@inflexa-ai/harness 0.48.4 → 0.48.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/agents/conversation-agent.js +5 -1
- package/dist/agents/sandbox/network-agent.js +1 -1
- package/dist/agents/sandbox/shared.js +3 -1
- package/dist/agents/sandbox/types.d.ts +1 -1
- package/dist/execution/run-event-stream.d.ts +2 -2
- package/dist/loop/chat-stream.d.ts +4 -1
- package/dist/loop/chat-stream.js +30 -13
- package/dist/prompts/sandbox/network-agent.d.ts +1 -1
- package/dist/prompts/sandbox/network-agent.js +4 -0
- package/dist/providers/errors.js +2 -1
- package/dist/tools/bio/humanbase.d.ts +32 -0
- package/dist/tools/bio/humanbase.js +180 -0
- package/dist/tools/bio/index.d.ts +3 -1
- package/dist/tools/bio/index.js +3 -1
- package/dist/tools/bio/resolve-gene-ids.d.ts +13 -0
- package/dist/tools/bio/resolve-gene-ids.js +67 -0
- package/dist/tools/lib/humanbase-client.d.ts +215 -0
- package/dist/tools/lib/humanbase-client.js +187 -0
- package/dist/tools/lib/mygene-client.d.ts +150 -0
- package/dist/tools/lib/mygene-client.js +109 -0
- package/dist/tools/script/run-script.js +48 -51
- package/package.json +1 -1
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@@ -20,7 +20,6 @@ import { z } from "zod";
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import { createSubAgentActivityTracker } from "../../contracts/subagent-activity.js";
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import { createNoopLogger } from "../../lib/console-logger.js";
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import { parseJsonAs } from "../../lib/parse-json.js";
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import { parseUnknownRecord, UnknownArraySchema } from "../../lib/unknown-containers.js";
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import { computeDetail, computeResultDetail } from "../../loop/tool-detail.js";
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import { buildFileReferenceCardData, MAX_FILES } from "../../memory/card-builders.js";
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import { defineTool, readToolCallRecord, readToolResultImages, withToolCallRecord, } from "../define-tool.js";
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@@ -59,8 +58,8 @@ function bounded(text) {
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function plainJson(value) {
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return value === undefined ? null : parseJsonAs(JSON.stringify(value), z.json());
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}
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function describeTool(tool) {
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return renderToolSample({ name: tool.id, description: tool.description, inputSchema:
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function describeTool(tool, schemas) {
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return renderToolSample({ name: tool.id, description: tool.description, inputSchema: schemas.input, outputSchema: schemas.output });
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}
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function issuesOf(error) {
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return error.issues.map((issue) => `${issue.path.join(".") || "input"}: ${issue.message}`).join("; ");
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@@ -129,12 +128,12 @@ function collectEffect(state, value) {
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* The script gets the JSON of a result, and the JSON has no pictures. Thus a result with pictures is a failed call: the
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* script would otherwise read the result as complete.
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*/
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function scriptToolOf(tool, ctx, state, log, inCallContext) {
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function scriptToolOf(tool, schemas, ctx, state, log, inCallContext) {
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return {
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name: tool.id,
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description: tool.description,
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inputSchema:
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outputSchema:
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inputSchema: schemas.input,
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outputSchema: schemas.output,
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execute: (args, options) => inCallContext(() => runNestedCall(tool, ctx, state, log, args, options.signal)),
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};
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}
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@@ -187,56 +186,54 @@ async function runNestedCall(tool, ctx, state, log, args, signal) {
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await finish("ok", computeResultDetail(tool, parsed.data, result.value, log) ?? detail);
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return plainJson(result.value);
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}
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/** A JSON schema without its prose: the types and the constraints stay, the descriptions and the examples go. */
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function withoutProse(schema) {
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const array = UnknownArraySchema.safeParse(schema);
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if (array.success)
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return array.data.map(withoutProse);
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const record = parseUnknownRecord(schema);
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if (record === undefined)
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return schema;
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return Object.fromEntries(Object.entries(record)
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.filter(([key]) => key !== "description" && key !== "examples")
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.map(([key, value]) => [key, withoutProse(value)]));
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}
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/**
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*
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* permissive (`add_block` does, thus a malformed block reaches its typed refusal). The type of such a
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* `unknown`, which hides the real shape, thus the empty member goes. The VM only renders the schema and
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* nothing, and the tool still parses each input with its own schema.
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* Shape one node of a JSON schema for a script. A tool can union its real shape with the empty schema to keep its
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* runtime parse permissive (`add_block` does, thus a malformed block reaches its typed refusal). The type of such a
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* union is `unknown`, which hides the real shape, thus the empty member goes. The VM only renders the schema and
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* validates nothing, and the tool still parses each input with its own schema. Without prose, the `description` and the
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* `examples` of the node go too. Zod calls this for each schema node and never for a field name, thus a field with the
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* name `description` stays.
