Chemical DB added

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)

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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+    {file = "greenlet-2.0.1.tar.gz", hash = "sha256:42e602564460da0e8ee67cb6d7236363ee5e131aa15943b6670e44e5c2ed0f67"},
+]
 
 [package.extras]
-docs = ["sphinx", "docutils (<0.18)"]
-test = ["objgraph", "psutil", "faulthandler"]
+docs = ["Sphinx", "docutils (<0.18)"]
+test = ["faulthandler", "objgraph", "psutil"]
+
+[[package]]
+name = "idna"
+version = "3.4"
+description = "Internationalized Domain Names in Applications (IDNA)"
+category = "main"
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "idna-3.4-py3-none-any.whl", hash = "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"},
+    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
+]
 
 [[package]]
 name = "importlib-metadata"
@@ -79,14 +243,50 @@ description = "Read metadata from Python packages"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "importlib_metadata-5.2.0-py3-none-any.whl", hash = "sha256:0eafa39ba42bf225fc00e67f701d71f85aead9f878569caf13c3724f704b970f"},
+    {file = "importlib_metadata-5.2.0.tar.gz", hash = "sha256:404d48d62bba0b7a77ff9d405efd91501bef2e67ff4ace0bed40a0cf28c3c7cd"},
+]
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8", "importlib-resources (>=1.3)"]
+testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"]
+
+[[package]]
+name = "infinity"
+version = "1.5"
+description = "All-in-one infinity value for Python. Can be compared to any object."
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "infinity-1.5.tar.gz", hash = "sha256:8daa7c15ce2100fdccfde212337e0cd5cf085869f54dc2634b6c30d61461ecda"},
+]
+
+[package.extras]
+test = ["Pygments (>=1.2)", "flake8 (>=2.4.0)", "isort (>=4.2.2)", "pytest (>=2.2.3)", "six (>=1.4.1)"]
+
+[[package]]
+name = "intervals"
+version = "0.9.2"
+description = "Python tools for handling intervals (ranges of comparable objects)."
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "intervals-0.9.2-py3-none-any.whl", hash = "sha256:7c963abf7b4be2be40322b84e036af5d4ebec0945b5d29df7da1a638b3fea768"},
+    {file = "intervals-0.9.2.tar.gz", hash = "sha256:c7ee568c583ca857c0d91af6d90ee5e0e8adef3f5646d0076bfb87305ae43090"},
+]
+
+[package.dependencies]
+infinity = ">=0.1.3"
+
+[package.extras]
+test = ["Pygments (>=1.2)", "flake8 (>=2.4.0)", "isort (>=4.2.2)", "pytest (>=2.2.3)"]
 
 [[package]]
 name = "itsdangerous"
@@ -95,6 +295,10 @@ description = "Safely pass data to untrusted environments and back."
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "itsdangerous-2.1.2-py3-none-any.whl", hash = "sha256:2c2349112351b88699d8d4b6b075022c0808887cb7ad10069318a8b0bc88db44"},
+    {file = "itsdangerous-2.1.2.tar.gz", hash = "sha256:5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a"},
+]
 
 [[package]]
 name = "jinja2"
@@ -103,6 +307,10 @@ description = "A very fast and expressive template engine."
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
+    {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
+]
 
 [package.dependencies]
 MarkupSafe = ">=2.0"
@@ -117,6 +325,48 @@ description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
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+]
 
 [[package]]
 name = "py-bcrypt"
@@ -125,6 +375,9 @@ description = "bcrypt password hashing and key derivation"
 category = "main"
 optional = false
 python-versions = "*"
+files = [
+    {file = "py-bcrypt-0.4.tar.gz", hash = "sha256:5fa13bce551468350d66c4883694850570f3da28d6866bb638ba44fe5eabda78"},
+]
 
 [[package]]
 name = "pycodestyle"
@@ -133,6 +386,22 @@ description = "Python style guide checker"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
+files = [
+    {file = "pycodestyle-2.10.0-py2.py3-none-any.whl", hash = "sha256:8a4eaf0d0495c7395bdab3589ac2db602797d76207242c17d470186815706610"},
+    {file = "pycodestyle-2.10.0.tar.gz", hash = "sha256:347187bdb476329d98f695c213d7295a846d1152ff4fe9bacb8a9590b8ee7053"},
+]
+
+[[package]]
+name = "six"
+version = "1.16.0"
+description = "Python 2 and 3 compatibility utilities"
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+files = [
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+]
 
