From 1b018ab3bed778adbe9f282a51315b26cde37427 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Fri, 9 Jul 2021 13:29:07 +0200
Subject: [PATCH] Add gene search form to sample page.

---
 ExonCov/forms.py                    | 23 +++++++++++++++++++
 ExonCov/static/css/exoncov.css      |  4 ++++
 ExonCov/templates/macros/forms.html |  2 +-
 ExonCov/templates/sample.html       | 15 ++++++++++++-
 ExonCov/views.py                    | 34 ++++++++++++++++++++++++-----
 5 files changed, 71 insertions(+), 7 deletions(-)

diff --git a/ExonCov/forms.py b/ExonCov/forms.py
index daf07db..0faecaa 100644
--- a/ExonCov/forms.py
+++ b/ExonCov/forms.py
@@ -368,3 +368,26 @@ def validate(self):
                 self.gene_id = gene.id
 
         return valid_form
+
+
+class SampleGeneForm(FlaskForm):
+    """Sample Form to query a specific gene."""
+    gene = StringField('Gene', validators=[validators.InputRequired()])
+    gene_id = ''
+
+    def validate(self):
+        """Extra validation to parse panel / gene selection"""
+        self.gene_id = ''
+        valid_form = True
+
+        if not FlaskForm.validate(self):
+            valid_form = False
+
+        if self.gene.data:
+            gene, error = get_gene(self.gene.data)
+            if error:
+                self.gene.errors.append(error)
+            else:
+                self.gene_id = gene.id
+
+        return valid_form
diff --git a/ExonCov/static/css/exoncov.css b/ExonCov/static/css/exoncov.css
index dfa3025..59f08e1 100644
--- a/ExonCov/static/css/exoncov.css
+++ b/ExonCov/static/css/exoncov.css
@@ -11,3 +11,7 @@ body {
     float: left;
     text-align: left;
 }
+
+.help-block-inline {
+    display: inline;
+}
\ No newline at end of file
diff --git a/ExonCov/templates/macros/forms.html b/ExonCov/templates/macros/forms.html
index 90b8d96..0142188 100644
--- a/ExonCov/templates/macros/forms.html
+++ b/ExonCov/templates/macros/forms.html
@@ -61,7 +61,7 @@
     {{ field.label(class_='control-label') }}
     {{ field(class_='form-control', size=40, **kwargs) }}
     {% for error in field.errors %}
-    <span class="help-block">{{error}}</span>
+    <span class="help-block help-block-inline">{{error}}</span>
     {% endfor %}
 </div>
 {% else %}
diff --git a/ExonCov/templates/sample.html b/ExonCov/templates/sample.html
index 42519e7..6e686dd 100644
--- a/ExonCov/templates/sample.html
+++ b/ExonCov/templates/sample.html
@@ -1,5 +1,5 @@
 {% from "macros/tables.html" import render_panel_measurement_td %}
-{% from "macros/forms.html" import render_sample_datatable_form %}
+{% from "macros/forms.html" import render_sample_datatable_form, render_inline_field %}
 {% extends 'base.html' %}
 
 {% block header %}{{ sample.name }}{% endblock %}
@@ -14,6 +14,19 @@
     </dl>
 </div>
 
+<div class="page-header"><h1>Search gene</h1></div>
+<div class="well">
+    <form method="POST" action="{{ url_for('sample', id=sample.id) }}" class="form-inline">
+        {{ form.csrf_token }}
+        {{ render_inline_field(form.gene) }}
+        <div class="form-group">
+            <div class="col-sm-offset-1 col-sm-10">
+                <button type="submit" class="btn btn-primary">Search</button>
+            </div>
+        </div>
+    </form>
+</div>
+
 {% if sample.custom_panels %}
 <div class="page-header"><h1>Custom panels</h1></div>
 <table class="table table-bordered table-hover table-condensed">
diff --git a/ExonCov/views.py b/ExonCov/views.py
index 1ca9ab9..d3b323e 100644
--- a/ExonCov/views.py
+++ b/ExonCov/views.py
@@ -17,7 +17,7 @@
 )
 from .forms import (
     MeasurementTypeForm, CustomPanelForm, CustomPanelNewForm, CustomPanelValidateForm, SampleForm,
-    CreatePanelForm, PanelNewVersionForm, PanelEditForm, PanelVersionEditForm, SampleSetPanelGeneForm
+    CreatePanelForm, PanelNewVersionForm, PanelEditForm, PanelVersionEditForm, SampleSetPanelGeneForm, SampleGeneForm
 )
 from .utils import weighted_average
 
@@ -54,18 +54,42 @@ def samples():
     return render_template('samples.html', form=sample_form, samples=samples)
 
 
-@app.route('/sample/<int:id>')
+@app.route('/sample/<int:id>', methods=['GET', 'POST'])
 @login_required
 def sample(id):
     """Sample page."""
-    sample = Sample.query.options(joinedload('sequencing_runs')).options(joinedload('project')).options(joinedload('custom_panels')).get_or_404(id)
+
+    # Setup gene form and validate
+    gene_form = SampleGeneForm()
+
+    if gene_form.validate_on_submit():
+        if gene_form.gene_id:
+            return redirect(url_for('sample_gene', sample_id=id, gene_id=gene_form.gene_id))
+
+    # Query Sample and panels
+    sample = (
+        Sample.query
+        .options(joinedload('sequencing_runs'))
+        .options(joinedload('project'))
+        .options(joinedload('custom_panels'))
+        .get_or_404(id)
+    )
+    query = (
+        db.session.query(PanelVersion, TranscriptMeasurement)
+        .filter_by(active=True)
+        .filter_by(validated=True)
+        .join(Transcript, PanelVersion.transcripts)
+        .join(TranscriptMeasurement)
+        .filter_by(sample_id=sample.id)
+        .order_by(PanelVersion.panel_name)
+        .all()
+    )
     measurement_types = {
         'measurement_mean_coverage': 'Mean coverage',
         'measurement_percentage10': '>10',
         'measurement_percentage15': '>15',
         'measurement_percentage30': '>30'
     }
-    query = db.session.query(PanelVersion, TranscriptMeasurement).filter_by(active=True).filter_by(validated=True).join(Transcript, PanelVersion.transcripts).join(TranscriptMeasurement).filter_by(sample_id=sample.id).order_by(PanelVersion.panel_name).all()
     panels = {}
 
     for panel, transcript_measurement in query:
@@ -84,7 +108,7 @@ def sample(id):
                     [panels[panel.id]['len'], transcript_measurement.len]
                 )
             panels[panel.id]['len'] += transcript_measurement.len
-    return render_template('sample.html', sample=sample, panels=panels, measurement_types=measurement_types)
+    return render_template('sample.html', sample=sample, panels=panels, measurement_types=measurement_types, form=gene_form)
 
 
 @app.route('/sample/<int:id>/inactive_panels')