@sura_ai/mcp-server 0.2.4 → 0.2.5

package/dist/index.js

@@ -232,4 +232,4 @@ Library mode results include \`bestBlockId\` and smart \`retrievalHint\`:
 ${QI()}`),note:G.string().min(1).describe("REQUIRED rationale (§5.9c): a concise free-text justification for asserting this typed relation. Domain specificity lives here; the predicate stays universal. Stored in `relation_note`; the structural `role` is left untouched.")}),lu=ob.extend({note:G.string().optional()}),e0={name:"update_artifact_link_relation",description:["Set the TYPED, queryable SEMANTIC relation on an existing artifact ↔ source link (an `artifact_links` row) — the epistemic/methodological layer the structural roles (input/output/derived_from/referenced) cannot express.","Use this to record what a node/record actually *does* relative to a linked artifact: tests a hypothesis, supports/refutes a claim, replicates a prior run, supersedes/corrects an entity, uses a protocol, or characterizes a sample.","This is SEPARATE from `link_artifact_to_node` (which creates the row + sets the structural `role`). It keys on the join-row `artifactLinkId` and writes ONLY `relation_type`/`relation_note`; the structural `role` is never changed.","The eight predicates are deliberately tight and universal — pick the one whose argument structure matches; put domain specificity in the REQUIRED `note`, never by inventing a predicate (unknown predicates are rejected).","Predicates (disjoint from structural roles — NEVER pass a structural role here):",QI(),"Re-calling with the same `artifactLinkId` re-types the relation in place."].join(`
 `)};var db=G.object({edgeId:G.string().uuid().optional().describe("OPTIONAL. Present → RE-TYPE mode: the mention already carries this `edgeId` prop (an already-promoted edge); the tool re-edits the typed metadata in place (DB-only, no document write). Absent → PROMOTION mode: the mention is currently untyped; the tool locates the mention inline in the source entity, mints a fresh `edgeId` into it (the durable anchor), then writes the typed edge. Promotion needs WebSocket config; re-type does not."),sourceEntityId:G.string().uuid().describe("UUID of the document/record the mention lives in (the edge subject)."),sourceEntityType:G.enum(["document","record"]).describe("Type of the source entity (document or record)."),targetEntityId:G.string().uuid().describe("UUID of the mentioned entity (the edge object)."),targetEntityType:G.enum(["literature","document","record","artifact","matrix"]).describe("Type of the mentioned (target) entity."),blockId:G.string().optional().describe("PROMOTION mode only. Optional block scope: when set, only that block is searched for the target mention; when omitted, the whole source entity body is searched. Pass this to disambiguate when the same entity is mentioned in multiple blocks (the tool returns an `ambiguous_mention` error telling you to.) Ignored in re-type mode."),occurrence:G.number().int().min(0).optional().describe("PROMOTION mode only. 0-based index among matching mentions within the search scope (default 0 = first match). Pass this to disambiguate when a single block contains multiple mentions of the same target entity (the tool returns an `ambiguous_mention` error telling you to). Ignored in re-type mode."),relationType:a0.describe(`The relation predicate. One of the eight ratified, disjoint-from-structural predicates:
 ${QI()}`),note:G.string().min(1).describe("REQUIRED rationale (§5.9c): a concise free-text justification for asserting this typed edge. Domain specificity lives here; the predicate stays universal."),direction:G.enum(["forward","inverse"]).describe("Reading orientation (§6.2). `forward` = subject → object (the source entity tests/uses/etc. the mentioned entity — the usual case). `inverse` = object → subject (e.g. the mentioned reviewer note *refutes* this document). Storage always keeps source = subject; this only flips the reading.")}),cu=db.extend({edgeId:G.string().uuid(),note:G.string().optional()}),s0={name:"update_edge",description:["Promote a plain @mention into a TYPED, queryable, convergence-preserved relationship edge — the epistemic/methodological layer the structural links (input/output/derived_from/referenced) cannot express.","Use this to record what a run/analysis/result actually *does* relative to another entity: tests a hypothesis, supports/refutes a claim, replicates a prior run, supersedes/corrects an entity, uses a protocol, or characterizes a sample.","The eight predicates are deliberately tight and universal — pick the one whose argument structure matches; put domain specificity in the REQUIRED `note`, never by inventing a predicate (unknown predicates are rejected).","Predicates (disjoint from structural roles — NEVER pass a structural role here):",QI(),"Two modes: (a) PROMOTION — omit `edgeId`; the tool finds the @mention of `targetEntity` inside `sourceEntity`, writes a durable edge anchor into the document, then types the edge. Disambiguate with `blockId` and/or `occurrence` if the tool reports `ambiguous_mention`. (b) RE-TYPE — pass the existing `edgeId` (an already-promoted mention) to re-edit the typed metadata in place. Either way, the metadata survives every document convergence."].join(`
