Analysis Agent

// src/agents/analysis/index.ts
export async function analysisAgent(input: {
  objective: string;
  datasets: Dataset[];
  type: AnalysisType;
  userId: string;
  conversationStateId: string;
  onPollUpdate?: OnPollUpdate;
}): Promise<AnalysisResult>;

type AnalysisType = "EDISON" | "BIO";

type Dataset = {
  filename: string;
  id: string;
  description: string;
  content?: Buffer;
  path?: string;
};

type AnalysisResult = {
  objective: string;
  output: string;
  jobId?: string;
  reasoning?: string[];
  start?: string;
  end?: string;
  artifacts?: Array<AnalysisArtifact>;
};

const result = await analysisAgent({
  objective: "Analyze gene expression patterns and identify key regulators",
  datasets: [
    {
      filename: "expression_data.csv",
      id: "dataset-123",
      description: "RNA-seq gene expression matrix",
      content: buffer
    }
  ],
  type: "EDISON",
  userId: "user-456",
  conversationStateId: "conv-789"
});

EDISON_API_URL=https://your-edison-api
EDISON_API_KEY=your_key
EDISON_TASK_TIMEOUT_MINUTES=30

const result = await analysisAgent({
  objective: "Perform statistical analysis of metabolite concentrations",
  datasets: [
    {
      filename: "metabolites.xlsx",
      id: "dataset-456",
      description: "Metabolomics data from mass spectrometry",
      path: "uploads/metabolites.xlsx"
    }
  ],
  type: "BIO",
  userId: "user-456",
  conversationStateId: "conv-789",
  onPollUpdate: (update) => {
    console.log(update.reasoning); // Real-time trace
  }
});

PRIMARY_ANALYSIS_AGENT=bio
DATA_ANALYSIS_API_URL=https://your-analysis-api
DATA_ANALYSIS_API_KEY=your_key
BIO_ANALYSIS_TASK_TIMEOUT_MINUTES=60

{
  "objective": "Analyze gene expression",
  "output": "Analysis identified 342 differentially expressed genes (FDR < 0.05). Key regulators include TP53 and MYC with log2 fold changes of -2.3 and 1.8 respectively. See plot_volcano.png for visualization.",
  "jobId": "bio-task-123",
  "artifacts": [
    {
      "id": "artifact-1",
      "filename": "plot_volcano.png",
      "type": "image/png",
      "path": "artifacts/conv-789/artifact-1/plot_volcano.png"
    },
    {
      "id": "artifact-2",
      "filename": "deg_table.csv",
      "type": "text/csv",
      "path": "artifacts/conv-789/artifact-2/deg_table.csv"
    }
  ]
}

// src/routes/deep-research/start.ts
const analysisTasks = plan.filter(t => t.type === "ANALYSIS");

for (const task of analysisTasks) {
  const result = await analysisAgent({
    objective: task.objective,
    datasets: task.datasets,
    type: analysisType,
    userId,
    conversationStateId: conversationState.id,
    onPollUpdate: (update) => {
      // Send real-time updates via WebSocket
      notifyJobUpdate(messageId, update);
    }
  });
  
  task.output = result.output;
  task.jobId = result.jobId;
  task.artifacts = result.artifacts;
}