@dxos/assistant-toolkit 0.8.4-main.e8ec1fe → 0.8.4-main.fcfe5033a5

package/dist/lib/neutral/chunk-7VH5RFBT.mjs

@@ -0,0 +1,392 @@
+import {
+  __export
+} from "./chunk-J5LGTIGS.mjs";
+
+// src/crud/graph.ts
+import * as Tool from "@effect/ai/Tool";
+import * as Toolkit from "@effect/ai/Toolkit";
+import * as Context from "effect/Context";
+import * as Effect from "effect/Effect";
+import * as Function from "effect/Function";
+import * as Option from "effect/Option";
+import * as Schema from "effect/Schema";
+import * as SchemaAST from "effect/SchemaAST";
+import { Entity, Filter, Obj, Query, Type } from "@dxos/echo";
+import { Database } from "@dxos/echo";
+import { isEncodedReference } from "@dxos/echo-protocol";
+import { ReferenceAnnotationId, RelationSourceDXNId, RelationSourceId, RelationTargetDXNId, RelationTargetId, createObject, getTypeAnnotation, getTypeIdentifierAnnotation } from "@dxos/echo/internal";
+import { mapAst } from "@dxos/effect";
+import { ContextQueueService } from "@dxos/functions";
+import { DXN, ObjectId } from "@dxos/keys";
+import { log } from "@dxos/log";
+import { deepMapValues, isNonNullable, trim } from "@dxos/util";
+var __dxlog_file = "/__w/dxos/dxos/packages/core/assistant-toolkit/src/crud/graph.ts";
+var Subgraph = Schema.Struct({
+  /** Objects and relations. */
+  objects: Schema.Array(Schema.Any)
+});
+var findRelatedSchema = async (db, anchor) => {
+  const allSchemas = await db.graph.schemaRegistry.query().run();
+  return allSchemas.filter((schema) => {
+    if (getTypeAnnotation(schema)?.kind !== Entity.Kind.Relation) {
+      return false;
+    }
+    return isSchemaAddressableByDxn(anchor, DXN.parse(getTypeAnnotation(schema).sourceSchema)) || isSchemaAddressableByDxn(anchor, DXN.parse(getTypeAnnotation(schema).targetSchema));
+  }).map((schema) => ({
+    kind: "relation",
+    schema
+  }));
+};
+var isSchemaAddressableByDxn = (schema, dxn) => {
+  if (getTypeIdentifierAnnotation(schema) === dxn.toString()) {
+    return true;
+  }
+  const t = dxn.asTypeDXN();
+  if (t) {
+    return t.type === Type.getTypename(schema);
+  }
+  return false;
+};
+var LocalSearchToolkit = Toolkit.make(Tool.make("search_local_search", {
+  description: "Search the local database for information using a vector index",
+  parameters: {
+    query: Schema.String.annotations({
+      description: "The query to search for. Could be a question or a topic or a set of keywords."
+    })
+  },
+  success: Schema.Unknown,
+  failure: Schema.Never,
+  dependencies: [
+    Database.Service
+  ]
+}));
+var LocalSearchHandler = LocalSearchToolkit.toLayer({
+  search_local_search: Effect.fn(function* ({ query: query2 }) {
+    const objects = yield* Database.runQuery(Query.select(Filter.text(query2, {
+      type: "vector"
+    })));
+    const results = [
+      ...objects
+    ];
+    const option = yield* Effect.serviceOption(ContextQueueService);
+    if (Option.isSome(option)) {
+      const queueObjects = yield* Effect.promise(() => option.value.queue.queryObjects());
+      results.push(...queueObjects);
+    }
+    return trim`
+      <local_context>
+        ${JSON.stringify(results, null, 2)}
+      </local_context>
+    `;
+  })
+});
+var GraphWriterSchema = class extends Context.Tag("@dxos/assistant/GraphWriterSchema")() {
+};
+var makeGraphWriterToolkit = ({ schema }) => {
+  return Toolkit.make(Tool.make("graph_writer", {
+    description: "Write to the local graph database",
+    parameters: createExtractionSchema(schema).fields,
+    success: Schema.Unknown,
+    failure: Schema.Never,
+    dependencies: [
+      Database.Service,
+      ContextQueueService
+    ]
