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-rw-r--r--app/__init__.py11
-rw-r--r--app/templates/about.html2
-rw-r--r--app/templates/base.html49
-rw-r--r--app/templates/display_photo.html7
-rw-r--r--app/templates/display_result.html8
-rw-r--r--app/templates/dock_upload.html2
-rw-r--r--app/templates/dock_upload_single.html2
-rw-r--r--app/templates/generate.html2
-rw-r--r--app/templates/home.html1
-rw-r--r--app/templates/job_status.html2
-rw-r--r--app/templates/molecule_editor.html2
-rw-r--r--app/templates/pdbqt_form.html2
-rw-r--r--app/templates/search-pubchem.html2
-rw-r--r--app/templates/search.html2
-rw-r--r--app/templates/visualise.html2
-rw-r--r--app/templates/wtform.html20
-rw-r--r--app/views.py34
-rw-r--r--requirements.txt1
18 files changed, 45 insertions, 106 deletions
diff --git a/app/__init__.py b/app/__init__.py
index 7f09da5..dd2f7ff 100644
--- a/app/__init__.py
+++ b/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')
diff --git a/app/templates/about.html b/app/templates/about.html
index b61bfed..c360003 100644
--- a/app/templates/about.html
+++ b/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>
diff --git a/app/templates/base.html b/app/templates/base.html
index 2e79a61..f92d59d 100644
--- a/app/templates/base.html
+++ b/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">
- <a class="nav-link" href="{{ url_for('basic_form') }}">Basic Form</a>
+ <li class="{{ 'nav-item dropdown active' if active_page == 'dock' else 'nav-item dropdown' }}">
+ <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
+ 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">
- <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">
+ <li class="{{ 'nav-item active' if active_page == 'generate' else 'nav-item' }}">
<a class="nav-link" href="{{ url_for('generate') }}">Generate</a>
</li>
- <li class="nav-item">
- <a class="nav-link" href="{{ url_for('status') }}">Job Status</a>
+ <li class="{{ 'nav-item dropdown active' if active_page == 'search' else 'nav-item dropdown' }}">
+ <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">
- <a class="nav-link" href="{{url_for('pubmed')}}">Search</a>
+ <li class="{{ 'nav-item dropdown active' if active_page == 'tool' else 'nav-item dropdown' }}">
+ <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>
diff --git a/app/templates/display_photo.html b/app/templates/display_photo.html
deleted file mode 100644
index 413e2e1..0000000
--- a/app/templates/display_photo.html
+++ /dev/null
@@ -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 %} \ No newline at end of file
diff --git a/app/templates/display_result.html b/app/templates/display_result.html
deleted file mode 100644
index 0174637..0000000
--- a/app/templates/display_result.html
+++ /dev/null
@@ -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 %} \ No newline at end of file
diff --git a/app/templates/dock_upload.html b/app/templates/dock_upload.html
index 26f1e99..43dcd63 100644
--- a/app/templates/dock_upload.html
+++ b/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">
diff --git a/app/templates/dock_upload_single.html b/app/templates/dock_upload_single.html
index 882675c..5329972 100644
--- a/app/templates/dock_upload_single.html
+++ b/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">
diff --git a/app/templates/generate.html b/app/templates/generate.html
index 629a2a3..7e6808d 100644
--- a/app/templates/generate.html
+++ b/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>
diff --git a/app/templates/home.html b/app/templates/home.html
index 14b5f71..1f7f9e5 100644
--- a/app/templates/home.html
+++ b/app/templates/home.html
@@ -1,4 +1,5 @@
{% extends 'base.html' %}
+{% set active_page = "home" %}
{% block main %}
<h2>Curie Web Demo</h2>
diff --git a/app/templates/job_status.html b/app/templates/job_status.html
index 97ce9b3..446d46a 100644
--- a/app/templates/job_status.html
+++ b/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>
diff --git a/app/templates/molecule_editor.html b/app/templates/molecule_editor.html
index 22d8481..2a8eab3 100644
--- a/app/templates/molecule_editor.html
+++ b/app/templates/molecule_editor.html
@@ -1,5 +1,5 @@
{% extends 'base.html' %}
-
+{% set active_page = "tool" %}
{% block main %}
<h2>Molecule Editor</h2>
diff --git a/app/templates/pdbqt_form.html b/app/templates/pdbqt_form.html
index 09cd1b0..af1bb37 100644
--- a/app/templates/pdbqt_form.html
+++ b/app/templates/pdbqt_form.html
@@ -1,6 +1,6 @@
{% extends 'base.html' %}
-
+{% set active_page = "tool" %}
{% block main %}
<h2>Generate PDBQTs</h2>
diff --git a/app/templates/search-pubchem.html b/app/templates/search-pubchem.html
index 9b8e7cb..d9f0c2b 100644
--- a/app/templates/search-pubchem.html
+++ b/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>
diff --git a/app/templates/search.html b/app/templates/search.html
index 1faf151..b2cdfdc 100644
--- a/app/templates/search.html
+++ b/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>
diff --git a/app/templates/visualise.html b/app/templates/visualise.html
index 67c3a1c..f1bb068 100644
--- a/app/templates/visualise.html
+++ b/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>
diff --git a/app/templates/wtform.html b/app/templates/wtform.html
deleted file mode 100644
index 6d9add5..0000000
--- a/app/templates/wtform.html
+++ /dev/null
@@ -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 %} \ No newline at end of file
diff --git a/app/views.py b/app/views.py
index 142229b..fc1620b 100644
--- a/app/views.py
+++ b/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):
diff --git a/requirements.txt b/requirements.txt
index 5534700..af8a46b 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -25,5 +25,4 @@ wget
lifelines
scikit-plot
pymed
-sentry-sdk[flask]
logzero
generated by cgit v1.2.3 (git 2.25.1) at 2024-09-19 22:06:48 +0000