Update operation on NCBI taxonomy

Content

• Generate NCBI taxonomy hierarchy
• Create link to parent for NCBI tax

Related Issue

Closes #16 (closed)

backend/app/app/api/endpoints/admin/db.py

 from celery.result import AsyncResult
-from fastapi import APIRouter
+from fastapi import APIRouter, status
 from fastapi.responses import JSONResponse
 
 
@@ -7,39 +7,90 @@ from app.celery.tasks.kegg import (
     create_or_update_all_ko,
     CREATE_KEGG_TASK_NAME,
 )
+from app.celery.tasks.ncbi_taxonomy import (
+    create_or_update_all_ncbi_tax,
+    generate_ncbi_tax_hierarchy,
+    CREATE_NCBI_TAX_TASK_NAME,
+    GENERATE_HIERARCHY_TASK_NAME,
+)
 from app.celery.utils import (
     is_running_task,
     get_task_id,
 )
+from app.db import reinit_db
+from app.core.schemas.tasks.base import CreateTask
+from app.core.schemas.tasks.db import TaskDbOperation
 
 
 router = APIRouter()
 
 
-@router.post("/create_kegg_ko")
+@router.delete("/reinit_db")
+def reinitialize_db():
+    reinit_db()
+    return JSONResponse({"empty": True}, status_code=201)
+
+
+@router.post(
+    "/create_kegg_ko", response_model=CreateTask, status_code=status.HTTP_201_CREATED
+)
 def create_kegg_ko():
     task_name = CREATE_KEGG_TASK_NAME
     if is_running_task(task_name):
         task_id = get_task_id(task_name)
-        return JSONResponse(
-            {"status": "Process already running", "task_id": task_id}, status_code=200
-        )
+        task_obj = CreateTask(task_status="STARTED", task_id=task_id)
+        return JSONResponse(status_code=status.HTTP_200_OK, content=task_obj.dict())
     task = create_or_update_all_ko.delay()
-    return JSONResponse({"task_id": task.id}, status_code=201)
+    task_obj = CreateTask(task_status="PENDING", task_id=task.id)
+    return task_obj
 
 
-@router.get("/tasks/{task_id}")
+@router.post(
+    "/create_ncbi_taxonomy",
+    response_model=CreateTask,
+    status_code=status.HTTP_201_CREATED,
+)
+def create_ncbi_taxonomy():
+    task_name = CREATE_NCBI_TAX_TASK_NAME
+    if is_running_task(task_name):
+        task_id = get_task_id(task_name)
+        task_obj = CreateTask(task_status="STARTED", task_id=task_id)
+        return JSONResponse(status_code=status.HTTP_200_OK, content=task_obj.dict())
+    task = create_or_update_all_ncbi_tax.delay()
+    task_obj = CreateTask(task_status="PENDING", task_id=task.id)
+    return task_obj
+
+
+@router.post(
+    "/ncbi_taxonomy_hierarchy",
+    response_model=CreateTask,
+    status_code=status.HTTP_201_CREATED,
+)
+def generate_ncbi_taxonomy_hierarchy():
+    task_name = GENERATE_HIERARCHY_TASK_NAME
+    if is_running_task(task_name):
+        task_id = get_task_id(task_name)
+        task_obj = CreateTask(task_status="STARTED", task_id=task_id)
+        return JSONResponse(status_code=status.HTTP_200_OK, content=task_obj.dict())
+    task = generate_ncbi_tax_hierarchy.delay()
+    task_obj = CreateTask(task_status="PENDING", task_id=task.id)
+    return task_obj
+
+
+@router.get(
+    "/tasks/{task_id}", response_model=TaskDbOperation, status_code=status.HTTP_200_OK
+)
 def get_status(task_id):
     task_result = AsyncResult(task_id)
     if task_result.failed():
         result = {
             "task_id": task_id,
-            "task_status": "failed",
+            "task_status": task_result.status,
         }
         return JSONResponse(result)
-    result = {
-        "task_id": task_id,
-        "task_status": task_result.status,
-        "task_result": task_result.result,
-    }
-    return JSONResponse(result)
+    result = TaskDbOperation(
+        task_id=task_id,
+        task_status=task_result.status,
+        task_result=task_result.result,
+    )
+    return result