+  }).annotateContext(Context.make(GraphWriterSchema, {
+    schema
+  })));
+};
+var makeGraphWriterHandler = (toolkit, { onAppend } = {}) => {
+  const { schema } = Context.get(toolkit.tools.graph_writer.annotations, GraphWriterSchema);
+  return toolkit.toLayer({
+    graph_writer: Effect.fn(function* (input) {
+      const { db } = yield* Database.Service;
+      const { queue } = yield* ContextQueueService;
+      const data = yield* Effect.promise(() => sanitizeObjects(schema, input, db, queue));
+      yield* Effect.promise(() => queue.append(data));
+      const dxns = data.map((obj) => Obj.getDXN(obj));
+      onAppend?.(dxns);
+      return dxns;
+    })
+  });
+};
+var createExtractionSchema = (types) => {
+  return Schema.Struct({
+    ...Object.fromEntries(types.map(preprocessSchema).map((schema, index) => [
+      `objects_${getSanitizedSchemaName(types[index])}`,
+      Schema.optional(Schema.Array(schema)).annotations({
+        description: `The objects of type: ${Type.getDXN(types[index])?.asTypeDXN().type}. ${SchemaAST.getDescriptionAnnotation(types[index].ast).pipe(Option.getOrElse(() => ""))}`
+      })
+    ]))
+  });
+};
+var getSanitizedSchemaName = (schema) => {
+  return Type.getDXN(schema).asTypeDXN().type.replaceAll(/[^a-zA-Z0-9]+/g, "_");
+};
+var sanitizeObjects = async (types, data, db, queue) => {
+  const entries = types.map((type) => data[`objects_${getSanitizedSchemaName(type)}`]?.map((object) => ({
+    data: object,
+    schema: type
+  })) ?? []).flat();
+  const idMap = /* @__PURE__ */ new Map();
+  const existingIds = /* @__PURE__ */ new Set();
+  const enitties = /* @__PURE__ */ new Map();
+  const resolveId = (id) => {
+    if (ObjectId.isValid(id)) {
+      existingIds.add(id);
+      return DXN.fromLocalObjectId(id);
+    }
+    const mappedId = idMap.get(id);
+    if (mappedId) {
+      return DXN.fromLocalObjectId(mappedId);
+    }
+    return void 0;
+  };
+  const res = entries.map((entry) => {
+    if (ObjectId.isValid(entry.data.id)) {
+      return entry;
+    }
+    idMap.set(entry.data.id, ObjectId.random());
+    entry.data.id = idMap.get(entry.data.id);
+    return entry;
+  }).map((entry) => {
+    const data2 = deepMapValues(entry.data, (value, recurse) => {
+      if (isEncodedReference(value)) {
+        const ref = value["/"];
+        const id = resolveId(ref);
+        if (id) {
+          return {
+            "/": id.toString()
+          };
+        } else {
+          return {
+            "/": `search:?q=${encodeURIComponent(ref)}`
+          };
+        }
+      }
+      return recurse(value);
+    });
+    if (Entity.getKind(entry.schema) === "relation") {
+      const sourceDxn = resolveId(data2.source);
+      if (!sourceDxn) {
+        log.warn("source not found", {
+          source: data2.source
+        }, {
+          F: __dxlog_file,
+          L: 273,
+          S: void 0,
+          C: (f, a) => f(...a)
+        });
+      }
+      const targetDxn = resolveId(data2.target);
+      if (!targetDxn) {
+        log.warn("target not found", {
+          target: data2.target
+        }, {
+          F: __dxlog_file,
+          L: 277,
+          S: void 0,
+          C: (f, a) => f(...a)
+        });
+      }
+      delete data2.source;
+      delete data2.target;
+      data2[RelationSourceDXNId] = sourceDxn;
+      data2[RelationTargetDXNId] = targetDxn;
+    }
+    return {
+      data: data2,
+      schema: entry.schema
+    };
+  }).filter((object) => !existingIds.has(object.data.id));
+  const dbObjects = await db.query(Query.select(Filter.id(...existingIds))).run();
+  const queueObjects = await queue?.getObjectsById([
+    ...existingIds
+  ]) ?? [];
