7102454002

Committed 05 Dec 2023 02:52PM UTC coverage: 0.0%. Remained the same

Build # 7102454002

Build Type

push

github

Committed by

web-flow

Commit Message

Update to pydantic v2 (#47) (patch)

Added
Move the models to pydantic v2

add Codeowners for automatic reviewer tagging

Run Details

0 of 89 new or added lines in 5 files covered. (0.0%)

28 existing lines in 5 files now uncovered.

0 of 699 relevant lines covered (0.0%)

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0.0

/arnold/api/api_v1/endpoints/flow_cell.py

from arnold.adapter import ArnoldAdapter
from arnold.crud.read.flow_cell import find_flow_cell, find_all_flow_cells

from arnold.crud import create
from arnold.models.database.flow_cell import FlowCell
from typing import List
from fastapi import APIRouter, Depends, status
from fastapi.responses import JSONResponse
import logging

from arnold.settings import get_arnold_adapter

LOG = logging.getLogger(__name__)

router = APIRouter()


@router.get("/flow_cell/{flow_cell_id}", response_model=FlowCell)
def get_flow_cell(
    flow_cell_id: str,
    adapter: ArnoldAdapter = Depends(get_arnold_adapter),
):
    """fetch a flow_cell by flow_cell id"""
    flow_cell: FlowCell = find_flow_cell(flow_cell_id=flow_cell_id, adapter=adapter)
    return flow_cell


@router.get("/flow_cells/", response_model=List[FlowCell])
def get_flow_cells(
    adapter: ArnoldAdapter = Depends(get_arnold_adapter),
):
    """Get all flow_cells"""
    flow_cells: List[FlowCell] = find_all_flow_cells(adapter=adapter)

    return flow_cells


@router.post("/flow_cell/")
def create_flow_cell(
    flow_cell: FlowCell, adapter: ArnoldAdapter = Depends(get_arnold_adapter)
) -> JSONResponse:
    if find_flow_cell(flow_cell_id=flow_cell.flow_cell_id, adapter=adapter):
        return JSONResponse(
            status_code=status.HTTP_405_METHOD_NOT_ALLOWED, content="flow_cell already in database"
        )
    try:
        create.create_flow_cell(adapter=adapter, flow_cell=flow_cell)
    except Exception as e:
        return JSONResponse(
            status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
            content=f"exception {e} ",
        )

    return JSONResponse(
        status_code=status.HTTP_200_OK, content=f"flow_cell {flow_cell.flow_cell_id} inserted to db"
    )

1	from arnold.adapter import ArnoldAdapter	×
2	from arnold.crud.read.flow_cell import find_flow_cell, find_all_flow_cells	×
3
4	from arnold.crud import create	×
5	from arnold.models.database.flow_cell import FlowCell	×
6	from typing import List	×
7	from fastapi import APIRouter, Depends, status	×
8	from fastapi.responses import JSONResponse	×
9	import logging	×
10
11	from arnold.settings import get_arnold_adapter	×
12
13	LOG = logging.getLogger(__name__)	×
14
15	router = APIRouter()	×
16
17
18	@router.get("/flow_cell/{flow_cell_id}", response_model=FlowCell)	×
19	def get_flow_cell(	×
20	flow_cell_id: str,
21	adapter: ArnoldAdapter = Depends(get_arnold_adapter),
22	):
23	"""fetch a flow_cell by flow_cell id"""
24	flow_cell: FlowCell = find_flow_cell(flow_cell_id=flow_cell_id, adapter=adapter)	×
25	return flow_cell	×
26
27
28	@router.get("/flow_cells/", response_model=List[FlowCell])	×
29	def get_flow_cells(	×
30	adapter: ArnoldAdapter = Depends(get_arnold_adapter),
31	):
32	"""Get all flow_cells"""
33	flow_cells: List[FlowCell] = find_all_flow_cells(adapter=adapter)	×
34
35	return flow_cells	×
36
37
38	@router.post("/flow_cell/")	×
39	def create_flow_cell(	×
40	flow_cell: FlowCell, adapter: ArnoldAdapter = Depends(get_arnold_adapter)
41	) -> JSONResponse:
42	if find_flow_cell(flow_cell_id=flow_cell.flow_cell_id, adapter=adapter):	×
43	return JSONResponse(	×
44	status_code=status.HTTP_405_METHOD_NOT_ALLOWED, content="flow_cell already in database"
45	)
46	try:	×
47	create.create_flow_cell(adapter=adapter, flow_cell=flow_cell)	×
48	except Exception as e:	×
49	return JSONResponse(	×
50	status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
51	content=f"exception {e} ",
52	)
53
54	return JSONResponse(	×
55	status_code=status.HTTP_200_OK, content=f"flow_cell {flow_cell.flow_cell_id} inserted to db"
56	)

Clinical-Genomics / arnold / 7102454002

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