added active link for all pages to navbar

added dropdowns
removed starter files
removed sentry completely

app/__init__.py

@@ -1,16 +1,5 @@
 from flask import Flask
 
-import sentry_sdk
-from sentry_sdk.integrations.flask import FlaskIntegration
-
-"""
-sentry_sdk.init(
-    dsn="https://7bc9916920c041479b69db97bdb279fa@o126149.ingest.sentry.io/5424142",
-    integrations=[FlaskIntegration()],
-    traces_sample_rate=1.0
-)
-"""
-
 import configparser
 config = configparser.ConfigParser()
 config.read('config.ini')

app/templates/about.html

@@ -1,5 +1,5 @@
 {% extends 'base.html' %}
-
+{% set active_page = "about" %}
 {% block main %}
     <h1>About Curie Web</h1>
     <p>Curie Web is a web interface for my private Python Library called "Curie", with some aditional superpowers.</p>

app/templates/base.html

@@ -23,30 +23,47 @@
       </button>
       <div class="collapse navbar-collapse" id="navbarNav">
         <ul class="navbar-nav">
-          <li class="nav-item active">
+          <li class="{{ 'nav-item active' if active_page == 'home' else 'nav-item' }}">
             <a class="nav-link" href="{{ url_for('home') }}">Home <span class="sr-only">(current)</span></a>
           </li>
-          <li class="nav-item">
+          <li class="{{ 'nav-item active' if active_page == 'about' else 'nav-item' }}">
             <a class="nav-link" href="{{ url_for('about') }}">About</a>
           </li>
-          <!--
+          <li class="{{ 'nav-item dropdown active' if active_page == 'dock' else 'nav-item dropdown' }}">
-          <li class="nav-item">
+            <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
-            <a class="nav-link" href="{{ url_for('basic_form') }}">Basic Form</a>
+              Dock and Report
+            </a>
+            <div class="dropdown-menu" aria-labelledby="navbarDropdown">
+              <a class="dropdown-item" href="{{ url_for('dock_upload') }}">Automatic</a>
+              <a class="dropdown-item" href="{{ url_for('dock_upload_single') }}">Manual</a>
+            </div>
           </li>
-          <li class="nav-item">
+          <li class="{{ 'nav-item active' if active_page == 'generate' else 'nav-item' }}">
-            <a class="nav-link" href="{{ url_for('wtform') }}">WTForms</a>
-          </li> -->
-          <li class="nav-item">
-            <a class="nav-link" href="{{ url_for('dock_upload') }}">Dock and Report</a>
-          </li>
-          <li class="nav-item">
             <a class="nav-link" href="{{ url_for('generate') }}">Generate</a>
           </li>
-          <li class="nav-item">
+          <li class="{{ 'nav-item dropdown active' if active_page == 'search' else 'nav-item dropdown' }}">
-            <a class="nav-link" href="{{ url_for('status') }}">Job Status</a>
+            <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
+              Research
+            </a>
+            <div class="dropdown-menu" aria-labelledby="navbarDropdown">
+              <a class="dropdown-item" href="{{url_for('pubmed')}}">PubMed</a>
+              <a class="dropdown-item" href="{{url_for('pubchem')}}">PubChem</a>
+              <div class="dropdown-divider"></div>
+              <a class="dropdown-item disabled" href="#">Qrious</a>
+            </div>
           </li>
-          <li class="nav-item">
+          <li class="{{ 'nav-item dropdown active' if active_page == 'tool' else 'nav-item dropdown' }}">
-            <a class="nav-link" href="{{url_for('pubmed')}}">Search</a>
+            <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
+              Other Tools
+            </a>
+            <div class="dropdown-menu" aria-labelledby="navbarDropdown">
+              <a class="dropdown-item" href="{{url_for('generate_pdbqts')}}">Generate PDBQTs</a>
+              <a class="dropdown-item" href="{{url_for('editor')}}">Molecule Editor</a>
+              <a class="dropdown-item" href="{{url_for('visualise')}}">Molecule Visualiser</a>
+            </div>
+          </li>
+          <li class="{{ 'nav-item active' if active_page == 'job_status' else 'nav-item' }}">
+            <a class="nav-link" href="{{ url_for('status') }}">Job Status</a>
           </li>
         </ul>
       </div>

app/templates/display_photo.html

@@ -1,7 +0,0 @@
-{% extends 'base.html' %}
-
-{% block main %}
-    <h2>Description: {{ description }}</h2>
-    <p>Succesfuly Submitted</p>
-    <!-- <img src="{{ url_for('static', filename="uploads/" + filename) }}" /> -->
-{% endblock %}

app/templates/display_result.html

@@ -1,8 +0,0 @@
-{% extends 'base.html' %}
-
-{% block main %}
-    <h2>Job ID: {{ job }}</h2>
-    <p>Succesfuly Submitted</p>
-    <b>Description: </b>{{description}}
-    <!-- <img src="{{ url_for('static', filename="uploads/" + filename) }}" /> -->
-{% endblock %}

app/templates/dock_upload.html

@@ -1,5 +1,5 @@
 {% extends 'base.html' %}
-
+{% set active_page = "dock" %}
 {% block main %}
     <h2>Enter Your Configuration</h2>
     <form action="{{ url_for('dock_upload') }}" method="post" enctype="multipart/form-data">

