app/routes/lab[.md].ts

Functions

Imports

It imports app/db/phages.ts, app/db/procedures.ts, app/db/registry.ts, app/kb/registry/catalog.mjs, app/kb/registry/route.ts, app/lib/context.ts, app/lib/markdown-twin.ts, app/lib/seo.ts. No module of this repo imports it.

Source

1import { listPhages } from "~/db/phages";
2import { listPublishedLibraryRecords } from "~/db/procedures";
3import { listRegistry } from "~/db/registry";
4import { getEnv } from "~/lib/context";
5import { canonicalLink } from "~/lib/markdown-twin";
6import {
7  LAB_PATH,
8  inventoryMarkdown,
9  inventoryRows,
10  itemPath,
11  kindFromSegment,
12  kindPath,
13  primerMarkdown,
14  primerRow,
15  primerRows,
16  primersMarkdown,
17  protocolsUsing,
18  protocolsUsingStrain,
19  equipmentItemMarkdown,
20  equipmentMarkdown,
21  equipmentRows,
22  reagentItemMarkdown,
23  reagentRows,
24  reagentsMarkdown,
25  strainMarkdown,
26  strainRows,
27  strainsMarkdown,
28  tmNote,
29} from "~/kb/registry/catalog.mjs";
30import { LAB_CACHE_TAGS } from "~/kb/registry/route";
31import { SHARED_CACHE_CONTROL, SITE_ORIGIN } from "~/lib/seo";
32
33import type { Route } from "./+types/lab[.md]";
34
35/**
36 * The registry's markdown twins: /research/lab.md, /research/lab/primers.md and /research/lab/primers/<id>.md, drawn from
37 * the same rows as the pages, so an agent reads the facts a person does. One module for the three addresses; each route
38 * entry names it, and the params say which. Published items only: a draft has no twin.
39 */
40export async function loader({ params, context }: Route.LoaderArgs) {
41  const env = getEnv(context);
42  const { kind: segment, id } = params as { kind?: string; id?: string };
43  const notFound = () => new Response("Not found\n", { status: 404, headers: { "content-type": "text/plain; charset=utf-8" } });
44  const respond = (body: string, canonical: string) =>
45    new Response(body, {
46      headers: {
47        "content-type": "text/markdown; charset=utf-8",
48        "cache-control": SHARED_CACHE_CONTROL,
49        "cache-tag": LAB_CACHE_TAGS,
50        "x-robots-tag": "noindex",
51        link: canonicalLink(canonical),
52      },
53    });
54
55  if (segment === undefined) {
56    const [items, phages] = await Promise.all([listRegistry(env, { published: true }), listPhages(env)]);
57    const rows = inventoryRows(items, phages);
58    return respond(
59      `# Lab registry\n\nThe lab's reference catalog, with the phages it has isolated. It records what a thing is, never how much of it the lab has or where it sits.\n\n${inventoryMarkdown(rows, SITE_ORIGIN)}\n`,
60      LAB_PATH,
61    );
62  }
63
64  const kind = kindFromSegment(segment);
65  if (kind !== "primer" && kind !== "strain" && kind !== "reagent" && kind !== "equipment") return notFound();
66  const published = await listRegistry(env, { kind, published: true });
67
68  if (kind === "equipment") {
69    const items = equipmentRows(published, await listPublishedLibraryRecords(env));
70    if (id !== undefined) {
71      const item = items.find((e) => e.id === id);
72      return item ? respond(equipmentItemMarkdown(item, SITE_ORIGIN), itemPath(kind, item.id)) : notFound();
73    }
74    return respond(
75      `# Equipment\n\nThe instruments and labware the lab's protocols list under Equipment, in one table. Each row lists the protocols that use it.\n\n${equipmentMarkdown(items, SITE_ORIGIN)}\n`,
76      kindPath(kind),
77    );
78  }
79
80  if (kind === "reagent") {
81    const reagents = reagentRows(published, await listPublishedLibraryRecords(env));
82    if (id !== undefined) {
83      const reagent = reagents.find((r) => r.id === id);
84      return reagent ? respond(reagentItemMarkdown(reagent, SITE_ORIGIN), itemPath(kind, reagent.id)) : notFound();
85    }
86    return respond(
87      `# Reagents\n\nThe substances the lab's protocols use, in one table. A reagent is bought (supplier and catalog number) or prepared in the lab (a recipe); each row lists the protocols that use it.\n\n${reagentsMarkdown(reagents, SITE_ORIGIN)}\n`,
88      kindPath(kind),
89    );
90  }
91
92  if (kind === "strain") {
93    const strains = strainRows(published, await listPhages(env));
94    if (id === undefined) {
95      return respond(
96        `# Strains\n\nThe bacterial hosts the lab's phages are isolated on. Each strain's phages are counted from the phages table.\n\n${strainsMarkdown(strains, SITE_ORIGIN)}\n`,
97        kindPath(kind),
98      );
99    }
100    const strain = strains.find((s) => s.id === id);
101    if (!strain) return notFound();
102    const usedBy = protocolsUsingStrain(strain, await listPublishedLibraryRecords(env));
103    return respond(strainMarkdown(strain, usedBy, SITE_ORIGIN), itemPath(kind, strain.id));
104  }
105
106  const primers = published.map(primerRow);
107
108  if (id === undefined) {
109    return respond(
110      `# Primers\n\nThe primers the lab's protocols use, with each sequence as stored. Length, GC content and melting temperature are computed from the sequence, and a pair's product is computed from where its primers bind a reference sequence.\n\n${primersMarkdown(primerRows(published), SITE_ORIGIN)}\n\n${tmNote().statement} ${tmNote().annealing}\n`,
111      kindPath(kind),
112    );
113  }
114
115  const primer = primers.find((p) => p.id === id);
116  if (!primer) return notFound();
117  const usedBy = protocolsUsing(primer, await listPublishedLibraryRecords(env));
118  return respond(primerMarkdown(primer, primers, usedBy, SITE_ORIGIN), itemPath(kind, primer.id));
119}