Tresholds (#99)

* X0 and XXX in place. Waiting for XXY and XYY treshold equations.

* tresholds for XXY and XYY

* truncating report

* Library_nM

* unique colors mm

* batch commetn

* Update CHANGELOG.md

* Update fetal_fraction_sex.py

* Update CHANGELOG.md

* Update __init__.py

CHANGELOG.md

@@ -1,11 +1,21 @@
 # Change Log
 
 This change log will document the notable changes to this project in this file and it is following [Semantic Versioning](https://semver.org/)
+## [x.x.x]
+### Added
 
+### Fixed
 
-## [x.x.x]
+## [1.2.0]
 ### Added
 - samples view
+- thresholds to the XY-plot
+- adding batch comment
+- unique colors in xy-plot and increased marker size
+
+### Fixed
+- truncates the html report
+- expands the XY-plot so no samples are hidden
 
 ## [1.1.0]
 

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

@@ -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 (
@@ -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
     )
@@ -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(
@@ -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(),
@@ -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
             ),

statina/API/external/api/api_v1/endpoints/download.py

@@ -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()
@@ -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(
@@ -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()

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

@@ -33,6 +33,7 @@ def statistics(
         "GC_Dropout",
         "AT_Dropout",
         "Bin2BinVariance",
+        "Library_nM",
     ]
 
     batches = get_last_batches(adapter=adapter, nr_of_batches=nr_batches)

statina/API/external/api/api_v1/endpoints/update.py

@@ -13,7 +13,7 @@
 from statina.crud import update
 from statina.crud.delete import delete_batches
 from statina.crud.find import find
-from statina.models.database import DataBaseSample, User
+from statina.models.database import DataBaseSample, User, Batch
 
 router = APIRouter()
 
@@ -85,6 +85,28 @@ async def set_sample_status(
     return RedirectResponse(request.headers.get("referer"))
 
 
+@router.post("/batch_comment")
+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"))
+
+
 @router.post("/sample_comment")
 async def sample_comment(
     request: Request,

statina/API/external/api/api_v1/templates/batch/header.html

@@ -9,33 +9,62 @@
         </div>
         <div class="row">
             <div class="col-lg-9"><big><em> Sequenced: {{ batch.SequencingDate }}</em></big></div>
-            <ul class="nav navbar-top-links navbar-right">
-                <li class="dropdown">
-                    <button class="btn btn-secondary dropdown-toggle" data-toggle="dropdown">
-                        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) }}">
-                            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>
-                        <li class="divider"></li>
-                        <a class="dropdown-item"
-                           href="{{ url_for('batch_download', file_id='result_file', file_name='result_file',batch_id=batch.batch_id) }}">Fluffy
-                            Result file</a>
-                        <li class="divider"></li>
-                        <a class="dropdown-item"
-                           href="{{ url_for('batch_download', file_id='segmental_calls', file_name=batch.batch_id+'.zip', batch_id=batch.batch_id) }}">Full Batch Archive</a>
-                    </ul>
-                </li>
-            </ul>
+        </div>
+        <br>
+        <div class="row">
+            <div class="col-lg-12">
+                {% if current_user.role in ['RW','admin'] %}
+                    <form action="{{ url_for('batch_comment') }}" method="post">
+
+                    <div class="form-group">
+                        <textarea class="form-control" rows="2" name="comment">{{ batch.comment }}</textarea>
+                    </div>
+                    <td>
+                        <input type=text name="form_id" value="set_batch_comment" hidden>
+                        <input type=text name="batch_id" value="{{ batch.batch_id }}" hidden>
+                    </td>
+                    <td>
+                        <p align="right">
+                            <input type="submit" class="btn" value="Save comment">
+                        </p>
+                    </td>
+                    </form>
+                {% else %}
+                    <div class="panel panel-default">
+                        <div class="panel-heading">Comment</div>
+                        <div class="panel-body">{{ batch.comment }}</div>
+                    </div>
+                {% endif %}
+            </div>
+            <div class="row">
+                <ul class="nav navbar-top-links navbar-right">
+                    <li class="dropdown">
+                        <button class="btn btn-secondary dropdown-toggle" data-toggle="dropdown">
+                            Batch Downloads <i class="fa fa-caret-down"></i>
+                        </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") }}">
+                                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>
+                            <li class="divider"></li>
+                            <a class="dropdown-item"
+                               href="{{ url_for('batch_download', file_id='result_file', file_name='result_file',batch_id=batch.batch_id) }}">Fluffy
+                                Result file</a>
+                            <li class="divider"></li>
+                            <a class="dropdown-item"
+                               href="{{ url_for('batch_download', file_id='segmental_calls', file_name=batch.batch_id+'.zip', batch_id=batch.batch_id) }}">Full
+                                Batch Archive</a>
+                        </ul>
+                    </li>
+                </ul>
+            </div>
         </div>
     </div> <!--jumbotron-->
+
     <ul class="nav nav-tabs" id="myTab">
         <li {% if page_id =='batches' %} class="active" {% endif %}><a
                 href="{{ url_for('batch', batch_id = batch.batch_id) }}">Batch Summary Table</a>