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sample.py
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sample.py
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from fastapi import APIRouter, Depends, Request
from NIPTool.adapter.plugin import NiptAdapter
from NIPTool.crud import find
from NIPTool.models.database import User
from NIPTool.API.external.utils import *
from NIPTool.API.external.api.deps import get_nipt_adapter
from fastapi.templating import Jinja2Templates
router = APIRouter()
templates = Jinja2Templates(directory="templates")
@router.get("/samples/{sample_id}/")
def sample(request: Request, sample_id: str, adapter: NiptAdapter = Depends(get_nipt_adapter)):
"""Sample view with sample information."""
sample: dict = find.sample(sample_id=sample_id, adapter=adapter).dict()
batch = find.batch(batch_id=sample.get("batch_id"), adapter=adapter)
return templates.TemplateResponse(
"sample/sample.html",
context=dict(
request=request,
current_user=User(username="mayapapaya", email="mayabrandi@123.com", role="RW"),
chrom_abnorm=CHROM_ABNORM,
sample=sample,
status_classes=STATUS_CLASSES,
batch=batch,
page_id="sample",
),
)
@router.get("/samples/{sample_id}/tris")
def sample_tris(request: Request, sample_id: str, adapter: NiptAdapter = Depends(get_nipt_adapter)):
"""Sample view with trisomi plot."""
sample: dict = find.sample(sample_id=sample_id, adapter=adapter).dict()
batch = find.batch(batch_id=sample.get("batch_id"), adapter=adapter)
abnormal_data, data_per_abnormaliy = get_abn_for_samp_tris_plot(adapter=adapter)
normal_data = get_normal_for_samp_tris_plot(adapter=adapter)
sample_data = get_sample_for_samp_tris_plot(sample)
return templates.TemplateResponse(
"sample/sample_tris.html",
context=dict(
request=request,
current_user=User(username="mayapapaya", email="mayabrandi@123.com", role="RW"),
tris_abn=data_per_abnormaliy,
normal_data=normal_data,
abnormal_data=abnormal_data,
sample_data=sample_data,
sample=sample,
batch=batch,
status_colors=STATUS_COLORS,
page_id="sample_tris",
),
)