nx_probiome_provenance.nx source

1// nx_probiome_provenance.nx -- R6d grounding: "research not bro science". 2// Maps each nx_probiome cite_id (1..22) to the REAL source file the Nishi 3// researcher fetched (nx_probiome_research_fetch -> knowledge/fetched/ 4// probiome_c<NN>_*.raw) and proves the file genuinely landed: it must be 5// at least PG_MIN_SOURCE_BYTES, so a 404 error page (~48 KB here) can 6// NEVER masquerade as a citation. This is the honest counterpart of the 7// food branch's nx_food_ground_gate ("N science rules cited to real 8// fetched sources"). 9// 10// Absolute paths (cwd-independent: the native-lane gate runs from bench/, 11// the researcher wrote from nxc2/, so a relative path would diverge). 12// 13// genealogy_id: nishi_food_ground_gate + rule4_verified_facts_not_assumptions 14 15import "nx_syscalls.nx" 16import "nx_probiome.nx" 17 18// A real fetched Wikipedia article here is >100 KB; the two 404 pages the 19// first pass saved were ~48-49 KB. 80 KB cleanly separates real from 404. 20const PG_MIN_SOURCE_BYTES: i64 = 80000 21const PG_CITE_N: i64 = 22 // cite ids 1..22 are all referenced by strains 22 23// cite_id -> absolute path of the fetched source (or a non-existent 24// sentinel for an unknown id, so the grounding check fails closed). 25func pg_cite_path(cite: i64) -> *u8 { 26 if cite == 1 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c01_listeria.raw" as *u8 } 27 if cite == 2 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c02_bacillus_subtilis.raw" as *u8 } 28 if cite == 3 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c03_bacillus_cereus.raw" as *u8 } 29 if cite == 4 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c04_enterococcus_faecium.raw" as *u8 } 30 if cite == 5 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c05_rhizobium.raw" as *u8 } 31 if cite == 6 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c06_azospirillum.raw" as *u8 } 32 if cite == 7 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c07_pseudomonas_fluorescens.raw" as *u8 } 33 if cite == 8 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c08_lactic_acid_bacteria.raw" as *u8 } 34 if cite == 9 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c09_bifidobacterium.raw" as *u8 } 35 if cite == 10 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c10_nitrosomonas.raw" as *u8 } 36 if cite == 11 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c11_pseudomonas_putida.raw" as *u8 } 37 if cite == 12 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c12_acetic_acid_bacteria.raw" as *u8 } 38 if cite == 13 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c13_saccharomyces_boulardii.raw" as *u8 } 39 if cite == 14 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c14_propionibacterium.raw" as *u8 } 40 if cite == 15 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c15_aspergillus_oryzae.raw" as *u8 } 41 if cite == 16 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c16_arbuscular_mycorrhiza.raw" as *u8 } 42 if cite == 17 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c17_trichoderma.raw" as *u8 } 43 if cite == 18 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c18_rhizopus.raw" as *u8 } 44 if cite == 19 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c19_penicillium_roqueforti.raw" as *u8 } 45 if cite == 20 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c20_leuconostoc.raw" as *u8 } 46 if cite == 21 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c21_bacillus_amyloliquefaciens.raw" as *u8 } 47 if cite == 22 { return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/probiome_c22_aflatoxin.raw" as *u8 } 48 return "/mnt/c/Users/elder/nishi-core/nxc2/knowledge/fetched/__no_such_source__.raw" as *u8 49} 50 51// File size in bytes via lseek(SEEK_END), or -1 if the file is absent. 52func pg_file_size(path: *u8) -> i64 { 53 let fd: i64 = sys_openat_rd(path) 54 if fd < 0 { return -1 } 55 let sz: i64 = sys_lseek(fd, 0, 2) 56 sys_close(fd) 57 return sz 58} 59 60// A cite is GROUNDED iff its fetched file exists and clears the byte floor 61// (so a 404 stub cannot count). 62func pg_cite_grounded(cite: i64) -> i64 { 63 let p: *u8 = pg_cite_path(cite) 64 if pg_file_size(p) >= PG_MIN_SOURCE_BYTES { return 1 } 65 return 0 66} 67 68// How many of the 22 referenced cites are grounded in a real source. 69func pg_count_grounded() -> i64 { 70 var n: i64 = 0 71 var c: i64 = 1 72 while c <= PG_CITE_N { 73 if pg_cite_grounded(c) == 1 { n = n + 1 } 74 c = c + 1 75 } 76 return n 77} 78 79// Anti-bro-science: is EVERY real catalog strain cited (cite_id >= 1)? 80// Returns the count of uncited strains (0 = all cited). 81func pg_uncited_strains() -> i64 { 82 var bad: i64 = 0 83 var id: i64 = 0 84 while id < PB_STR_N { 85 let s: *NxProbiomeStrain = nx_probiome_strain(id) 86 if s.cite_id < 1 { bad = bad + 1 } 87 id = id + 1 88 } 89 return bad 90}