@sura_ai/mcp-server 0.1.20 → 0.1.21

package/dist/index.js

@@ -60,9 +60,9 @@ ${N}
 +++ after
 ${A}`}function q3($){let X=[];X.push(`[workspace context | default org:${$.defaults.orgId}${$.defaults.workspaceId?` ws:${$.defaults.workspaceId}`:""}]`);let W=0,Q=[];for(let G of $.orgs)for(let Y of G.workspaces)if(Y.spaces.length===0)Q.push(c1([G.name,G.id,Y.name,Y.id,Y.type,"","",""])),W++;else for(let U of Y.spaces)Q.push(c1([G.name,G.id,Y.name,Y.id,Y.type,U.name,U.id,U.type])),W++;return X.push(`{org,orgId,workspace,wsId,wsType,space,spaceId,spaceType}[${W}]:`),X.push(...Q),X.join(`
 `)}function L3($){let{mode:X,found:W,hasMore:Q}=$;if(W===0)return`[results:0 found, ${X}]
-No results.`;let G=[X,...Q?["hasMore"]:[]].join(", "),Y=[`[results:${W} found, ${G}]`];if(X==="library"){let U=$.results,J=U.some((z)=>z.literatureMetadata),H=J?"{type,title,id,relevance,doi,firstAuthor,year,journal,snippet}":"{type,title,id,relevance,snippet}";Y.push(`${H}[${U.length}]:`);for(let z of U){let B=z.bestSnippet??z.snippet??"",D=B.length>120?`${B.slice(0,117)}...`:B;if(J){let w=z.literatureMetadata;Y.push(c1([z.entityType,z.entityTitle,z.entityId,z.relevance,w?.doi??"",w?.firstAuthor??"",w?.year??"",w?.journal??"",D]))}else Y.push(c1([z.entityType,z.entityTitle,z.entityId,z.relevance,D]))}}else{let U=$.results;Y.push(`{type,title,entityId,blockId,snippet}[${U.length}]:`);for(let J of U){let H=J.bestSnippet??J.snippet??"",z=H.length>120?`${H.slice(0,117)}...`:H;Y.push(c1([J.entityType,J.entityTitle,J.entityId,J.blockId,z]))}}return Y.join(`
+No results.`;let G=[X,...Q?["hasMore"]:[]].join(", "),Y=[`[results:${W} found, ${G}]`];if(X==="library"){let U=$.results,J=U.some((z)=>z.literatureMetadata),H=J?"{type,title,id,relevance,tags,doi,firstAuthor,year,journal,snippet}":"{type,title,id,relevance,tags,snippet}";Y.push(`${H}[${U.length}]:`);for(let z of U){let B=z.bestSnippet??z.snippet??"",D=B.length>120?`${B.slice(0,117)}...`:B,w=z.tags?.join(" | ")??"";if(J){let N=z.literatureMetadata;Y.push(c1([z.entityType,z.entityTitle,z.entityId,z.relevance,w,N?.doi??"",N?.firstAuthor??"",N?.year??"",N?.journal??"",D]))}else Y.push(c1([z.entityType,z.entityTitle,z.entityId,z.relevance,w,D]))}}else{let U=$.results;Y.push(`{type,title,entityId,blockId,snippet}[${U.length}]:`);for(let J of U){let H=J.bestSnippet??J.snippet??"",z=H.length>120?`${H.slice(0,117)}...`:H;Y.push(c1([J.entityType,J.entityTitle,J.entityId,J.blockId,z]))}}return Y.join(`
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-`)}function rv($,X){return`${{literature:"lit",document:"doc",record:"rec",artifact:"art"}[$]??$.slice(0,3)}-${X.slice(0,8)}`}function I3($){let X=[];if(X.push(`**"${$.entityTitle}"** - ${$.entityType}`),$.bibliographic){let W=$.bibliographic,Q=[];if(W.authors?.length)Q.push(W.authors.length<=3?W.authors.join(", "):`${W.authors[0]} et al.`);if(W.journal)Q.push(W.journal);if(W.volume){let G=W.volume;if(W.issue)G+=`(${W.issue})`;if(W.pages)G+=`, ${W.pages}`;Q.push(G)}if(W.year)Q.push(String(W.year));if(Q.length>0)X.push(Q.join(", "));if(W.doi)X.push(`DOI: ${W.doi}`);if(W.pmid)X.push(`PMID: ${W.pmid}`);if(W.arxivId)X.push(`arXiv: ${W.arxivId}`)}if($.error)return X.push(""),X.push(`**Error:** ${$.error}`),X.join(`
+`)}function rv($,X){return`${{literature:"lit",document:"doc",record:"rec",artifact:"art"}[$]??$.slice(0,3)}-${X.slice(0,8)}`}function I3($){let X=[];if(X.push(`**"${$.entityTitle}"** - ${$.entityType}`),$.bibliographic){let W=$.bibliographic,Q=[];if(W.authors?.length)Q.push(W.authors.length<=3?W.authors.join(", "):`${W.authors[0]} et al.`);if(W.journal)Q.push(W.journal);if(W.volume){let G=W.volume;if(W.issue)G+=`(${W.issue})`;if(W.pages)G+=`, ${W.pages}`;Q.push(G)}if(W.year)Q.push(String(W.year));if(Q.length>0)X.push(Q.join(", "));if(W.doi)X.push(`DOI: ${W.doi}`);if(W.pmid)X.push(`PMID: ${W.pmid}`);if(W.arxivId)X.push(`arXiv: ${W.arxivId}`);if(W.tags&&W.tags.length>0)X.push(`Tags: ${W.tags.join(", ")}`)}if($.error)return X.push(""),X.push(`**Error:** ${$.error}`),X.join(`
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 `)}function V3($){if(!$.success)return`Failed to create document: ${$.error}`;return`Document created successfully.
