@seqyuan/annodex 0.1.15 → 0.1.17

package/.next/server/app/page_client-reference-manifest.js

@@ -1 +1 @@
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package/.next/server/app-paths-manifest.json

@@ -17,23 +17,23 @@
   "/api/sessions/route": "app/api/sessions/route.js",
   "/api/soul/route": "app/api/soul/route.js",
   "/api/agent/[id]/events/route": "app/api/agent/[id]/events/route.js",
-  "/api/auth/api-key/[provider]/route": "app/api/auth/api-key/[provider]/route.js",
   "/api/auth/login/[provider]/route": "app/api/auth/login/[provider]/route.js",
   "/api/auth/logout/[provider]/route": "app/api/auth/logout/[provider]/route.js",
+  "/api/auth/api-key/[provider]/route": "app/api/auth/api-key/[provider]/route.js",
   "/api/auth/all-providers/route": "app/api/auth/all-providers/route.js",
   "/api/auth/providers/route": "app/api/auth/providers/route.js",
-  "/api/models-config/discover/route": "app/api/models-config/discover/route.js",
   "/api/internal/runtime/route": "app/api/internal/runtime/route.js",
+  "/api/models-config/discover/route": "app/api/models-config/discover/route.js",
   "/api/models-config/route": "app/api/models-config/route.js",
-  "/api/models/route": "app/api/models/route.js",
   "/api/models-config/test/route": "app/api/models-config/test/route.js",
   "/api/reports/[id]/route": "app/api/reports/[id]/route.js",
-  "/api/sessions/[id]/route": "app/api/sessions/[id]/route.js",
+  "/api/models/route": "app/api/models/route.js",
   "/api/settings/route": "app/api/settings/route.js",
+  "/api/sessions/[id]/route": "app/api/sessions/[id]/route.js",
+  "/api/skills/install/route": "app/api/skills/install/route.js",
   "/api/version/route": "app/api/version/route.js",
-  "/api/skills/route": "app/api/skills/route.js",
   "/api/skills/search/route": "app/api/skills/search/route.js",
-  "/api/skills/install/route": "app/api/skills/install/route.js",
+  "/api/skills/route": "app/api/skills/route.js",
   "/login/page": "app/login/page.js",
   "/page": "app/page.js"
 }

package/.next/server/chunks/402.js

@@ -1,2 +1,2 @@
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package/.next/server/chunks/5399.js

@@ -1,8 +1,8 @@
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package/.next/server/chunks/6429.js

