app/kb/procedures/primer-dependents.server.ts

Functions

Imports

It imports app/kb/procedures/parse.mjs, app/kb/procedures/save.server.ts, app/lib/cache-purge.server.ts, app/lib/editor/github.server.ts. Imported by app/kb/registry/save.server.ts, app/lib/operator/sync-tools.server.ts.

Source

1// The protocols that print a registry primer, or name a registry strain, carry its facts in their record (compile.mjs), so a
2// change to one must reach them. A registry save and sync_registry call this after the primer's own row is written: each protocol that names
3// a changed primer is recompiled from its file, which reads the primer again, and its row and search records are
4// rewritten through the one write door a procedure save uses. Nothing here reads D1's primer row: the repository is the
5// source, so a primer edited through git and a primer saved through Carrel converge the same way.
6//
7// A protocol that no longer compiles with the new primer (the primer was deleted, or made a draft) stops the refresh and
8// the error names it, so the registry never reports success over a protocol it left reading the old sequence.
9
10import { purgeProcedures } from "~/lib/cache-purge.server";
11import { readFile } from "~/lib/editor/github.server";
12
13import { procedurePath } from "./parse.mjs";
14import { compile, writeRow } from "./save.server";
15
16type ProcedureEnv = Env & { GITHUB_TOKEN?: string };
17
18/** The record field each kind's items are named in. */
19const NAMED_IN = {
20  primer: [{ field: "$.primers", id: "$.id" }],
21  // The organism list is the ids themselves.
22  strain: [
23    { field: "$.hostStrains", id: "$.id" },
24    { field: "$.organisms", id: null },
25  ],
26  reagent: [{ field: "$.materials", id: "$.reagent.id" }],
27  equipment: [{ field: "$.equipment", id: "$.item.id" }],
28} as const;
29export type NamedKind = keyof typeof NAMED_IN;
30
31/** The slugs of the procedures whose stored record names one of these items (of these kinds), or any item of the kinds when `ids` is null. */
32async function procedureSlugsNaming(env: ProcedureEnv, ids: string[] | null, kinds: NamedKind[] = ["primer"]): Promise<string[]> {
33  const wanted = ids === null ? null : new Set(ids);
34  const slugs = new Set<string>();
35  for (const kind of kinds) {
36    for (const { field, id } of NAMED_IN[kind]) {
37      // A list of items has the id inside each (at the path given); a list of ids is the ids themselves.
38      const rows = await env.DB.prepare(
39        `SELECT DISTINCT p.slug AS slug, CASE WHEN ?2 IS NULL THEN j.value ELSE json_extract(j.value, ?2) END AS item
40         FROM procedures p, json_each(json_extract(p.record, ?1)) j`,
41      )
42        .bind(field, id)
43        .all<{ slug: string; item: string }>();
44      for (const row of rows.results ?? []) if (wanted === null || wanted.has(row.item)) slugs.add(row.slug);
45    }
46  }
47  return [...slugs];
48}
49
50/** Recompiles and rewrites every protocol that names one of these items (null: every protocol that names any item of the kinds). */
51export async function refreshProceduresNaming(env: ProcedureEnv, ids: string[] | null, kinds: NamedKind[] = ["primer"]): Promise<string[]> {
52  const slugs = await procedureSlugsNaming(env, ids, kinds);
53  for (const slug of slugs) {
54    const file = await readFile(env, procedurePath(slug));
55    if (!file) throw new Error(`the protocol ${slug} names a registry item but has no file (${procedurePath(slug)}), so it was not refreshed`);
56    const compiled = await compile(env, slug, file.content);
57    if (!compiled.ok) {
58      throw new Error(
59        `the protocol ${slug} no longer compiles with the registry as it now stands, so it was not refreshed: ${compiled.errors.join("; ")}`,
60      );
61    }
62    await writeRow(env, compiled);
63  }
64  if (slugs.length > 0) await purgeProcedures(`registry refresh ${slugs.join(", ")}`);
65  return slugs;
66}