 Title: ${$.title}
@@ -116,7 +116,7 @@ Batch mode: provide blocks array for multiple blocks in one call (more efficient
 - Add paragraph: \`insert_block(afterBlockId="...", content="New text")\`
 - Add heading: \`insert_block(afterBlockId="...", blockType="heading", headingLevel=2, content="Methods")\`
 - Add checklist: \`insert_block(afterBlockId="...", blockType="checkListItem", checked=false, content="Run analysis")\`
-- Batch insert section: \`insert_block(afterBlockId="...", blocks=[{blockType:"heading", headingLevel:2, content:"Results"}, {blockType:"paragraph", content:"We observed..."}])\``};var S3=b.object({query:b.string().min(1).optional().describe("Search query keywords"),mode:b.enum(["library","blocks"]).default("library").describe('Search mode: "library" returns unique entities (papers/docs), "blocks" returns block-level results'),scope:b.object({type:b.enum(["literature","document","record","artifact"]).optional().describe("Filter by entity type"),entityId:b.string().uuid().optional().describe("Search within specific entity (blocks mode only)")}).optional().describe("Optional scope to narrow search"),orgId:b.string().uuid().optional().describe("Organization ID - use the one from workspace context"),workspaceId:b.string().uuid().optional().describe("Filter by workspace ID"),spaceId:b.string().uuid().optional().describe("Filter by space ID"),limit:b.number().min(1).max(50).default(10).describe("Max results. Default: 10"),authorName:b.string().optional().describe('Filter by author name (partial match). Example: "Shen" finds papers by authors named Shen'),journalName:b.string().optional().describe('Filter by journal name (partial match). Example: "Nano Letters" finds papers from Nano Letters'),yearMin:b.number().int().min(1900).max(2100).optional().describe("Minimum publication year (inclusive)"),yearMax:b.number().int().min(1900).max(2100).optional().describe("Maximum publication year (inclusive)"),artifactType:b.string().optional().describe('Filter by artifact type: "sample", "dataset", "protocol", "file", "equipment", "chemical", "model"'),artifactStatus:b.string().optional().describe('Filter by artifact status: "active", "depleted", "archived", "draft"')}),S9={name:"search",description:`Search across literature, documents, records, and artifacts.
+- Batch insert section: \`insert_block(afterBlockId="...", blocks=[{blockType:"heading", headingLevel:2, content:"Results"}, {blockType:"paragraph", content:"We observed..."}])\``};var S3=b.object({query:b.string().min(1).optional().describe("Search query keywords"),mode:b.enum(["library","blocks"]).default("library").describe('Search mode: "library" returns unique entities (papers/docs), "blocks" returns block-level results'),scope:b.object({type:b.enum(["literature","document","record","artifact"]).optional().describe("Filter by entity type"),entityId:b.string().uuid().optional().describe("Search within specific entity (blocks mode only)")}).optional().describe("Optional scope to narrow search"),orgId:b.string().uuid().optional().describe("Organization ID - use the one from workspace context"),workspaceId:b.string().uuid().optional().describe("Filter by workspace ID"),spaceId:b.string().uuid().optional().describe("Filter by space ID"),limit:b.number().min(1).max(50).default(10).describe("Max results. Default: 10"),authorName:b.string().optional().describe('Filter by author name (partial match). Example: "Shen" finds papers by authors named Shen'),journalName:b.string().optional().describe('Filter by journal name (partial match). Example: "Nano Letters" finds papers from Nano Letters'),yearMin:b.number().int().min(1900).max(2100).optional().describe("Minimum publication year (inclusive)"),yearMax:b.number().int().min(1900).max(2100).optional().describe("Maximum publication year (inclusive)"),tags:b.array(b.string()).optional().describe("Filter by tags. Matches entities that have any of the provided tags."),artifactType:b.string().optional().describe('Filter by artifact type: "sample", "dataset", "protocol", "file", "equipment", "chemical", "model"'),artifactStatus:b.string().optional().describe('Filter by artifact status: "active", "depleted", "archived", "draft"')}),S9={name:"search",description:`Search across literature, documents, records, and artifacts.
