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meljendy
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proteinea

Sleeping

Mahmoud Eljendy

feat: Antibody Studio — AI-native antibody design workspace by Proteinea

30cc31a 6 months ago

4.93 kB

export interface StreamEvent {
  type:
    | "text_delta"
    | "tool_use"
    | "tool_result"
    | "done"
    | "error"
    // ---- v2 events ----
    | "kb_lookup"      // best-practice retrieval, with timing
    | "plan"           // structured plan with tool chips per step
    | "trace"          // execution trace entry
    | "artifact"       // file produced by the agent
    | "citation"       // inline source citation chip for the previous text run
    | "step_status";   // live status pulse for a plan step (Biomni-style todo)
  text?: string;
  tool?: string;
  input?: Record<string, unknown>;
  result?: unknown;
  response?: string;
  error?: string;
  // ---- v2 fields ----
  kb?: { name: string; ms: number };
  plan?: PlanProposal;
  trace?: TraceEntry;
  artifact?: Artifact;
  citation?: Citation;
  step?: { index: number; status: StepStatus };
}

export interface ChatMessage {
  id: string;
  role: "user" | "assistant";
  content: string;
  toolCalls?: ToolCall[];
  kbLookups?: KBLookup[];
  trace?: TraceEntry[];
  plan?: PlanProposal;
  artifacts?: Artifact[];
  citations?: Citation[];
  /** Per-step live status, parallel-indexed with `plan.steps`. */
  stepStatus?: StepStatus[];
  isStreaming?: boolean;
}

export interface ToolCall {
  tool: string;
  input: Record<string, unknown>;
  result?: unknown;
  status: "running" | "completed" | "error";
}

// ---- v2 types ----

export interface KBLookup {
  name: string;
  ms: number;
}

export interface PlanStepProto {
  label: string;
  tools: string[];
}

export interface PlanProposal {
  title: string;
  steps: PlanStepProto[];
}

export interface TraceEntry {
  ts: number;          // ms epoch
  kind: "thought" | "tool_call" | "tool_result" | "text";
  label: string;       // short human-readable summary
  detail?: string;     // optional verbose body
}

export interface Artifact {
  id: string;          // stable id
  name: string;        // user-visible filename
  bytes: number;       // size in bytes
  mime: string;        // MIME type
  url: string;         // download URL (relative)
  createdAt: number;   // ms epoch
  hubOutputData?: Record<string, unknown>; // Hub job output_data (scores, PDB, sequences, etc.)
}

export interface Citation {
  label: string;       // chip text e.g. "clinicaltrials.gov/data-api"
  url?: string;        // optional href
}

// ---- Task persistence ----

export interface TaskRecord {
  id: string;          // sess_xxxxxxxx
  projectId: string;   // proj_xxxxxxxx
  title: string;
  createdAt: number;
  updatedAt: number;
  messages: ChatMessage[];
  artifacts: Artifact[];
}

export interface ProjectRecord {
  id: string;          // proj_xxxxxxxx
  name: string;
  createdAt: number;
}

export interface Benchmark {
  source: string;
  paper_title: string;
  paper_url: string;
  paper_date: string;
  avg_hit_rate_vhh: number | null;
  avg_hit_rate_mab: number | null;
  target_coverage: number | null;
  best_affinity_pM: number | null;
  total_designs_tested: number;
  code_available: boolean;
  weights_available: boolean;
  developability: { overall_pass_rate: number | null } | null;
  targets: { name: string; target_class: string }[];
  binding_results: {
    target: string;
    antibody_format: string;
    hit_rate: number | null;
    best_affinity_nM: number | null;
    assay: string;
    notes: string;
  }[];
  notes: string;
}

export interface Skill {
  id: string;
  name: string;
  description: string;
  version: string;
  author: string;
  inputs: Record<string, unknown>;
  outputs: Record<string, unknown>;
  // ---- Optional fields populated from the Hub registry passthrough ----
  category?: string;
  tier?: string;
  gpu?: boolean;
  gpuType?: string;
  minRamGb?: number;
  typicalRuntimeSeconds?: number;
}

// ---- Dataset connector types ----

export interface DatasetSearchResult {
  id: string;
  source: "sabdab" | "oas" | "imgt" | "fc";
  title: string;
  summary: string;
  organism?: string;
  data_type: "structure" | "sequence" | "gene";
}

export interface DatasetSearchResponse {
  results: Record<string, DatasetSearchResult[]>;
  errors: Record<string, string>;
  query: Record<string, unknown>;
}

export interface SyncStatusEntry {
  source: string;
  last_synced: string | null;
  entry_count: number;
  size_bytes: number;
  status: "synced" | "syncing" | "error" | "not_synced" | "not_configured";
}

export type ResourceKind = "target" | "benchmark" | "model" | "skill" | "sabdab" | "imgt" | "oas";

export interface ResourceRef {
  type: ResourceKind;
  id: string;
  label: string;
  sublabel?: string;
}

export interface ModelEntry {
  name: string;
  version: string;
  source: string;
  capabilities: string[];
  repo_url: string | null;
  license: string | null;
  gpu_required: boolean;
  min_vram_gb: number;
  antibody_formats: string[];
  notes: string;
}

export type StepStatus = "pending" | "running" | "done" | "error";

	export interface StreamEvent {
	type:
	\| "text_delta"
	\| "tool_use"
	\| "tool_result"
	\| "done"
	\| "error"
	// ---- v2 events ----
	\| "kb_lookup" // best-practice retrieval, with timing
	\| "plan" // structured plan with tool chips per step
	\| "trace" // execution trace entry
	\| "artifact" // file produced by the agent
	\| "citation" // inline source citation chip for the previous text run
	\| "step_status"; // live status pulse for a plan step (Biomni-style todo)
	text?: string;
	tool?: string;
	input?: Record<string, unknown>;
	result?: unknown;
	response?: string;
	error?: string;
	// ---- v2 fields ----
	kb?: { name: string; ms: number };
	plan?: PlanProposal;
	trace?: TraceEntry;
	artifact?: Artifact;
	citation?: Citation;
	step?: { index: number; status: StepStatus };
	}

	export interface ChatMessage {
	id: string;
	role: "user" \| "assistant";
	content: string;
	toolCalls?: ToolCall[];
	kbLookups?: KBLookup[];
	trace?: TraceEntry[];
	plan?: PlanProposal;
	artifacts?: Artifact[];
	citations?: Citation[];
	/** Per-step live status, parallel-indexed with `plan.steps`. */
	stepStatus?: StepStatus[];
	isStreaming?: boolean;
	}

	export interface ToolCall {
	tool: string;
	input: Record<string, unknown>;
	result?: unknown;
	status: "running" \| "completed" \| "error";
	}

	// ---- v2 types ----

	export interface KBLookup {
	name: string;
	ms: number;
	}

	export interface PlanStepProto {
	label: string;
	tools: string[];
	}

	export interface PlanProposal {
	title: string;
	steps: PlanStepProto[];
	}

	export interface TraceEntry {
	ts: number; // ms epoch
	kind: "thought" \| "tool_call" \| "tool_result" \| "text";
	label: string; // short human-readable summary
	detail?: string; // optional verbose body
	}

	export interface Artifact {
	id: string; // stable id
	name: string; // user-visible filename
	bytes: number; // size in bytes
	mime: string; // MIME type
	url: string; // download URL (relative)
	createdAt: number; // ms epoch
	hubOutputData?: Record<string, unknown>; // Hub job output_data (scores, PDB, sequences, etc.)
	}

	export interface Citation {
	label: string; // chip text e.g. "clinicaltrials.gov/data-api"
	url?: string; // optional href
	}

	// ---- Task persistence ----

	export interface TaskRecord {
	id: string; // sess_xxxxxxxx
	projectId: string; // proj_xxxxxxxx
	title: string;
	createdAt: number;
	updatedAt: number;
	messages: ChatMessage[];
	artifacts: Artifact[];
	}

	export interface ProjectRecord {
	id: string; // proj_xxxxxxxx
	name: string;
	createdAt: number;
	}

	export interface Benchmark {
	source: string;
	paper_title: string;
	paper_url: string;
	paper_date: string;
	avg_hit_rate_vhh: number \| null;
	avg_hit_rate_mab: number \| null;
	target_coverage: number \| null;
	best_affinity_pM: number \| null;
	total_designs_tested: number;
	code_available: boolean;
	weights_available: boolean;
	developability: { overall_pass_rate: number \| null } \| null;
	targets: { name: string; target_class: string }[];
	binding_results: {
	target: string;
	antibody_format: string;
	hit_rate: number \| null;
	best_affinity_nM: number \| null;
	assay: string;
	notes: string;
	}[];
	notes: string;
	}

	export interface Skill {
	id: string;
	name: string;
	description: string;
	version: string;
	author: string;
	inputs: Record<string, unknown>;
	outputs: Record<string, unknown>;
	// ---- Optional fields populated from the Hub registry passthrough ----
	category?: string;
	tier?: string;
	gpu?: boolean;
	gpuType?: string;
	minRamGb?: number;
	typicalRuntimeSeconds?: number;
	}

	// ---- Dataset connector types ----

	export interface DatasetSearchResult {
	id: string;
	source: "sabdab" \| "oas" \| "imgt" \| "fc";
	title: string;
	summary: string;
	organism?: string;
	data_type: "structure" \| "sequence" \| "gene";
	}

	export interface DatasetSearchResponse {
	results: Record<string, DatasetSearchResult[]>;
	errors: Record<string, string>;
	query: Record<string, unknown>;
	}

	export interface SyncStatusEntry {
	source: string;
	last_synced: string \| null;
	entry_count: number;
	size_bytes: number;
	status: "synced" \| "syncing" \| "error" \| "not_synced" \| "not_configured";
	}

	export type ResourceKind = "target" \| "benchmark" \| "model" \| "skill" \| "sabdab" \| "imgt" \| "oas";

	export interface ResourceRef {
	type: ResourceKind;
	id: string;
	label: string;
	sublabel?: string;
	}

	export interface ModelEntry {
	name: string;
	version: string;
	source: string;
	capabilities: string[];
	repo_url: string \| null;
	license: string \| null;
	gpu_required: boolean;
	min_vram_gb: number;
	antibody_formats: string[];
	notes: string;
	}

	export type StepStatus = "pending" \| "running" \| "done" \| "error";