sovling merge conflict with master

NIPTool/API/external/api/api_v1/endpoints/batches.py

@@ -5,6 +5,7 @@
 from NIPTool.API.external.utils import *
 from NIPTool.API.external.constants import TRISOMI_TRESHOLDS
 from NIPTool.API.external.api.deps import get_nipt_adapter
+
 from fastapi.templating import Jinja2Templates
 
 router = APIRouter()
@@ -68,6 +69,7 @@ def batch(request: Request, batch_id: str, adapter: NiptAdapter = Depends(get_ni
 @router.post("/{batch_id}/")
 def batch(request: Request, batch_id: str, adapter: NiptAdapter = Depends(get_nipt_adapter)):
     """Batch view with table of all samples in the batch."""
+
     samples: List[Sample] = find.batch_samples(batch_id=batch_id, adapter=adapter)
     return templates.TemplateResponse(
         "batch/tabs/table.html",
@@ -85,6 +87,7 @@ def batch(request: Request, batch_id: str, adapter: NiptAdapter = Depends(get_ni
 def NCV(request: Request, batch_id: str, ncv, adapter: NiptAdapter = Depends(get_nipt_adapter)):
     """Batch view with with NCV plot"""
     batch: Batch = find.batch(batch_id=batch_id, adapter=adapter)
+
     return templates.TemplateResponse(
         "batch/tabs/NCV.html",
         context=dict(
@@ -107,6 +110,7 @@ def fetal_fraction_XY(
 ):
     """Batch view with fetal fraction (X against Y) plot"""
     batch: Batch = find.batch(batch_id=batch_id, adapter=adapter)
+
     control = get_ff_control_normal(adapter)
     abnormal = get_ff_control_abnormal(adapter)
     return templates.TemplateResponse(
@@ -131,6 +135,7 @@ def fetal_fraction(
 ):
     """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(
@@ -149,6 +154,7 @@ def coverage(request: Request, batch_id: str, adapter: NiptAdapter = Depends(get
     """Batch view with coverage plot"""
     batch: Batch = find.batch(batch_id=batch_id, adapter=adapter)
     samples: List[Sample] = find.batch_samples(batch_id=batch_id, adapter=adapter)
+
     scatter_data = get_scatter_data_for_coverage_plot(samples)
     box_data = get_box_data_for_coverage_plot(samples)
     return templates.TemplateResponse(
@@ -173,6 +179,7 @@ def report(
 
     batch: Batch = find.batch(batch_id=batch_id, adapter=adapter)
     samples: List[Sample] = find.batch_samples(batch_id=batch_id, adapter=adapter)
+
     scatter_data = get_scatter_data_for_coverage_plot(samples)
     box_data = get_box_data_for_coverage_plot(samples)
     control = get_ff_control_normal(adapter)

NIPTool/API/external/api/api_v1/endpoints/sample.py

@@ -4,6 +4,7 @@
 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()

NIPTool/API/external/api/api_v1/endpoints/statistics.py

@@ -9,6 +9,7 @@
     get_statistics_for_scatter_plot,
 )
 from NIPTool.API.external.api.deps import get_nipt_adapter
+
 from fastapi.templating import Jinja2Templates
 
 router = APIRouter()
@@ -35,6 +36,7 @@ def statistics(request: Request, adapter: NiptAdapter = Depends(get_nipt_adapter
     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(

NIPTool/API/external/utils.py

@@ -24,6 +24,7 @@ def get_sample_info(sample: Sample):
         "FFY",
         "Zscore_X",
     ]
+
     for key in sample_info_keys:
         val = sample.get(key)
         if isinstance(val, (float, int)):
@@ -82,6 +83,7 @@ def _get_ff_warning(fetal_fraction):
 def get_sample_warnings(sample: Sample):
     """"""
     sample = sample.dict()
+
     sample_warnings = {}
     fetal_fraction = sample.get("FF_Formatted")
     sample_warnings["FF_Formatted"] = _get_ff_warning(fetal_fraction)
@@ -258,6 +260,7 @@ def get_tris_control_normal(adapter, chr):
     if not list(find.sample_aggregate(pipe=pipe, adapter=adapter)):
         return []
     data = list(find.sample_aggregate(pipe=pipe, adapter=adapter))[0]
+
     data["values"] = [value for value in data.get("values", [])]
 
     return data
@@ -286,6 +289,7 @@ def get_tris_control_abnormal(adapter, chr, x_axis):
     ]
 
     for status_dict in find.sample_aggregate(pipe=pipe, adapter=adapter):
+
         status = status_dict["_id"][f"status_{chr}"]
         plot_data[status] = {
             "values": [value for value in status_dict.get("values")],
@@ -389,6 +393,7 @@ def get_statistics_for_scatter_plot(batches: list, fields: list) -> dict:
     for batch in batches:
         batch_id = batch.get("batch_id")
         scatter_plot_data[batch_id] = {"date": batch.get("SequencingDate")}
+
         for field in fields:
             scatter_plot_data[batch_id][field] = batch.get(field)
 

NIPTool/adapter/plugin.py

@@ -5,6 +5,7 @@
 
 from mongo_adapter import MongoAdapter
 
+
 LOG = logging.getLogger(__name__)
 
 

NIPTool/models/database/batch.py

@@ -4,7 +4,7 @@
 
 
 class Batch(BaseModel):
-    batch_id: str=Field(..., alias='SampleProject')
+    batch_id: str = Field(..., alias="SampleProject")
     result_file: Optional[str]
     multiqc_report: Optional[str]
     segmental_calls: Optional[str]

NIPTool/models/database/sample.py

@@ -4,8 +4,8 @@
 
 
 class Sample(BaseModel):
-    sample_id: str= Field(..., alias='SampleID')
-    batch_id: str= Field(..., alias='SampleProject')
+    sample_id: str = Field(..., alias="SampleID")
+    batch_id: str = Field(..., alias="SampleProject")
     SampleType: Optional[str]
     Description: Optional[str]
     Flowcell: Optional[str]