+  const objects = [
+    ...dbObjects,
+    ...queueObjects
+  ].filter(isNonNullable);
+  log.info("objects", {
+    dbObjects,
+    queueObjects,
+    existingIds
+  }, {
+    F: __dxlog_file,
+    L: 298,
+    S: void 0,
+    C: (f, a) => f(...a)
+  });
+  const missing = Array.from(existingIds).filter((id) => !objects.some((object) => object.id === id));
+  if (missing.length > 0) {
+    throw new Error(`Object IDs do not point to existing objects: ${missing.join(", ")}`);
+  }
+  return res.flatMap(({ data: data2, schema }) => {
+    let skip = false;
+    if (RelationSourceDXNId in data2) {
+      const id = data2[RelationSourceDXNId].asEchoDXN()?.echoId;
+      const obj = objects.find((object) => object.id === id) ?? enitties.get(id);
+      if (obj) {
+        delete data2[RelationSourceDXNId];
+        data2[RelationSourceId] = obj;
+      } else {
+        skip = true;
+      }
+    }
+    if (RelationTargetDXNId in data2) {
+      const id = data2[RelationTargetDXNId].asEchoDXN()?.echoId;
+      const obj = objects.find((object) => object.id === id) ?? enitties.get(id);
+      if (obj) {
+        delete data2[RelationTargetDXNId];
+        data2[RelationTargetId] = obj;
+      } else {
+        skip = true;
+      }
+    }
+    if (!skip) {
+      const obj = createObject(schema, data2);
+      enitties.set(obj.id, obj);
+      return [
+        obj
+      ];
+    }
+    return [];
+  });
+};
+var SoftRef = Schema.Struct({
+  "/": Schema.String
+}).annotations({
+  description: "Reference to another object."
+});
+var preprocessSchema = (schema) => {
+  const isRelationSchema = Entity.getKind(schema) === "relation";
+  const go = (ast, visited = /* @__PURE__ */ new Set()) => {
+    if (visited.has(ast)) {
+      return ast;
+    }
+    visited.add(ast);
+    if (SchemaAST.getAnnotation(ast, ReferenceAnnotationId).pipe(Option.isSome)) {
+      return SoftRef.ast;
+    }
+    return mapAst(ast, (child) => go(child, visited));
+  };
+  return Schema.make(mapAst(schema.ast, (ast) => go(ast))).pipe(Schema.omit("id"), Schema.extend(Schema.Struct({
+    id: Schema.String.annotations({
+      description: "The id of this object. Come up with a unique id based on your judgement."
+    })
+  })), isRelationSchema ? Schema.extend(Schema.Struct({
+    source: Schema.String.annotations({
+      description: "The id of the source object for this relation."
+    }),
+    target: Schema.String.annotations({
+      description: "The id of the target object for this relation."
+    })
+  })) : Function.identity);
+};
+
+// src/blueprints/research/types/ResearchGraph.ts
+var ResearchGraph_exports = {};
+__export(ResearchGraph_exports, {
+  LegacyResearchGraph: () => LegacyResearchGraph,
+  ResearchGraph: () => ResearchGraph,
+  ResearchGraphV1: () => ResearchGraphV1,
+  contextQueueLayer: () => contextQueueLayer,
+  create: () => create,
+  migrations: () => migrations,
+  query: () => query
+});
+import * as Effect2 from "effect/Effect";
+import * as Layer from "effect/Layer";
+import * as Schema2 from "effect/Schema";
+import { Database as Database2, Feed, Migration, Obj as Obj2, Query as Query2, Ref, Type as Type2 } from "@dxos/echo";
+import { Queue } from "@dxos/echo-db";
+import { SystemTypeAnnotation } from "@dxos/echo/internal";
+import { ContextQueueService as ContextQueueService2, QueueService } from "@dxos/functions";
+var LegacyResearchGraph = Schema2.Struct({
+  queue: Ref.Ref(Queue)
+}).pipe(Type2.object({
+  typename: "org.dxos.type.research-graph",
+  version: "0.1.0"
+}), SystemTypeAnnotation.set(true));
+var ResearchGraphV1 = Schema2.Struct({
+  queue: Ref.Ref(Queue)
+}).pipe(Type2.object({
