import path from "path"import fs from "fs/promises"import z from "zod"import { Global } from "../global"import { Log } from "../util/log" // Outbound domain allow-list. A catalog of curated science-connector domain// sets (each toggleable as a group) plus a free-form list of custom domains.// Persisted as a single JSON document under the ~/.openscience data dir and readable// by the backend via `Network.allowlist()`.export namespace Network { const log = Log.create({ service: "settings.network" }) export const Group = z.object({ id: z.string(), label: z.string(), description: z.string(), domains: z.array(z.string()), }) export type Group = z.infer<typeof Group> // Curated groups wired to the science connectors the agents actually reach. export const CATALOG: Group[] = [ { id: "package-management", label: "Package management", description: "Python, R, JS, Rust package indexes and source hosting.", domains: [ "pypi.org", "files.pythonhosted.org", "registry.npmjs.org", "conda.anaconda.org", "cran.r-project.org", "crates.io", "github.com", "raw.githubusercontent.com", "objects.githubusercontent.com", ], }, { id: "ncbi-nih", label: "NCBI / NIH", description: "PubMed, Entrez E-utilities, and NIH data services.", domains: [ "ncbi.nlm.nih.gov", "www.ncbi.nlm.nih.gov", "eutils.ncbi.nlm.nih.gov", "pubmed.ncbi.nlm.nih.gov", "ftp.ncbi.nlm.nih.gov", "nih.gov", ], }, { id: "genomics-biology", label: "Genomics & biology", description: "Ensembl, UCSC Genome Browser, and EBI resources.", domains: [ "ensembl.org", "rest.ensembl.org", "ucsc.edu", "genome.ucsc.edu", "genome-euro.ucsc.edu", "ebi.ac.uk", "www.ebi.ac.uk", ], }, { id: "proteomics", label: "Proteomics", description: "UniProt, RCSB PDB, and AlphaFold structure services.", domains: [ "uniprot.org", "rest.uniprot.org", "rcsb.org", "files.rcsb.org", "alphafold.ebi.ac.uk", "www.ebi.ac.uk", ], }, { id: "literature-citations", label: "Literature & citations", description: "Preprint servers, Semantic Scholar, Crossref, and DOIs.", domains: [ "arxiv.org", "biorxiv.org", "medrxiv.org", "semanticscholar.org", "api.semanticscholar.org", "crossref.org", "api.crossref.org", "doi.org", "europepmc.org", ], }, { id: "clinical-pharma", label: "Clinical & pharma", description: "Clinical trials, drug databases, and regulatory agencies.", domains: ["clinicaltrials.gov", "go.drugbank.com", "fda.gov", "api.fda.gov", "who.int", "ema.europa.eu"], }, ] export const State = z.object({ // When false the allow-list is advisory only (agent may reach any domain). allowlistEnabled: z.boolean(), // Enabled catalog group ids. enabled: z.array(z.string()), // Custom user-added domains. custom: z.array(z.string()), }) export type State = z.infer<typeof State> const file = path.join(Global.Path.data, "settings", "network.json") function defaultState(): State { return { allowlistEnabled: false, enabled: ["package-management"], custom: [] } } export async function get(): Promise<State> { const text = await Bun.file(file) .text() .catch(() => undefined) if (!text) return defaultState() try { const parsed = State.safeParse(JSON.parse(text)) if (parsed.success) return parsed.data } catch (e) { log.error("failed to parse network state", { error: e }) } return defaultState() } export async function set(state: State): Promise<State> { await fs.mkdir(path.dirname(file), { recursive: true }) await Bun.write(file, JSON.stringify(state, null, 2)) return state } // Effective flat list of allowed domains (enabled groups ∪ custom). Readable // by any backend caller that wants to gate outbound access. export async function allowlist(): Promise<string[]> { const state = await get() const domains = new Set<string>(state.custom.map((d) => d.trim()).filter(Boolean)) for (const group of CATALOG) { if (!state.enabled.includes(group.id)) continue for (const domain of group.domains) domains.add(domain) } return [...domains].sort() }}
import path from "path"
import fs from "fs/promises"
import z from "zod"
import { Global } from "../global"
import { Log } from "../util/log"
// Outbound domain allow-list. A catalog of curated science-connector domain
// sets (each toggleable as a group) plus a free-form list of custom domains.