-`)};var mu=G.record(G.string(),G.union([G.string(),G.number(),G.boolean(),G.null()])).describe("Row match: every provided key/value must equal the row's current value. Matches all rows where the criteria hold (not just the first)."),ru=G.object({rowIndex:G.number().int().min(0).optional().describe("Target a single row by 0-based index in the current rows array."),rowMatch:mu.optional(),values:q1.describe("Partial row patch. **Keys MUST match `col.key` (the column id), NOT `col.label`.** Keys present here overwrite the matching rows' cells. Keys not in `values` retain their existing values. Set a key to null to clear a cell.")}).refine(($)=>{let I=$.rowIndex!==void 0,U=$.rowMatch!==void 0;return I!==U},{message:"Provide exactly one of `rowIndex` (absolute) or `rowMatch` (by column values).",path:["rowIndex"]}),S5=G.object({matrixId:G.string().uuid().describe("UUID of the target data_matrix."),updates:G.array(ru).min(1).describe("List of row patches. Each entry targets rows by `rowIndex` OR `rowMatch` and supplies a partial `values` patch."),version:G.number().int().min(0).describe("Current matrix version (optimistic locking). Must equal the server's stored version; otherwise returns a matrix_version_conflict error.")}),$D={name:"update_matrix_rows",description:["Patch cells in an existing data matrix. Each update targets rows by `rowIndex` (absolute 0-based) OR `rowMatch` (every provided column/value must equal the row's current cell); partial column updates are allowed.","**All row-keyed objects (`values`, `rowMatch`) MUST use `col.key` as the object key, NOT `col.label`.** Read the schema first via `get_content` on the owning entity — its matrix TOON shows `cols: key(Label,type[,unit])` and a `{key1,key2,...}` row header. Mismatched keys persist as opaque JSONB that the UI cannot render.","Match mode updates every row that satisfies the criteria — use it when the match is unique, or when you intend to update a whole group at once.","Bumps `version` on success; stale `version` returns a structured `matrix_version_conflict` error with the current server version so you can re-fetch and retry.","Set a `values` entry to null to clear a cell. Keys not present in `values` are untouched.","Only draft records are writable; completed/locked records return a `record_not_draft` error.",'**Stoichiometry matrices** (`kind=stoichiometry` in the matrix header): clearing a numeric cell to null re-enables client-side derivation via the chemistry identities (n = m/M, n = V·c, m = V·ρ·purity, n = stockMolarity·V, n = stockWtPercent·ρ_soln·V/M, n_i = equiv_i · n_limiting, equiv_i = n_i / n_limiting). Keys not in `values` stay untouched — use this to preserve the hidden `compoundId` link to a chemical artifact while patching other cells. Do not manually recompute derived quantities; write only measured or locked-in values. For aqueous stock solutions, set `stockMolarity` (mol/L) or `stockWtPercent` (0–100) rather than approximating via `purity` × `density`. The displayed `c` is computed against a per-row reference volume controlled by two hidden keys: `cBasis` (`null` | `"none"` | `"phase"` | `"total"` | `"manual"`; null = engine picks default by role+phase, "phase" = c relative to V_phase, "total" = c relative to V_total, "manual" = c relative to `cBasisManualVolume`, "none" = blank c) and `cBasisManualVolume` (mL, only used when cBasis="manual"). Leave both null unless the user explicitly set them.'].join(" ")};var j5=G.object({nodeId:G.string().uuid().describe("UUID of the existing procedure node to update."),label:G.string().min(1).optional().describe("New label (skip to keep existing)."),type:F1.optional().describe('New type (skip to keep existing). Changing type to "observation" forces copyable=false.'),copyable:G.boolean().optional().describe('Template-copyable flag. When the resulting type is "observation" this must be false (or omitted).'),analyticalData:G.array(E1).optional().describe("Replace the current `analyticalData` list with this one. Pass an empty array to clear it; omit to leave it untouched.")