Browse Source

Chemical DB added

master
Tei Kim 2 years ago
parent
commit
14bb186ae6
  1. 149
      app.py
  2. 565
      poetry.lock
  3. 3
      pyproject.toml
  4. 6
      templates/admin.html
  5. 1
      templates/base.html
  6. 31
      templates/create_chemical.html
  7. 5
      templates/delete_chemical.html
  8. 11
      templates/index.html
  9. 69
      templates/search.html
  10. 30
      templates/view_chemical.html

149
app.py

@ -1,8 +1,11 @@
#!/usr/bin/env python3
from flask import Flask, render_template, session, request, abort, redirect, url_for
from flask import Flask, render_template, session, request, abort, redirect, url_for, jsonify
from flask_sqlalchemy import SQLAlchemy
from sqlalchemy import inspect, or_, and_
from flask_wtf import FlaskForm
import bcrypt
from wtforms_alchemy import model_form_factory
db: SQLAlchemy = SQLAlchemy()
app = Flask(__name__)
@ -11,6 +14,13 @@ app.config["SQLALCHEMY_DATABASE_URI"] = "sqlite:///project.db"
app.secret_key = '98d31240f9fbe14c8083586db49c19c3a8d3f726'
BaseModelForm = model_form_factory(FlaskForm)
class ModelForm(BaseModelForm):
@classmethod
def get_session(self):
return db.session
class Admin(db.Model):
id = db.Column(db.Integer, primary_key=True)
username = db.Column(db.String, unique=True, nullable=False)
@ -40,16 +50,43 @@ class Admin(db.Model):
if not session.get('admin'):
return redirect(url_for("admin_login"))
def object_as_dict(obj):
return {c.key: getattr(obj, c.key)
for c in inspect(obj).mapper.column_attrs}
class Chemical(db.Model):
query: db.Query
id = db.Column(db.Integer, primary_key=True)
pubchem_cid = db.Column(db.Integer, nullable=False)
# all fields after here are included in the database
chemical_db_id = db.Column(db.String)
library = db.Column(db.String)
# important fields
name = db.Column(db.String, nullable=False)
formula = db.Column(db.String, nullable=False)
mass = db.Column(db.Float, nullable=False)
mz = db.Column(db.Float, nullable=False)
rt = db.Column(db.Float, nullable=False)
pubchem_cid = db.Column(db.Integer)
pubmed_refcount = db.Column(db.Integer)
standard_class = db.Column(db.String)
inchikey = db.Column(db.String)
inchikey14 = db.Column(db.String)
final_mz = db.Column(db.Float, nullable=False)
final_rt = db.Column(db.Float, nullable=False)
final_adduct = db.Column(db.String)
adduct = db.Column(db.String)
detected_adducts = db.Column(db.String)
adduct_calc_mz = db.Column(db.String)
msms_detected = db.Column(db.Boolean)
msms_purity = db.Column(db.Float)
class ChemicalForm(ModelForm):
class Meta:
csrf = False
model = Chemical
#exclude = ['id']
# Error Handlers
@ -116,11 +153,111 @@ def home():
else:
return redirect(url_for("admin_create"))
# Routes for CRUD operations on chemicals
@app.route("/chemical/create", methods=['GET', 'POST'])
def chemical_create():
if not session.get('admin'):
abort(403)
if request.method == "POST":
form = ChemicalForm(**request.form)
if form.validate():
new_chemical = Chemical(**form.data)
db.session.add(new_chemical)
db.session.commit()