 
 **Modes:**
 - \`library\` (default): Returns unique entities ranked by relevance. Use when browsing/discovering.
@@ -149,9 +149,11 @@ Batch mode: provide blocks array for multiple blocks in one call (more efficient
 - \`authorName\`: Filter by author (partial match, e.g., "Shen" finds authors named Shen)
 - \`journalName\`: Filter by journal (partial match)
 - \`yearMin\`/\`yearMax\`: Filter by publication year range
+- \`tags\`: Filter by document/record/literature tags
 
 These filters can be combined with \`query\` to narrow content search results:
 \`search(query="catalysis", authorName="Shen")\` -> Papers by Shen mentioning catalysis
+\`search(workspaceId="...", tags=["teaching", "rag"])\` -> Tagged entities in that workspace
 
 **Artifact Search:**
 Search artifacts (samples, chemicals, equipment, etc.) by name and type/status:
@@ -163,4 +165,4 @@ Requires \`workspaceId\`. Returns artifact names, types, and retrieval hints.
 **Retrieval Hints:**
 Library mode results include \`bestBlockId\` and smart \`retrievalHint\`:
 - High relevance: Jump directly to the best block via \`blockIds=['bestBlockId']\`
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Set SURA_API_KEY environment variable or use --api-key flag."),R4.error("Get your API key at https://app.sura.science/settings/api-keys"),process.exit(1);var jl=await pF({apiUrl:Sl,apiKey:UE}),JE=new tH({name:"sura",version:"0.1.0"});QE(JE,jl);var HE=new eH,zE=async($)=>{R4.info(`Received ${$}, shutting down...`),await HE.close(),process.exit(0)};process.on("SIGTERM",()=>zE("SIGTERM"));process.on("SIGINT",()=>zE("SIGINT"));process.on("uncaughtException",($)=>{R4.error("Uncaught exception:",$)});process.on("unhandledRejection",($)=>{R4.error("Unhandled rejection:",$)});R4.info("Connecting stdio transport...");await JE.connect(HE);R4.info("SURA MCP Server ready");
+- Medium/Low relevance: Start with \`overview=true\` to explore structure first`};var j3=b.object({entityType:m1.describe('Entity type: "document" or "record"'),entityId:b.string().uuid().describe("Document or record ID"),blockId:b.string().describe("Block ID to edit"),oldText:b.string().describe("Exact text to find and replace (must match exactly)"),newText:b.string().describe("Text to replace with")}),j9={name:"str_replace_block",description:"Replace text content in a specific block. Works like Claude Code str_replace - find exact text and replace it. oldText must match exactly (case-sensitive). Use get_content first to see exact block content. Content supports SURA markdown inline syntax: **bold**, *italic*, ~~strike~~, `code`, {u}underline{/u}, {color:red}text color{/color}, {bg:yellow}background{/bg}. 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(${Q})`}})}function $E($,X){A6($,X,{definition:v9,schema:E3,createExecutor:(W)=>{return async(Q)=>{if(W.workspaceContext&&!Q.forceRefresh)return W.workspaceContext;let G=await W.client.getWorkspaceContext();return W.workspaceContext=G,G}},formatOutput:q3,getLogMessage:(W)=>W.forceRefresh?"force refresh":"cached"})}function XE($,X){A6($,X,{definition:E9,schema:RY,createExecutor:(W)=>{return async(Q)=>{return await W.client.insertBlock(Q)}},formatOutput:F3,getLogMessage:(W)=>{let Q;if(W.parentBlockId)Q=`in:${W.parentBlockId.slice(0,8)}`;else if(W.beforeBlockId)Q=`before:${W.beforeBlockId.slice(0,8)}`;else if(W.afterBlockId)Q=`after:${W.afterBlockId.slice(0,8)}`;else Q="start";if(W.blocks&&W.blocks.length>0)return`${W.entityType}/${W.entityId.slice(0,8)} ${Q} (batch: ${W.blocks.length} blocks)`;return`${W.entityType}/${W.entityId.slice(0,8)} ${Q} (${W.blockType??"paragraph"})`}})}function vl($,X){if($>0){if($<0.5)return"high";if($<1.5)return"medium";return"low"}return X>0?"medium":"low"}function WE($,X){A6($,X,{definition:S9,schema:S3,createExecutor:(W)=>{return async(Q)=>{let G=Q.mode??"library",Y=Q.limit??10;if(Q.scope?.type==="artifact"&&G==="library"&&Q.workspaceId){let z=await W.client.searchArtifacts({workspaceId:Q.workspaceId,query:Q.query,artifactType:Q.artifactType,artifactStatus:Q.artifactStatus,limit:Y}),B=z.results.map((D)=>{let w=D.description?D.description.length>100?