app/kb/registry/strain.mjs

Functions

Imports

It imports app/kb/procedures/validate.mjs, app/kb/registry/primer.mjs. Imported by app/kb/registry/catalog.mjs, app/kb/registry/host.server.ts, app/kb/registry/kinds.mjs, app/kb/registry/search-inputs.mjs.

Source

1// The strain kind of the lab registry (docs/REGISTRY.md): the bacterial hosts the lab's phage work grows. A strain record
2// states what the lab's own pages state about one host (its organism, the strain designation where it has one, the culture
3// collection and the number the collection gives it, the SEA-PHAGES Guide's page for it) and the biosafety level, which is
4// Dustin's to set and is MISSING until the biosafety officer check is done (core.md).
5//
6// The strain's id is the phages' host key (app/lib/phages/compile.mjs HOSTS), so a phage's host and a strain are one word,
7// and what follows from it is COMPUTED: the phages isolated on the host are read from the phages table, the protocols that use
8// the strain are read from the protocols (which name their host strains by id), and the strain's full name is its organism and
9// designation, which the record's `name` must equal.
10
11import { BIOSAFETY_LEVELS } from "../procedures/validate.mjs";
12import { stated } from "./primer.mjs";
13
14const LINE = /^[^\r\n]+$/;
15
16/** @param {unknown} value @param {number} max */
17const oneLine = (value, max) =>
18  typeof value === "string" && LINE.test(value) && value === value.trim() && value.length <= max ? null : `is one line of at most ${max} characters`;
19
20/** @type {import("./kinds.mjs").KindSpec} */
21export const STRAIN = {
22  singular: "strain",
23  plural: "strains",
24  fields: {
25    organism: { required: true, check: (value) => oneLine(value, 120) },
26    // The lab's designation within the species, where there is one apart from the collection's number (mc²155).
27    strain: { check: (value) => oneLine(value, 60) },
28    collection: { required: true, check: (value) => oneLine(value, 60) },
29    collection_number: { required: true, check: (value) => oneLine(value, 40) },
30    guide_url: { check: (value) => (typeof value === "string" && /^https:\/\/[^\s]+$/.test(value) ? null : "is an https address") },
31    // Dustin's to set: a gap until the biosafety officer check is done.
32    biosafety_level: {
33      required: true,
34      check: (value) => (BIOSAFETY_LEVELS.includes(/** @type {any} */ (value)) ? null : `is one of ${BIOSAFETY_LEVELS.join(", ")}, or "MISSING: <why>" until Dustin sets it`),
35    },
36  },
37  /** The name is the organism and its designation, so it is stated once and cannot say a different strain than the fields do. */
38  setErrors(items) {
39    /** @type {string[]} */
40    const errors = [];
41    for (const { id, name, fields } of items) {
42      const organism = stated(fields.organism);
43      const designation = designationOf(fields);
44      if (organism && designation && name !== `${organism} ${designation}`) {
45        errors.push(`strain/${id} is named "${name}", but its organism and designation make "${organism} ${designation}"; the name is computed from them`);
46      }
47    }
48    return errors;
49  },
50};
51
52/**
53 * How the strain is designated: the lab's own designation where there is one, otherwise the collection and its number.
54 *
55 * @param {Record<string, unknown>} fields
56 */
57export function designationOf(fields) {
58  const strain = stated(fields.strain);
59  if (strain) return strain;
60  const collection = stated(fields.collection);
61  const number = stated(fields.collection_number);
62  return collection && number ? `${collection} ${number}` : null;
63}
64
65/**
66 * A strain as a protocol carries it (`StoredStrain` in app/kb/procedures/render.mjs): the stated facts, none computed, so the
67 * protocol's page, twin and frozen versions name one strain.
68 *
69 * @param {import("./kinds.mjs").RegistryItem} item
70 * @returns {import("../procedures/render.mjs").StoredStrain}
71 */
72export function storedStrain(item) {
73  const f = /** @type {Record<string, unknown>} */ (item.fields);
74  return {
75    id: item.id,
76    name: item.name,
77    status: item.status,
78    organism: stated(f.organism),
79    strain: stated(f.strain),
80    collection: stated(f.collection),
81    collectionNumber: stated(f.collection_number),
82  };
83}