@graphty/graph-io 0.3.46 → 0.3.48

package/dist/sources-ndex.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"sources-ndex.js","sources":["../src/sources/ndex/client.ts","../src/sources/ndex/expand.ts","../src/sources/ndex/share-url.ts","../src/sources/ndex/index.ts"],"sourcesContent":["/**\n * What every NDEx call shares: the checks on the endpoint and the network UUID, and a fetch that\n * classifies NDEx's failures.\n */\n\nimport { failOn } from \"../fail.js\";\nimport { type SourceContext } from \"../types.js\";\n\n/** An NDEx network UUID. */\nconst UUID = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i;\n\n/** The query parameter NDEx reads a link-share access key from. */\nexport const ACCESS_KEY_QUERY = \"accesskey\";\n\n/** The statuses whose JSON body (NDEx's errorCode) is read; every other failure is classified by status alone. */\nconst READ_STATUSES = [401, 403, 404] as const;\n\n/**\n * Refuse an access key in the endpoint: it belongs in a credential, which is never logged.\n * @param ctx - the context\n */\nexport function checkEndpoint(ctx: SourceContext): void {\n    if (ctx.endpoint?.searchParams.has(ACCESS_KEY_QUERY) === true) {\n        failOn(ctx.report, \"E_SOURCE_PARAM\", \"an access key goes in a credential, never in the endpoint\", {\n            name: \"endpoint\",\n            reason: \"credentials-in-url\",\n        });\n    }\n}\n\n/**\n * Check a call's endpoint and network UUID.\n * @param uuid - the network UUID\n * @param ctx - the context\n * @returns the UUID, lowercase and URL-safe\n */\nexport function checkedUuid(uuid: unknown, ctx: SourceContext): string {\n    checkEndpoint(ctx);\n    const value = String(uuid);\n    if (/accesskey/i.test(value)) {\n        failOn(ctx.report, \"E_SOURCE_PARAM\", \"an access key goes in a credential, never in the uuid\", {\n            name: \"uuid\",\n            reason: \"credentials-in-url\",\n        });\n    }\n    if (!UUID.test(value)) {\n        failOn(ctx.report, \"E_SOURCE_PARAM\", \"the uuid is not a network UUID\", { name: \"uuid\", reason: \"format\" });\n    }\n    return value.toLowerCase();\n}\n\n/**\n * Fetch from NDEx, turning a 401, 403 or 404 into its coded error with NDEx's own errorCode.\n * @param ctx - the context\n * @param path - the path, relative to the endpoint\n * @param uuid - the network the request is about, for E_SOURCE_NOT_FOUND\n * @param init - the request init\n * @returns the response, status 2xx\n */\nexport async function ndexFetch(\n    ctx: SourceContext,\n    path: string,\n    uuid: string | null,\n    init: RequestInit & { readonly idempotent?: boolean } = {},\n): Promise<Response> {\n    const response = await ctx.fetch(path, { ...init, allowStatus: READ_STATUSES });\n    if (response.ok) {\n        return response;\n    }\n    const url = new URL(path, ctx.endpoint ?? undefined);\n    const serverCode = await errorCode(response);\n    const { status } = response;\n    if (status === 401) {\n        failOn(ctx.report, \"E_SOURCE_AUTH\", `NDEx answered ${String(status)}`, {\n            origin: url.origin,\n            status,\n            scheme: response.headers.get(\"www-authenticate\")?.split(/\\s/)[0] ?? null,\n            serverCode,\n        });\n    }\n    if (status === 403) {\n        failOn(ctx.report, \"E_SOURCE_FORBIDDEN\", \"NDEx answered 403\", { status, serverCode });\n    }\n    return failOn(ctx.report, \"E_SOURCE_NOT_FOUND\", \"NDEx has no such network\", {\n        what: uuid === null ? \"url\" : \"network\",\n        value: uuid ?? `${url.origin}${url.pathname}`,\n    });\n}\n\n/**\n * NDEx's own error code from a JSON error body, never its message or stack trace.\n * @param response - the failed response\n * @returns the code, or null\n */\nasync function errorCode(response: Response): Promise<string | null> {\n    try {\n        const body = (await response.json()) as { errorCode?: unknown };\n        return typeof body.errorCode === \"string\" ? body.errorCode.slice(0, 100) : null;\n    } catch {\n        return null;\n    }\n}\n","/**\n * The NDEx source's expand: NDEx's neighborhood query (`POST /v2/search/network/{uuid}/query`),\n * which answers CX1, read by the CX importer. Seeds are node ids, sent as `nodeIds`; NDEx's CX1\n * answer keeps the ids of the CX2 download (checked on 2026-10-17), so an expansion merges into a\n * loaded network by id. With `idAttribute`, seeds are values of that node attribute instead,\n * matched by NDEx's node search.