+  typename: "org.dxos.type.researchGraph",
+  version: "0.1.0"
+}), SystemTypeAnnotation.set(true));
+var ResearchGraph = Schema2.Struct({
+  queue: Ref.Ref(Feed.Feed)
+}).pipe(Type2.object({
+  typename: "org.dxos.type.researchGraph",
+  version: "0.2.0"
+}), SystemTypeAnnotation.set(true));
+var create = Effect2.fn("createResearchGraph")(function* () {
+  const feed = yield* Database2.add(Feed.make());
+  return yield* Database2.add(Obj2.make(ResearchGraph, {
+    queue: Ref.make(feed)
+  }));
+});
+var query = Effect2.fn("queryResearchGraph")(function* () {
+  const objects = yield* Database2.runQuery(Query2.type(ResearchGraph));
+  return objects.at(0);
+});
+var contextQueueLayer = Layer.unwrapEffect(Effect2.gen(function* () {
+  const researchGraph = (yield* query()) ?? (yield* create());
+  const researchFeed = yield* Database2.load(researchGraph.queue);
+  const feedDxn = Feed.getQueueDxn(researchFeed);
+  if (!feedDxn) {
+    throw new Error("ResearchGraph feed must be stored in a space");
+  }
+  const { queues } = yield* QueueService;
+  return ContextQueueService2.layer(queues.get(feedDxn));
+}));
+var migrations = [
+  Migration.define({
+    from: ResearchGraphV1,
+    to: ResearchGraph,
+    transform: async (from, { db }) => {
+      const feed = Feed.unsafeFromQueueDXN(from.queue.dxn);
+      const existing = db.getObjectById(feed.id);
+      const dbFeed = existing ?? db.add(feed);
+      return {
+        queue: Ref.make(dbFeed)
+      };
+    },
+    onMigration: async () => {
+    }
+  })
+];
+
+// src/blueprints/research/types/index.ts
+import { Text } from "@dxos/schema";
+import { Event, HasConnection, HasRelationship, LegacyOrganization, LegacyPerson, Pipeline, Task } from "@dxos/types";
+var ResearchDataTypes = [
+  // Objects
+  Event.Event,
+  Task.Task,
+  Text.Text,
+  // TODO(wittjosiah): Until views (e.g., Table) support relations this needs to be expressed via organization ref.
+  // Employer.Employer,
+  // Organization.Organization,
+  LegacyPerson,
+  LegacyOrganization,
+  Pipeline.Pipeline,
+  // Relations
+  HasRelationship.HasRelationship,
+  HasConnection.HasConnection
+];
+
+export {
+  Subgraph,
+  findRelatedSchema,
+  LocalSearchToolkit,
+  LocalSearchHandler,
+  makeGraphWriterToolkit,
+  makeGraphWriterHandler,
+  createExtractionSchema,
+  getSanitizedSchemaName,
+  sanitizeObjects,
+  ResearchGraph_exports,
+  ResearchDataTypes
+};
+//# sourceMappingURL=chunk-7VH5RFBT.mjs.map

package/dist/lib/neutral/chunk-7VH5RFBT.mjs.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../../src/crud/graph.ts", "../../../src/blueprints/research/types/ResearchGraph.ts", "../../../src/blueprints/research/types/index.ts"],
+  "sourcesContent": ["//\n// Copyright 2025 DXOS.org\n//\n\nimport * as Tool from '@effect/ai/Tool';\nimport * as Toolkit from '@effect/ai/Toolkit';\nimport * as Context from 'effect/Context';\nimport * as Effect from 'effect/Effect';\nimport * as Function from 'effect/Function';\nimport * as Option from 'effect/Option';\nimport * as Schema from 'effect/Schema';\nimport * as SchemaAST from 'effect/SchemaAST';\n\nimport { Entity, Filter, Obj, Query, Type } from '@dxos/echo';\nimport { Database } from '@dxos/echo';\nimport { type Queue } from '@dxos/echo-db';\nimport { isEncodedReference } from '@dxos/echo-protocol';\nimport {\n  ReferenceAnnotationId,\n  RelationSourceDXNId,\n  RelationSourceId,\n  RelationTargetDXNId,\n  RelationTargetId,\n  createObject,\n  getTypeAnnotation,\n  getTypeIdentifierAnnotation,\n} from '@dxos/echo/internal';\nimport { mapAst } from '@dxos/effect';\nimport { ContextQueueService } from '@dxos/functions';\nimport { DXN, ObjectId } from '@dxos/keys';\nimport { log } from '@dxos/log';\nimport { deepMapValues, isNonNullable, trim } from '@dxos/util';\n\n// TODO(burdon): Unify with the graph schema.