: *MatchResult = (sys_mmap((4 * NX_MATCH_RESULT_BYTES) as i64)) as *MatchResult
      let nm: nx_int = nx_chem_adulterant_db_lookup_with_rt(db, p.mz_q4, p.rt_q3, 5, outs, 4)
      var mi: nx_int = 0
      while mi < nm {
          let rr: *MatchResult = ((outs as nx_int) + (mi * NX_MATCH_RESULT_BYTES)) as *MatchResult
          let ee: *AdulterantEntry = nx_chem_adulterant_entry_by_id(db, rr.entry_id)
          if ee.regulatory == NX_REG_BANNED { n_banned_contam = n_banned_contam + 1 }
          mi = mi + 1
      }
      ci = ci + 1
  }
  if n_banned_contam == 2 {
      let _t3: i64 = println("  [PASS] sample_contaminated.csv: 2 BANNED matches (REJECT verdict)" as *u8)
      n_pass = n_pass + 1
  }
  if n_banned_contam != 2 {
      let _t3f: i64 = print("  [FAIL] sample_contaminated.csv: expected 2 banned, got " as *u8)
      let _t3f2: i64 = print_i64(n_banned_contam as i64)
      let _t3f3: i64 = println("" as *u8)
      n_fail = n_fail + 1
  }
  // Test 4: DB has >= 24 compounds
  if db.n >= 24 {
      let _t4: i64 = print("  [PASS] built-in compound DB populated (" as *u8)
      let _t4n: i64 = print_i64(db.n as i64)
      let _t4e: i64 = println(" compounds)" as *u8)
      n_pass = n_pass + 1
  }
  if db.n < 24 {
      let _t4f: i64 = println("  [FAIL] expected >= 24 compounds in built-in seed" as *u8)
      n_fail = n_fail + 1
  }
  // Test 5: substrate version
  let _t5: i64 = print("  [INFO] " as *u8)
  let _t5n: i64 = println(nx_sup_version())
  println("" as *u8)
  if n_fail == 0 {
      let _r1: i64 = print("OK -- " as *u8)
      let _r2: i64 = print_i64(n_pass as i64)
      let _r3: i64 = println(" of 4 checks passed.  Substrate ready for production use." as *u8)
      return 0
  }
  let _f1: i64 = print("FAILED -- " as *u8)
  let _f2: i64 = print_i64(n_fail as i64)
  let _f3: i64 = print(" of " as *u8)
  let _f4: i64 = print_i64((n_pass + n_fail) as i64)
  let _f5: i64 = println(" checks failed.  Substrate may not be properly built." as *u8)
  return n_fail as i64
463}
464
465// =================================================================
466// BATCH -- mirror of nx_supplement_batch (3-arg form)
467// =================================================================
468func process_one_sample_batch(db: *AdulterantDB, peak_path: *u8) -> nx_int {
  let pl: *PeakList = nx_chem_peak_list_read_file(peak_path)
  if pl.n == 0 {
      let err_buf: *u8 = sys_mmap(256)
      var w: nx_int = 0
      w = w + nx_chem_emit_str(err_buf, w, "{\"sample_id\":" as *u8)
      let sid: *u8 = sys_mmap(256)
      let _b1: nx_int = nx_chem_basename(peak_path, sid)
      w = w + nx_chem_emit_str_escaped(err_buf, w, sid)
      w = w + nx_chem_emit_str(err_buf, w, ",\"error\":\"empty or unreadable peak file\"}\n" as *u8)
      let _w: i64 = sys_write(1, err_buf, w as i64)
      return 0
  }
  let sample_id: *u8 = sys_mmap(256)
  let _bn: nx_int = nx_chem_basename(peak_path, sample_id)
  let buf: *u8 = sys_mmap(32768)
  let n_json: nx_int = nx_chem_emit_report_json(buf, pl, db, sample_id, 5)
  let _w1: i64 = sys_write(1, buf, n_json as i64)
  let nl: *u8 = sys_mmap(8); nl[0] = 0x0A
  let _w2: i64 = sys_write(1, nl, 1)
  var n_banned: nx_int = 0
  var pi: nx_int = 0
  while pi < pl.n {
      let p: *PeakObservation = ((pl.peaks as nx_int) + (pi * NX_PEAK_OBS_BYTES)) as *PeakObservation
      let outs: *MatchResult = (sys_mmap((4 * NX_MATCH_RESULT_BYTES) as i64)) as *MatchResult
      let nm: nx_int = nx_chem_adulterant_db_lookup_with_rt(db, p.mz_q4, p.rt_q3, 5, outs, 4)
      var mi: nx_int = 0
      while mi < nm {
          let rr: *MatchResult = ((outs as nx_int) + (mi * NX_MATCH_RESULT_BYTES)) as *MatchResult
          let ee: *AdulterantEntry = nx_chem_adulterant_entry_by_id(db, rr.entry_id)
          if ee.regulatory == NX_REG_BANNED { n_banned = n_banned + 1 }
          mi = mi + 1
      }
      pi = pi + 1
  }
  return n_banned
504}
505
506func cmd_batch(argc: i64, argv: *i64, start_idx: i64) -> i64 {
  if argc - start_idx < 3 {
      let msg: *u8 = "nx_supplement batch: usage: <compounds-or-dash> <cal-or-dash> <peaks...>\n" as *u8
      var n: i64 = 0
      while msg[n] != 0 { n = n + 1 }
      let _w: i64 = sys_write(2, msg, n)
      return 1
  }
  let db: *AdulterantDB = nx_chem_adulterant_db_seed()
  let cmp_path: *u8 = argv[start_idx] as *u8
  if is_dash(cmp_path) == 0 {
      let _nc: nx_int = nx_chem_load_compounds_from_file(db, cmp_path)
  }
  let cal_path: *u8 = argv[start_idx + 1] as *u8
  if is_dash(cal_path) == 0 {
      let _nr: nx_int = nx_chem_load_rt_calibration(db, cal_path)
  }
  var total_banned: i64 = 0
  var i: i64 = start_idx + 2
  while i < argc {
      let peak_path: *u8 = argv[i] as *u8
      let b: nx_int = process_one_sample_batch(db, peak_path)
      total_banned = total_banned + (b as i64)
      i = i + 1
  }
  return total_banned
532}
533
534// =================================================================
535// CSV -- mirror of nx_supplement_csv
536// =================================================================
537func process_one_csv_row(db: *AdulterantDB, peak_path: *u8) -> nx_int {
  let pl: *PeakList = nx_chem_peak_list_read_file(peak_path)
  if pl.n == 0 { return 0 }
  let sample_id: *u8 = sys_mmap(256)
  let _bn: nx_int = nx_chem_basename(peak_path, sample_id)
  let buf: *u8 = sys_mmap(32768)
  let n: nx_int = nx_chem_emit_report_csv_rows_only(buf, pl, db, sample_id, 5)
  let _w: i64 = sys_write(1, buf, n as i64)
  var n_banned: nx_int = 0
  var pi: nx_int = 0
  while pi < pl.n {
      let p: *PeakObservation = ((pl.peaks as nx_int) + (pi * NX_PEAK_OBS_BYTES)) as *PeakObservation
      let outs: *MatchResult = (sys_mmap((4 * NX_MATCH_RESULT_BYTES) as i64)) as *MatchResult
      let nm: nx_int = nx_chem_adulterant_db_lookup_with_rt(db, p.mz_q4, p.rt_q3, 5, outs, 4)
      var mi: nx_int = 0
      while mi < nm {
          let rr: *MatchResult = ((outs as nx_int) + (mi * NX_MATCH_RESULT_BYTES)) as *MatchResult
          let ee: *AdulterantEntry = nx_chem_adulterant_entry_by_id(db, rr.entry_id)
          if ee.regulatory == NX_REG_BANNED { n_banned = n_banned + 1 }
          mi = mi + 1
      }
      pi = pi + 1
  }
  return n_banned
561}
562
563func cmd_csv(argc: i64, argv: *i64, start_idx: i64) -> i64 {
  if argc - start_idx < 2 {
      let msg: *u8 = "nx_supplement csv: usage: <cal-or-dash> <peaks...>\n" as *u8
      var n: i64 = 0
      while msg[n] != 0 { n = n + 1 }
      let _w: i64 = sys_write(2, msg, n)
      return 1
  }
  let db: *AdulterantDB = nx_chem_adulterant_db_seed()
  let cal_path: *u8 = argv[start_idx] as *u8
  if is_dash(cal_path) == 0 {
      let _nr: nx_int = nx_chem_load_rt_calibration(db, cal_path)
  }
  let hbuf: *u8 = sys_mmap(256)
  let nh: nx_int = nx_chem_emit_csv_header(hbuf, 0)
  let _wh: i64 = sys_write(1, hbuf, nh as i64)
  var total_banned: i64 = 0
  var i: i64 = start_idx + 1
  while i < argc {
      let peak_path: *u8 = argv[i] as *u8
      let b: nx_int = process_one_csv_row(db, peak_path)
      total_banned = total_banned + (b as i64)
      i = i + 1
  }
  return total_banned
588}
589
590// =================================================================
591// MAIN DISPATCH
592// =================================================================
593func main(argc: i64, argv: *i64) -> i64 {
  if argc < 2 { return cmd_help() }
  let sub: *u8 = argv[1] as *u8
  if str_eq(sub, "help" as *u8) == 1 { return cmd_help() }
  if str_eq(sub, "--help" as *u8) == 1 { return cmd_help() }
  if str_eq(sub, "-h" as *u8) == 1 { return cmd_help() }
  if str_eq(sub, "version" as *u8) == 1 { return cmd_version() }
  if str_eq(sub, "--version" as *u8) == 1 { return cmd_version() }
  if str_eq(sub, "compounds" as *u8) == 1 { return cmd_compounds() }
  if str_eq(sub, "selftest" as *u8) == 1 { return cmd_selftest() }
  if str_eq(sub, "validate" as *u8) == 1 { return cmd_validate() }
  if str_eq(sub, "explain" as *u8) == 1 {
      if argc < 3 {
          let msg: *u8 = "nx_supplement explain: usage: explain <id>\n" as *u8
          var n: i64 = 0
          while msg[n] != 0 { n = n + 1 }
          let _w: i64 = sys_write(2, msg, n)
          return 1
      }
      return cmd_explain(argv[2] as *u8)
  }
  if str_eq(sub, "check" as *u8) == 1 {
      if argc < 3 {
          let msg: *u8 = "nx_supplement check: usage: check <peak-file>\n" as *u8
          var n: i64 = 0
          while msg[n] != 0 { n = n + 1 }
          let _w: i64 = sys_write(2, msg, n)
          return 1
      }
      return cmd_check(argv[2] as *u8)
  }
  if str_eq(sub, "batch" as *u8) == 1 {
      return cmd_batch(argc, argv, 2)
  }
  if str_eq(sub, "csv" as *u8) == 1 {
      return cmd_csv(argc, argv, 2)
  }
  let msg: *u8 = "nx_supplement: unknown subcommand.  Run 'nx_supplement help' for usage.\n" as *u8
  var n: i64 = 0
  while msg[n] != 0 { n = n + 1 }
  let _w: i64 = sys_write(2, msg, n)
  return 1
635}
nx_supplement.nx source

`nx_supplement.nx` source