}).refine(($)=>{if($.type!=="observation")return!0;return $.copyable===void 0||$.copyable===!1},{message:'copyable must be false (or omitted) when type is "observation".',path:["copyable"]}).refine(($)=>$.label!==void 0||$.type!==void 0||$.copyable!==void 0||$.analyticalData!==void 0,{message:"Provide at least one field to update (label, type, copyable, analyticalData)."}),ID={name:"update_procedure_node",description:["Update non-structural fields of a procedure-tree node (label, type, copyable, analyticalData).","Structural changes (move / reorder) go through `reorder_procedure_nodes` — this tool never touches parentId or order.",'`type === "observation"` implies `copyable = false`; setting both to a conflicting combination is rejected.',"Passing an empty `analyticalData` array clears the file-ref list; omitting the field leaves it untouched.","Only draft records are writable; completed/locked records return a `record_not_draft` error."].join(" ")};var k5=[i0,g0,o0,d0,h0,K0,P0,T0,j0,k0,R0,S0,y0,x0,m0,F0,f0,ID,n0,Z0,v0,$D,E0,C0,r0,V0,l0,_0,u0,p0,c0,e0,s0,v5,b5,N5,M5,O5],nu=k5.map(($)=>$.name),iu=Object.fromEntries(k5.map(($)=>[$.name,$]));function P5($){return{content:[{type:"text",text:$}]}}function R5($){return{content:[{type:"text",text:$}],isError:!0}}function g($,I,U){let{definition:A,schema:D,createExecutor:w,formatOutput:b,formatError:N=(Q)=>Q.message,getLogMessage:O=(Q)=>JSON.stringify(Q).slice(0,100)}=U,X=w(I),W=D.shape;$.tool(A.name,A.description,W,async(Q)=>{let B=Q,Y=O(B);I.log.info(`${A.name}: ${Y}`);try{let J=await X(B),H=b(J,B);return I.log.info(`${A.name}: completed`),P5(H)}catch(J){let H=J instanceof Error?N(J,B):"Unknown error";return I.log.error(`${A.name} failed:`,J),R5(`${A.name} error: ${H}`)}})}function pb($,I,U){let{definition:A,schema:D,createExecutor:w,formatSuccess:b,formatNotFound:N=(B)=>JSON.stringify({found:!1,error:B.error??"Not 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literature: "${U.title.slice(0,30)}${U.title.length>30?"...":""}"${U.doi?` (DOI: ${U.doi})`:""}`})}function KF($,I){g($,I,{definition:P0,schema:v7,createExecutor:(U)=>{return async(A)=>{return await U.client.createMatrixFromArtifact(A)}},formatOutput:C7,getLogMessage:(U)=>`Deriving matrix from artifact ${U.artifactId.slice(0,8)}`})}function vF($,I){g($,I,{definition:R0,schema:V7,createExecutor:(U)=>{return async(A)=>{return await U.client.createRecord(A)}},formatOutput:h7,getLogMessage:(U)=>`Creating record: "${U.title.slice(0,30)}${U.title.length>30?"...":""}"${U.initialTree?` + ${U.initialTree.length} node(s)`:""}`})}function VF($,I){g($,I,{definition:T0,schema:rb,createExecutor:(U)=>{return async(A)=>{return await U.client.deleteBlock(A)}},formatOutput:x7,getLogMessage:(U)=>{if(U.blockIds&&U.blockIds.length>0)return`${U.entityType}/${U.entityId.slice(0,8)} batch delete ${U.blockIds.length} blocks`;return`${U.entityType}/${U.entityId.slice(0,8)} block ${U.blockId?.slice(0,8)??"unknown"}`}})}function qF($,I){g($,I,{definition:_0,schema:q7,createExecutor:(U)=>{return async(A)=>{return await U.client.deleteMatrix(A)}},formatOutput:a7,getLogMessage:(U)=>`Deleting matrix ${U.matrixId.slice(0,8)} (+ block)`})}function FF($,I){g($,I,{definition:C0,schema:F7,createExecutor:(U)=>{return async(A)=>{return await U.client.deleteMatrixRows(A)}},formatOutput:p7,getLogMessage:(U)=>{return`Deleting rows (${U.rowIndices?`${U.rowIndices.length} index(es)`:"match"}) from matrix ${U.matrixId.slice(0,8)}`}})}function EF($,I){g($,I,{definition:Z0,schema:E7,createExecutor:(U)=>{return async(A)=>{return await U.client.deleteProcedureNode(A)}},formatOutput:n7,getLogMessage:(U)=>`Deleting procedure node ${U.nodeId.slice(0,8)} (cascade)`})}function SF($,I){pb($,I,{definition:g0,schema:X5,createExecutor:(U)=>{return async(A)=>{return U.client.getContent(A)}},formatSuccess:P7,formatNotFound:(U)=>JSON.stringify({found:!1,error:U.error??"Entity not found"}),getLogMessage:(U)=>{let A=U.blockIds?`blocks:${U.blockIds.length}`:U.segment?`segment:"${U.segment}"`:U.from_section&&U.to_section?`range:"${U.from_section}"-"${U.to_section}"`:U.node?`node:"${U.node}"${U.depth!==void 0?`,depth=${U.depth}`:""}`:U.section?`section:"${U.section}"${U.depth!==void 0?`,depth=${U.depth}`:""}`:U.refs?`refs:${U.refs.length}`:"overview";return`${U.entityId.slice(0,8)}... (${A})`}})}function jF($,I){g($,I,{definition:x0,schema:W5,createExecutor:(U)=>{return async(A)=>{if(U.workspaceContext&&!A.forceRefresh)return U.workspaceContext;let D=await U.client.getWorkspaceContext();return U.workspaceContext=D,D}},formatOutput:S7,getLogMessage:(U)=>U.forceRefresh?"force refresh":"cached"})}function kF($,I){g($,I,{definition:h0,schema:ib,createExecutor:(U)=>{return async(A)=>{return await U.client.insertBlock(A)}},formatOutput:g7,getLogMessage:(U)=>{let A;if(U.parentBlockId)A=`in:${U.parentBlockId.slice(0,8)}`;else if(U.beforeBlockId)A=`before:${U.beforeBlockId.slice(0,8)}`;else if(U.afterBlockId)A=`after:${U.afterBlockId.slice(0,8)}`;else A="start";if(U.blocks&&U.blocks.length>0)return`${U.entityType}/${U.entityId.slice(0,8)} ${A} (batch: ${U.blocks.length} blocks)`;return`${U.entityType}/${U.entityId.slice(0,8)} ${A} (${U.blockType??"paragraph"})`}})}function PF($,I){g($,I,{definition:K0,schema:Y7,createExecutor:(U)=>{return async(A)=>{return await U.client.insertMatrix(A)}},formatOutput:(U)=>_7(U),getLogMessage:(U)=>`"${U.label.slice(0,30)}${U.label.length>30?"...":""}"`})}function RF($,I){g($,I,{definition:f0,schema:G5,createExecutor:(U)=>{return async(A)=>{return await U.client.insertProcedureNode(A)}},formatOutput:f7,getLogMessage:(U)=>`Inserting procedure node "${U.label.slice(0,30)}" into record ${U.recordId.slice(0,8)}`})}function TF($,I){g($,I,{definition:y0,schema:Q5,createExecutor:(U)=>{return async(A)=>{return await U.client.instantiateArtifactTemplate(A)}},formatOutput:c7,getLogMessage:(U)=>`Instantiating template ${U.templateId.slice(0,8)} → "${U.name}"`})}function _F($,I){g($,I,{definition:u0,schema:Y5,createExecutor:(U)=>{return async(A)=>{return await U.client.linkArtifactToNode(A)}},formatOutput:$5,getLogMessage:(U)=>`Linking artifact ${U.artifactId.slice(0,8)} → node ${U.nodeId.slice(0,8)} (${U.role})`})}function CF($,I){g($,I,{definition:l0,schema:B5,createExecutor:(U)=>{return async(A)=>{return await U.client.listMatrixReferences(A)}},formatOutput:s7,getLogMessage:(U)=>`Listing references for matrix ${U.matrixId.slice(0,8)}`})}function ZF($,I){g($,I,{definition:c0,schema:J5,createExecutor:(U)=>{return async(A)=>{return await U.client.listNodeArtifactLinks(A)}},formatOutput:A5,getLogMessage:(U)=>`Listing artifact links for node ${U.nodeId.slice(0,8)}`})}function gF($,I){g($,I,{definition:m0,schema:H5,createExecutor:(U)=>{return async(A)=>{return await U.client.listProcedureNodes(A)}},formatOutput:w5,getLogMessage:(U)=>`Listing procedure nodes for record ${U.recordId.slice(0,8)}`})}function xF($,I){g($,I,{definition:r0,schema:L5,createExecutor:(U)=>{return async(A)=>{return await U.client.rebindMatrixToNode(A)}},formatOutput:t7,getLogMessage:(U)=>{let A=U.nodeRef?U.nodeRef.slice(0,8):"(body)";return`Rebinding matrix ${U.matrixId.slice(0,8)} → ${A}`}})}function hF($,I){g($,I,{definition:n0,schema:z5,createExecutor:(U)=>{return async(A)=>{return await U.client.reorderProcedureNodes(A)}},formatOutput:r7,getLogMessage:(U)=>`Reordering ${U.moves.length} procedure node(s) in record ${U.recordId.slice(0,8)}`})}function ou($,I){if($>0){if($<0.5)return"high";if($<1.5)return"medium";return"low"}return I>0?"medium":"low"}function fF($,I){g($,I,{definition:i0,schema:K5,createExecutor:(U)=>{return async(A)=>{let D=A.mode??"library",w=A.limit??10;if(A.scope?.type==="artifact"&&D==="library"&&A.workspaceId){let X=await U.client.searchArtifacts({workspaceId:A.workspaceId,query:A.query,artifactType:A.artifactType,artifactStatus:A.artifactStatus,limit:w}),W=X.results.map((Q)=>{let B=Q.description?Q.description.length>100?`${Q.description.slice(0,97)}...`:Q.description:`${Q.artifactType}, ${Q.status}`;return{entityType:"artifact",entityId:Q.id,entityTitle:Q.name,matchCount:1,bestBlockId:"",snippet:B,relevance:"high",retrievalHint:{recommended:"overview",usage:`get_content(entityId="${Q.id}")`}}});return{mode:"library",found:W.length,results:W,hasMore:X.hasMore}}let b=await U.client.search({query:A.query,mode:D,entityType:A.scope?.type,entityId:A.scope?.entityId,orgId:A.orgId,workspaceId:A.workspaceId,spaceId:A.spaceId,limit:w,offset:0,authorName:A.authorName,yearMin:A.yearMin,yearMax:A.yearMax,journalName:A.journalName}),N=b.results??[];if(D==="library"){let X=N.map((W)=>{let{bestMatch:Q}=W,B=ou(Q.rank,W.matchCount),Y={entityType:W.entityType,entityId:W.entityId,entityTitle:W.entityTitle,matchCount:W.matchCount,bestBlockId:Q.blockId,snippet:Q.snippet,relevance:B,tags:W.tags,retrievalHint:Q.blockId?