\nexport const Subgraph = Schema.Struct({\n  /** Objects and relations. */\n  objects: Schema.Array(Schema.Any),\n});\n\nexport interface Subgraph extends Schema.Schema.Type<typeof Subgraph> {}\n\nexport type RelatedSchema = {\n  schema: Type.AnyEntity;\n  kind: 'reference' | 'relation';\n};\n\n/**\n * Find all schemas that are related to the given schema.\n *\n * @param db\n * @param schema\n * @returns\n */\nexport const findRelatedSchema = async (db: Database.Database, anchor: Type.AnyEntity): Promise<RelatedSchema[]> => {\n  // TODO(dmaretskyi): Query stored schemas.\n  const allSchemas = await db.graph.schemaRegistry.query().run();\n\n  // TODO(dmaretskyi): Also do references.\n  return allSchemas\n    .filter((schema) => {\n      if (getTypeAnnotation(schema)?.kind !== Entity.Kind.Relation) {\n        return false;\n      }\n\n      return (\n        isSchemaAddressableByDxn(anchor, DXN.parse(getTypeAnnotation(schema)!.sourceSchema!)) ||\n        isSchemaAddressableByDxn(anchor, DXN.parse(getTypeAnnotation(schema)!.targetSchema!))\n      );\n    })\n    .map(\n      (schema): RelatedSchema => ({\n        kind: 'relation',\n        schema,\n      }),\n    );\n};\n\n/**\n * Non-strict DXN comparison.\n * Returns true if the DXN could be resolved to the schema.\n */\nconst isSchemaAddressableByDxn = (schema: Type.AnyEntity, dxn: DXN): boolean => {\n  if (getTypeIdentifierAnnotation(schema) === dxn.toString()) {\n    return true;\n  }\n\n  const t = dxn.asTypeDXN();\n  if (t) {\n    return t.type === Type.getTypename(schema);\n  }\n\n  return false;\n};\n\n/**\n * Perform vector search in the local database.\n */\n// TODO(dmaretskyi): Rename `GraphReadToolkit`.\nexport const LocalSearchToolkit = Toolkit.make(\n  Tool.make('search_local_search', {\n    description: 'Search the local database for information using a vector index',\n    parameters: {\n      query: Schema.String.annotations({\n        description: 'The query to search for. Could be a question or a topic or a set of keywords.',\n      }),\n    },\n    success: Schema.Unknown,\n    failure: Schema.Never,\n    dependencies: [Database.Service],\n  }),\n);\n\nexport const LocalSearchHandler = LocalSearchToolkit.toLayer({\n  search_local_search: Effect.fn(function* ({ query }) {\n    const objects = yield* Database.runQuery(Query.select(Filter.text(query, { type: 'vector' })));\n    const results = [...objects];\n\n    const option = yield* Effect.serviceOption(ContextQueueService);\n    if (Option.isSome(option)) {\n      const queueObjects = yield* Effect.promise(() => option.value.queue.queryObjects());\n      // TODO(dmaretskyi): Text search on the queue.\n      results.push(...queueObjects);\n    }\n\n    return trim`\n      <local_context>\n        ${JSON.stringify(results, null, 2)}\n      </local_context>\n    `;\n  }),\n});\n\n/**\n * Attached as an annotation to the writer tool.\n */\nclass GraphWriterSchema extends Context.Tag('@dxos/assistant/GraphWriterSchema')<\n  GraphWriterSchema,\n  {\n    schema: Type.AnyEntity[];\n  }\n>() {}\n\n/**\n * Forms typed objects that can be written to the graph database.