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*/
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function
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const members = UnknownArraySchema.safeParse(out[key]);
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if (!members.success)
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continue;
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const shaped = members.data.filter((member) => Object.keys(parseUnknownRecord(member) ?? {}).length > 0);
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if (shaped.length === 0 || shaped.length === members.data.length)
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continue;
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const rest = Object.fromEntries(Object.entries(out).filter(([name]) => name !== key));
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out = shaped.length > 1 ? { ...rest, [key]: shaped } : { ...rest, ...parseUnknownRecord(shaped[0]) };
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function shapeForScript(jsonSchema, prose) {
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if (!prose) {
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delete jsonSchema.description;
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delete jsonSchema.examples;
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}
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const anyOf = shapedMembers(jsonSchema.anyOf);
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if (anyOf !== undefined) {
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delete jsonSchema.anyOf;
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Object.assign(jsonSchema, anyOf.length > 1 ? { anyOf } : anyOf[0]);
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}
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const oneOf = shapedMembers(jsonSchema.oneOf);
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if (oneOf !== undefined) {
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delete jsonSchema.oneOf;
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Object.assign(jsonSchema, oneOf.length > 1 ? { oneOf } : oneOf[0]);
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}
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}
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/** The members of a union that are not the empty schema, or `undefined` when the union keeps each member. */
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function shapedMembers(members) {
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if (members === undefined)
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return undefined;
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const shaped = members.filter((member) => Object.keys(member).length > 0);
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return shaped.length === 0 || shaped.length === members.length ? undefined : shaped;
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}
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/** The
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function
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/** The schemas of a tool as a script reads them, built with the same options as the schemas of {@link defineTool}. */
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function scriptSchemasOf(tool, prose) {
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const override = ({ jsonSchema }) => shapeForScript(jsonSchema, prose);
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const { $schema: _inputDialect, ...input } = z.toJSONSchema(tool.inputSchema, { override });
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if (tool.outputSchema === undefined)
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return { input };
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const { $schema: _outputDialect, ...output } = z.toJSONSchema(tool.outputSchema, { io: "output", unrepresentable: "any", override });
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return { input, output };
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}
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/** The longest result type that the catalog shows. A longer type shows as `unknown`, and `describe()` gives it whole. */
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const MAX_CATALOG_RESULT_TYPE_CHARS = 800;
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/** One catalog entry: the first sentence of the description, then the signature with no prose. */
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function catalogEntry(tool) {
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const
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const { input, output } = scriptSchemasOf(tool, false);
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const resultType = output === undefined ? "unknown" : schemaToType(output, { maxChars: MAX_CATALOG_RESULT_TYPE_CHARS });
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// pi renders a signature with no result schema as `...: Promise<unknown>;`, thus the catalog puts its capped type there.
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const untyped = renderToolSignature({ name: tool.id, inputSchema:
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const untyped = renderToolSignature({ name: tool.id, inputSchema: input });
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const signature = `${untyped.slice(0, -"unknown>;".length)}${resultType}>;`;
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return `/** ${firstSentence(tool.description)} */\n${signature}`;
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}
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/** The `run_script` tool over the script tools of an agent. */
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export function createRunScriptTool(scriptTools, runtime = {}, options = {}) {
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const vm = sandboxRuntimeOf(runtime);
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const byId = new Map(scriptTools.map((tool) => [tool.id, tool]));
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const byId = new Map(scriptTools.map((tool) => [tool.id, { tool, schemas: scriptSchemasOf(tool, true) }]));
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const log = (options.logger ?? createNoopLogger()).named("run-script");
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const { scratch } = options;
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return defineTool({
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@@ -312,7 +309,7 @@ export function createRunScriptTool(scriptTools, runtime = {}, options = {}) {
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scratch?.recordRun(record.run);
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for (const entry of record.nested) {
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try {
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byId.get(entry.tool)?.foldCallRecord?.(entry.record);
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byId.get(entry.tool)?.tool.foldCallRecord?.(entry.record);
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}
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catch (err) {
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log.error("the call record of a nested call did not fold", { tool: entry.tool, ...log.errorFields(err) });
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// example the durable step of the call, which DBOS keeps in an AsyncLocalStorage.
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const inCallContext = AsyncLocalStorage.snapshot();
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const sandbox = new CodemodeSandbox({
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tools:
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tools: [...byId.values()].map(({ tool, schemas }) => scriptToolOf(tool, schemas, ctx, state, log, inCallContext)),
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globals: [
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{
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name: "describe",
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execute: (name) => {
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const
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if (
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const entry = typeof name === "string" ? byId.get(name) : undefined;
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if (entry === undefined)
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throw new Error(`no script tool ${JSON.stringify(name)}; the tools are ${[...byId.keys()].join(", ")}`);
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return describeTool(tool);
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return describeTool(entry.tool, entry.schemas);
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},
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},
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],
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package/package.json
CHANGED