{recommended:"blockIds",usage:`blockIds=['${Q.blockId}']`}:{recommended:"overview",usage:"overview=true"}};if(W.literatureMetadata)Y.literatureMetadata=W.literatureMetadata;if(W.creatorId)Y.creatorId=W.creatorId;if(W.creatorName)Y.creatorName=W.creatorName;return Y});return{mode:"library",found:X.length,results:X,hasMore:b.hasMore}}let O=N.map((X)=>{let W={entityType:X.entityType,entityId:X.entityId,entityTitle:X.entityTitle,blockId:"blockId"in X?X.blockId:"",snippet:"snippet"in X?X.snippet:"",relevance:"medium",retrievalHint:{recommended:"blockIds",usage:`blockIds=['${"blockId"in X?X.blockId:""}']`}},Q=X.creatorId,B=X.creatorName;if(Q)W.creatorId=Q;if(B)W.creatorName=B;return W});return{mode:"blocks",found:O.length,results:O,hasMore:b.hasMore}}},formatOutput:(U)=>j7(U),getLogMessage:(U)=>U.query?`"${U.query}"`:"metadata filters"})}function yF($,I){pb($,I,{definition:o0,schema:V5,createExecutor:(U)=>{return async(A)=>{return U.client.situate(A)}},formatSuccess:k7,formatNotFound:(U)=>JSON.stringify({found:!1,error:U.error??"Entity not found"}),getLogMessage:(U)=>`${U.entityId.slice(0,8)}... (depth ${U.depth??2})`})}function uF($,I){g($,I,{definition:d0,schema:q5,createExecutor:(U)=>{return async(A)=>{return await U.client.strReplaceBlock(A)}},formatOutput:Z7,getLogMessage:(U)=>`${U.entityType}/${U.entityId.slice(0,8)} block ${U.blockId.slice(0,8)}`})}function lF($,I){g($,I,{definition:p0,schema:F5,createExecutor:(U)=>{return async(A)=>{return await U.client.unlinkArtifactFromNode(A)}},formatOutput:D5,getLogMessage:(U)=>`Unlinking artifact link ${U.linkId.slice(0,8)}`})}function cF($,I){g($,I,{definition:E0,schema:L7,createExecutor:(U)=>{return async(A)=>{return await U.client.updateArtifact(A)}},formatOutput:m7,getLogMessage:(U)=>`Updating artifact ${U.id.slice(0,8)}`})}function mF($,I){g($,I,{definition:e0,schema:ob,createExecutor:(U)=>{return async(A)=>{return await U.client.updateArtifactLinkRelation(A)}},formatOutput:U5,getLogMessage:(U)=>`Typing artifact link ${U.artifactLinkId.slice(0,8)} as "${U.relationType}"`})}function rF($,I){g($,I,{definition:s0,schema:db,createExecutor:(U)=>{return async(A)=>{return await U.client.updateEdge(A)}},formatOutput:I5,getLogMessage:(U)=>U.edgeId?`Re-typing edge ${U.edgeId.slice(0,8)} as "${U.relationType}" (${U.direction})`:`Promoting @mention → "${U.relationType}" edge (${U.direction})`})}function nF($,I){g($,I,{definition:$D,schema:S5,createExecutor:(U)=>{return async(A)=>{return await U.client.updateMatrixRows(A)}},formatOutput:d7,getLogMessage:(U)=>`Updating ${U.updates.length} row target(s) in matrix ${U.matrixId.slice(0,8)}`})}function iF($,I){g($,I,{definition:ID,schema:j5,createExecutor:(U)=>{return async(A)=>{return await U.client.updateProcedureNode(A)}},formatOutput:y7,getLogMessage:(U)=>`Updating procedure node ${U.nodeId.slice(0,8)}`})}function oF($,I){I.log.info("Registering tools..."),fF($,I),SF($,I),yF($,I),uF($,I),kF($,I),PF($,I),KF($,I),VF($,I),zF($,I),MF($,I),vF($,I),jF($,I),gF($,I),HF($,I),RF($,I),iF($,I),hF($,I),EF($,I),BF($,I),nF($,I),FF($,I),xF($,I),qF($,I),JF($,I),CF($,I),LF($,I),cF($,I),TF($,I),_F($,I),lF($,I),ZF($,I),mF($,I),rF($,I),I.log.info("All tools registered")}function du(){let $=process.argv.slice(2),I={};for(let U=0;U<$.length;U++){let A=$[U],D=$[U+1];if((A==="--api-key"||A==="-k")&&D)I.apiKey=D,U++;else if((A==="--api-url"||A==="-u")&&D)I.apiUrl=D,U++;else if(A==="--help"||A==="-h")process.exit(0)}return I}A4.info("Starting SURA MCP Server...");var dF=du(),pF=dF.apiKey??process.env.SURA_API_KEY,pu=dF.apiUrl??process.env.SURA_API_URL??"https://api.sura.science";if(!pF)A4.error("Missing API key. Set SURA_API_KEY environment variable or use --api-key flag."),A4.error("Get your API key at https://app.sura.science/settings/api-keys"),process.exit(1);var tu=await UV({apiUrl:pu,apiKey:pF}),tF=new pW({name:"sura",version:"0.1.0"});oF(tF,tu);var aF=new aW,eF=async($)=>{A4.info(`Received ${$}, shutting down...`),await aF.close(),process.exit(0)};process.on("SIGTERM",()=>eF("SIGTERM"));process.on("SIGINT",()=>eF("SIGINT"));process.on("uncaughtException",($)=>{A4.error("Uncaught exception:",$)});process.on("unhandledRejection",($)=>{A4.error("Unhandled rejection:",$)});A4.info("Connecting stdio transport...");await tF.connect(aF);A4.info("SURA MCP Server ready");