\n */\nexport const makeGraphWriterToolkit = ({ schema }: { schema: Type.AnyEntity[] }) => {\n  return Toolkit.make(\n    Tool.make('graph_writer', {\n      description: 'Write to the local graph database',\n      parameters: createExtractionSchema(schema).fields,\n      success: Schema.Unknown,\n      failure: Schema.Never,\n      dependencies: [Database.Service, ContextQueueService],\n    }).annotateContext(Context.make(GraphWriterSchema, { schema })),\n  );\n};\n\nexport const makeGraphWriterHandler = (\n  toolkit: ReturnType<typeof makeGraphWriterToolkit>,\n  {\n    onAppend,\n  }: {\n    onAppend?: (object: DXN[]) => void;\n  } = {},\n) => {\n  const { schema } = Context.get(\n    toolkit.tools.graph_writer.annotations as Context.Context<GraphWriterSchema>,\n    GraphWriterSchema,\n  );\n\n  return toolkit.toLayer({\n    graph_writer: Effect.fn(function* (input) {\n      const { db } = yield* Database.Service;\n      const { queue } = yield* ContextQueueService;\n      const data = yield* Effect.promise(() => sanitizeObjects(schema, input as any, db, queue));\n      yield* Effect.promise(() => queue.append(data as Obj.Unknown[]));\n\n      const dxns = data.map((obj) => Obj.getDXN(obj));\n      onAppend?.(dxns);\n      return dxns;\n    }),\n  });\n};\n\n/**\n * Create a schema for structured data extraction.\n */\nexport const createExtractionSchema = (types: Type.AnyEntity[]) => {\n  return Schema.Struct({\n    ...Object.fromEntries(\n      types.map(preprocessSchema).map((schema, index) => [\n        `objects_${getSanitizedSchemaName(types[index])}`,\n        Schema.optional(Schema.Array(schema)).annotations({\n          description: `The objects of type: ${Type.getDXN(types[index])?.asTypeDXN()!.type}. ${SchemaAST.getDescriptionAnnotation(types[index].ast).pipe(Option.getOrElse(() => ''))}`,\n        }),\n      ]),\n    ),\n  });\n};\n\nexport const getSanitizedSchemaName = (schema: Type.AnyEntity) => {\n  return Type.getDXN(schema)!\n    .asTypeDXN()!\n    .type.replaceAll(/[^a-zA-Z0-9]+/g, '_');\n};\n\nexport const sanitizeObjects = async (\n  types: Type.AnyEntity[],\n  data: Record<string, readonly unknown[]>,\n  db: Database.Database,\n  queue?: Queue,\n): Promise<Obj.Unknown[]> => {\n  const entries = types\n    .map(\n      (type) =>\n        data[`objects_${getSanitizedSchemaName(type)}`]?.map((object: any) => ({\n          data: object,\n          schema: type,\n        })) ?? [],\n    )\n    .flat();\n\n  const idMap = new Map<string, string>();\n  const existingIds = new Set<ObjectId>();\n  const enitties = new Map<ObjectId, Entity.Unknown>();\n\n  const resolveId = (id: string): DXN | undefined => {\n    if (ObjectId.isValid(id)) {\n      existingIds.add(id);\n      return DXN.fromLocalObjectId(id);\n    }\n\n    const mappedId = idMap.get(id);\n    if (mappedId) {\n      return DXN.fromLocalObjectId(mappedId);\n    }\n\n    return undefined;\n  };\n\n  const res = entries\n    .map((entry) => {\n      // This entry mutates existing object.\n      if (ObjectId.isValid(entry.data.id)) {\n        return entry;\n      }\n\n      idMap.set(entry.data.id, ObjectId.random());\n      entry.data.id = idMap.get(entry.data.id);\n      return entry;\n    })\n    .map((entry) => {\n      const data = deepMapValues(entry.data, (value, recurse) => {\n        if (isEncodedReference(value)) {\n          const ref = value['/'];\n          const id = resolveId(ref);\n\n          if (id) {\n            // Link to an existing object.\n            return { '/': id.toString() };\n          } else {\n            // Search URIs?\n            return { '/': `search:?q=${encodeURIComponent(ref)}` };\n          }\n        }\n\n        return recurse(value);\n      });\n\n      if (Entity.getKind(entry.schema) === 'relation') {\n        const sourceDxn = resolveId(data.source);\n        if (!sourceDxn) {\n          log.warn('source not found', { source: data.source });\n        }\n        const targetDxn = resolveId(data.target);\n        if (!targetDxn) {\n          log.warn('target not found', { target: data.target });\n        }\n        delete data.source;\n        delete data.target;\n        data[RelationSourceDXNId] = sourceDxn;\n        data[RelationTargetDXNId] = targetDxn;\n      }\n\n      return {\n        data,\n        schema: entry.schema,\n      };\n    })\n    .filter((object) => !existingIds.has(object.data.id)); // TODO(dmaretskyi): This dissallows updating existing objects.