Update webforms.

Added new parameter 'distance_group_seeds' to view, routes, and templates. defaults to 15.

app/routes.py

@@ -121,6 +121,7 @@ def upload():
     session['query_rayt'] = None
     session['treefile'] = None
     session['min_nmer_occurrence'] = None
+    session['distance_group_seeds'] = None
     session['nmer_length'] = None
     session['e_value_cutoff'] = None
     session['analyse_repins'] = None
@@ -181,6 +182,7 @@ def submit():
 
         session['treefile'] = treefile
         session['nmer_length'] = request.form.get('nmer_length')
+        session['distance_group_seeds'] = request.form.get('distance_group_seeds', 15)
         session['e_value_cutoff'] = request.form.get('e_value_cutoff')
         session['analyse_repins'] = request.form.get('analyse_repins')
         session['email'] = request.form.get('email', None)
@@ -253,6 +255,7 @@ def submit():
                 "reference_strain": session['reference_strain'],
                 "min_nmer_occurrence": session['min_nmer_occurrence'],
                 "nmer_length": session['nmer_length'],
+                "distance_group_seeds": session.get('distance_group_seeds', 15),
                 "query_rayt_fname": query_rayt_fname,
                 "treefile": session['treefile'],
                 "e_value_cutoff": session['e_value_cutoff'],
@@ -477,6 +480,8 @@ def rerun():
     submit_form.min_nmer_occurrence.data = dbjob.setup.get('min_nmer_occurrence')
     session['nmer_length'] = dbjob.setup.get('nmer_length')
     submit_form.nmer_length.data = dbjob.setup.get('nmer_length')
+    session['distance_group_seeds'] = dbjob.setup.get('distance_group_seeds', 15)
+    submit_form.distance_group_seeds.data = dbjob.setup.get('distance_group_seeds', 15)
     session['analyse_repins'] = dbjob.setup.get('analyse_repins')
     submit_form.analyse_repins.data = dbjob.setup.get('analyse_repins')
     session['e_value_cutoff'] = dbjob.setup.get('e_value_cutoff')

app/templates/submit.html

@@ -7,26 +7,22 @@
     <form action="{{ url_for('submit') }}" method="post" enctype="multipart/form-data">
         <p>
             {{ submit_form.reference_strain.label }}
-            <!-- <span title="{{submit_form.reference_strain.description}}" style="cursor:default">(?)</span> -->
     </br>
     {{ submit_form.reference_strain(title=submit_form.reference_strain.description) }}
     </br></br>
         </p>
         <p>
             {{ submit_form.query_rayt.label }}
-            <!-- <span title="{{submit_form.query_rayt.description}}" style="cursor:default">(?)</span> -->
     </br>
             {{ submit_form.query_rayt(title=submit_form.query_rayt.description) }}</br></br>
         </p>
         <p>
             {{ submit_form.treefile.label }}
-            <!-- <span title="{{submit_form.treefile.description}}" style="cursor:default">(?)</span> -->
     </br>
             {{ submit_form.treefile(title=submit_form.treefile.description) }}</br></br>
         </p>
         <p>
             {{ submit_form.min_nmer_occurrence.label }}
-            <!-- <span title="{{submit_form.min_nmer_occurrence.description}}" style="cursor:default">(?)</span> -->
     </br>
     {{ submit_form.min_nmer_occurrence(title=submit_form.min_nmer_occurrence.description) }}
             </br>
@@ -39,7 +35,6 @@
         </p>
         <p>
             {{ submit_form.nmer_length.label }}
-            <!-- <span title="{{submit_form.nmer_length.description}}" style="cursor:default">(?)</span> -->
     </br>
     {{ submit_form.nmer_length(title=submit_form.nmer_length.description) }}
             </br>
@@ -49,9 +44,19 @@
             {% endfor %}
             </br>
         </p>
+        <p>
+            {{ submit_form.distance_group_seeds.label }}
+    </br>
+    {{ submit_form.distance_group_seeds(title=submit_form.distance_group_seeds.description) }}
+    </br>
+    {% for error in submit_form.distance_group_seeds.errors %}
+    <span style="color: red;">
+        [{{ error }}]</span>
+    {% endfor %}
+    </br>
+        </p>
         <p>
             {{ submit_form.e_value_cutoff.label }}
-            <!-- <span title="{{submit_form.e_value_cutoff.description}}" style="cursor:default">(?)</span> -->
     </br>
     {{ submit_form.e_value_cutoff(title=submit_form.e_value_cutoff.description) }}</br>
     {% for error in submit_form.e_value_cutoff.errors %}
@@ -63,13 +68,11 @@
         </p>
         <p>
             {{ submit_form.analyse_repins.label }}
-            <!-- <span title="{{submit_form.analyse_repins.description}}" style="cursor:default">(?)</span> -->
     </br>
     {{ submit_form.analyse_repins(title=submit_form.analyse_repins.description) }}</br>
         </p>
         <p>
             {{ submit_form.email.label }}
-            <!-- <span title="{{submit_form.email.description}}" style="cursor:default">(?)</span> -->
     </br>
     {{ submit_form.email(title=submit_form.email.description) }}</br>
     {% for error in submit_form.email.errors %}
@@ -81,7 +84,6 @@
         </p>
         <p>
             {{ submit_form.submit(title=submit_form.submit.description) }}
-            <!-- <span title="{{submit_form.submit.description}}" style="cursor:default">(?)</span> -->
         </p>
     </form>
 {% endblock %}

app/views.py

@@ -80,6 +80,11 @@ class SubmitForm(FlaskForm):
         description="Set the Seed length (in basepairs). Only sequences of this length that occur more frequently than 'min. Seed occurrence (see above) will be considered in the REP/REPIN analysis.",
                              validators=[validators.DataRequired(message="Please enter the nmer length as an integer!")]
                              )
+    distance_group_seeds= IntegerField("Distance group seeds", 
+                             default=15, 
+        description="Set the group seeds distance (???)",
+                             validators=[validators.DataRequired(message="Please enter an integer number > 0.")]
+                             )
 
     e_value_cutoff = FloatField("e value cutoff",
                                 default=1.0e-30,