+`)};var mu=G.record(G.string(),G.union([G.string(),G.number(),G.boolean(),G.null()])).describe("Row match: every provided key/value must equal the row's current value. Matches all rows where the criteria hold (not just the first)."),ru=G.object({rowIndex:G.number().int().min(0).optional().describe("Target a single row by 0-based index in the current rows array."),rowMatch:mu.optional(),values:q1.describe("Partial row patch. **Keys MUST match `col.key` (the column id), NOT `col.label`.** Keys present here overwrite the matching rows' cells. Keys not in `values` retain their existing values. Set a key to null to clear a cell.")}).refine(($)=>{let I=$.rowIndex!==void 0,U=$.rowMatch!==void 0;return I!==U},{message:"Provide exactly one of `rowIndex` (absolute) or `rowMatch` (by column values).",path:["rowIndex"]}),S5=G.object({matrixId:G.string().uuid().describe("UUID of the target data_matrix."),updates:G.array(ru).min(1).describe("List of row patches. Each entry targets rows by `rowIndex` OR `rowMatch` and supplies a partial `values` patch."),version:G.number().int().min(0).describe("Current matrix version (optimistic locking). Must equal the server's stored version; otherwise returns a matrix_version_conflict error.")}),$D={name:"update_matrix_rows",description:["Patch cells in an existing data matrix. Each update targets rows by `rowIndex` (absolute 0-based) OR `rowMatch` (every provided column/value must equal the row's current cell); partial column updates are allowed.","**All row-keyed objects (`values`, `rowMatch`) MUST use `col.key` as the object key, NOT `col.label`.** Read the schema first via `get_content` on the owning entity — its matrix TOON shows `cols: key(Label,type[,unit])` and a `{key1,key2,...}` row header. Mismatched keys persist as opaque JSONB that the UI cannot render.","Match mode updates every row that satisfies the criteria — use it when the match is unique, or when you intend to update a whole group at once.","Bumps `version` on success; stale `version` returns a structured `matrix_version_conflict` error with the current server version so you can re-fetch and retry.","Set a `values` entry to null to clear a cell. Keys not present in `values` are untouched.","Only draft records are writable; completed/locked records return a `record_not_draft` error.",'**Stoichiometry matrices** (`kind=stoichiometry` in the matrix header): clearing a numeric cell to null re-enables client-side derivation via the chemistry identities (n = m/M, n = V·c, m = V·ρ·purity, n = stockMolarity·V, n = stockWtPercent·ρ_soln·V/M, n_i = equiv_i · n_limiting, equiv_i = n_i / n_limiting). Keys not in `values` stay untouched — use this to preserve the hidden `compoundId` link to a chemical artifact while patching other cells. Do not manually recompute derived quantities; write only measured or locked-in values. For aqueous stock solutions, set `stockMolarity` (mol/L) or `stockWtPercent` (0–100) rather than approximating via `purity` × `density`. The displayed `c` is computed against a per-row reference volume controlled by two hidden keys: `cBasis` (`null` | `"none"` | `"phase"` | `"total"` | `"manual"`; null = engine picks default by role+phase, "phase" = c relative to V_phase, "total" = c relative to V_total, "manual" = c relative to `cBasisManualVolume`, "none" = blank c) and `cBasisManualVolume` (mL, only used when cBasis="manual"). Leave both null unless the user explicitly set them.'].join(" ")};var j5=G.object({nodeId:G.string().uuid().describe("UUID of the existing procedure node to update."),label:G.string().min(1).optional().describe("New label (skip to keep existing)."),type:F1.optional().describe('New type (skip to keep existing). Changing type to "observation" forces copyable=false.'),copyable:G.boolean().optional().describe('Template-copyable flag. When the resulting type is "observation" this must be false (or omitted).'),analyticalData:G.array(E1).optional().describe("Replace the current `analyticalData` list with this one. Pass an empty array to clear it; omit to leave it untouched.")}).refine(($)=>{if($.type!=="observation")return!0;return $.copyable===void 0||$.copyable===!1},{message:'copyable must be false (or omitted) when type is "observation".',path:["copyable"]}).refine(($)=>$.label!==void 0||$.type!==void 0||$.copyable!==void 0||$.analyticalData!==void 0,{message:"Provide at least one field to update (label, type, copyable, analyticalData)."