Schema not includes time

.gitignore

@@ -160,3 +160,5 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+/R
+.swp

2-5-23.txt

@@ -0,0 +1,12 @@
+# Changes to Make
+
+- Show how to make a network request in R to the server
+- Version Control (what date a compound was added)
+  - createdAt, but configurable.
+  - Compare the database to the list of compunds and you only want compounds
+    from that date or before?
+
+- Emphasizing Local? - Accessible through a url.
+
+- Shiny app
+  - Permissions System (revoke, access API keys)

app.py

@@ -6,22 +6,21 @@ from sqlalchemy import inspect, and_
 from flask_wtf import FlaskForm
 import bcrypt
 from wtforms_alchemy import model_form_factory
+from flask_migrate import Migrate
 
-db: SQLAlchemy = SQLAlchemy()
 app = Flask(__name__)
-
 app.config["SQLALCHEMY_DATABASE_URI"] = "sqlite:///project.db"
 app.secret_key = '98d31240f9fbe14c8083586db49c19c3a8d3f726'
 
-db.init_app(app)
-
+db: SQLAlchemy = SQLAlchemy(app)
+migrate = Migrate(app, db)
 
 BaseModelForm = model_form_factory(FlaskForm)
 
 
 class ModelForm(BaseModelForm):
     @classmethod
-    def get_session(self):
+    def get_session(cls):
         return db.session
 
 
@@ -87,6 +86,8 @@ class Chemical(db.Model):
     msms_detected = db.Column(db.Boolean)
     msms_purity = db.Column(db.Float)
 
+    createdAt = db.Column(db.Date)
+
 
 class ChemicalForm(ModelForm):
     class Meta:
@@ -228,7 +229,6 @@ def chemical_all():
         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')

entrypoint.sh

@@ -1,4 +1,5 @@
 #!/bin/sh
 
+flask db upgrade
 ./initialize_db.py
 gunicorn -b 0.0.0.0:5000 app:app

flake.lock

@@ -0,0 +1,43 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "locked": {
+        "lastModified": 1667395993,
+        "narHash": "sha256-nuEHfE/LcWyuSWnS8t12N1wc105Qtau+/OdUAjtQ0rA=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "5aed5285a952e0b949eb3ba02c12fa4fcfef535f",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1675600654,
+        "narHash": "sha256-ipsDTkzRq1CAl2g5tYd7ugjVMSKF6KLh9F+5Kso0lT0=",
+        "owner": "nixos",
+        "repo": "nixpkgs",
+        "rev": "cff83d5032a21aad4f69bf284e95b5f564f4a54e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nixos",
+        "ref": "nixos-22.11",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}

flake.nix

@@ -0,0 +1,30 @@
+{
+  description = "Juni's Vanilla Flake Template";
+  inputs = {
+    nixpkgs.url = "github:nixos/nixpkgs/nixos-22.11";
+    flake-utils = {
+      url = "github:numtide/flake-utils";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    with flake-utils.lib;
+    eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs { inherit system; };
+        version = "0.1.0";
+        name = "package name";
+        myR = pkgs.rWrapper.override{ packages = with pkgs.rPackages; [ crul ]; };
+      in {
+
+        devShell = pkgs.mkShell {
+          buildInputs = with pkgs; [ python3 poetry myR ];
+        };
+
+        defaultPackage = pkgs.stdenv.mkDerivation { inherit name version; };
+
+        formatter = nixpkgs.legacyPackages."${system}".nixfmt;
+
+      });
+}

migrations/README

@@ -0,0 +1 @@
+Single-database configuration for Flask.