return render_template("create_chemical.html", form=form, success=True)
else:
return render_template("create_chemical.html", form=ChemicalForm(), invalid=True)
else:
form = ChemicalForm()
return render_template("create_chemical.html", form=form)
@app.route("/chemical/<int:id>/update", methods=['GET', 'POST'])
def chemical_update(id:int):
if not session.get('admin'):
abort(403)
current_chemical:Chemical = Chemical.query.filter_by(id=id).one_or_404()
dct = object_as_dict(current_chemical)
if request.method == "POST":
form = ChemicalForm(**request.form)
if form.validate():
# take the row with id and update it.
for k in form.data:
setattr(current_chemical, k, form.data[k])
db.session.commit()
return render_template("create_chemical.html", form=form, success=True, id=id)
else:
form = ChemicalForm(**dct)
return render_template("create_chemical.html", form=form, invalid=True, id=id)
else:
form = ChemicalForm(**dct)
return render_template("create_chemical.html", form=form, id=id)
@app.route("/chemical/<int:id>/delete")
def chemical_delete(id:int):
if not session.get('admin'):
abort(403)
current_chemical:Chemical = Chemical.query.filter_by(id=id).one_or_404()
db.session.delete(current_chemical)
db.session.commit()
return render_template("delete_chemical.html", id=id)
@app.route("/chemical/<int:id>/view")
def chemical_view(id:int):
current_chemical:Chemical = Chemical.query.filter_by(id=id).one_or_404()
dct = object_as_dict(current_chemical)
return render_template("view_chemical.html", id=id, chemical=dct)
@app.route("/chemical/all")
def chemical_all():
if not session.get('admin'):
abort(403)
result = Chemical.query.all()
data = []
for x in result:
data.append({"url": url_for("chemical_view", id=x.id), "name": x.name, "mz": x.final_mz, "rt": x.final_rt})
return jsonify(data)
@app.route("/chemical/search")
def search_api():
mz_min, mz_max = request.args.get('mz_min'), request.args.get('mz_max')
rt_min, rt_max = request.args.get('rt_min'), request.args.get('rt_max')
if (mz_min is None and mz_max is None) or (rt_min is None and rt_max is None):
abort(400)
try:
if mz_min is not None and mz_max is None:
mz_max = float(mz_min) + 3
elif mz_max is not None and mz_min is None:
mz_min = float(mz_max) - 3
if rt_min is not None and rt_max is None:
rt_max = float(rt_min) + 3
elif rt_max is not None and rt_min is None:
rt_min = rt_max - 3
mz_min, mz_max = float(mz_min), float(mz_max)
rt_min, rt_max = float(rt_min), float(rt_max)
except ValueError:
abort(400)
print(mz_min, mz_max, " ", rt_min, rt_max)
mz_filter = and_(mz_max > Chemical.final_mz, Chemical.final_mz > mz_min)
rt_filter = and_(rt_max > Chemical.final_rt, Chemical.final_rt > rt_min)
result = Chemical.query.filter(
or_(mz_filter, rt_filter)
).limit(20).all()
print("Got Result", result)
data = []
for x in result:
data.append({"url": url_for("chemical_view", id=x.id), "name": x.name, "mz": x.final_mz, "rt": x.final_rt})
return jsonify(data)
@app.route("/search")
def search():
return "searching url"
return render_template("search.html")
if __name__ == "__main__":
db.init_app(app)