\n */\n\nimport { type GraphSink } from \"@graphty/graph-format\";\n\nimport { cxImporter } from \"../../formats/cx/importer.js\";\nimport { type ImportReport } from \"../../types.js\";\nimport { failOn } from \"../fail.js\";\nimport { type ExpandRequest, type SourceContext } from \"../types.js\";\nimport { checkedUuid, ndexFetch } from \"./client.js\";\nimport { type NdexParams } from \"./params.js\";\n\n/** The deepest neighborhood asked for, as for every built-in source. */\nconst MAX_DEPTH = 10;\n\n/**\n * Quote a value for NDEx's search syntax.\n * @param value - the value\n * @returns the quoted term\n */\nfunction term(value: string): string {\n    const escaped = value.replaceAll(/[\"\\\\]/g, String.raw`\\$&`);\n    return `\"${escaped}\"`;\n}\n\n/**\n * The query body: the seeds as node ids, or as values of `idAttribute`.\n * @param request - the expand request\n * @param ctx - the context\n * @returns the body NDEx's query takes\n */\nfunction queryBody(request: ExpandRequest<NdexParams>, ctx: SourceContext): Record<string, unknown> {\n    const { ids } = request;\n    const { idAttribute } = request.params;\n    const depth = request.depth ?? 1;\n    if (!Number.isInteger(depth) || depth < 1 || depth > MAX_DEPTH) {\n        failOn(ctx.report, \"E_SOURCE_PARAM\", \"depth is an integer from 1 to 10\", { name: \"depth\", reason: \"range\" });\n    }\n    if (ids.length === 0) {\n        failOn(ctx.report, \"E_SOURCE_PARAM\", \"an expansion needs at least one id\", { name: \"ids\", reason: \"required\" });\n    }\n    const limit = request.limit === undefined ? {} : { edgeLimit: request.limit, errorWhenLimitIsOver: false };\n    if (idAttribute !== undefined) {\n        if (!/^[A-Za-z_][\\w.]*$/.test(idAttribute)) {\n            failOn(ctx.report, \"E_SOURCE_PARAM\", \"idAttribute is not an attribute name\", {\n                name: \"idAttribute\",\n                reason: \"identifier\",\n            });\n        }\n        const searchString = ids.map((id) => `${idAttribute}:${term(String(id))}`).join(\" \");\n        return { searchString, searchDepth: depth, ...limit };\n    }\n    const nodeIds = ids.map(Number);\n    if (nodeIds.some((n) => !Number.isSafeInteger(n))) {\n        failOn(ctx.report, \"E_SOURCE_PARAM\", \"NDEx node ids are integers; set idAttribute to seed by name\", {\n            name: \"ids\",\n            reason: \"type\",\n        });\n    }\n    return { searchString: \"\", searchDepth: depth, nodeIds, ...limit };\n}\n\n/**\n * Fetch the neighborhood of some nodes of an NDEx network into a sink.\n * @param request - the seeds, depth and limit; `limit` caps the edges NDEx returns\n * @param sink - where to write\n * @param ctx - the context\n * @returns the report\n */\nexport async function expandNdex(\n    request: ExpandRequest<NdexParams>,\n    sink: GraphSink,\n    ctx: SourceContext,\n): Promise<ImportReport> {\n    const uuid = checkedUuid(request.params.uuid, ctx);\n    if (request.direction !== undefined && request.direction !== \"both\") {\n        failOn(ctx.report, \"E_SOURCE_UNSUPPORTED\", \"NDEx expands in both directions only\", {\n            feature: \"direction\",\n            needs: \"both\",\n        });\n    }\n    if ((request.relationshipTypes ?? []).length > 0) {\n        failOn(ctx.report, \"E_SOURCE_UNSUPPORTED\", \"NDEx cannot filter an expansion by relationship type\", {\n            feature: \"relationshipTypes\",\n        });\n    }\n    const response = await ndexFetch(ctx, `v2/search/network/${uuid}/query`, uuid, {\n        method: \"POST\",\n        idempotent: true,\n        headers: { \"Content-Type\": \"application/json\", Accept: \"application/json\" },\n        body: JSON.stringify(queryBody(request, ctx)),\n    });\n    ctx.report.include(await cxImporter.import(response.body ?? \"\", sink, { signal: ctx.signal }));\n    return ctx.finish();\n}\n","/**\n * NDEx share links: a network's page or API URL, possibly carrying a link-share access key.