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 new_user(request: Request):
"""Log in view."""
return templates.TemplateResponse("new_user.html",
context={
"request": request,
"current_user": ""
})
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 index(request: Request):
"""Log in view."""
return templates.TemplateResponse(
"index.html",
context={
"request": request,
"current_user": "",
"info_type": request.cookies.get("info_type"),
"user_info": request.cookies.get("user_info"),
},
)
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",
),
)
def batches(
request: Request,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""List of all batches"""
all_batches: List[Batch] = find.batches(adapter=adapter)
return templates.TemplateResponse(
"batches.html",
context={
"request": request,
"batches": all_batches,
"current_user": user,
"page_id": "all_batches",
},
)
def samples(
request: Request,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Get sample with id"""
samples: List[DataBaseSample] = find.samples(adapter=adapter)
return templates.TemplateResponse(
"sample/samples.html",
context=dict(
request=request,
current_user=user,
sample_info=[Sample(**sample.dict()) for sample in samples],
page_id="samples",
),
)
def statistics(
request: Request,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Statistics view."""
nr_batches = 20
scatter_plots = ["Stdev_13", "Stdev_18", "Stdev_21"]
box_plots = [
"Chr13_Ratio",
"Chr18_Ratio",
"Chr21_Ratio",
"FF_Formatted",
"DuplicationRate",
"MappedReads",
"GC_Dropout",
"AT_Dropout",
"Bin2BinVariance",
"Library_nM",
]
batches = get_last_batches(adapter=adapter, nr_of_batches=nr_batches)
batch_ids = [batch.get("batch_id") for batch in batches]
box_stat = get_statistics_for_box_plot(adapter=adapter,
batches=batch_ids,
fields=box_plots)
scatter_stat = get_statistics_for_scatter_plot(batches=batches,
fields=scatter_plots)
return templates.TemplateResponse(
"statistics.html",
context=dict(
request=request,
current_user=user,
ticks=list(range(0, nr_batches)),
nr_batches=nr_batches,
batch_ids=batch_ids,
box_stat=box_stat,
box_plots=box_plots,
scatter_stat=scatter_stat,
scatter_plots=scatter_plots,
page_id="statistics",
),
)
def users(
request: Request,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Admin view with table of all users."""
if user.role != "admin":
CredentialsError(message="Only admin users can access the users page")
user_list: List[User] = find.users(adapter=adapter)
return templates.TemplateResponse(
"users.html",
context={
"request": request,
"users": user_list,
"page_id": "users",
"current_user": user,
},
)
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 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",
),
)