\n\n  // TODO(dmaretskyi): Use ref resolver.\n  const dbObjects = await db.query(Query.select(Filter.id(...existingIds))).run();\n  const queueObjects = (await queue?.getObjectsById([...existingIds])) ?? [];\n  const objects = [...dbObjects, ...queueObjects].filter(isNonNullable);\n\n  // TODO(dmaretskyi): Returns everything if IDs are empty!\n  log.info('objects', { dbObjects, queueObjects, existingIds });\n  const missing = Array.from(existingIds).filter((id) => !objects.some((object) => object.id === id));\n  if (missing.length > 0) {\n    throw new Error(`Object IDs do not point to existing objects: ${missing.join(', ')}`);\n  }\n\n  return res.flatMap(({ data, schema }) => {\n    let skip = false;\n    if (RelationSourceDXNId in data) {\n      const id = (data[RelationSourceDXNId] as DXN).asEchoDXN()?.echoId;\n      const obj = objects.find((object) => object.id === id) ?? enitties.get(id!);\n      if (obj) {\n        delete data[RelationSourceDXNId];\n        data[RelationSourceId] = obj;\n      } else {\n        skip = true;\n      }\n    }\n    if (RelationTargetDXNId in data) {\n      const id = (data[RelationTargetDXNId] as DXN).asEchoDXN()?.echoId;\n      const obj = objects.find((object) => object.id === id) ?? enitties.get(id!);\n      if (obj) {\n        delete data[RelationTargetDXNId];\n        data[RelationTargetId] = obj;\n      } else {\n        skip = true;\n      }\n    }\n    if (!skip) {\n      const obj = createObject(schema, data);\n      enitties.set(obj.id, obj);\n      return [obj];\n    }\n    return [];\n  });\n};\n\nconst SoftRef = Schema.Struct({\n  '/': Schema.String,\n}).annotations({\n  description: 'Reference to another object.',\n});\n\nconst preprocessSchema = (schema: Schema.Schema.AnyNoContext) => {\n  const isRelationSchema = Entity.getKind(schema) === 'relation';\n\n  const go = (ast: SchemaAST.AST, visited = new Set<SchemaAST.AST>()): SchemaAST.AST => {\n    if (visited.has(ast)) {\n      // Already visited this node, prevent infinite recursion.\n      return ast;\n    }\n    visited.add(ast);\n\n    if (SchemaAST.getAnnotation(ast, ReferenceAnnotationId).pipe(Option.isSome)) {\n      return SoftRef.ast;\n    }\n\n    return mapAst(ast, (child) => go(child, visited));\n  };\n\n  return Schema.make<any, any, never>(mapAst(schema.ast, (ast) => go(ast))).pipe(\n    Schema.omit('id'),\n    Schema.extend(\n      Schema.Struct({\n        id: Schema.String.annotations({\n          description: 'The id of this object. Come up with a unique id based on your judgement.',\n        }),\n      }),\n    ),\n    isRelationSchema\n      ? Schema.extend(\n          Schema.Struct({\n            source: Schema.String.annotations({\n              description: 'The id of the source object for this relation.',\n            }),\n            target: Schema.String.annotations({\n              description: 'The id of the target object for this relation.',\n            }),\n          }),\n        )\n      : Function.identity<Schema.Schema.AnyNoContext>,\n  );\n};\n", "//\n// Copyright 2025 DXOS.org\n//\n\nimport * as Effect from 'effect/Effect';\nimport * as Layer from 'effect/Layer';\nimport * as Schema from 'effect/Schema';\n\nimport { Database, Feed, Migration, Obj, Query, Ref, Type } from '@dxos/echo';\nimport { Queue } from '@dxos/echo-db';\nimport { SystemTypeAnnotation } from '@dxos/echo/internal';\nimport { ContextQueueService, QueueService } from '@dxos/functions';\n\n/** @deprecated Use ResearchGraph instead. */\nexport const LegacyResearchGraph = Schema.Struct({\n  queue: Ref.Ref(Queue),\n}).pipe(\n  Type.object({\n    typename: 'org.dxos.type.research-graph',\n    version: '0.1.0',\n  }),\n  SystemTypeAnnotation.set(true),\n);\n\nexport interface LegacyResearchGraph extends Schema.Schema.Type<typeof LegacyResearchGraph> {}\n\n/** @deprecated Migration target of LegacyResearchGraph; migrated to ResearchGraph (v0.2.0) with feed ref. */\nexport const ResearchGraphV1 = Schema.Struct({\n  queue: Ref.Ref(Queue),\n}).pipe(\n  Type.object({\n    typename: 'org.dxos.type.researchGraph',\n    version: '0.1.0',\n  }),\n  SystemTypeAnnotation.set(true),\n);\n\nexport interface ResearchGraphV1 extends Schema.Schema.Type<typeof ResearchGraphV1> {}\n\n/**\n * Container for a set of ephemeral research results.\n */\nexport const ResearchGraph = Schema.Struct({\n  queue: Ref.Ref(Feed.Feed),\n}).pipe(\n  Type.object({\n    typename: 'org.dxos.type.researchGraph',\n    version: '0.2.0',\n  }),\n  SystemTypeAnnotation.set(true),\n);\n\nexport interface ResearchGraph extends Schema.Schema.Type<typeof ResearchGraph> {}\n\nexport const create: () => Effect.Effect<ResearchGraph, never, Database.Service | QueueService> = Effect.fn(\n  'createResearchGraph',\n)(function* () {\n  const feed = yield* Database.add(Feed.make());\n  return yield* Database.add(Obj.make(ResearchGraph, { queue: Ref.make(feed) }));\n});\n\nexport const query: () => Effect.Effect<ResearchGraph | undefined, never, Database.Service> = Effect.fn(\n  'queryResearchGraph',\n)(function* () {\n  const objects = yield* Database.runQuery(Query.type(ResearchGraph));\n  return objects.at(0);\n});\n\nexport const contextQueueLayer = Layer.unwrapEffect(\n  Effect.gen(function* () {\n    const researchGraph = (yield* query()) ?? (yield* create());\n    const researchFeed = yield* Database.load(researchGraph.queue);\n    const feedDxn = Feed.getQueueDxn(researchFeed);\n    if (!feedDxn) {\n      throw new Error('ResearchGraph feed must be stored in a space');\n    }\n    const { queues } = yield* QueueService;\n    return ContextQueueService.layer(queues.get(feedDxn));\n  }),\n);\n\nexport const migrations = [\n  Migration.define({\n    from: ResearchGraphV1,\n    to: ResearchGraph,\n    transform: async (from, { db }) => {\n      const feed = Feed.unsafeFromQueueDXN(from.queue.dxn);\n      const existing = db.getObjectById<Feed.Feed>(feed.id);\n      const dbFeed = existing ?? db.add(feed);\n      return {\n        queue: Ref.make(dbFeed),\n      };\n    },\n    onMigration: async () => {},\n  }),\n];\n", "//\n// Copyright 2026 DXOS.org\n//\n\nimport { type Type } from '@dxos/echo';\nimport { Text } from '@dxos/schema';\nimport { Event, HasConnection, HasRelationship, LegacyOrganization, LegacyPerson, Pipeline, Task } from '@dxos/types';\n\nexport * as ResearchGraph from './ResearchGraph';\n\n/**\n * Data types for research.\n */\n// TODO(burdon): This should not be hardcoded.\nexport const ResearchDataTypes: Type.AnyEntity[] = [\n  // Objects\n  Event.Event,\n  Task.Task,\n  Text.Text,\n\n  // TODO(wittjosiah): Until views (e.g., Table) support relations this needs to be expressed via organization ref.\n  // Employer.Employer,\n  // Organization.Organization,\n  LegacyPerson,\n  LegacyOrganization,\n\n  Pipeline.Pipeline,\n\n  // Relations\n  HasRelationship.HasRelationship,\n  HasConnection.HasConnection,\n];\n"],
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+}