Scaich Integration with the Bioagent-plugin

.env.example

@@ -1,3 +1,4 @@
+# .env.example
 ## Deployed Eliza URL
 PROD_URL=https://your-production-url.com
 DEV_URL=https://your-dev-url.com
@@ -33,14 +34,6 @@ OPENAI_API_KEY=your_openai_api_key  # Starting with sk-
 # Anthropic Configuration
 ANTHROPIC_API_KEY=your_anthropic_api_key  # For Claude
 
-# OriginTrail DKG
-DKG_ENVIRONMENT="testnet"  # Values: "development", "testnet", "mainnet"
-DKG_HOSTNAME="your_dkg_hostname"
-DKG_PORT="8900"
-DKG_PUBLIC_KEY="your_dkg_public_key"
-DKG_PRIVATE_KEY="your_dkg_private_key"
-DKG_BLOCKCHAIN_NAME="base:84532"  # Values: (mainnet) "base:8453", "gnosis:100", "otp:2043" (testnet) "base:84532", "gnosis:10200", "otp:20430"
-
 # Unstructured API Key
 UNSTRUCTURED_API_KEY=your_unstructured_api_key
 

.gitignore

@@ -2,4 +2,4 @@ node_modules
 .env
 .migration-complete
 drizzle
-oxigraph
+oxigraph

README.scaich.md

@@ -0,0 +1,26 @@
+# ScaiCh Plugin 🤖📚
+
+A plugin for researchers to search literature via SCAI API, process Google Drive documents, and generate biological hypotheses. Integrates with RDF stores like [OriginTrail DKG](https://origintrail.io) or [Oxigraph](https://github.com/oxigraph/oxigraph).
+
+## 🚀 Features
+
+- **Literature Search**: Query SCAI API for scientific articles and store as Knowledge Assets.
+- **Google Drive Monitoring**: Auto-process new PDFs into Knowledge Assets.
+- **Hypothesis Generation**: Generate and evaluate biological hypotheses, scored by JudgeLLM.
+
+> [!NOTE] Under development. Google Drive webhooks require public URLs (e.g., ngrok).
+
+```
+{
+  "action": "SCAI_SEARCH",
+  "content": "The History of Sci-hub"
+}
+```
+
+## 📋 Notes
+
+- SCAI API requires no authentication for now.
+- Logs: Set `DEFAULT_LOG_LEVEL=debug` in `.env`.
+- Issues? Check logs or submit to [GitHub](https://github.com/bio-xyz/plugin-scaich).
+
+

src/actions/index.ts

@@ -1 +1,2 @@
-export * from "./dkgInsert.ts";
+// src/actions/index.ts
+export * from "./scaichSearch";

src/actions/scaichSearch.ts

@@ -0,0 +1,33 @@
+// src/actions/scaichSearch.ts
+import { searchLiterature } from "../services/scaich/client";
+import { processScaiResults } from "../services/scaich/processResults";
+import { logger } from "@elizaos/core";
+
+export const SCAI_SEARCH_ACTION = "SCAI_SEARCH";
+
+export const scaichSearch = {
+  name: SCAI_SEARCH_ACTION,
+  description: "Search scientific literature using the SCAI API",
+  validate: async () => {
+    // 移除 SCAI_API_KEY 检查，因为 API 不需要认证
+    return { valid: true };
+  },
+  handler: async ({ message, runtime }) => {
+    const query = message.content.trim();
+    if (!query) {
+      return { response: "Please provide a search query" };
+    }
+
+    try {
+      const response = await searchLiterature(query, 10, false);
+      const jsonLdGraph = await processScaiResults(response);
+      return {
+        response: `Found ${response.results.length} articles for query "${query}". Results stored in knowledge graph.`,
+        data: jsonLdGraph,
+      };
+    } catch (error) {
+      logger.error(`SCAI search failed: ${error.message}`);
+      return { response: `Error searching literature: ${error.message}` };
+    }
+  },
+};