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a=d.mimeType||"image/png";c.push({type:"image",url:`data:${a};base64,${d.data}`})}return c.length>0?c:[{type:"text",text:"",text_elements:[]}]}(a,b),...this.cwd?{cwd:this.cwd}:{},...(this._wireModel??this._currentModel)?.modelId?{model:(this._wireModel??this._currentModel).modelId}:{},...(this._wireModel??this._currentModel)?.provider?{modelProvider:(this._wireModel??this._currentModel).provider}:{},approvalPolicy:"never",sandboxPolicy:{type:"workspaceWrite",writableRoots:[this.cwd],readOnlyAccess:{type:"fullAccess"},networkAccess:!0,excludeTmpdirEnvVar:!1,excludeSlashTmp:!1}});this._activeTurnId=c.turn?.id??null}catch(a){this._isStreaming=!1,this.emit({type:"agent_end",error:a instanceof Error?a.message:String(a)})}}async abort(){if(this._activeTurnId)try{await this.connection.request("turn/interrupt",{threadId:this.threadId,turnId:this._activeTurnId})}catch{}this._isStreaming=!1,this._activeTurnId=null}async 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this.connection.request("thread/name/set",{threadId:this.threadId,name:a})}catch{}}destroy(){if(this._alive){for(let a of(this._alive=!1,this._isStreaming=!1,this.cleanupFns))try{a()}catch{}this.cleanupFns=[],this.listeners=[]}}}async function j(a,b){let c=await a.request("thread/start",{cwd:b.cwd,...b.baseInstructions?{baseInstructions:b.baseInstructions}:{},...b.model?{model:(b.wireModel??b.model).modelId,modelProvider:(b.wireModel??b.model).provider}:{},approvalPolicy:"never",sandbox:"workspace-write",experimentalRawEvents:!1,persistExtendedHistory:!0}),d=c.thread?.id;if(!d)throw Error("Failed to create codex thread: no thread.id returned");let f=new l(d,b.cwd,a,b.baseInstructions);return b.model?f.setModel(b.model.provider,b.model.modelId,b.wireModel):b.acceptReturnedModel&&c.model&&f.setModel((0,e.g8)(c.modelProvider)??"codex",c.model,c.modelProvider?{provider:c.modelProvider,modelId:c.model}:void 0),f}async function k(a,b,c){let d=null,f=await a.request("thread/read",{threadId:b,includeTurns:!0});f?.model&&(d={provider:(0,e.g8)(f.modelProvider??f.thread?.modelProvider)??"codex",modelId:f.model});let g=new l(b,c,a);return d&&g.setModel(d.provider,d.modelId),g.restoreActiveTurnFromThread(f.thread),g}d()}catch(a){d(a)}})},56429:(a,b,c)=>{c.a(a,async(a,d)=>{try{c.d(b,{A4:()=>t,Bj:()=>u,OF:()=>v});var e=c(11002),f=c(46983),g=c(55132),h=c(9805),i=c(71887),j=c(29021),k=c(33873),l=c(21820),m=c(40402),n=c(26257),o=c(72801),p=a([e,f,m]);[e,f,m]=p.then?(await p)():p;class w{constructor(a){this.inner=a,this.listeners=[],this.cleanupEventSub=null,this.idleTimer=null,this.onDestroyCallback=null,this.busyOperations=new Set,this._alive=!0,this._thinkingLevel="auto",this._serverConnection=a.connection}get sessionId(){return this.inner.sessionId}get sessionFile(){return this.inner.sessionFile}get cwd(){return this.inner.cwd}isAlive(){return this._alive&&this.inner.isAlive}isBusy(){return this.busyOperations.size>0||this.inner.isStreaming||this.inner.isCompacting}getRuntimeStatus(){return{sessionId:this.sessionId,sessionFile:this.sessionFile,busy:this.isBusy(),operations:[...this.busyOperations],isStreaming:this.inner.isStreaming,isCompacting:this.inner.isCompacting}}start(){this.cleanupEventSub?.(),this.cleanupEventSub=this.inner.onEvent(a=>{for(let b of(this.resetIdleTimer(),this.listeners))b(a)}),this.resetIdleTimer()}resetIdleTimer(){this.idleTimer&&clearTimeout(this.idleTimer),this.idleTimer=setTimeout(()=>{this.isBusy()?this.resetIdleTimer():this.destroy()},6e5)}onEvent(a){return this.listeners.push(a),()=>{let b=this.listeners.indexOf(a);-1!==b&&this.listeners.splice(b,1)}}onDestroy(a){this.onDestroyCallback=a}async send(a){this.resetIdleTimer();let b=a.type;switch(b){case"prompt":{if(this.inner.isStreaming)throw Error("Session already has a running turn");let b=a.images,c=a.message;return this.trackBusy("prompt",this.inner.prompt(c,b?.map(a=>({data:a.data,mimeType:a.mimeType})))).catch(()=>{}),null}case"abort":return await this.inner.abort(),null;case"get_state":{let a=(0,o.l)((0,m.bd)(this.inner.sessionId),this.inner.model?.modelId);return{sessionId:this.inner.sessionId,sessionFile:"",isStreaming:this.inner.isStreaming,isCompacting:this.inner.isCompacting,autoCompactionEnabled:!0,autoRetryEnabled:!0,model:this.inner.model?