Reply Agent

// src/agents/reply/index.ts
export async function replyAgent(input: {
  conversationState: ConversationState;
  message: Message;
  completedMaxTasks: PlanTask[];
  hypothesis?: string;
  nextPlan: PlanTask[];
  isFinal?: boolean;
}): Promise<ReplyResult>;

type ReplyResult = {
  reply: string;
  summary?: string;
  start: string;
  end: string;
};

const replyText = await generateChatReply(
  question,
  {
    completedTasks,
    hypothesis,
    nextPlan: [], // No next plan in chat mode
    keyInsights,
    discoveries,
    methodology,
    currentObjective,
    uploadedDatasets
  },
  {
    maxTokens: 1024,
    messageId,
    usageType: "chat"
  }
);

// Example output:
// "Based on literature search, rapamycin extends lifespan in mice by up to 60% 
// through mTOR pathway inhibition (Harrison et al., 2009). The mechanism involves..."

const result = await replyAgent({
  conversationState,
  message,
  completedMaxTasks,
  hypothesis,
  nextPlan,
  isFinal: true
});

// Example output:
// "I completed literature search on mTOR and aging. Key findings:
// 
// 1. mTOR inhibition extends lifespan across species
// 2. Rapamycin is the primary mTOR inhibitor studied
// 
// Current hypothesis: mTOR-dependent translation control regulates aging.
// 
// Next steps:
// - ANALYSIS: Analyze gene expression data for mTOR targets
// - LITERATURE: Search for mTOR downstream effectors
// 
// Does this plan look good? Feel free to modify or add tasks."

// src/routes/chat.ts
const replyText = await generateChatReply(
  message,
  {
    completedTasks,
    hypothesis: hypothesisText,
    nextPlan: [], // No next plan
    keyInsights: conversationState.values.keyInsights || [],
    discoveries: conversationState.values.discoveries || [],
    methodology: conversationState.values.methodology,
    currentObjective: conversationState.values.currentObjective,
    uploadedDatasets: conversationState.values.uploadedDatasets || []
  },
  {
    maxTokens: 1024,
    messageId: createdMessage.id,
    usageType: "chat"
  }
);

// src/routes/deep-research/start.ts
const replyResult = await replyAgent({
  conversationState,
  message,
  completedMaxTasks,
  hypothesis: hypothesisText,
  nextPlan,
  isFinal: !shouldContinue // Ask for feedback if not continuing
});

const replyText = replyResult.reply;

// src/agents/reply/index.ts
const conversationHistory = await fetchConversationHistory(
  message.conversation_id
);

const resolvedQuestion = await resolveQuestionForReply(
  message.question,
  conversationHistory
);

Input: "(Rapamycin extends lifespan)[10.1038/nature.2009.1234]"
Output: "Based on research, rapamycin extends lifespan (Harrison et al., 2009)."