 [[package]]
 name = "sqlalchemy"
@@ -141,31 +410,103 @@ description = "Database Abstraction Library"
 category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
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+]
 
 [package.dependencies]
 greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"}
 
 [package.extras]
-aiomysql = ["greenlet (!=0.4.17)", "aiomysql"]
-aiosqlite = ["typing_extensions (!=3.10.0.1)", "greenlet (!=0.4.17)", "aiosqlite"]
+aiomysql = ["aiomysql", "greenlet (!=0.4.17)"]
+aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
-asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4)"]
-mariadb_connector = ["mariadb (>=1.0.1,!=1.1.2)"]
+asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)"]
 mssql = ["pyodbc"]
-mssql_pymssql = ["pymssql"]
-mssql_pyodbc = ["pyodbc"]
-mypy = ["sqlalchemy2-stubs", "mypy (>=0.910)"]
-mysql = ["mysqlclient (>=1.4.0,<2)", "mysqlclient (>=1.4.0)"]
-mysql_connector = ["mysql-connector-python"]
-oracle = ["cx_oracle (>=7,<8)", "cx_oracle (>=7)"]
+mssql-pymssql = ["pymssql"]
+mssql-pyodbc = ["pyodbc"]
+mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"]
+mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"]
+mysql-connector = ["mysql-connector-python"]
+oracle = ["cx-oracle (>=7)", "cx-oracle (>=7,<8)"]
 postgresql = ["psycopg2 (>=2.7)"]
-postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"]
-postgresql_pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
-postgresql_psycopg2binary = ["psycopg2-binary"]
-postgresql_psycopg2cffi = ["psycopg2cffi"]
-pymysql = ["pymysql (<1)", "pymysql"]
+postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
+postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
+postgresql-psycopg2binary = ["psycopg2-binary"]
+postgresql-psycopg2cffi = ["psycopg2cffi"]
+pymysql = ["pymysql", "pymysql (<1)"]
 sqlcipher = ["sqlcipher3-binary"]
 
+[[package]]
+name = "sqlalchemy-utils"
+version = "0.39.0"
+description = "Various utility functions for SQLAlchemy."
+category = "main"
+optional = false
+python-versions = "~=3.6"
+files = [
+    {file = "SQLAlchemy-Utils-0.39.0.tar.gz", hash = "sha256:b37240917d81c14fe1b6e5096a402bace472b179121384e47c10d854dbf5af92"},
+    {file = "SQLAlchemy_Utils-0.39.0-py3-none-any.whl", hash = "sha256:9da26a9b20c6979167772ba5dc2a1d01265648f18c82995f082279a399ea308b"},
+]
+
+[package.dependencies]
+SQLAlchemy = ">=1.3"
+
+[package.extras]
+arrow = ["arrow (>=0.3.4)"]
+babel = ["Babel (>=1.3)"]
+color = ["colour (>=0.0.4)"]
+encrypted = ["cryptography (>=0.6)"]
+intervals = ["intervals (>=0.7.1)"]
+password = ["passlib (>=1.6,<2.0)"]
+pendulum = ["pendulum (>=2.0.5)"]
+phone = ["phonenumbers (>=5.9.2)"]
+test = ["Jinja2 (>=2.3)", "Pygments (>=1.2)", "backports.zoneinfo", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "isort (>=4.2.2)", "pg8000 (>=1.12.4)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
+test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "backports.zoneinfo", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
+timezone = ["python-dateutil"]
+url = ["furl (>=0.4.1)"]
+
 [[package]]
 name = "tomli"
 version = "2.0.1"
@@ -173,6 +514,10 @@ description = "A lil' TOML parser"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
+    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+]
 
 [[package]]
 name = "types-flask-sqlalchemy"
@@ -181,6 +526,10 @@ description = "Typing stubs for Flask-SQLAlchemy"
 category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "types-Flask-SQLAlchemy-2.5.9.tar.gz", hash = "sha256:be198f073dcde90d05eb9f198bede58bf0f63f965a0fbdc0b9f917e123591d77"},
+    {file = "types_Flask_SQLAlchemy-2.5.9-py3-none-any.whl", hash = "sha256:324d88456bc14cb023f93e869341d14f7a06294dd11c621959ad72ee810d7ae9"},
+]
 
