sample search view (#98)

* sample search view * Update CHANGELOG.md
Clinical-Genomics · Jul 9, 2021 · 24ab085 · 24ab085
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,8 @@ This change log will document the notable changes to this project in this file a
 
 
 ## [x.x.x]
+### Added
+- samples view
 
 ## [1.1.0]
 

diff --git a/statina/API/external/api/api_v1/endpoints/sample.py b/statina/API/external/api/api_v1/endpoints/sample.py
@@ -1,4 +1,4 @@
-from typing import Dict
+from typing import Dict, List
 
 from fastapi import APIRouter, Depends, Request
 
@@ -19,6 +19,25 @@
 router = APIRouter()
 
 
+@router.get("/samples/")
+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",
+        ),
+    )
+
+
 @router.get("/samples/{sample_id}/")
 def sample(
     request: Request,

diff --git a/statina/API/external/api/api_v1/templates/layout/navigation.html b/statina/API/external/api/api_v1/templates/layout/navigation.html
@@ -18,6 +18,8 @@
                         <li class="divider"></li>
                         <a class="active" href={{ url_for('logout') }}><i class="fa fa-sign-out"></i> Sign Out</a>
                         <li class="divider"></li>
+                        <a class="active" href={{ url_for('samples') }}><i class="fa fa-sign-out"></i> All samples</a>
+                        <li class="divider"></li>
                         {% if current_user.role=='admin' %}
                             <a class="active" href="{{ url_for('users') }}"><i class="fa fa-home"></i> Users</a>
                         {% endif %}

diff --git a/statina/API/external/api/api_v1/templates/sample/samples.html b/statina/API/external/api/api_v1/templates/sample/samples.html
@@ -0,0 +1,89 @@
+{% extends 'layout/layout.html' %}
+{% include 'layout/navigation.html' %}
+
+{% block body %}
+    <div class="container-fluid">
+        <div class="jumbotron vertical-center">
+            <div class="row">
+                <div class="col-lg-12">
+                    <h1 class="page-header"><strong>NIPT Samples</strong></h1>
+                </div>
+            </div>
+        </div>
+        <div class="row">
+            <div class="col-lg-12">
+                <div class="panel panel-default">
+                    <div id="batch_list">
+                        <div class="panel-body">
+                         <div class="table-responsive">
+                            <table id="sample_table" class="table table-bordered table-hover" >
+                                    <thead>
+                                        <tr>
+                                            <th>Sample Name</th>
+                                            <th>Batch ID</th>
+                                            <th>Zscore 13</th>
+                                            <th>Zscore 18</th>
+                                            <th>Zscore 21</th>
+                                            <th>Zscore X</th>
+                                            <th>FF-PF (%)</th>
+                                            <th>FF-X (%)</th>
+                                            <th>FF-Y (%)</th>
+                                            <th>Sex</th>
+                                            <th>CNVSegment</th>
+                                            <th><a href="#" data-toggle="tooltip" data-placement="bottom" title="Warning for chomosome abnormality. Automatically generated. Based on pre defined Zscore and Fetal Fraction trsholds">Warning</a></th>
+                                            <th>QC Flagg</th>
+                                            <th><a href="#" data-toggle="tooltip" data-placement="bottom" title="Chomosome abnormalies. Manually classified by user through the sample page">Status</a></th>
+                                            <th>Download</th>
+                                            <th><a href="#" data-toggle="tooltip" data-placement="bottom" title="Samples checked in the 'Include' column are added to the validation sample set for comparison. Check the checkboxes for samples to include and save. If all samples are ok, just press 'set all OK'.">Include</a></th>
+                                            <th>Comment</th>
+                                            <th>Last Change</th>
+                                        </tr>
+                                    </thead>
+                                    <tbody>
+                                        {% for sample in sample_info %}
+                                        <tr>
+                                            <td width="10%"> <a href={{ url_for('sample', sample_id=sample.sample_id) }}>{{ sample.sample_id }}</a></td>
+                                            <td width="10%"> <a href={{ url_for('batch', batch_id=sample.batch_id) }}>{{ sample.batch_id }}</a></td>
+                                            <td width="3%" class = "{{ sample.warnings.Zscore_13}}">{{ sample.Zscore_13 }}</td>
+                                            <td width="3%" class = "{{ sample.warnings.Zscore_18}}">{{ sample.Zscore_18 }}</td>
+                                            <td width="3%" class = "{{ sample.warnings.Zscore_21}}">{{ sample.Zscore_21 }}</td>
+                                            <td width="3%" class = "{{ sample.warnings.Zscore_X}}">{{ sample.Zscore_X }}</td>
+                                            <td width="3%" class = "{{sample.warnings.FF_Formatted}}">{{sample.FF_Formatted}}</td>
+                                            <td width="3%" class = "default">{{sample.FFX}}</td>
+                                            <td width="3%" class =  "{{sample.warnings.FFY}}">{{sample.FFY}}</td>
+                                            <td width="3%" class = "default">{{sample.sex}}</td>
+                                            <td width="3%" class = "default">{{sample.CNVSegment}}</td>
+                                            <td width="3%"><p> <small>{{ sample.text_warning }}</small></p></td>
+                                            <td width="3%" class = "default">{{sample.QCFlag}}</td>
+                                            <td><p> <small>{{ sample.status }}</small></p></td>
+                                            <td><a class="dropdown-item" href="{{ url_for('sample_download', file_id='segmental_calls', sample_id=sample.sample_id) }}">segmental calls</a></td>
+                                            <td width="1%" {% if sample.include %}class="success"{% endif %}>{{sample.include }}</td>
+                                            <td width="18%">{{sample.comment}}</td>
+                                            <td ><small>{{sample.change_include_date}}</small></td>
+                                        </tr>
+                                        {% endfor %}
+                                    </tbody>
+                                </table>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+{% endblock %}
+
+{% block scripts %}
+    <script>
+        $(document).ready(function () {
+            var table = $('#sample_table').DataTable({
+                order: [[1, "dec"]],
+                paging: true
+            });
+
+            table.buttons().container()
+                .appendTo('#sample_table_wrapper .col-sm-6:eq(0)');
+        });
+    </script>
+{% endblock %}
+
diff --git a/statina/crud/find/find.py b/statina/crud/find/find.py
@@ -28,6 +28,13 @@ def user(
     return User(**raw_user)
 
 
+def samples(adapter: StatinaAdapter) -> List[DataBaseSample]:
+    """Return all batches from the batch collection"""
+
+    raw_samples: Iterable[dict] = adapter.sample_collection.find()
+    return parse_obj_as(List[DataBaseSample], list(raw_samples))
+
+
 def sample(adapter: StatinaAdapter, sample_id: str) -> Optional[DataBaseSample]:
     """Find one sample from the sample collection"""