`${D.description.slice(0,97)}...`:D.description:`${D.artifactType}, ${D.status}`;return{entityType:"artifact",entityId:D.id,entityTitle:D.name,matchCount:1,bestBlockId:"",snippet:w,relevance:"high",retrievalHint:{recommended:"overview",usage:`get_content(entityId="${D.id}")`}}});return{mode:"library",found:B.length,results:B,hasMore:z.hasMore}}let U=await W.client.search({query:Q.query,mode:G,entityType:Q.scope?.type,entityId:Q.scope?.entityId,orgId:Q.orgId,workspaceId:Q.workspaceId,spaceId:Q.spaceId,limit:Y,offset:0,authorName:Q.authorName,yearMin:Q.yearMin,yearMax:Q.yearMax,journalName:Q.journalName,tags:Q.tags}),J=U.results??[];if(G==="library"){let z=J.map((B)=>{let{bestMatch:D}=B,w=vl(D.rank,B.matchCount),N={entityType:B.entityType,entityId:B.entityId,entityTitle:B.entityTitle,matchCount:B.matchCount,bestBlockId:D.blockId,snippet:D.snippet,relevance:w,tags:B.tags,retrievalHint:D.blockId?{recommended:"blockIds",usage:`blockIds=['${D.blockId}']`}:{recommended:"overview",usage:"overview=true"}};if(B.literatureMetadata)N.literatureMetadata=B.literatureMetadata;return N});return{mode:"library",found:z.length,results:z,hasMore:U.hasMore}}let H=J.map((z)=>({entityType:z.entityType,entityId:z.entityId,entityTitle:z.entityTitle,blockId:"blockId"in z?z.blockId:"",snippet:"snippet"in z?z.snippet:"",relevance:"medium",retrievalHint:{recommended:"blockIds",usage:`blockIds=['${"blockId"in z?z.blockId:""}']`}}));return{mode:"blocks",found:H.length,results:H,hasMore:U.hasMore}}},formatOutput:(W)=>L3(W),getLogMessage:(W)=>W.query?`"${W.query}"`:"metadata filters"})}function GE($,X){A6($,X,{definition:j9,schema:j3,createExecutor:(W)=>{return async(Q)=>{return await W.client.strReplaceBlock(Q)}},formatOutput:K3,getLogMessage:(W)=>`${W.entityType}/${W.entityId.slice(0,8)} block ${W.blockId.slice(0,8)}`})}function QE($,X){X.log.info("Registering tools..."),WE($,X),sv($,X),GE($,X),XE($,X),ev($,X),tv($,X),av($,X),$E($,X),X.log.info("All tools registered")}function El(){let $=process.argv.slice(2),X={};for(let W=0;W<$.length;W++){let Q=$[W],G=$[W+1];if((Q==="--api-key"||Q==="-k")&&G)X.apiKey=G,W++;else if((Q==="--api-url"||Q==="-u")&&G)X.apiUrl=G,W++;else if(Q==="--help"||Q==="-h")process.exit(0)}return X}R4.info("Starting SURA MCP Server...");var YE=El(),UE=YE.apiKey??process.env.SURA_API_KEY,Sl=YE.apiUrl??process.env.SURA_API_URL??"https://api.sura.science";if(!UE)R4.error("Missing API key. Set SURA_API_KEY environment variable or use --api-key flag."),R4.error("Get your API key at https://app.sura.science/settings/api-keys"),process.exit(1);var jl=await pF({apiUrl:Sl,apiKey:UE}),JE=new tH({name:"sura",version:"0.1.0"});QE(JE,jl);var HE=new eH,zE=async($)=>{R4.info(`Received ${$}, shutting down...`),await HE.close(),process.exit(0)};process.on("SIGTERM",()=>zE("SIGTERM"));process.on("SIGINT",()=>zE("SIGINT"));process.on("uncaughtException",($)=>{R4.error("Uncaught exception:",$)});process.on("unhandledRejection",($)=>{R4.error("Unhandled rejection:",$)});R4.info("Connecting stdio transport...");await JE.connect(HE);R4.info("SURA MCP Server ready");

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sura_ai/mcp-server",
-  "version": "0.1.20",
+  "version": "0.1.21",
   "description": "SURA MCP server - search, read, and edit your research workspace from any AI assistant",
   "type": "module",
   "bin": {