// Persisted as a single JSON document under the ~/.openscience data dir and readable
// by the backend via `Network.allowlist()`.
export namespace Network {
const log = Log.create({ service: "settings.network" })
export const Group = z.object({
id: z.string(),
label: z.string(),
description: z.string(),
domains: z.array(z.string()),
})
export type Group = z.infer<typeof Group>
// Curated groups wired to the science connectors the agents actually reach.
export const CATALOG: Group[] = [
{
id: "package-management",
label: "Package management",
description: "Python, R, JS, Rust package indexes and source hosting.",
domains: [
"pypi.org",
"files.pythonhosted.org",
"registry.npmjs.org",
"conda.anaconda.org",
"cran.r-project.org",
"crates.io",
"github.com",
"raw.githubusercontent.com",
"objects.githubusercontent.com",
],
},
{
id: "ncbi-nih",
label: "NCBI / NIH",
description: "PubMed, Entrez E-utilities, and NIH data services.",
domains: [
"ncbi.nlm.nih.gov",
"www.ncbi.nlm.nih.gov",
"eutils.ncbi.nlm.nih.gov",
"pubmed.ncbi.nlm.nih.gov",
"ftp.ncbi.nlm.nih.gov",
"nih.gov",
],
},
{
id: "genomics-biology",
label: "Genomics & biology",
description: "Ensembl, UCSC Genome Browser, and EBI resources.",
domains: [
"ensembl.org",
"rest.ensembl.org",
"ucsc.edu",
"genome.ucsc.edu",
"genome-euro.ucsc.edu",
"ebi.ac.uk",
"www.ebi.ac.uk",
],
},
{
id: "proteomics",
label: "Proteomics",
description: "UniProt, RCSB PDB, and AlphaFold structure services.",
domains: [
"uniprot.org",
"rest.uniprot.org",
"rcsb.org",
"files.rcsb.org",
"alphafold.ebi.ac.uk",
"www.ebi.ac.uk",
],
},
{
id: "literature-citations",
label: "Literature & citations",
description: "Preprint servers, Semantic Scholar, Crossref, and DOIs.",
domains: [
"arxiv.org",
"biorxiv.org",
"medrxiv.org",
"semanticscholar.org",
"api.semanticscholar.org",
"crossref.org",
"api.crossref.org",
"doi.org",
"europepmc.org",
],
},
{
id: "clinical-pharma",
label: "Clinical & pharma",
description: "Clinical trials, drug databases, and regulatory agencies.",
domains: ["clinicaltrials.gov", "go.drugbank.com", "fda.gov", "api.fda.gov", "who.int", "ema.europa.eu"],
},
]
export const State = z.object({
// When false the allow-list is advisory only (agent may reach any domain).
allowlistEnabled: z.boolean(),
// Enabled catalog group ids.
enabled: z.array(z.string()),
// Custom user-added domains.
custom: z.array(z.string()),
})
export type State = z.infer<typeof State>
const file = path.join(Global.Path.data, "settings", "network.json")
function defaultState(): State {
return { allowlistEnabled: false, enabled: ["package-management"], custom: [] }
}
export async function get(): Promise<State> {
const text = await Bun.file(file)
.text()
.catch(() => undefined)
if (!text) return defaultState()
try {
const parsed = State.safeParse(JSON.parse(text))
if (parsed.success) return parsed.data
} catch (e) {
log.error("failed to parse network state", { error: e })
}
return defaultState()
}
export async function set(state: State): Promise<State> {
await fs.mkdir(path.dirname(file), { recursive: true })
await Bun.write(file, JSON.stringify(state, null, 2))
return state
}
// Effective flat list of allowed domains (enabled groups ∪ custom). Readable
// by any backend caller that wants to gate outbound access.
export async function allowlist(): Promise<string[]> {
const state = await get()
const domains = new Set<string>(state.custom.map((d) => d.trim()).filter(Boolean))
for (const group of CATALOG) {
if (!state.enabled.includes(group.id)) continue
for (const domain of group.domains) domains.add(domain)
}
return [...domains].sort()
}
}