\n */\n\nimport { credentials } from \"../credentials.js\";\nimport { failAlone } from \"../fail.js\";\nimport { NDEX_SOURCE_ID } from \"../ids.js\";\nimport { type Credential } from \"../types.js\";\nimport { ACCESS_KEY_QUERY } from \"./client.js\";\n\n/** A network UUID anywhere in a URL's path or hash. */\nconst UUID_IN_URL = /[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}/i;\n\n/**\n * What a share link says: the network, the NDEx server, and the access key as a credential.\n * Experimental.\n * @category Network sources\n */\nexport interface NdexShareLink {\n    /** The params to load the network with. */\n    readonly params: {\n        /** The network's NDEx id. */\n        readonly uuid: string;\n    };\n    /** The NDEx server the link points at (\"https://www.ndexbio.org/\"). */\n    readonly endpoint: string;\n    /** The link's access key, sent only to that server; absent when the link has none. */\n    readonly credential?: Credential | undefined;\n}\n\n/**\n * Read an NDEx share link (`https://www.ndexbio.org/viewer/networks/<uuid>?accesskey=<key>`, the\n * older `#/network/<uuid>` form, or an API URL). The access key leaves the URL and becomes a\n * credential bound to the link's server, so it is never logged or stored with the params.\n * Rejects with `E_SOURCE_PARAM` (`name: \"url\"`): `reason: \"format\"` when the text is not a URL\n * naming a network, `\"credentials-in-url\"` when it carries a user name or password. Experimental.\n * @param url - the link\n * @returns the params, endpoint and credential to load it with\n * @example\n * ```ts\n * const link = parseShareUrl(sharedUrl);\n * const { snapshot } = await loadFromSource(\"ndex\", link.params, {\n *     endpoint: link.endpoint,\n *     credential: link.credential,\n * });\n * ```\n * @category Network sources\n */\nexport function parseShareUrl(url: string | URL): NdexShareLink {\n    let parsed: URL;\n    try {\n        parsed = new URL(url);\n    } catch {\n        return refuse(\"format\");\n    }\n    if (parsed.username !== \"\" || parsed.password !== \"\") {\n        return refuse(\"credentials-in-url\");\n    }\n    // the older viewer keeps the network and its key in the hash\n    const hash = new URL(parsed.hash.replace(/^#/, \"\"), \"https://hash.invalid/\");\n    const uuid = UUID_IN_URL.exec(`${parsed.pathname} ${hash.pathname}`)?.[0];\n    if (uuid === undefined || (parsed.protocol !== \"https:\" && parsed.protocol !== \"http:\")) {\n        return refuse(\"format\");\n    }\n    // the bare host redirects to www without CORS headers, so a page cannot follow it\n    const host = parsed.host.toLowerCase() === \"ndexbio.org\" ? \"www.ndexbio.org\" : parsed.host;\n    const endpoint = `${parsed.protocol}//${host}/`;\n    const key = parsed.searchParams.get(ACCESS_KEY_QUERY) ?? hash.searchParams.get(ACCESS_KEY_QUERY);\n    const params = { uuid: uuid.toLowerCase() };\n    if (key === null || key === \"\") {\n        return { params, endpoint };\n    }\n    const credential = credentials.apiKey({ query: ACCESS_KEY_QUERY }, key, { origins: [new URL(endpoint).origin] });\n    return { params, endpoint, credential };\n}\n\n/**\n * Reject a share link.\n * @param reason - why\n * @returns never\n */\nfunction refuse(reason: \"format\" | \"credentials-in-url\"): never {\n    return failAlone(\"E_SOURCE_PARAM\", \"not an NDEx share link\", { name: \"url\", reason }, `source:${NDEX_SOURCE_ID}`);\n}\n","/**\n * `@graphty/graph-io/sources/ndex`: the NDEx source (design section 12.1). Experimental.\n *\n * - load: the network's summary first (counts, download size, modification time), checked against\n *   the caps before a byte of the network is read; then the CX2 (or CX) download, streamed into\n *   the CX2 (or CX) importer.\n * - probe: the summary. list: NDEx's v2 network search. validate: the summary's modificationTime.\n * - expand: NDEx's neighborhood query (`expand.ts`).\n *\n * Errors are classified by status; a body is read only from a 401, 403 or 404 (NDEx's own\n * `errorCode`, passed through as `serverCode`), so a 500 with a Java stack trace never reaches a\n * report.