migrations/alembic.ini

@@ -0,0 +1,50 @@
+# A generic, single database configuration.
+
+[alembic]
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic,flask_migrate
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[logger_flask_migrate]
+level = INFO
+handlers =
+qualname = flask_migrate
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

migrations/env.py

@@ -0,0 +1,110 @@
+import logging
+from logging.config import fileConfig
+
+from flask import current_app
+
+from alembic import context
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+logger = logging.getLogger('alembic.env')
+
+
+def get_engine():
+    try:
+        # this works with Flask-SQLAlchemy<3 and Alchemical
+        return current_app.extensions['migrate'].db.get_engine()
+    except TypeError:
+        # this works with Flask-SQLAlchemy>=3
+        return current_app.extensions['migrate'].db.engine
+
+
+def get_engine_url():
+    try:
+        return get_engine().url.render_as_string(hide_password=False).replace(
+            '%', '%%')
+    except AttributeError:
+        return str(get_engine().url).replace('%', '%%')
+
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+config.set_main_option('sqlalchemy.url', get_engine_url())
+target_db = current_app.extensions['migrate'].db
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def get_metadata():
+    if hasattr(target_db, 'metadatas'):
+        return target_db.metadatas[None]
+    return target_db.metadata
+
+
+def run_migrations_offline():
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url, target_metadata=get_metadata(), literal_binds=True
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online():
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+
+    # this callback is used to prevent an auto-migration from being generated
+    # when there are no changes to the schema
+    # reference: http://alembic.zzzcomputing.com/en/latest/cookbook.html
+    def process_revision_directives(context, revision, directives):
+        if getattr(config.cmd_opts, 'autogenerate', False):
+            script = directives[0]
+            if script.upgrade_ops.is_empty():
+                directives[:] = []
+                logger.info('No changes in schema detected.')
+
+    connectable = get_engine()
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection,
+            target_metadata=get_metadata(),
+            process_revision_directives=process_revision_directives,
+            **current_app.extensions['migrate'].configure_args
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

migrations/script.py.mako

@@ -0,0 +1,24 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
+
+
+def upgrade():
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade():
+    ${downgrades if downgrades else "pass"}

migrations/versions/7e9528cf1416_first_migration.py

@@ -0,0 +1,58 @@
+"""first migration
+
+Revision ID: 7e9528cf1416
+Revises: 
+Create Date: 2023-02-05 19:02:36.284051
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '7e9528cf1416'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('admin',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('username', sa.String(), nullable=False),
+    sa.Column('password', sa.String(), nullable=False),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('username')
+    )
+    op.create_table('chemical',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('chemical_db_id', sa.String(), nullable=True),
+    sa.Column('library', sa.String(), nullable=True),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.Column('formula', sa.String(), nullable=False),
+    sa.Column('mass', sa.Float(), nullable=False),
+    sa.Column('pubchem_cid', sa.Integer(), nullable=True),
+    sa.Column('pubmed_refcount', sa.Integer(), nullable=True),
+    sa.Column('standard_class', sa.String(), nullable=True),
+    sa.Column('inchikey', sa.String(), nullable=True),
+    sa.Column('inchikey14', sa.String(), nullable=True),
+    sa.Column('final_mz', sa.Float(), nullable=False),
+    sa.Column('final_rt', sa.Float(), nullable=False),
+    sa.Column('final_adduct', sa.String(), nullable=True),
+    sa.Column('adduct', sa.String(), nullable=True),
+    sa.Column('detected_adducts', sa.String(), nullable=True),
+    sa.Column('adduct_calc_mz', sa.String(), nullable=True),
+    sa.Column('msms_detected', sa.Boolean(), nullable=True),
+    sa.Column('msms_purity', sa.Float(), nullable=True),
+    sa.Column('createdAt', sa.Date(), nullable=True),
+    sa.PrimaryKeyConstraint('id')
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('chemical')
+    op.drop_table('admin')
+    # ### end Alembic commands ###

poetry.lock

@@ -1,3 +1,18 @@
+[[package]]
+name = "alembic"
+version = "1.9.2"
+description = "A database migration tool for SQLAlchemy."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+Mako = "*"
+SQLAlchemy = ">=1.3.0"
+
+[package.extras]
+tz = ["python-dateutil"]
+
 [[package]]
 name = "autopep8"
 version = "2.0.1"
@@ -39,27 +54,28 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "dnspython"
-version = "2.2.1"
+version = "2.3.0"
 description = "DNS toolkit"
 category = "main"
 optional = false
-python-versions = ">=3.6,<4.0"
+python-versions = ">=3.7,<4.0"
 
