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",
),
)
async def set_sample_status(
request: Request,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Update the manualy interpreted chromosome abnormality status for a sample."""
form = await request.form()
if user.role not in ["RW", "admin"]:
return RedirectResponse(request.headers.get("referer"))
sample_id: str = form["sample_id"]
sample: dict = find.sample(sample_id=sample_id, adapter=adapter).dict()
for abnormality in CHROM_ABNORM:
new_abnormality_status: str = form[abnormality]
abnormality_key: str = f"status_{abnormality}"
if sample.get(abnormality_key) == new_abnormality_status:
continue
LOG.debug(
"Updating %s to %s for sample %s",
abnormality_key,
new_abnormality_status,
sample_id,
)
time_stamp: str = datetime.now().strftime("%Y/%m/%d %H:%M:%S")
sample[abnormality_key] = new_abnormality_status
sample[f"status_change_{abnormality}"] = f"{user.username} {time_stamp}"
update.sample(adapter=adapter, sample=DataBaseSample(**sample))
return RedirectResponse(request.headers.get("referer"))
def include_all_samples(samples: Iterable[str], adapter: StatinaAdapter, user: User):
"""Function to set sample.include=True for all samples."""
time_stamp: str = datetime.now().strftime("%Y/%m/%d %H:%M:%S")
for sample_id in samples:
sample: DataBaseSample = find.sample(sample_id=sample_id, adapter=adapter)
if sample.include:
continue
sample.include = True
sample.change_include_date = f"{user.username} {time_stamp}"
update.sample(adapter=adapter, sample=sample)
def save_samples(samples: Iterable[str], form: FormData, adapter: StatinaAdapter, user: User):
"""Function to update sample.comment and sample.include."""
time_stamp: str = datetime.now().strftime("%Y/%m/%d %H:%M:%S")
for sample_id in samples:
sample: DataBaseSample = find.sample(sample_id=sample_id, adapter=adapter)
comment: str = form.get(f"comment_{sample_id}")
include: bool = form.get(f"include_{sample_id}")
if comment != sample.comment:
sample.comment = comment
if include and not sample.include:
sample.include = True
sample.change_include_date = f"{user.username} {time_stamp}"
elif not include and sample.include:
sample.include = False
update.sample(adapter=adapter, sample=sample)
def sample_download(
request: Request,
sample_id: str,
file_id: str,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""View for sample downloads"""
sample: DataBaseSample = find.sample(adapter=adapter, sample_id=sample_id)
file_path = sample.dict().get(file_id)
if not validate_file_path(file_path):
# warn file missing!
return RedirectResponse(request.headers.get("referer"))
file = Path(file_path)
return FileResponse(str(file.absolute()),
media_type="application/octet-stream",
filename=file.name)
async def sample_comment(
request: Request,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Update sample comment"""
form = await request.form()
if user.role not in ["RW", "admin"]:
return RedirectResponse(request.headers.get("referer"))
sample_id: str = form["sample_id"]
sample: DataBaseSample = find.sample(sample_id=sample_id, adapter=adapter)
comment: str = form.get("comment")
if comment != sample.comment:
sample.comment = comment
update.sample(adapter=adapter, sample=sample)
return RedirectResponse(request.headers.get("referer"))
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",
),
)