7114672788

Committed 06 Dec 2023 12:43PM UTC coverage: 0.0%. Remained the same

Build # 7114672788

Build Type

push

github

Committed by

web-flow

Commit Message

add(bioinfo models) (#49) (patch)

## Added
Adds Bioinfo models to arnold

## Changed
Renamed "Sample" model to "LimsSample" to make a better distinction between LAB and BIOINFO related metrics.
Not sure if this will persist later on or these will me merged in some way.

Run Details

0 of 190 new or added lines in 18 files covered. (0.0%)

2 existing lines in 1 file now uncovered.

0 of 862 relevant lines covered (0.0%)

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Source File
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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 find_sample, find_all_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 = find_sample(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] = find_all_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.find_sample(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	×
3	from arnold.crud.read.sample import find_sample, find_all_samples	×
4	from arnold.crud.read.step import find_sample_fields	×
NEW 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
NEW 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 = find_sample(sample_id=sample_id, adapter=adapter)	×
33	return sample	×
34
35
NEW 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] = find_all_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:
50	if arnold.crud.read.sample.find_sample(sample_id=sample.sample_id, adapter=adapter):	×
51	return JSONResponse(	×
52	status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
53	content=f"Sample: sample.sample_id is already in database",
54	)
55	try:	×
56	create.create_sample(adapter=adapter, sample=sample)	×
57	except Exception as e:	×
58	return JSONResponse(	×
59	status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
60	content=f"exception {e} ",
61	)
62
63	return JSONResponse(	×
64	status_code=status.HTTP_200_OK,
65	content=f"Sample: {sample.sample_id} inserted to database",
66	)
67
68
69	@router.post("/samples/")	×
70	def create_samples(	×
71	samples: List[LimsSample], adapter: ArnoldAdapter = Depends(get_arnold_adapter)
72	) -> JSONResponse:
73	try:	×
74	create.create_samples(adapter=adapter, samples=samples)	×
75	except Exception as e:	×
76	return JSONResponse(	×
77	status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
78	content=f"exception {e} ",
79	)
80	return JSONResponse(status_code=status.HTTP_200_OK, content="Samples inserted to db")	×
81
82
83	@router.put("/sample/")	×
84	def update_sample(	×
85	sample: LimsSample, adapter: ArnoldAdapter = Depends(get_arnold_adapter)
86	) -> JSONResponse:
87	try:	×
88	update.update_sample(adapter=adapter, sample=sample)	×
89	except Exception as e:	×
90	return JSONResponse(	×
91	status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
92	content=f"exception {e} ",
93	)
94
95	return JSONResponse(	×
96	status_code=status.HTTP_200_OK,
97	content=f"Sample: {sample.sample_id} inserted to database",
98	)
99
100
101	@router.put("/samples/")	×
102	def update_samples(	×
103	samples: List[LimsSample], adapter: ArnoldAdapter = Depends(get_arnold_adapter)
104	) -> JSONResponse:
105	try:	×
106	update.update_samples(adapter=adapter, samples=samples)	×
107	except Exception as e:	×
108	return JSONResponse(	×
109	status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
110	content=f"exception {e} ",
111	)
112	return JSONResponse(status_code=status.HTTP_200_OK, content="Samples inserted to db")	×

Clinical-Genomics / arnold / 7114672788

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