{id:this.inner.model.modelId,provider:this.inner.model.provider,...a.contextUsage?.contextWindow?{contextWindow:a.contextUsage.contextWindow}:{}}:void 0,messageCount:0,pendingMessageCount:0,contextUsage:a.contextUsage,systemPrompt:this.inner.baseInstructions??"",thinkingLevel:this._thinkingLevel}}case"set_model":{let{provider:b,modelId:c}=a,d=(0,g.Dw)(),e=(0,g.wB)(d,b),h=(0,g.AX)(d,c,e??b),i=h?.provider.id??e??b,j=h?.modelId??c,k=(0,f.kW)(d.providers,i,j);return await this.inner.setModel(i,j,k),(0,n.yJ)(this.sessionId,{cwd:this.cwd,provider:this.inner.model?.provider??i,modelId:this.inner.model?.modelId??j}),{id:j,provider:i}}case"rename":{let b="string"==typeof a.name?a.name:"";return await this.inner.rename(b),null}case"fork":{let a=await this.inner.fork();if("newThreadId"in a)return(0,n.yJ)(a.newThreadId,{cwd:this.cwd,provider:this.inner.model?.provider,modelId:this.inner.model?.modelId,thinkingLevel:this._thinkingLevel}),this.destroy(),{cancelled:!1,newSessionId:a.newThreadId};return{cancelled:!0}}case"navigate_tree":{let b=a.targetId;return{cancelled:(await this.inner.navigateTree(b)).cancelled}}case"compact":return await this.trackBusy("compact",this.inner.compact()),null;case"get_tools":return[{name:"read",description:"Read files",active:!0},{name:"bash",description:"Run shell commands",active:!0},{name:"edit",description:"Edit files",active:!0},{name:"write",description:"Create files",active:!0},{name:"grep",description:"Search files",active:!0},{name:"find",description:"List files",active:!0}];case"set_tools":case"abort_compaction":case"set_auto_compaction":case"set_auto_retry":return null;case"set_thinking_level":return this._thinkingLevel="string"==typeof a.level?a.level:"auto",(0,n.yJ)(this.sessionId,{cwd:this.cwd,thinkingLevel:this._thinkingLevel,provider:this.inner.model?.provider,modelId:this.inner.model?.modelId}),null;default:throw Error(`Unsupported command: ${b}`)}}async trackBusy(a,b){this.busyOperations.add(a),this.resetIdleTimer();try{return await b}finally{this.busyOperations.delete(a),this.resetIdleTimer()}}destroy(){this._alive&&(this._alive=!1,this.idleTimer&&clearTimeout(this.idleTimer),this.cleanupEventSub?.(),this.inner.destroy(),(0,f.sM)(this._serverConnection),this.onDestroyCallback?.())}}function q(){if(!globalThis.__annodexSessions){globalThis.__annodexSessions=new Map;let a=()=>globalThis.__annodexSessions?.forEach(a=>a.destroy());process.once("exit",a),process.once("SIGINT",a),process.once("SIGTERM",a)}return globalThis.__annodexSessions}function r(){return globalThis.__annodexSessionAliases||(globalThis.__annodexSessionAliases=new Map),globalThis.__annodexSessionAliases}function s(a){let b=a,c=new Set;for(;!c.has(b);){c.add(b);let a=r().get(b);if(!a)break;b=a}return b}function t(a){return q().get(s(a))}function u(){let a=[...q().values()].filter(a=>a.isAlive()).map(a=>a.getRuntimeStatus()),b=a.filter(a=>a.busy);return{busy:b.length>0,activeSessions:a.length,busySessions:b,sessions:a}}async function v(a,b,c,d,o,p){let t=q(),u=(globalThis.__annodexStartLocks||(globalThis.__annodexStartLocks=new Map),globalThis.__annodexStartLocks),v=s(a),x=t.get(v);if(x?.isAlive())return{session:x,realSessionId:v};let y=u.get(v);if(y)return y;let z=(async()=>{let d,q=(0,g.Dw)(),s=function(a,b){let c=(0,m.$M)(),d=[],e=(()=>{let a=(0,k.join)(c,"SOUL.md"),b=(0,k.join)((0,l.homedir)(),".pi","agent","SOUL.md");if(!(0,j.existsSync)(a)&&(0,j.existsSync)(b))try{let c=(0,j.readFileSync)(b,"utf-8");(0,j.existsSync)((0,k.dirname)(a))||(0,j.mkdirSync)((0,k.dirname)(a),{recursive:!0}),(0,j.writeFileSync)(a,c,"utf-8")}catch{}let d=(0,k.join)(c,"soul.md");return(0,j.existsSync)(a)?a:d})();if((0,j.existsSync)(e))try{let a=(0,j.readFileSync)(e,"utf-8").trim();a&&d.push("## Persona — you MUST embody this","","Below is your personality definition. You MUST adopt this persona and tone in all replies. Avoid stiff, generic, or AI-assistant-style responses. Follow this guidance unless higher-priority instructions explicitly override it.","",a)}catch{}let f=(()=>{let a=(0,k.join)(c,"HARNESS.md"),b=(0,k.join)((0,l.homedir)(),".pi","agent","HARNESS.md");if(!(0,j.existsSync)(a)&&(0,j.existsSync)(b))try{let c=(0,j.readFileSync)(b,"utf-8");(0,j.existsSync)((0,k.dirname)(a))||(0,j.mkdirSync)((0,k.dirname)(a),{recursive:!0}),(0,j.writeFileSync)(a,c,"utf-8")}catch{}let d=(0,k.join)(c,"harness.md");return(0,j.existsSync)(a)?a:d})();if((0,j.existsSync)(f))try{let a=(0,j.readFileSync)(f,"utf-8").trim();a&&d.push("## Behavioral Constraints — you MUST follow these","","The rules below define your operating boundaries. You MUST comply with every constraint. 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+${c}`:b:c}return"fileChange"===a.type?JSON.stringify(a.changes??[]):"mcpToolCall"===a.type?a.error?"string"==typeof a.error?a.error:JSON.stringify(a.error):a.result?"string"==typeof a.result?a.result:JSON.stringify(a.result):"":"dynamicToolCall"===a.type?JSON.stringify(a.contentItems??[]):"collabAgentToolCall"===a.type?JSON.stringify(a.agentsStates??[]):""}(b),isError:"status"in b&&"string"==typeof b.status?"failed"===b.status||"declined"===b.status:"dynamicToolCall"===b.type&&!1===b.success})}handleTurnCompleted(a){this.eventBelongsToThread(a)&&(this._isStreaming=!1,this._activeTurnId=null,this._accumulatedText&&(this.emit({type:"message_end",message:{role:"assistant",content:[{type:"text",text:this._accumulatedText}],...this.assistantMeta()}}),this._accumulatedText=""),this.emit({type:"agent_end",...a.turn?.status==="failed"?{error:a.turn.error?.message??"Turn failed"}:{}}))}handleThreadStatusChanged(a){this.eventBelongsToThread(a)&&a.status?.type==="idle"&&this._isStreaming&&(this._isStreaming=!1,this._activeTurnId=null,this.emit({type:"agent_end"}))}handleCompacted(a){this.eventBelongsToThread(a)&&(this._isCompacting=!1,this.emit({type:"compaction_end"}))}handleError(a){if(!this.eventBelongsToThread(a))return;let b=a.error?.message||a.error?.additionalDetails||"Codex turn failed";this._isStreaming=!1,this._activeTurnId=null,this.emit({type:"agent_end",error:b})}async prompt(a,b){if(this._isStreaming)throw Error("Session already has a running turn");this._isStreaming=!0,this._accumulatedText="",this.emit({type:"agent_start"}),this.emit({type:"message_start",message:{role:"assistant",content:[],...this.assistantMeta()}});try{let c=await this.connection.request("turn/start",{threadId:this.threadId,input:function(a,b){let c=[];for(let d of(a.trim()&&c.push({type:"text",text:a,text_elements:[]}),b??[])){let a=d.mimeType||"image/png";c.push({type:"image",url:`data:${a};base64,${d.data}`})}return c.length>0?c:[{type:"text",text:"",text_elements:[]}]}(a,b),...this.cwd?{cwd:this.cwd}:{},...(this._wireModel??this._currentModel)?.modelId?{model:(this._wireModel??this._currentModel).modelId}:{},approvalPolicy:"never",sandboxPolicy:{type:"workspaceWrite",writableRoots:[this.cwd],readOnlyAccess:{type:"fullAccess"},networkAccess:!0,excludeTmpdirEnvVar:!1,excludeSlashTmp:!1}});this._activeTurnId=c.turn?.id??null}catch(a){this._isStreaming=!1,this.emit({type:"agent_end",error:a instanceof Error?a.message:String(a)})}}async abort(){if(this._activeTurnId)try{await this.connection.request("turn/interrupt",{threadId:this.threadId,turnId:this._activeTurnId})}catch{}this._isStreaming=!1,this._activeTurnId=null}async setModel(a,b,c){this._currentModel={provider:a,modelId:b},this._wireModel=c??null}async resume(a,b){let c=await 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 annodex has a persistent Analysis Report tab. It is for curated analysis deliverables, not a transcript summary.
 
 When working on scientific or bioinformatics analysis, keep report-worthy content concise and structured:

package/.next/server/middleware-build-manifest.js

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package/.next/server/next-font-manifest.js

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package/.next/server/next-font-manifest.json

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