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Merge 0cc03a8 into 2ce5357
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@mayabrandi
mayabrandi committed Jul 9, 2021
2 parents 2ce5357 + 0cc03a8 commit 47efbaa
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Showing 14 changed files with 399 additions and 234 deletions.
17 changes: 10 additions & 7 deletions statina/API/external/api/api_v1/endpoints/batches.py
View file
Expand Up @@ -5,7 +5,7 @@
import statina.crud.find.plots.fetal_fraction_plot_data as get_fetal_fraction
from statina.adapter import StatinaAdapter
from statina.API.external.api.deps import get_current_user
from statina.API.external.constants import TRISOMI_TRESHOLDS
from statina.API.external.constants import TRISOMI_TRESHOLDS, COLORS
from statina.config import get_nipt_adapter, templates
from statina.crud.find import find
from statina.crud.find.plots.coverage_plot_data import (
Expand Down Expand Up @@ -151,6 +151,7 @@ def fetal_fraction_XY(

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
)
Expand All @@ -165,8 +166,8 @@ def fetal_fraction_XY(
},
)

x_max = max(control.FFX) + 1
x_min = min(control.FFX) - 1
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(
Expand All @@ -176,15 +177,16 @@ def fetal_fraction_XY(
"XY_fetal_fraction_y": sex_thresholds.XY_fetal_fraction_y(),
"XX_lower": sex_thresholds.XX_lower(),
"XX_upper": sex_thresholds.XX_upper(),
# "XY_lower": sex_thresholds.XY_lower(),
# "XY_upper": sex_thresholds.XY_upper(),
# "XXY": sex_thresholds.XXY(),
"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=get_fetal_fraction.samples(adapter=adapter, batch_id=batch_id),
cases=cases,
max_x=x_max,
min_x=x_min,
batch=batch.dict(),
Expand All @@ -207,6 +209,7 @@ def fetal_fraction(
context=dict(
request=request,
current_user=user,
colors=COLORS,
control=get_fetal_fraction.samples(
adapter=adapter, batch_id=batch_id, control_samples=True
),
Expand Down
70 changes: 29 additions & 41 deletions statina/API/external/api/api_v1/endpoints/download.py
View file
Expand Up @@ -5,33 +5,23 @@
from starlette.requests import Request
from starlette.responses import StreamingResponse

from statina.API.external.constants import TRISOMI_TRESHOLDS

from statina.API.external.constants import COLORS
from statina.adapter.plugin import StatinaAdapter
from statina.API.external.api.deps import get_current_user
from statina.config import get_nipt_adapter, templates
from statina.crud.find import find
from statina.crud.find.plots import fetal_fraction_plot_data as get_fetal_fraction
from statina.crud.find.plots.coverage_plot_data import (
get_scatter_data_for_coverage_plot,
get_box_data_for_coverage_plot,
)
from statina.crud.find.plots.zscore_plot_data import (
get_samples_for_samp_tris_plot,
get_normal_for_samp_tris_plot,
get_abnormal_for_samp_tris_plot,
)
from statina.models.server.plots.coverage import CoveragePlotSampleData
from statina.models.server.plots.fetal_fraction import (
FetalFractionSamples,
FetalFractionControlAbNormal,
)
from statina.models.server.plots.fetal_fraction_sex import SexChromosomeThresholds
from statina.models.server.sample import Sample
from zipfile import ZIP_DEFLATED, ZipFile
import io
from os import PathLike
from typing import Union, List, Dict
from statina.models.database import DataBaseSample, User
from typing import Union, List
from statina.models.database import DataBaseSample, User, Batch
from statina.parse.batch import validate_file_path

router = APIRouter()
Expand Down Expand Up @@ -96,23 +86,22 @@ def sample_download(
)


@router.get("/batches/{batch_id}/report/{coverage}/{file_name}")
@router.get("/batches/{batch_id}/report/{file_name}")
def report(
request: Request,
batch_id: str,
file_name: str,
coverage: str,
adapter: StatinaAdapter = Depends(get_nipt_adapter),
user: User = Depends(get_current_user),
):
"""Report view, collecting all tables and plots from one batch."""

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)
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(
adapter=adapter, batch_id=batch_id, control_samples=True
batch_id=batch_id, adapter=adapter, control_samples=True
)
abnormal: FetalFractionControlAbNormal = get_fetal_fraction.control_abnormal(adapter)
abnormal_dict = abnormal.dict(
Expand All @@ -125,35 +114,34 @@ def report(
},
)

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),
# Zscore
tris_thresholds=TRISOMI_TRESHOLDS,
chromosomes=["13", "18", "21"],
ncv_chrom_data=get_samples_for_samp_tris_plot(adapter, batch_id=batch_id).dict(
by_alias=True
),
normal_data=get_normal_for_samp_tris_plot(adapter).dict(by_alias=True),
abnormal_data=get_abnormal_for_samp_tris_plot(adapter),
# Fetal Fraction preface
control=control,
cases=get_fetal_fraction.samples(adapter=adapter, batch_id=batch_id),
# 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,
max_x=max(control.FFX) + 1,
min_x=min(control.FFX) - 1,
cases=cases,
colors=COLORS,
max_x=x_max,
min_x=x_min,
# table
sample_info=samples,
# coverage
coverage=coverage,
x_axis=list(range(1, 23)),
scatter_data=scatter_data,
box_data=box_data,
page_id="batches",
sample_info=[Sample(**sample.dict()) for sample in samples],
)

in_mem_file = io.StringIO()
Expand Down
1 change: 1 addition & 0 deletions statina/API/external/api/api_v1/endpoints/statistics.py
View file
Expand Up @@ -33,6 +33,7 @@ def statistics(
"GC_Dropout",
"AT_Dropout",
"Bin2BinVariance",
"Library_nM",
]

batches = get_last_batches(adapter=adapter, nr_of_batches=nr_batches)
Expand Down
5 changes: 1 addition & 4 deletions statina/API/external/api/api_v1/templates/batch/header.html
View file
Expand Up @@ -15,12 +15,9 @@
Batch Downloads
</button>
<ul class="dropdown-menu">
<a class="dropdown-item" href="{{ url_for('report', batch_id=batch.batch_id , file_name=batch.batch_id+"_report.html", coverage=0) }}">
<a class="dropdown-item" href="{{ url_for('report', batch_id=batch.batch_id , file_name=batch.batch_id+"_report.html") }}">
Report</a>
<li class="divider"></li>
<a class="dropdown-item" href="{{ url_for('report', batch_id=batch.batch_id , file_name=batch.batch_id+"_coverage_report.html", coverage=1) }}">
Coverage Report</a>
<li class="divider"></li>
<a class="dropdown-item"
href="{{ url_for('batch_download', file_id='multiqc_report', file_name='multiqc_report', batch_id=batch.batch_id) }}">Multi
QC</a>
Expand Down

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