 [package.dependencies]
 types-SQLAlchemy = "*"
@@ -192,6 +541,27 @@ description = "Typing stubs for SQLAlchemy"
 category = "dev"
 optional = false
 python-versions = "*"
+files = [
+    {file = "types-SQLAlchemy-1.4.53.19.tar.gz", hash = "sha256:8f0cc6bff76e63433daa744da5adff66a49bca2ccc05073d5f211c96ef49ed3f"},
+    {file = "types_SQLAlchemy-1.4.53.19-py3-none-any.whl", hash = "sha256:42e7a2332a260f29cb65278d92201c59a9743e01657a3380d8e3e076f6c027d5"},
+]
+
+[[package]]
+name = "validators"
+version = "0.20.0"
+description = "Python Data Validation for Humans™."
+category = "main"
+optional = false
+python-versions = ">=3.4"
+files = [
+    {file = "validators-0.20.0.tar.gz", hash = "sha256:24148ce4e64100a2d5e267233e23e7afeb55316b47d30faae7eb6e7292bc226a"},
+]
+
+[package.dependencies]
+decorator = ">=3.4.0"
+
+[package.extras]
+test = ["flake8 (>=2.4.0)", "isort (>=4.2.2)", "pytest (>=2.2.3)"]
 
 [[package]]
 name = "werkzeug"
@@ -200,6 +570,10 @@ description = "The comprehensive WSGI web application library."
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "Werkzeug-2.2.2-py3-none-any.whl", hash = "sha256:f979ab81f58d7318e064e99c4506445d60135ac5cd2e177a2de0089bfd4c9bd5"},
+    {file = "Werkzeug-2.2.2.tar.gz", hash = "sha256:7ea2d48322cc7c0f8b3a215ed73eabd7b5d75d0b50e31ab006286ccff9e00b8f"},
+]
 
 [package.dependencies]
 MarkupSafe = ">=2.1.1"
@@ -207,6 +581,77 @@ MarkupSafe = ">=2.1.1"
 [package.extras]
 watchdog = ["watchdog"]
 