565
poetry.lock

@ -1,3 +1,5 @@
# This file is automatically @generated by Poetry and should not be changed by hand.
[[package]]
name = "autopep8"
version = "2.0.1"
@ -5,6 +7,10 @@ description = "A tool that automatically formats Python code to conform to the P
category = "dev"
optional = false
python-versions = ">=3.6"
files = [
{file = "autopep8-2.0.1-py2.py3-none-any.whl", hash = "sha256:be5bc98c33515b67475420b7b1feafc8d32c1a69862498eda4983b45bffd2687"},
{file = "autopep8-2.0.1.tar.gz", hash = "sha256:d27a8929d8dcd21c0f4b3859d2d07c6c25273727b98afc984c039df0f0d86566"},
]
[package.dependencies]
pycodestyle = ">=2.10.0"
@ -17,6 +23,10 @@ description = "Composable command line interface toolkit"
category = "main"
optional = false
python-versions = ">=3.7"
files = [
{file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"},
{file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},
]
[package.dependencies]
colorama = {version = "*", markers = "platform_system == \"Windows\""}
@ -28,6 +38,58 @@ description = "Cross-platform colored terminal text."
category = "main"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
files = [
{file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
{file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
]
[[package]]
name = "decorator"
version = "5.1.1"
description = "Decorators for Humans"
category = "main"
optional = false
python-versions = ">=3.5"
files = [
{file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
{file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
]
[[package]]
name = "dnspython"
version = "2.2.1"
description = "DNS toolkit"
category = "main"
optional = false
python-versions = ">=3.6,<4.0"
files = [
{file = "dnspython-2.2.1-py3-none-any.whl", hash = "sha256:a851e51367fb93e9e1361732c1d60dab63eff98712e503ea7d92e6eccb109b4f"},
{file = "dnspython-2.2.1.tar.gz", hash = "sha256:0f7569a4a6ff151958b64304071d370daa3243d15941a7beedf0c9fe5105603e"},
]
[package.extras]
curio = ["curio (>=1.2,<2.0)", "sniffio (>=1.1,<2.0)"]
dnssec = ["cryptography (>=2.6,<37.0)"]
doh = ["h2 (>=4.1.0)", "httpx (>=0.21.1)", "requests (>=2.23.0,<3.0.0)", "requests-toolbelt (>=0.9.1,<0.10.0)"]
idna = ["idna (>=2.1,<4.0)"]
trio = ["trio (>=0.14,<0.20)"]
wmi = ["wmi (>=1.5.1,<2.0.0)"]
[[package]]
name = "email-validator"
version = "1.3.0"
description = "A robust email address syntax and deliverability validation library."
category = "main"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
files = [
{file = "email_validator-1.3.0-py2.py3-none-any.whl", hash = "sha256:816073f2a7cffef786b29928f58ec16cdac42710a53bb18aa94317e3e145ec5c"},
{file = "email_validator-1.3.0.tar.gz", hash = "sha256:553a66f8be2ec2dea641ae1d3f29017ab89e9d603d4a25cdaac39eefa283d769"},
]
[package.dependencies]
dnspython = ">=1.15.0"
idna = ">=2.0.0"
[[package]]
name = "flask"
@ -36,6 +98,10 @@ description = "A simple framework for building complex web applications."
category = "main"
optional = false
python-versions = ">=3.7"
files = [
{file = "Flask-2.2.2-py3-none-any.whl", hash = "sha256:b9c46cc36662a7949f34b52d8ec7bb59c0d74ba08ba6cb9ce9adc1d8676d9526"},
{file = "Flask-2.2.2.tar.gz", hash = "sha256:642c450d19c4ad482f96729bd2a8f6d32554aa1e231f4f6b4e7e5264b16cca2b"},
]
[package.dependencies]
click = ">=8.0"
@ -55,11 +121,35 @@ description = "Add SQLAlchemy support to your Flask application."
category = "main"
optional = false
python-versions = ">=3.7"
files = [
{file = "Flask-SQLAlchemy-3.0.2.tar.gz", hash = "sha256:16199f5b3ddfb69e0df2f52ae4c76aedbfec823462349dabb21a1b2e0a2b65e9"},
{file = "Flask_SQLAlchemy-3.0.2-py3-none-any.whl", hash = "sha256:7d0cd9cf73e64a996bb881a1ebd01633fc5a6d11c36ea27f7b5e251dc45476e7"},
]
[package.dependencies]
Flask = ">=2.2"
SQLAlchemy = ">=1.4.18"
[[package]]
name = "flask-wtf"
version = "1.0.1"
description = "Form rendering, validation, and CSRF protection for Flask with WTForms."
category = "main"
optional = false
python-versions = ">=3.6"
files = [
{file = "Flask-WTF-1.0.1.tar.gz", hash = "sha256:34fe5c6fee0f69b50e30f81a3b7ea16aa1492a771fe9ad0974d164610c09a6c9"},
{file = "Flask_WTF-1.0.1-py3-none-any.whl", hash = "sha256:9d733658c80be551ce7d5bc13c7a7ac0d80df509be1e23827c847d9520f4359a"},
]
[package.dependencies]
Flask = "*"
itsdangerous = "*"
WTForms = "*"
[package.extras]
email = ["email-validator"]
[[package]]
name = "greenlet"
version = "2.0.1"
@ -67,10 +157,84 @@ description = "Lightweight in-process concurrent programming"
category = "main"
optional = false
python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
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autopep8 = []
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colorama = []
flask = []
flask-sqlalchemy = []
greenlet = []
importlib-metadata = []
itsdangerous = []
jinja2 = [
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py-bcrypt = []
pycodestyle = []
sqlalchemy = []
tomli = [
{file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
{file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
]
types-flask-sqlalchemy = []
types-sqlalchemy = []
werkzeug = []
zipp = []
content-hash = "2bf62dac3f38c6f5d62cd5a4dfdef4916bfaa6a1db6be9c68cc842bbdf719795"

3
pyproject.toml

@ -9,6 +9,9 @@ python = "^3.9"
flask-sqlalchemy = "^3.0.2"
Flask = "^2.2.2"
py-bcrypt = "^0.4"
wtforms = "^3.0.1"
wtforms-alchemy = "^0.18.0"
flask-wtf = "^1.0.1"
[tool.poetry.dev-dependencies]
autopep8 = "^2.0.1"

