app/kb/procedures/taxonomy.mjs

Functions

Imports

It imports no other module of this repo. Imported by app/kb/form-fields.mjs, app/kb/libraries.mjs, app/kb/procedures/cite.mjs, app/kb/procedures/compile.mjs, app/kb/procedures/library.mjs, app/kb/procedures/render.mjs, app/kb/procedures/validate.mjs, app/routes.ts, app/routes/kb-library.tsx, app/routes/protocols.tsx.

Source

1// The closed lists a procedure's `method`, `organism` and `course` are chosen from, so the protocol library can
2// filter by them (docs/PROCEDURES.md): a value is an id from here or the save is refused, which keeps "PCR" from
3// being "pcr", "PCR" and "polymerase chain reaction" on three pages. A procedure's `target` (the gene or region it
4// amplifies, the sample it works on) is free text, because targets are as many as the experiments.
5//
6// The organism ids are the phages' host keys (app/lib/phages/compile.mjs HOSTS) where a host exists, so a protocol's
7// organism and a phage's host are the same word. When the lab registry holds host strains, these become records
8// and this list is read from them.
9
10/** What a procedure is mostly doing: the library's "method" facet. */
11export const METHODS = Object.freeze({
12  pcr: "PCR",
13  plating: "Plating and titering",
14  culture: "Culture",
15  extraction: "Nucleic acid extraction",
16  sequencing: "Sequencing",
17  annotation: "Genome annotation",
18  media: "Media and reagents",
19  microscopy: "Microscopy",
20});
21
22/**
23 * The organisms a procedure works with or on that are not a cultured strain. The rest of the list is the lab registry's strains
24 * (docs/REGISTRY.md): a strain's id is an organism id, and its organism is the words, so a strain added to the registry is an
25 * organism a protocol can name with no edit here.
26 */
27export const NON_STRAIN_ORGANISMS = Object.freeze({
28  avian: "Birds",
29});
30
31/** The courses a procedure is taught in, each with the page that describes it. */
32export const COURSES = Object.freeze({
33  "phage-discovery": { label: "Phage Discovery Program", path: "/teaching/phage-discovery" },
34  "virus-isolation": { label: "Virus Isolation Course", path: "/teaching/virus-isolation" },
35  "phage-bioinformatics": { label: "Phage Bioinformatics Course", path: "/teaching/phage-bioinformatics" },
36});
37
38/**
39 * Where a protocol stands in the lab, a closed list so the editor offers a choice and the page says it in one set of words
40 * (Dustin, 2026-10-09, the form editor). Each is the protocol's `status`, or "MISSING: <why>" until someone sets it.
41 */
42export const PROTOCOL_STATUSES = Object.freeze({
43  "in-use": "In use",
44  "in-development": "In development",
45  retired: "Retired",
46});
47
48/** A status id's words, or the id itself. @param {string} id */
49export function statusLabel(id) {
50  return /** @type {Record<string, string>} */ (PROTOCOL_STATUSES)[id] ?? id;
51}
52
53/**
54 * The phage workflow the library draws as a strip, in the order a phage takes through the lab: each stage is the
55 * methods that carry it out. A stage with no protocol yet is drawn without a link, so the strip is the lab's own
56 * path and a protocol appears under its stage the moment one is saved. `tools` are the ids of the calculators
57 * (TOOLS in phage-tools.mjs) a person uses at that stage, so the strip links them from the one place that says so.
58 */
59export const PHAGE_PIPELINE = Object.freeze([
60  { id: "isolate", label: "Isolate and purify", methods: ["plating", "culture"], tools: ["titer", "dilution", "webbed-plate", "lysate-volume"] },
61  { id: "extract", label: "Extract DNA", methods: ["extraction"], tools: [] },
62  { id: "sequence", label: "Sequence", methods: ["sequencing"], tools: [] },
63  { id: "annotate", label: "Annotate", methods: ["annotation"], tools: [] },
64]);
65
66/**
67 * The tabs above the library: the lab's two kinds of work, each the methods that make it up. "All" is implied. A tab
68 * is a link to the library narrowed to its methods, so it is also what the method facet would give.
69 */
70export const LIBRARY_TABS = Object.freeze([
71  { id: "phage", label: "Phage work", methods: PHAGE_PIPELINE.flatMap((stage) => stage.methods) },
72  { id: "pcr", label: "PCR and primers", methods: ["pcr"] },
73]);
74
75/** The page that lists the phage calculators (docs/PHAGE-TOOLS.md): the library's Calculators tab goes there. */
76export const CALCULATORS_PATH = "/research/tools";
77
78/** The words for an id in a closed list, or the id itself when the list does not know it. */
79export function methodLabel(/** @type {string} */ id) {
80  return /** @type {Record<string, string>} */ (METHODS)[id] ?? id;
81}
82/**
83 * The words for an organism id: a non-strain organism's own, else the registry strain's organism, as the protocols' records carry
84 * it (compile.mjs reads it from the registry; `libraryItems` hands it here), else the id. The facet's label function is given a
85 * value and nothing else, so the words read so far are kept by id; each request's `libraryItems` refreshes them from its records.
86 */
87const organismWords = /** @type {Map<string, string>} */ (new Map());
88export function rememberOrganisms(/** @type {Record<string, string>} */ names) {
89  for (const [id, words] of Object.entries(names)) organismWords.set(id, words);
90}
91export function organismLabel(/** @type {string} */ id) {
92  return /** @type {Record<string, string>} */ (NON_STRAIN_ORGANISMS)[id] ?? organismWords.get(id) ?? id;
93}
94export function courseLabel(/** @type {string} */ id) {
95  return /** @type {Record<string, { label: string }>} */ (COURSES)[id]?.label ?? id;
96}
97
98/** The protocol library's address; its filters are query parameters on it, so the canonical stays this path. */
99export const LIBRARY_PATH = "/research/protocols";