src/constants.ts

@@ -1,76 +1,76 @@
 import { z } from "zod";
 // TODO: add isConnectedTo field or similar which you will use to connect w other KAs
 export const dkgMemoryTemplate = {
-    "@context": "http://schema.org",
-    "@type": "SocialMediaPosting",
-    headline: "<describe memory in a short way, as a title here>",
-    articleBody:
-        "Check out this amazing project on decentralized cloud networks! @DecentralCloud #Blockchain #Web3",
-    author: {
-        "@type": "Person",
-        "@id": "uuid:john:doe",
-        name: "John Doe",
-        identifier: "@JohnDoe",
-        url: "https://twitter.com/JohnDoe",
+  "@context": "http://schema.org",
+  "@type": "SocialMediaPosting",
+  headline: "<describe memory in a short way, as a title here>",
+  articleBody:
+    "Check out this amazing project on decentralized cloud networks! @DecentralCloud #Blockchain #Web3",
+  author: {
+    "@type": "Person",
+    "@id": "uuid:john:doe",
+    name: "John Doe",
+    identifier: "@JohnDoe",
+    url: "https://twitter.com/JohnDoe",
+  },
+  dateCreated: "yyyy-mm-ddTHH:mm:ssZ",
+  interactionStatistic: [
+    {
+      "@type": "InteractionCounter",
+      interactionType: {
+        "@type": "LikeAction",
+      },
+      userInteractionCount: 150,
     },
-    dateCreated: "yyyy-mm-ddTHH:mm:ssZ",
-    interactionStatistic: [
-        {
-            "@type": "InteractionCounter",
-            interactionType: {
-                "@type": "LikeAction",
-            },
-            userInteractionCount: 150,
-        },
-        {
-            "@type": "InteractionCounter",
-            interactionType: {
-                "@type": "ShareAction",
-            },
-            userInteractionCount: 45,
-        },
-    ],
-    mentions: [
-        {
-            "@type": "Person",
-            name: "Twitter account mentioned name goes here",
-            identifier: "@TwitterAccount",
-            url: "https://twitter.com/TwitterAccount",
-        },
-    ],
-    keywords: [
-        {
-            "@type": "Text",
-            "@id": "uuid:keyword1",
-            name: "keyword1",
-        },
-        {
-            "@type": "Text",
-            "@id": "uuid:keyword2",
-            name: "keyword2",
-        },
-    ],
-    about: [
-        {
-            "@type": "Thing",
-            "@id": "uuid:thing1",
-            name: "Blockchain",
-            url: "https://en.wikipedia.org/wiki/Blockchain",
-        },
-        {
-            "@type": "Thing",
-            "@id": "uuid:thing2",
-            name: "Web3",
-            url: "https://en.wikipedia.org/wiki/Web3",
-        },
-        {
-            "@type": "Thing",
-            "@id": "uuid:thing3",
-            name: "Decentralized Cloud",
-            url: "https://example.com/DecentralizedCloud",
-        },
-    ],
-    url: "https://twitter.com/JohnDoe/status/1234567890",
+    {
+      "@type": "InteractionCounter",
+      interactionType: {
+        "@type": "ShareAction",
+      },
+      userInteractionCount: 45,
+    },
+  ],
+  mentions: [
+    {
+      "@type": "Person",
+      name: "Twitter account mentioned name goes here",
+      identifier: "@TwitterAccount",
+      url: "https://twitter.com/TwitterAccount",
+    },
+  ],
+  keywords: [
+    {
+      "@type": "Text",
+      "@id": "uuid:keyword1",
+      name: "keyword1",
+    },
+    {
+      "@type": "Text",
+      "@id": "uuid:keyword2",
+      name: "keyword2",
+    },
+  ],
+  about: [
+    {
+      "@type": "Thing",
+      "@id": "uuid:thing1",
+      name: "Blockchain",
+      url: "https://en.wikipedia.org/wiki/Blockchain",
+    },
+    {
+      "@type": "Thing",
+      "@id": "uuid:thing2",
+      name: "Web3",
+      url: "https://en.wikipedia.org/wiki/Web3",
+    },
+    {
+      "@type": "Thing",
+      "@id": "uuid:thing3",
+      name: "Decentralized Cloud",
+      url: "https://example.com/DecentralizedCloud",
+    },
+  ],
+  url: "https://twitter.com/JohnDoe/status/1234567890",
 };
 
 export const combinedSparqlExample = `
@@ -99,7 +99,7 @@ SELECT DISTINCT ?headline ?articleBody
     LIMIT 10`;
 
 export const sparqlExamples = [
-    `
+  `
     SELECT DISTINCT ?headline ?articleBody
     WHERE {
       ?s a <http://schema.org/SocialMediaPosting> .
@@ -124,7 +124,7 @@ export const sparqlExamples = [
     }
     LIMIT 10
     `,
-    `
+  `
     SELECT DISTINCT ?headline ?articleBody
     WHERE {
       ?s a <http://schema.org/SocialMediaPosting> .
@@ -136,7 +136,7 @@ export const sparqlExamples = [
       )
     }
     `,
-    `
+  `
     SELECT DISTINCT ?headline ?articleBody ?keywordName
     WHERE {
       ?s a <http://schema.org/SocialMediaPosting> .
@@ -150,7 +150,7 @@ export const sparqlExamples = [
       )
     }
     `,
-    `
+  `
     SELECT DISTINCT ?headline ?articleBody ?aboutName
     WHERE {
       ?s a <http://schema.org/SocialMediaPosting> .
@@ -177,6 +177,6 @@ export const generalSparqlQuery = `
   `;
 
 export const DKG_EXPLORER_LINKS = {
-    testnet: "https://dkg-testnet.origintrail.io/explore?ual=",
-    mainnet: "https://dkg.origintrail.io/explore?ual=",
+  testnet: "https://dkg-testnet.origintrail.io/explore?ual=",
+  mainnet: "https://dkg.origintrail.io/explore?ual=",
 };

src/index.ts

@@ -4,6 +4,7 @@ import { dkgInsert } from "./actions/dkgInsert";
 import { HypothesisService } from "./services";
 import { initWithMigrations } from "./helper";
 import { gdriveManualSync, gdriveWebhook, health } from "./routes";
+import { scaichSearch } from "./actions/scaichSearch";
 
 export const dkgPlugin: Plugin = {
   init: async (config: Record<string, string>, runtime: IAgentRuntime) => {
@@ -13,10 +14,9 @@ export const dkgPlugin: Plugin = {
       await initWithMigrations(runtime);
     }, 20000); // prevent `undefined` error, the db property is not available immediately
   },
-  name: "dkg",
-  description:
-    "Agent DKG which allows you to store memories on the OriginTrail Decentralized Knowledge Graph",
-  actions: [dkgInsert],
+  name: "scaichplugin",
+  description: "A plugin for literature search using SCAI API and knowledge graph integration with BioAgent Plugin",
+  actions: [dkgInsert, scaichSearch],
   providers: [],
   evaluators: [],
   services: [HypothesisService],

src/services/scaich/client.ts

@@ -0,0 +1,30 @@
+// src/services/scaich/client.ts
+import axios from "axios";
+import { logger } from "@elizaos/core";
+
+const SCAI_API_URL = "https://api.scai.sh/search";
+
+/**
+ * Sends a search query to the SCAI API and returns the response.
+ * @param query - The search query string
+ * @param limit - Maximum number of results to return
+ * @param oa - Whether to restrict to open access articles
+ * @returns The API response data
+ */
+export async function searchLiterature(
+  query: string,
+  limit: number = 10,
+  oa: boolean = false
+): Promise<any> {
+  try {
+    const response = await axios.get(SCAI_API_URL, {
+      params: { query, limit, oa },
+      timeout: 10000, // 10 seconds timeout
+    });
+    logger.info(`SCAI API request successful for query: ${query}`);
+    return response.data;
+  } catch (error) {
+    logger.error(`SCAI API request failed: ${error.message}`);
+    throw error;
+  }
+}

src/services/scaich/index.ts

@@ -0,0 +1,4 @@
+// src/services/scaich/index.ts
+export * from "./client";
+export * from "./processResults";
+export * from "./types";

src/services/scaich/processResults.ts

@@ -0,0 +1,48 @@
+// src/services/scaich/processResults.ts
+import { ScaiResponse, ScaiSearchResult } from "./types";
+import { logger } from "@elizaos/core";
+import { storeJsonLd } from "../gdrive/storeJsonLdToKg"; // 重用现有存储逻辑
+
+/**
+ * Converts SCAI search results to JSON-LD and stores them in the knowledge graph.
+ * @param response - The SCAI API response
+ * @returns The generated JSON-LD graph
+ */
+export async function processScaiResults(response: ScaiResponse): Promise<Record<string, any>> {
+  const jsonLdGraph: Record<string, any> = {
+    "@context": "http://schema.org",
+    "@type": "ScholarlyArticle",
+    "query": response.query,
+    "articles": [],
+  };
+
+  for (const result of response.results) {
+    const article = {
+      "@id": result.doi,
+      "@type": "ScholarlyArticle",
+      "name": result.title,
+      "abstract": result.abstract,
+      "author": result.author.split(", ").map((name) => ({ "@type": "Person", "name": name })),
+      "url": result.url,
+      "sameAs": result.scihub_url,
+      "datePublished": result.year.toString(),
+      "identifier": result.doi,
+      "keywords": response.summary.sum.split(", "),
+    };
+    jsonLdGraph.articles.push(article);
+  }
+
+  try {
+    // 存储到知识图谱
+    const success = await storeJsonLd(jsonLdGraph);
+    if (success) {
+      logger.info(`Successfully stored SCAI search results for query: ${response.query}`);
+    } else {
+      logger.error("Failed to store JSON-LD to knowledge graph");
+    }
+  } catch (error) {
+    logger.error(`Error storing JSON-LD: ${error.message}`);
+  }
+
+  return jsonLdGraph;
+}