7130299646

Committed 07 Dec 2023 03:25PM UTC coverage: 0.0%. Remained the same

Build # 7130299646

Build Type

push

github

Committed by

web-flow

Commit Message

refactor( refactor arnold add tests) (#52) (patch)

# Added
This PR refactors some parts of arnold and adds test for the crud modules related to the flow cell and sample model

Run Details

0 of 39 new or added lines in 11 files covered. (0.0%)

5 existing lines in 5 files now uncovered.

0 of 897 relevant lines covered (0.0%)

0.0 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

0.0

/arnold/api/api_v1/endpoints/sample.py

from arnold.adapter import ArnoldAdapter
from arnold.crud import create, update
from arnold.crud.read.sample import get_sample_by_id, get_samples
from arnold.crud.read.step import find_sample_fields
from arnold.models.database import LimsSample
from typing import List
from fastapi import APIRouter, Depends, status
from fastapi.responses import JSONResponse
import logging
import arnold.crud.read.sample
from arnold.settings import get_arnold_adapter

LOG = logging.getLogger(__name__)

router = APIRouter()


@router.get("/sample/fields")
def get_sample_fields(
    adapter: ArnoldAdapter = Depends(get_arnold_adapter),
):
    """Get sample fields"""
    return find_sample_fields(adapter=adapter)


@router.get("/sample/{sample_id}", response_model=LimsSample)
def get_sample(
    sample_id: str,
    adapter: ArnoldAdapter = Depends(get_arnold_adapter),
):
    """fetch a sample by sample id"""
    sample: LimsSample = get_sample_by_id(sample_id=sample_id, adapter=adapter)
    return sample


@router.get("/samples/", response_model=List[LimsSample])
def get_samples(
    adapter: ArnoldAdapter = Depends(get_arnold_adapter),
):
    """Get all samples"""
    samples: List[LimsSample] = get_samples(adapter=adapter)

    return samples


@router.post("/sample/")
def create_sample(
    sample: LimsSample, adapter: ArnoldAdapter = Depends(get_arnold_adapter)
) -> JSONResponse:
    if arnold.crud.read.sample.get_sample_by_id(
        sample_id=sample.sample_id, adapter=adapter
    ):
        return JSONResponse(
            status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
            content=f"Sample: sample.sample_id is already in database",
        )
    try:
        create.create_sample(adapter=adapter, sample=sample)
    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"Sample: {sample.sample_id} inserted to database",
    )


@router.post("/samples/")
def create_samples(
    samples: List[LimsSample], adapter: ArnoldAdapter = Depends(get_arnold_adapter)
) -> JSONResponse:
    try:
        create.create_samples(adapter=adapter, samples=samples)
    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="Samples inserted to db"
    )


@router.put("/sample/")
def update_sample(
    sample: LimsSample, adapter: ArnoldAdapter = Depends(get_arnold_adapter)
) -> JSONResponse:
    try:
        update.update_sample(adapter=adapter, sample=sample)
    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"Sample: {sample.sample_id} inserted to database",
    )


@router.put("/samples/")
def update_samples(
    samples: List[LimsSample], adapter: ArnoldAdapter = Depends(get_arnold_adapter)
) -> JSONResponse:
    try:
        update.update_samples(adapter=adapter, samples=samples)
    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="Samples inserted to db"
    )

1	from arnold.adapter import ArnoldAdapter	×
2	from arnold.crud import create, update	×
NEW 3	from arnold.crud.read.sample import get_sample_by_id, get_samples	×
4	from arnold.crud.read.step import find_sample_fields	×
5	from arnold.models.database import LimsSample	×
6	from typing import List	×
7	from fastapi import APIRouter, Depends, status	×
8	from fastapi.responses import JSONResponse	×
9	import logging	×
10	import arnold.crud.read.sample	×
11	from arnold.settings import get_arnold_adapter	×
12
13	LOG = logging.getLogger(__name__)	×
14
15	router = APIRouter()	×
16
17
18	@router.get("/sample/fields")	×
19	def get_sample_fields(	×
20	adapter: ArnoldAdapter = Depends(get_arnold_adapter),
21	):
22	"""Get sample fields"""
23	return find_sample_fields(adapter=adapter)	×
24
25
26	@router.get("/sample/{sample_id}", response_model=LimsSample)	×
27	def get_sample(	×
28	sample_id: str,
29	adapter: ArnoldAdapter = Depends(get_arnold_adapter),
30	):
31	"""fetch a sample by sample id"""
NEW 32	sample: LimsSample = get_sample_by_id(sample_id=sample_id, adapter=adapter)	×
33	return sample	×
34
35
36	@router.get("/samples/", response_model=List[LimsSample])	×
37	def get_samples(	×
38	adapter: ArnoldAdapter = Depends(get_arnold_adapter),
39	):
40	"""Get all samples"""
NEW 41	samples: List[LimsSample] = get_samples(adapter=adapter)	×
42
43	return samples	×
44
45
46	@router.post("/sample/")	×
47	def create_sample(	×
48	sample: LimsSample, adapter: ArnoldAdapter = Depends(get_arnold_adapter)
49	) -> JSONResponse:
NEW 50	if arnold.crud.read.sample.get_sample_by_id(	×
51	sample_id=sample.sample_id, adapter=adapter
52	):
UNCOV 53	return JSONResponse(	×
54	status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
55	content=f"Sample: sample.sample_id is already in database",
56	)
57	try:	×
58	create.create_sample(adapter=adapter, sample=sample)	×
59	except Exception as e:	×
60	return JSONResponse(	×
61	status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
62	content=f"exception {e} ",
63	)
64
65	return JSONResponse(	×
66	status_code=status.HTTP_200_OK,
67	content=f"Sample: {sample.sample_id} inserted to database",
68	)
69
70
71	@router.post("/samples/")	×
72	def create_samples(	×
73	samples: List[LimsSample], adapter: ArnoldAdapter = Depends(get_arnold_adapter)
74	) -> JSONResponse:
75	try:	×
76	create.create_samples(adapter=adapter, samples=samples)	×
77	except Exception as e:	×
78	return JSONResponse(	×
79	status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
80	content=f"exception {e} ",
81	)
NEW 82	return JSONResponse(	×
83	status_code=status.HTTP_200_OK, content="Samples inserted to db"
84	)
85
86
87	@router.put("/sample/")	×
88	def update_sample(	×
89	sample: LimsSample, adapter: ArnoldAdapter = Depends(get_arnold_adapter)
90	) -> JSONResponse:
91	try:	×
92	update.update_sample(adapter=adapter, sample=sample)	×
93	except Exception as e:	×
94	return JSONResponse(	×
95	status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
96	content=f"exception {e} ",
97	)
98
99	return JSONResponse(	×
100	status_code=status.HTTP_200_OK,
101	content=f"Sample: {sample.sample_id} inserted to database",
102	)
103
104
105	@router.put("/samples/")	×
106	def update_samples(	×
107	samples: List[LimsSample], adapter: ArnoldAdapter = Depends(get_arnold_adapter)
108	) -> JSONResponse:
109	try:	×
110	update.update_samples(adapter=adapter, samples=samples)	×
111	except Exception as e:	×
112	return JSONResponse(	×
113	status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
114	content=f"exception {e} ",
115	)
NEW 116	return JSONResponse(	×
117	status_code=status.HTTP_200_OK, content="Samples inserted to db"
118	)

Clinical-Genomics / arnold / 7130299646

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous