def coverage(
request: Request,
batch_id: str,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Batch view with coverage plot"""
batch: Batch = find.batch(batch_id=batch_id, adapter=adapter)
db_samples: List[DataBaseSample] = find.batch_samples(batch_id=batch_id,
adapter=adapter)
samples: List[Sample] = [
Sample(**db_sample.dict()) for db_sample in db_samples
]
scatter_data: Dict[
str,
CoveragePlotSampleData] = get_scatter_data_for_coverage_plot(samples)
box_data: Dict[int, List[float]] = get_box_data_for_coverage_plot(samples)
return templates.TemplateResponse(
"batch/tabs/coverage.html",
context=dict(
request=request,
current_user=user,
batch=batch.dict(),
x_axis=list(range(1, 23)),
scatter_data=scatter_data,
box_data=box_data,
page_id="batches_cov",
),
)
def Zscore(
request: Request,
batch_id: str,
ncv: str,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Batch view with with Zscore plot"""
batch: Batch = find.batch(batch_id=batch_id, adapter=adapter)
return templates.TemplateResponse(
"batch/tabs/Zscore.html",
context=dict(
request=request,
tris_thresholds=TRISOMI_TRESHOLDS,
batch=batch.dict(),
chromosomes=[ncv],
ncv_chrom_data={
ncv: get_tris_samples(adapter=adapter,
chr=ncv,
batch_id=batch_id)
},
normal_data={ncv: get_tris_control_normal(adapter, ncv)},
abnormal_data={ncv: get_tris_control_abnormal(adapter, ncv, 0)},
page_id=f"batches_NCV{ncv}",
current_user=user,
),
)
def sample_tris(
request: Request,
sample_id: str,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Sample view with trisomi plot."""
sample: DataBaseSample = find.sample(sample_id=sample_id, adapter=adapter)
batch: Batch = find.batch(batch_id=sample.batch_id, adapter=adapter)
abnormal_data: Dict[str, ZscoreSamples] = get_abn_for_samp_tris_plot(
adapter=adapter)
normal_data: Zscore131821 = get_normal_for_samp_tris_plot(adapter=adapter)
sample_data: ZscoreSamples = get_sample_for_samp_tris_plot(sample)
return templates.TemplateResponse(
"sample/sample_tris.html",
context=dict(
request=request,
current_user=user,
normal_data=normal_data.dict(exclude_none=True, by_alias=True),
abnormal_data=abnormal_data,
sample_data=sample_data,
sample=Sample(**sample.dict()),
batch=batch,
status_colors=STATUS_COLORS,
page_id="sample_tris",
),
)
def fetal_fraction_XY(
request: Request,
batch_id: str,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Batch view with fetal fraction (X against Y) plot"""
batch: Batch = find.batch(batch_id=batch_id, adapter=adapter)
cases = get_fetal_fraction.samples(adapter=adapter, batch_id=batch_id)
control: FetalFractionSamples = get_fetal_fraction.samples(
batch_id=batch_id, adapter=adapter, control_samples=True)
abnormal: FetalFractionControlAbNormal = get_fetal_fraction.control_abnormal(
adapter)
abnormal_dict = abnormal.dict(
exclude_none=True,
exclude={
"X0": {"status_data_"},
"XXX": {"status_data_"},
"XXY": {"status_data_"},
"XYY": {"status_data_"},
},
)
x_max = max(control.FFX + cases.FFX) + 1
x_min = min(control.FFX + cases.FFX) - 1
sex_thresholds = SexChromosomeThresholds(x_min=x_min, x_max=x_max)
return templates.TemplateResponse(
"batch/tabs/FF_XY.html",
context=dict(
sex_thresholds={
"XY_fetal_fraction_y": sex_thresholds.XY_fetal_fraction_y(),
"XX_lower": sex_thresholds.XX_lower(),
"XX_upper": sex_thresholds.XX_upper(),
"XY_upper": sex_thresholds.XY_upper(),
"XY_lower": sex_thresholds.XY_lower(),
"XXY": sex_thresholds.XXY(),
},
request=request,
current_user=user,
colors=COLORS,
control=control,
abnormal=abnormal_dict,
cases=cases,
max_x=x_max,
min_x=x_min,
batch=batch.dict(),
page_id="batches_FF_XY",
),
)
async def batch_comment(
request: Request,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Update batch comment"""
form = await request.form()
if user.role not in ["RW", "admin"]:
return RedirectResponse(request.headers.get("referer"))
batch_id: str = form["batch_id"]
batch: Batch = find.batch(batch_id=batch_id, adapter=adapter)
comment: str = form.get("comment")
if comment != batch.comment:
batch.comment = comment
update.update_batch(adapter=adapter, batch=batch)
return RedirectResponse(request.headers.get("referer"))
def batch(
request: Request,
batch_id: str,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Batch view with table of all samples in the batch."""
samples: List[DataBaseSample] = find.batch_samples(batch_id=batch_id,
adapter=adapter)
return templates.TemplateResponse(
"batch/tabs/table.html",
context={
"request": request,
"batch": find.batch(batch_id=batch_id, adapter=adapter),
"sample_info": [Sample(**sample.dict()) for sample in samples],
"page_id": "batches",
"current_user": user,
},
)
def batch(
response: Response,
batch_files: BatchRequestBody,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
):
"""Function to load batch data into the database with rest"""
nipt_results = Path(batch_files.result_file)
if not nipt_results.exists():
response.status_code = status.HTTP_422_UNPROCESSABLE_ENTITY
return {"message": "Results file missing."}
samples: List[DataBaseSample] = get_samples(nipt_results)
batch: Batch = get_batch(nipt_results)
if find.batch(adapter=adapter, batch_id=batch.batch_id):
return "batch already in database"
insert_batch(adapter=adapter, batch=batch, batch_files=batch_files)
insert_samples(adapter=adapter,
samples=samples,
segmental_calls=batch_files.segmental_calls)
response.status_code = status.HTTP_200_OK
return {"message": f"Batch {batch.batch_id} inserted to the database"}
def batch_download(
request: Request,
batch_id: str,
file_id: str,
file_name: str,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""View for batch downloads"""
batch: dict = find.batch(adapter=adapter, batch_id=batch_id).dict()
file_path = batch.get(file_id)
if not validate_file_path(file_path):
return RedirectResponse(request.headers.get("referer"))
path = Path(file_path)
if path.is_dir():
file_obj = zip_dir(source_dir=file_path)
return StreamingResponse(file_obj, media_type="application/text")
return FileResponse(str(path.absolute()),
media_type="application/octet-stream",
filename=path.name)
def sample(
request: Request,
sample_id: str,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Post sample with id"""
sample: DataBaseSample = find.sample(sample_id=sample_id, adapter=adapter)
batch: Batch = find.batch(batch_id=sample.batch_id, adapter=adapter)
return templates.TemplateResponse(
"sample/sample.html",
context=dict(
request=request,
current_user=user,
chrom_abnorm=CHROM_ABNORM,
sample=Sample(**sample.dict()),
status_classes=STATUS_CLASSES,
batch=batch,
page_id="sample",
),
)
def fetal_fraction(
request: Request,
batch_id: str,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Batch view with fetal fraction plot"""
batch: Batch = find.batch(batch_id=batch_id, adapter=adapter)
return templates.TemplateResponse(
"batch/tabs/FF.html",
context=dict(
request=request,
current_user=user,
colors=COLORS,
control=get_fetal_fraction.samples(adapter=adapter,
batch_id=batch_id,
control_samples=True),
cases=get_fetal_fraction.samples(adapter=adapter,
batch_id=batch_id),
batch=batch.dict(),
page_id="batches_FF",
),
)
def report(
request: Request,
batch_id: str,
file_name: str,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Report view, collecting all tables and plots from one batch."""
samples: List[DataBaseSample] = find.batch_samples(batch_id=batch_id,
adapter=adapter)
batch: Batch = find.batch(batch_id=batch_id, adapter=adapter)
cases = get_fetal_fraction.samples(adapter=adapter, batch_id=batch_id)
control: FetalFractionSamples = get_fetal_fraction.samples(
batch_id=batch_id, adapter=adapter, control_samples=True)
abnormal: FetalFractionControlAbNormal = get_fetal_fraction.control_abnormal(
adapter)
abnormal_dict = abnormal.dict(
exclude_none=True,
exclude={
"X0": {"status_data_"},
"XXX": {"status_data_"},
"XXY": {"status_data_"},
"XYY": {"status_data_"},
},
)
x_max = max(control.FFX + cases.FFX) + 1
x_min = min(control.FFX + cases.FFX) - 1
sex_thresholds = SexChromosomeThresholds(x_min=x_min, x_max=x_max)
template = templates.get_template("batch/report.html")
output_from_parsed_template = template.render(
# common
request=request,
current_user=user,
batch=find.batch(batch_id=batch_id, adapter=adapter),
# Fetal Fraction XY
sex_thresholds={
"XY_fetal_fraction_y": sex_thresholds.XY_fetal_fraction_y(),
"XX_lower": sex_thresholds.XX_lower(),
"XX_upper": sex_thresholds.XX_upper(),
"XY_upper": sex_thresholds.XY_upper(),
"XY_lower": sex_thresholds.XY_lower(),
"XXY": sex_thresholds.XXY(),
},
control=control,
abnormal=abnormal_dict,
cases=cases,
colors=COLORS,
max_x=x_max,
min_x=x_min,
# table
sample_info=[Sample(**sample.dict()) for sample in samples],
)
in_mem_file = io.StringIO()
in_mem_file.seek(0)
in_mem_file.write(output_from_parsed_template)
in_mem_file.seek(0)
return StreamingResponse(in_mem_file, media_type="application/text")