}),ID={name:"update_procedure_node",description:["Update non-structural fields of a procedure-tree node (label, type, copyable, analyticalData).","Structural changes (move / reorder) go through `reorder_procedure_nodes` — this tool never touches parentId or order.",'`type === "observation"` implies `copyable = false`; setting both to a conflicting combination is rejected.',"Passing an empty `analyticalData` array clears the file-ref list; omitting the field leaves it untouched.","Only draft records are writable; completed/locked records return a `record_not_draft` error."].join(" ")};var k5=[i0,g0,o0,d0,h0,K0,P0,T0,j0,k0,R0,S0,y0,x0,m0,F0,f0,ID,n0,Z0,v0,$D,E0,C0,r0,V0,l0,_0,u0,p0,c0,e0,s0,v5,b5,N5,M5,O5],nu=k5.map(($)=>$.name),iu=Object.fromEntries(k5.map(($)=>[$.name,$]));function P5($){return{content:[{type:"text",text:$}]}}function R5($){return{content:[{type:"text",text:$}],isError:!0}}function g($,I,U){let{definition:A,schema:D,createExecutor:w,formatOutput:b,formatError:N=(Q)=>Q.message,getLogMessage:O=(Q)=>JSON.stringify(Q).slice(0,100)}=U,X=w(I),W=D.shape;$.tool(A.name,A.description,W,async(Q)=>{let B=Q,Y=O(B);I.log.info(`${A.name}: ${Y}`);try{let J=await X(B),H=b(J,B);return I.log.info(`${A.name}: completed`),P5(H)}catch(J){let H=J instanceof Error?N(J,B):"Unknown error";return I.log.error(`${A.name} failed:`,J),R5(`${A.name} error: ${H}`)}})}function pb($,I,U){let{definition:A,schema:D,createExecutor:w,formatSuccess:b,formatNotFound:N=(B)=>JSON.stringify({found:!1,error:B.error??"Not 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U.client.insertMatrix(A)}},formatOutput:(U)=>_7(U),getLogMessage:(U)=>`"${U.label.slice(0,30)}${U.label.length>30?"...":""}"`})}function RF($,I){g($,I,{definition:f0,schema:G5,createExecutor:(U)=>{return async(A)=>{return await U.client.insertProcedureNode(A)}},formatOutput:f7,getLogMessage:(U)=>`Inserting procedure node "${U.label.slice(0,30)}" into record ${U.recordId.slice(0,8)}`})}function TF($,I){g($,I,{definition:y0,schema:Q5,createExecutor:(U)=>{return async(A)=>{return await U.client.instantiateArtifactTemplate(A)}},formatOutput:c7,getLogMessage:(U)=>`Instantiating template ${U.templateId.slice(0,8)} → "${U.name}"`})}function _F($,I){g($,I,{definition:u0,schema:Y5,createExecutor:(U)=>{return async(A)=>{return await U.client.linkArtifactToNode(A)}},formatOutput:$5,getLogMessage:(U)=>`Linking artifact ${U.artifactId.slice(0,8)} → node ${U.nodeId.slice(0,8)} (${U.role})`})}function CF($,I){g($,I,{definition:l0,schema:B5,createExecutor:(U)=>{return async(A)=>{return await U.client.listMatrixReferences(A)}},formatOutput:s7,getLogMessage:(U)=>`Listing references for matrix ${U.matrixId.slice(0,8)}`})}function ZF($,I){g($,I,{definition:c0,schema:J5,createExecutor:(U)=>{return async(A)=>{return await U.client.listNodeArtifactLinks(A)}},formatOutput:A5,getLogMessage:(U)=>`Listing artifact links for node ${U.nodeId.slice(0,8)}`})}function gF($,I){g($,I,{definition:m0,schema:H5,createExecutor:(U)=>{return async(A)=>{return await U.client.listProcedureNodes(A)}},formatOutput:w5,getLogMessage:(U)=>`Listing procedure nodes for record ${U.recordId.slice(0,8)}`})}function xF($,I){g($,I,{definition:r0,schema:L5,createExecutor:(U)=>{return async(A)=>{return await U.client.rebindMatrixToNode(A)}},formatOutput:t7,getLogMessage:(U)=>{let A=U.nodeRef?U.nodeRef.slice(0,8):"(body)";return`Rebinding matrix ${U.matrixId.slice(0,8)} → ${A}`}})}function hF($,I){g($,I,{definition:n0,schema:z5,createExecutor:(U)=>{return async(A)=>{return await U.client.reorderProcedureNodes(A)}},formatOutput:r7,getLogMessage:(U)=>`Reordering ${U.moves.length} procedure node(s) in record ${U.recordId.slice(0,8)}`})}function ou($,I){if($>0){if($<0.5)return"high";if($<1.5)return"medium";return"low"}return I>0?"medium":"low"}function fF($,I){g($,I,{definition:i0,schema:K5,createExecutor:(U)=>{return async(A)=>{let D=A.mode??"library",w=A.limit??10;if(A.scope?.type==="artifact"&&D==="library"&&A.workspaceId){let X=await U.client.searchArtifacts({workspaceId:A.workspaceId,query:A.query,artifactType:A.artifactType,artifactStatus:A.artifactStatus,limit:w}),W=X.results.map((Q)=>{let B=Q.description?Q.description.length>100?`${Q.description.slice(0,97)}...`:Q.description:`${Q.artifactType}, ${Q.status}`;return{entityType:"artifact",entityId:Q.id,entityTitle:Q.name,matchCount:1,bestBlockId:"",snippet:B,relevance:"high",retrievalHint:{recommended:"overview",usage:`get_content(entityId="${Q.id}")`}}});return{mode:"library",found:W.length,results:W,hasMore:X.hasMore}}let b=await U.client.search({query:A.query,mode:D,entityType:A.scope?.type,entityId:A.scope?.entityId,orgId:A.orgId,workspaceId:A.workspaceId,spaceId:A.spaceId,limit:w,offset:0,authorName:A.authorName,yearMin:A.yearMin,yearMax:A.yearMax,journalName:A.journalName}),N=b.results??[];if(D==="library"){let X=N.map((W)=>{let{bestMatch:Q}=W,B=ou(Q.rank,W.matchCount),Y={entityType:W.entityType,entityId:W.entityId,entityTitle:W.entityTitle,matchCount:W.matchCount,bestBlockId:Q.blockId,snippet:Q.snippet,relevance:B,tags:W.tags,retrievalHint:Q.blockId?