\n * @module @graphty/graph-io/sources/ndex\n */\n\nimport { defineSource } from \"../define.js\";\nimport { failOn } from \"../fail.js\";\nimport { NDEX_SOURCE_ID } from \"../ids.js\";\nimport {\n    type GraphSource,\n    type SourceContext,\n    type SourceFreshness,\n    type SourceListing,\n    type SourceListQuery,\n    type SourceProbe,\n    type SourceValidators,\n} from \"../types.js\";\nimport { checkedUuid, checkEndpoint, ndexFetch } from \"./client.js\";\nimport { NDEX_DESCRIPTOR } from \"./descriptor.js\";\nimport { expandNdex } from \"./expand.js\";\nimport { type NdexParams } from \"./params.js\";\n\nexport { NDEX_DESCRIPTOR } from \"./descriptor.js\";\nexport { type NdexParams } from \"./params.js\";\nexport { type NdexShareLink, parseShareUrl } from \"./share-url.js\";\n\n/** The fields of a network summary this source reads. */\ninterface NdexSummary {\n    readonly nodeCount?: number;\n    readonly edgeCount?: number;\n    readonly cxFileSize?: number;\n    readonly cx2FileSize?: number;\n    readonly modificationTime?: number;\n    readonly creationTime?: number;\n    readonly visibility?: string;\n    readonly properties?: Readonly<Record<string, { readonly v?: unknown } | undefined>>;\n}\n\n/** One network of a v2 search answer. */\ninterface NdexSearchHit {\n    readonly externalId?: string;\n    readonly name?: string;\n    readonly nodeCount?: number;\n    readonly edgeCount?: number;\n    readonly modificationTime?: number;\n}\n\n/**\n * Read a network's summary.\n * @param uuid - the checked UUID\n * @param ctx - the context\n * @returns the summary and the bytes it took\n */\nasync function readSummary(uuid: string, ctx: SourceContext): Promise<{ summary: NdexSummary; bytes: number }> {\n    const response = await ndexFetch(ctx, `v3/networks/${uuid}/summary`, uuid, {\n        headers: { Accept: \"application/json\" },\n    });\n    const text = await response.text();\n    try {\n        return { summary: JSON.parse(text) as NdexSummary, bytes: new TextEncoder().encode(text).byteLength };\n    } catch {\n        return failOn(ctx.report, \"E_SOURCE_RESPONSE\", \"the NDEx summary is not JSON\", {\n            expected: \"json\",\n            contentType: response.headers.get(\"content-type\"),\n        });\n    }\n}\n\n/**\n * An NDEx time (epoch milliseconds) as an ISO string.\n * @param ms - the time\n * @returns the ISO string, or undefined\n */\nfunction iso(ms: number | undefined): string | undefined {\n    return typeof ms === \"number\" && Number.isFinite(ms) ? new Date(ms).toISOString() : undefined;\n}\n\n/**\n * The download size the summary gives for a format.\n * @param summary - the summary\n * @param format - \"cx2\" or \"cx\"\n * @returns the size in bytes, or undefined\n */\nfunction sizeOf(summary: NdexSummary, format: string): number | undefined {\n    return format === \"cx\" ? summary.cxFileSize : summary.cx2FileSize;\n}\n\n/**\n * Stop the load before its first byte when the summary says a cap would cut it: a network file cut\n * short is not a graph, so this is E_SOURCE_LIMIT under either `onLimit`.\n * @param summary - the summary\n * @param format - the download format\n * @param ctx - the context\n */\nfunction checkCaps(summary: NdexSummary, format: string, ctx: SourceContext): void {\n    const caps: [string, number | undefined, number | undefined][] = [\n        [\"maxNodes\", summary.nodeCount, ctx.limits.maxNodes],\n        [\"maxEdges\", summary.edgeCount, ctx.limits.maxEdges],\n        [\"maxBytes\", sizeOf(summary, format), ctx.limits.maxBytes],\n    ];\n    for (const [limit, value, cap] of caps) {\n        if (value !== undefined && cap !== undefined && value > cap) {\n            failOn(ctx.report, \"E_SOURCE_LIMIT\", `the network's ${limit} of ${String(value)} is over the cap`, {\n                limit,\n                value,\n            });\n        }\n    }\n}\n\n/**\n * The graph facts a summary adds: when it changed, and who may use it.\n * @param summary - the summary\n * @returns the facts\n */\nfunction metaOf(summary: NdexSummary): Record<string, string> {\n    const meta: Record<string, string> = {};\n    const modified = iso(summary.modificationTime);\n    if (modified !== undefined) {\n        meta.modified = modified;\n    }\n    if (typeof summary.visibility === \"string\") {\n        meta.visibility = summary.visibility;\n    }\n    for (const key of [\"rights\", \"rightsHolder\"]) {\n        const value = summary.properties?.[key]?.v;\n        if (typeof value === \"string\") {\n            meta[key] = value;\n        }\n    }\n    return meta;\n}\n\n/**\n * The validators of a summary.