Update biopython/mcp_output/mcp_plugin/mcp_service.py

biopython/mcp_output/mcp_plugin/mcp_service.py

@@ -356,64 +356,28 @@ def blast_get_result(payload: dict):
 # BLAST 搜索工具 - BLAST Search Tools (同步版本，保留用于小序列)
 # ==============================================
 
-@mcp.tool(name="blast_search", description="Search NCBI database using BLAST to find similar sequences")
-def blast_search(payload: dict):
-    """
-    使用 BLAST 搜索相似序列（稳定版）
-    Required fields: sequence
-    Optional fields: 
-      - database (nt/nr/refseq_rna, default refseq_rna)
-      - program (blastn/blastp, default blastn)
-      - hitlist_size (default 20)
-      - expect (default 1e-10)
-    """
-    try:
-        sequence = str(payload.get("sequence", "")).strip()
-        if not sequence:
-            return {"success": False, "result": None, "error": "sequence is required"}
-
-        # 清理序列
-        sequence = "".join(sequence.split()).upper()
+# 全局存储任务结果
+BLAST_TASKS = {}
 
-        # 参数
-        database = payload.get("database", "refseq_rna")
-        program = payload.get("program", "blastn")
-        hitlist_size = int(payload.get("hitlist_size", 20))
-        hitlist_size = 5
-        expect = float(payload.get("expect", 1e-10))
-
-        # 提示信息
-        if database == "nt":
-            print("⚠️ Warning: 'nt' database is very large and may take 5-15 minutes!")
-            print("💡 Consider using 'refseq_rna' for faster results")
-
-        print(f"🔍 Submitting BLAST search: {len(sequence)} bp, database={database}, hits={hitlist_size}")
-        print("⏳ Please wait...")
-
-        # 提交 BLAST
-        try:
-            handle = NCBIWWW.qblast(
-                program=program,
-                database=database,
-                sequence=sequence,
-                hitlist_size=hitlist_size,
-                expect=expect,
-                format_type="XML"
-            )
-        except Exception as blast_error:
-            return {
-                "success": False,
-                "result": None,
-                "error": f"BLAST submission failed: {str(blast_error)}"
-            }
+# --------------------------
+# 异步 BLAST 执行函数
+# --------------------------
+def run_blast_task(task_id, sequence, database, program, hitlist_size, expect):
+    try:
+        handle = NCBIWWW.qblast(
+            program=program,
+            database=database,
+            sequence=sequence,
+            hitlist_size=hitlist_size,
+            expect=expect,
+            format_type="XML"
+        )
 
-        # 迭代解析 XML
         hits = []
         for blast_record in NCBIXML.parse(handle):
             for idx, alignment in enumerate(blast_record.alignments[:hitlist_size]):
                 if not alignment.hsps:
                     continue
-
                 hsp = alignment.hsps[0]
                 align_len = int(hsp.align_length)
                 identities = int(hsp.identities)
@@ -432,25 +396,78 @@ def blast_search(payload: dict):
                     "align_length": int(align_len)
                 })
 
-                # 输出进度，保持 SSE 活跃
-                print(f"Processing alignment {idx+1}/{min(hitlist_size, len(blast_record.alignments))}")
-
         handle.close()
-        print(f"✅ BLAST search completed: {len(hits)} alignments found")
 
-        # 构建返回结果
-        result = {
-            "query_length": int(len(sequence)),
-            "database": str(database),
-            "program": str(program),
-            "total_hits": int(len(hits)),
-            "hits": hits
+        BLAST_TASKS[task_id] = {
+            "status": "completed",
+            "result": {
+                "query_length": len(sequence),
+                "database": database,
+                "program": program,
+                "total_hits": len(hits),
+                "hits": hits
+            },
+            "error": None
         }
 
-        return {"success": True, "result": result, "error": None}
-
     except Exception as e:
-        return {"success": False, "result": None, "error": str(e)}
+        BLAST_TASKS[task_id] = {
+            "status": "failed",
+            "result": None,
+            "error": str(e)
+        }
+
+# --------------------------
+# 单工具：blast_search
+# --------------------------
+@mcp.tool(name="blast_search", description="Asynchronous BLAST search: returns task_id immediately")
+def blast_search(payload: dict):
+    """
+    Single MCP tool for asynchronous BLAST search.
+    Required: sequence
+    Optional: database (refseq_rna/nt/nr), program (blastn/blastp), hitlist_size, expect
+    """
+
+    sequence = payload.get("sequence", "")
+    if not sequence:
+        return {"success": False, "result": None, "error": "sequence is required"}
+
+    database = payload.get("database", "refseq_rna")
+    program = payload.get("program", "blastn")
+    hitlist_size = int(payload.get("hitlist_size", 5))
+    expect = float(payload.get("expect", 1e-10))
+
+    task_id = str(uuid.uuid4())
+    BLAST_TASKS[task_id] = {"status": "running", "result": None, "error": None}
+
+    # 后��线程执行 BLAST
+    thread = threading.Thread(
+        target=run_blast_task,
+        args=(task_id, sequence, database, program, hitlist_size, expect)
+    )
+    thread.start()
+
+    # 立即返回 task_id
+    return {
+        "success": True,
+        "result": {"task_id": task_id, "status": "running"},
+        "error": None
+    }
+
+# --------------------------
+# 查询结果接口（同工具内可选）
+# --------------------------
+@mcp.tool(name="blast_check_task", description="Check BLAST task result by task_id")
+def blast_check_task(payload: dict):
+    task_id = payload.get("task_id", "")
+    if not task_id:
+        return {"success": False, "result": None, "error": "task_id is required"}
+
+    task = BLAST_TASKS.get(task_id)
+    if not task:
+        return {"success": False, "result": None, "error": "task_id not found"}
+
+    return {"success": True, "result": task, "error": None}
 
 
 @mcp.tool(name="filter_blast_hits", description="Filter BLAST hits by identity percentage threshold")