6
templates/admin.html

@ -1,5 +1,11 @@
{% extends "base.html" %}
{% block content %}
<h1>Admin Dashboard</h1>
<article>
<p>You are {{user}}</p>
<a href="{{url_for('chemical_create')}}">
<button>
Add a Chemical
</button></a>
</article>
{% endblock %}

1
templates/base.html

@ -15,6 +15,7 @@
<header>
<nav>
<a href="{{ url_for('home') }}">Home</a>
<a href="{{ url_for('search') }}">Search</a>
{% if session.admin %}
<a href="{{ url_for('admin_root') }}">Admin</a>
<a href="{{ url_for('admin_logout') }}">Logout</a>

31
templates/create_chemical.html

@ -0,0 +1,31 @@
{% extends "base.html" %}
{% block content %}
{% if id %}
<h2>Editing Chemical {{id}}</h2>
{% endif %}
{% if invalid %}
<p style="color: red;">Invalid Form!</p>
{% endif %}
{% if success %}
<p style="color: green;">Success!</p>
{% endif %}
<form method="post">
<table>
{% for field in form %}
<tr>
<td>
<strong>
{{ field.label }}{% if field.flags.required %}*{% endif %}
</strong>
</td>
<td>
{{ field }}
</td>
</tr>
{% endfor %}
</table>
<input type="submit" value="Submit">
</form>
{% endblock %}

5
templates/delete_chemical.html

@ -0,0 +1,5 @@
{% extends "base.html" %}
{% block content %}
<h2>Successfully Deleted Chemical with id {{id}}</h2>
{% endblock %}

11
templates/index.html

@ -1,3 +1,10 @@
{% extends 'base.html' %} {%block content%}
<h1>Exposome Database Website</h1>
{% extends 'base.html' %}
{%block content%}
<article>
<h1>Exposome Database Website</h1>
<p>
This website consists of a searchable database of chemicals.
</p>
</article>
{%endblock%}

69
templates/search.html

@ -0,0 +1,69 @@
{% extends "base.html" %}
{% block content %}
<script type="module">
import { createApp } from 'https://unpkg.com/petite-vue?module'
createApp({
mz_min:0,
mz_max:0,
rt_min:0,
rt_max:0,
results: [],
error: null,
// methods
async fetch_data() {
try {
console.log("called...")
const json = (await fetch(`/chemical/search?mz_min=${mz_min.value}&mz_max=${mz_max.value}&rt_min=${rt_min.value}&rt_max=${rt_max.value}`))
this.results = await json.json();
} catch(e) {
console.error(e);
error = true;
}
}
}).mount()
</script>
<h1>Search Box</h1>
<main>
<label for="mz_min">Mz Min</label>
<input id="mz_min" type="number" name="mz_min" v-model="mz_min">
<label for="mz_min">Mz Max</label>
<input id="mz_max" type="number" name="mz_max" v-model="mz_max">
<label for="mz_min">RT Min</label>
<input id="rt_min" type="number" name="rt_min" v-model="rt_min">
<label for="mz_min">RT Max</label>
<input id="rt_max" type="number" name="rt_max" v-model="rt_max">
<br>
<button @click="fetch_data()">Search</button>
</main>
<hr>
{% raw %}
<div id="search">
<div v-if="error" style="background-color: red;">
Uh Oh! There is an Error!
</div>
<div v-for="result in results">
<a :href="result.url">
<h3>{{result.name}}</h3>
</a>
<table>
<tr>
<td>Rt</td>
<td>{{result.rt}}</td>
</tr>
<tr>
<td>Mz</td>
<td>{{result.mz}}</td>
</tr>
</table>
<hr>
</div>
</div>
{% endraw %}
{% endblock %}

30
templates/view_chemical.html

@ -0,0 +1,30 @@
{% extends "base.html" %}
{% block content %}
<h2>Viewing Chemical {{id}}</h2>
{% if session.admin %}
<div>
<a href="{{ url_for('chemical_update', id=id) }}">
<button>Edit Chemical</button>
</a>
<a href="{{ url_for('chemical_delete', id=id) }}">
<button style="background-color: red;">Delete Chemical</button>
</a>
</div>
{% endif %}
<table>
{% for k,v in chemical.items() %}
<tr>
<td>
<strong>{{k}}</strong>
</td>
<td>
{% if v is not none %}
{{ v }}
{% endif %}
</td>
</tr>
{% endfor %}
</table>
{% endblock %}
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