\n * @param summary - the summary\n * @returns `{ modified }` when NDEx gave a modification time\n */\nfunction validatorsOf(summary: NdexSummary): SourceValidators {\n    const modified = iso(summary.modificationTime);\n    return modified === undefined ? {} : { modified };\n}\n\n/**\n * The NDEx source. Experimental.\n * @category Network sources\n */\nexport const ndexSource: GraphSource<NdexParams> = defineSource<NdexParams>({\n    id: NDEX_SOURCE_ID,\n    descriptor: NDEX_DESCRIPTOR,\n    async file(params, ctx) {\n        const uuid = checkedUuid(params.uuid, ctx);\n        const format = params.format ?? \"cx2\";\n        const { summary, bytes } = await readSummary(uuid, ctx);\n        checkCaps(summary, format, ctx);\n        const size = sizeOf(summary, format);\n        // progress counts every byte read, the summary's included\n        ctx.progress(bytes, size === undefined ? undefined : bytes + size, \"bytes\");\n        // records the validators in report.source; the file path keeps them\n        ctx.finish({ validators: validatorsOf(summary) });\n        const path = format === \"cx\" ? `v2/network/${uuid}` : `v3/networks/${uuid}`;\n        const body = await ndexFetch(ctx, path, uuid);\n        return { body, format, meta: metaOf(summary) };\n    },\n    async probe(params, ctx): Promise<SourceProbe> {\n        const uuid = checkedUuid(params.uuid, ctx);\n        const { summary } = await readSummary(uuid, ctx);\n        return {\n            ok: true,\n            counts: {\n                nodes: summary.nodeCount,\n                edges: summary.edgeCount,\n                bytes: sizeOf(summary, params.format ?? \"cx2\"),\n            },\n        };\n    },\n    async list(query: SourceListQuery<NdexParams>, ctx): Promise<SourceListing> {\n        checkEndpoint(ctx);\n        const start = Number(query.cursor?.start ?? 0);\n        const size = query.size ?? 25;\n        const body = await ctx.fetchJson<{ networks?: unknown; numFound?: unknown }>(\n            `v2/search/network?start=${String(start)}&size=${String(size)}`,\n            {\n                method: \"POST\",\n                idempotent: true,\n                headers: { \"Content-Type\": \"application/json\" },\n                body: JSON.stringify({ searchString: query.search ?? \"\" }),\n            },\n        );\n        const networks = Array.isArray(body.networks)\n            ? (body.networks as readonly NdexSearchHit[])\n            : failOn(ctx.report, \"E_SOURCE_RESPONSE\", \"the NDEx search answer has no networks\", {\n                  expected: \"ndex-search\",\n                  contentType: \"application/json\",\n              });\n        const { numFound } = body;\n        const items = networks.flatMap((n) =>\n            typeof n.externalId === \"string\"\n                ? [\n                      {\n                          params: { uuid: n.externalId },\n                          name: n.name ?? n.externalId,\n                          nodeCount: n.nodeCount,\n                          edgeCount: n.edgeCount,\n                          modified: iso(n.modificationTime),\n                      },\n                  ]\n                : [],\n        );\n        const total = typeof numFound === \"number\" ? numFound : undefined;\n        const more = total === undefined ? networks.length === size : start + networks.length < total;\n        return { items, next: more && networks.length > 0 ? { start: start + networks.length } : null, total };\n    },\n    async validate(params, seen, ctx): Promise<SourceFreshness> {\n        const uuid = checkedUuid(params.uuid, ctx);\n        const validators = validatorsOf((await readSummary(uuid, ctx)).summary);\n        if (seen.modified === undefined || validators.modified === undefined) {\n            return { status: \"unverifiable\", validators };\n        }\n        return seen.modified === validators.modified\n            ? { status: \"current\", via: \"modified\", validators }\n            : { status: \"changed\", via: \"modified\", changedAt: validators.modified, validators };\n    },\n    expand: 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package/dist/sources-rest.d.ts

@@ -0,0 +1 @@
+export * from "./src/sources/rest/index.js";