{recommended:"blockIds",usage:`blockIds=['${Q.blockId}']`}:{recommended:"overview",usage:"overview=true"}};if(W.literatureMetadata)Y.literatureMetadata=W.literatureMetadata;if(W.creatorId)Y.creatorId=W.creatorId;if(W.creatorName)Y.creatorName=W.creatorName;if(W.updatedAt instanceof Date)Y.updatedAt=W.updatedAt.toISOString().slice(0,10);else if(typeof W.updatedAt==="string")Y.updatedAt=W.updatedAt.slice(0,10);return Y});return{mode:"library",found:X.length,results:X,hasMore:b.hasMore}}let O=N.map((X)=>{let W={entityType:X.entityType,entityId:X.entityId,entityTitle:X.entityTitle,blockId:"blockId"in X?X.blockId:"",snippet:"snippet"in X?X.snippet:"",relevance:"medium",retrievalHint:{recommended:"blockIds",usage:`blockIds=['${"blockId"in X?X.blockId:""}']`}},Q=X.creatorId,B=X.creatorName;if(Q)W.creatorId=Q;if(B)W.creatorName=B;return W});return{mode:"blocks",found:O.length,results:O,hasMore:b.hasMore}}},formatOutput:(U)=>j7(U),getLogMessage:(U)=>U.query?`"${U.query}"`:"metadata filters"})}function yF($,I){pb($,I,{definition:o0,schema:V5,createExecutor:(U)=>{return async(A)=>{return U.client.situate(A)}},formatSuccess:k7,formatNotFound:(U)=>JSON.stringify({found:!1,error:U.error??"Entity not found"}),getLogMessage:(U)=>`${U.entityId.slice(0,8)}... (depth ${U.depth??2})`})}function uF($,I){g($,I,{definition:d0,schema:q5,createExecutor:(U)=>{return async(A)=>{return await U.client.strReplaceBlock(A)}},formatOutput:Z7,getLogMessage:(U)=>`${U.entityType}/${U.entityId.slice(0,8)} block ${U.blockId.slice(0,8)}`})}function lF($,I){g($,I,{definition:p0,schema:F5,createExecutor:(U)=>{return async(A)=>{return await U.client.unlinkArtifactFromNode(A)}},formatOutput:D5,getLogMessage:(U)=>`Unlinking artifact link ${U.linkId.slice(0,8)}`})}function cF($,I){g($,I,{definition:E0,schema:L7,createExecutor:(U)=>{return async(A)=>{return await U.client.updateArtifact(A)}},formatOutput:m7,getLogMessage:(U)=>`Updating artifact ${U.id.slice(0,8)}`})}function mF($,I){g($,I,{definition:e0,schema:ob,createExecutor:(U)=>{return async(A)=>{return await U.client.updateArtifactLinkRelation(A)}},formatOutput:U5,getLogMessage:(U)=>`Typing artifact link ${U.artifactLinkId.slice(0,8)} as "${U.relationType}"`})}function rF($,I){g($,I,{definition:s0,schema:db,createExecutor:(U)=>{return async(A)=>{return await U.client.updateEdge(A)}},formatOutput:I5,getLogMessage:(U)=>U.edgeId?`Re-typing edge ${U.edgeId.slice(0,8)} as "${U.relationType}" (${U.direction})`:`Promoting @mention → "${U.relationType}" edge (${U.direction})`})}function nF($,I){g($,I,{definition:$D,schema:S5,createExecutor:(U)=>{return async(A)=>{return await U.client.updateMatrixRows(A)}},formatOutput:d7,getLogMessage:(U)=>`Updating ${U.updates.length} row target(s) in matrix ${U.matrixId.slice(0,8)}`})}function iF($,I){g($,I,{definition:ID,schema:j5,createExecutor:(U)=>{return async(A)=>{return await U.client.updateProcedureNode(A)}},formatOutput:y7,getLogMessage:(U)=>`Updating procedure node ${U.nodeId.slice(0,8)}`})}function oF($,I){I.log.info("Registering tools..."),fF($,I),SF($,I),yF($,I),uF($,I),kF($,I),PF($,I),KF($,I),VF($,I),zF($,I),MF($,I),vF($,I),jF($,I),gF($,I),HF($,I),RF($,I),iF($,I),hF($,I),EF($,I),BF($,I),nF($,I),FF($,I),xF($,I),qF($,I),JF($,I),CF($,I),LF($,I),cF($,I),TF($,I),_F($,I),lF($,I),ZF($,I),mF($,I),rF($,I),I.log.info("All tools registered")}function du(){let $=process.argv.slice(2),I={};for(let U=0;U<$.length;U++){let A=$[U],D=$[U+1];if((A==="--api-key"||A==="-k")&&D)I.apiKey=D,U++;else if((A==="--api-url"||A==="-u")&&D)I.apiUrl=D,U++;else if(A==="--help"||A==="-h")process.exit(0)}return I}A4.info("Starting SURA MCP Server...");var dF=du(),pF=dF.apiKey??process.env.SURA_API_KEY,pu=dF.apiUrl??process.env.SURA_API_URL??"https://api.sura.science";if(!pF)A4.error("Missing API key. Set SURA_API_KEY environment variable or use --api-key flag."),A4.error("Get your API key at https://app.sura.science/settings/api-keys"),process.exit(1);var tu=await UV({apiUrl:pu,apiKey:pF}),tF=new pW({name:"sura",version:"0.1.0"});oF(tF,tu);var aF=new aW,eF=async($)=>{A4.info(`Received ${$}, shutting down...`),await aF.close(),process.exit(0)};process.on("SIGTERM",()=>eF("SIGTERM"));process.on("SIGINT",()=>eF("SIGINT"));process.on("uncaughtException",($)=>{A4.error("Uncaught exception:",$)});process.on("unhandledRejection",($)=>{A4.error("Unhandled rejection:",$)});A4.info("Connecting stdio transport...");await tF.connect(aF);A4.info("SURA MCP Server ready");

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sura_ai/mcp-server",
-  "version": "0.2.4",
+  "version": "0.2.5",
   "description": "SURA MCP server - search, read, and edit your research workspace from any AI assistant",
   "type": "module",
   "bin": {