app/templates/dock_upload_single.html

@@ -1,5 +1,5 @@
 {% extends 'base.html' %}
-
+{% set active_page = "dock" %}
 {% block main %}
     <h2>Enter Your Configuration</h2>
     <form action="{{ url_for('dock_upload_single') }}" method="post" enctype="multipart/form-data">

app/templates/generate.html

@@ -1,5 +1,5 @@
 {% extends 'base.html' %}
-
+{% set active_page = "generate" %}
 {% block main %}
     <h1>Curie Generate</h1>
     <p>The model {{expName}} has been trained for {{epochs}} epochs using the {{optimizer}} optimization algorithm. Option for finetuning coming soon.</p>

app/templates/home.html

@@ -1,4 +1,5 @@
 {% extends 'base.html' %}
+{% set active_page = "home" %}
 
 {% block main %}
     <h2>Curie Web Demo</h2>

app/templates/job_status.html

@@ -1,5 +1,7 @@
 {% extends 'base.html' %}
 
+{% set active_page = "job_status" %}
+
 {% block main %}
     <h2>Job ID: {{ ID }}</h2>
     <b>Submitted On: </b>{{subDate}}<br>

app/templates/molecule_editor.html

@@ -1,5 +1,5 @@
 {% extends 'base.html' %}
-
+{% set active_page = "tool" %}
 {% block main %}
 
 <h2>Molecule Editor</h2>

app/templates/pdbqt_form.html

@@ -1,6 +1,6 @@
 
 {% extends 'base.html' %}
-
+{% set active_page = "tool" %}
 {% block main %}
     <h2>Generate PDBQTs</h2>
 

app/templates/search-pubchem.html

@@ -1,5 +1,5 @@
 {% extends 'base.html' %}
-
+{% set active_page = "search" %}
 {% block main %}
     <h1>SMILES Search</h1>
     <p>Get Compound SMILES through PubChem.</p>

app/templates/search.html

@@ -1,5 +1,5 @@
 {% extends 'base.html' %}
-
+{% set active_page = "search" %}
 {% block main %}
     <h1>Curie Search</h1>
     <p>Search PubMed articles.</p>

app/templates/visualise.html

@@ -1,5 +1,5 @@
 {% extends 'base.html' %}
-
+{% set active_page = "tool" %}
 {% block main %}
     <h1>Curie Visualise</h1>
     <p>placeholder uwu</p>

app/templates/wtform.html

@@ -1,20 +0,0 @@
-{% extends 'base.html' %}
-
-{% block main %}
-    <h2>WTForms in Flask</h2>
-    <p>Here we are using the Flask-WTF library to create and process a form. Flask-WTF also comes with CSRF protection and validation classes.</p>
-    <form method="post" action="{{ url_for('wtform') }}">
-        {% include 'flash_messages.html' %}
-        {{ form.csrf_token }}
-        <div class="form-group">
-            {{ form.firstname.label }} {{ form.firstname(class="form-control") }}
-        </div>
-        <div class="form-group">
-            {{ form.lastname.label }} {{ form.lastname(class="form-control") }}
-        </div>
-        <div class="form-group">
-            {{ form.email.label }} {{ form.email(class="form-control", placeholder="jdoe@example.com") }}
-        </div>
-    <button type="submit" class="btn btn-primary">Submit</button>
-</form>
-{% endblock %}

app/views.py

@@ -152,37 +152,6 @@ def status():
         flash_errors(taskStatusForm)
     return render_template('job_status_form.html',form=taskStatusForm)
         
-@app.route('/basic-form', methods=['GET', 'POST'])
-def basic_form():
-    if request.method == 'POST':
-        firstname = request.form['firstname']
-        lastname = request.form['lastname']
-        email = request.form['email']
-
-        return render_template('result.html',
-                               firstname=firstname,
-                               lastname=lastname,
-                               email=email)
-
-    return render_template('form.html')
-
-@app.route('/wtform', methods=['GET', 'POST'])
-def wtform():
-    myform = MyForm()
-
-    if request.method == 'POST':
-        if myform.validate_on_submit():
-            # Note the difference when retrieving form data using Flask-WTF
-            # Here we use myform.firstname.data instead of request.form['firstname']
-            firstname = myform.firstname.data
-            lastname = myform.lastname.data
-            email = myform.email.data
-
-            flash('You have successfully filled out the form', 'success')
-            return render_template('result.html', firstname=firstname, lastname=lastname, email=email)
-
-        flash_errors(myform)
-    return render_template('wtform.html', form=myform)
 
 @app.route('/PDBQTs',methods=['GET','POST'])
 def generate_pdbqts():
@@ -406,9 +375,6 @@ def send_text_file(file_name):
     file_dot_text = file_name + '.txt'
     return app.send_static_file(file_dot_text)
 
-@app.route('/debug-sentry')
-def trigger_error():
-    division_by_zero = 1 / 0
 
 @app.after_request
 def add_header(response):

requirements.txt

@@ -25,5 +25,4 @@ wget
 lifelines 
 scikit-plot
 pymed
-sentry-sdk[flask]
 logzero