+[[package]]
+name = "wtforms"
+version = "3.0.1"
+description = "Form validation and rendering for Python web development."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "WTForms-3.0.1-py3-none-any.whl", hash = "sha256:837f2f0e0ca79481b92884962b914eba4e72b7a2daaf1f939c890ed0124b834b"},
+    {file = "WTForms-3.0.1.tar.gz", hash = "sha256:6b351bbb12dd58af57ffef05bc78425d08d1914e0fd68ee14143b7ade023c5bc"},
+]
+
+[package.dependencies]
+MarkupSafe = "*"
+
+[package.extras]
+email = ["email-validator"]
+
+[[package]]
+name = "wtforms-alchemy"
+version = "0.18.0"
+description = "Generates WTForms forms from SQLAlchemy models."
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "WTForms-Alchemy-0.18.0.tar.gz", hash = "sha256:7748494056bdd96a7566186b8f422180465c337b2e892ad8e82a063cd6c76ca7"},
+    {file = "WTForms_Alchemy-0.18.0-py3-none-any.whl", hash = "sha256:c14cec7f76e27351a5777182ff39fcba64b7c46a561401835426605e6c83f216"},
+]
+
+[package.dependencies]
+SQLAlchemy = ">=1.0"
+SQLAlchemy-Utils = ">=0.32.6"
+WTForms = ">=2.2"
+WTForms-Components = ">=0.9.2"
+
+[package.extras]
+arrow = ["arrow (>=0.3.4)"]
+babel = ["Babel (>=1.3)"]
+color = ["colour (>=0.0.4)"]
+i18n = ["SQLAlchemy-i18n (>=0.8.2)"]
+intervals = ["intervals (>=0.2.0)"]
+password = ["passlib (>=1.6,<2.0)"]
+phone = ["phonenumbers (>=5.9.2)"]
+test = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "SQLAlchemy-i18n (>=0.8.2)", "WTForms-Test (>=0.1.1)", "arrow (>=0.3.4)", "colour (>=0.0.4)", "docutils (>=0.10)", "enum34", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "intervals (>=0.2.0)", "isort (>=3.9.6)", "natsort (==3.5.6)", "passlib (>=1.6,<2.0)", "phonenumbers (>=5.9.2)", "pytest (>=2.3)", "python-dateutil"]
+timezone = ["python-dateutil"]
+
+[[package]]
+name = "wtforms-components"
+version = "0.10.5"
+description = "Additional fields, validators and widgets for WTForms."
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "WTForms_Components-0.10.5-py2.py3-none-any.whl", hash = "sha256:7d0d83dec6d5352c661e522be628f49c2de3aa78cd79c9caf0c1cc3bff4e3872"},
+]
+
+[package.dependencies]
+email-validator = ">=1.0.0"
+intervals = ">=0.6.0"
+MarkupSafe = ">=1.0.0"
+six = ">=1.4.1"
+validators = ">=0.5.0"
+WTForms = ">=1.0.4"
+
+[package.extras]
+color = ["colour (>=0.0.4)"]
+test = ["WTForms-Test (>=0.1.1)", "colour (>=0.0.4)", "flake8 (==3.8.4)", "flexmock (>=0.9.7)", "isort (==4.3.21)", "pytest (>=2.2.3)", "python-dateutil"]
+timezone = ["python-dateutil"]
+
 [[package]]
 name = "zipp"
 version = "3.11.0"
@@ -214,82 +659,16 @@ description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
 python-versions = ">=3.7"
+files = [
+    {file = "zipp-3.11.0-py3-none-any.whl", hash = "sha256:83a28fcb75844b5c0cdaf5aa4003c2d728c77e05f5aeabe8e95e56727005fbaa"},
+    {file = "zipp-3.11.0.tar.gz", hash = "sha256:a7a22e05929290a67401440b39690ae6563279bced5f314609d9d03798f56766"},
+]
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "jaraco.functools", "more-itertools", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"]
+testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [metadata]
-lock-version = "1.1"
+lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "54b3e8cb9fa3e9c6b85642bc519182772dac7ede4030fa8209e2510ccdbcd90c"
-
-[metadata.files]
-autopep8 = []
-click = [
-    {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"},
-    {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},
-]
-colorama = []
-flask = []
-flask-sqlalchemy = []
-greenlet = []
-importlib-metadata = []
-itsdangerous = []
-jinja2 = [
-    {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
-    {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
-]
-markupsafe = [
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-    {file = "MarkupSafe-2.1.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:f121a1420d4e173a5d96e47e9a0c0dcff965afdf1626d28de1460815f7c4ee7a"},
-    {file = "MarkupSafe-2.1.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a49907dd8420c5685cfa064a1335b6754b74541bbb3706c259c02ed65b644b3e"},
-    {file = "MarkupSafe-2.1.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:10c1bfff05d95783da83491be968e8fe789263689c02724e0c691933c52994f5"},
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-    {file = "MarkupSafe-2.1.1-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:b09bf97215625a311f669476f44b8b318b075847b49316d3e28c08e41a7a573f"},
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-    {file = "MarkupSafe-2.1.1-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:671cd1187ed5e62818414afe79ed29da836dde67166a9fac6d435873c44fdd02"},
-    {file = "MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3799351e2336dc91ea70b034983ee71cf2f9533cdff7c14c90ea126bfd95d65a"},
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-    {file = "MarkupSafe-2.1.1-cp39-cp39-win32.whl", hash = "sha256:d4306c36ca495956b6d568d276ac11fdd9c30a36f1b6eb928070dc5360b22e1c"},
-    {file = "MarkupSafe-2.1.1-cp39-cp39-win_amd64.whl", hash = "sha256:46d00d6cfecdde84d40e572d63735ef81423ad31184100411e6e3388d405e247"},
-    {file = "MarkupSafe-2.1.1.tar.gz", hash = "sha256:7f91197cc9e48f989d12e4e6fbc46495c446636dfc81b9ccf50bb0ec74b91d4b"},
-]
-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"

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"

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 %}

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>

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 %}

templates/delete_chemical.html

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

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%}

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 %}

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 %}