 [package.extras]
-dnssec = ["cryptography (>=2.6,<37.0)"]
+doq = ["aioquic (>=0.9.20)"]
+dnssec = ["cryptography (>=2.6,<40.0)"]
 curio = ["curio (>=1.2,<2.0)", "sniffio (>=1.1,<2.0)"]
-doh = ["h2 (>=4.1.0)", "httpx (>=0.21.1)", "requests (>=2.23.0,<3.0.0)", "requests-toolbelt (>=0.9.1,<0.10.0)"]
+doh = ["h2 (>=4.1.0)", "httpx (>=0.21.1)", "requests (>=2.23.0,<3.0.0)", "requests-toolbelt (>=0.9.1,<0.11.0)"]
 idna = ["idna (>=2.1,<4.0)"]
-trio = ["trio (>=0.14,<0.20)"]
+trio = ["trio (>=0.14,<0.23)"]
 wmi = ["wmi (>=1.5.1,<2.0.0)"]
 
 [[package]]
 name = "email-validator"
-version = "1.3.0"
+version = "1.3.1"
 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"
+python-versions = ">=3.5"
 
 [package.dependencies]
 dnspython = ">=1.15.0"
@@ -84,9 +100,22 @@ Werkzeug = ">=2.2.2"
 async = ["asgiref (>=3.2)"]
 dotenv = ["python-dotenv"]
 
+[[package]]
+name = "flask-migrate"
+version = "4.0.4"
+description = "SQLAlchemy database migrations for Flask applications using Alembic."
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+alembic = ">=1.9.0"
+Flask = ">=0.9"
+Flask-SQLAlchemy = ">=1.0"
+
 [[package]]
 name = "flask-sqlalchemy"
-version = "3.0.2"
+version = "3.0.3"
 description = "Add SQLAlchemy support to your Flask application."
 category = "main"
 optional = false
@@ -98,11 +127,11 @@ SQLAlchemy = ">=1.4.18"
 
 [[package]]
 name = "flask-wtf"
-version = "1.0.1"
+version = "1.1.1"
 description = "Form rendering, validation, and CSRF protection for Flask with WTForms."
 category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 
 [package.dependencies]
 Flask = "*"
@@ -114,7 +143,7 @@ email = ["email-validator"]
 
 [[package]]
 name = "greenlet"
-version = "2.0.1"
+version = "2.0.2"
 description = "Lightweight in-process concurrent programming"
 category = "main"
 optional = false
@@ -122,7 +151,7 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
 
 [package.extras]
 docs = ["sphinx", "docutils (<0.18)"]
-test = ["objgraph", "psutil", "faulthandler"]
+test = ["objgraph", "psutil"]
 
 [[package]]
 name = "gunicorn"
@@ -148,7 +177,7 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "importlib-metadata"
-version = "5.2.0"
+version = "6.0.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
@@ -209,9 +238,25 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
+name = "mako"
+version = "1.2.4"
+description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+MarkupSafe = ">=0.9.2"
+
+[package.extras]
+babel = ["babel"]
+lingua = ["lingua"]
+testing = ["pytest"]
+
 [[package]]
 name = "markupsafe"
-version = "2.1.1"
+version = "2.1.2"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "main"
 optional = false
@@ -243,7 +288,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "sqlalchemy"
-version = "1.4.45"
+version = "1.4.46"
 description = "Database Abstraction Library"
 category = "main"
 optional = false
@@ -308,7 +353,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "types-flask-sqlalchemy"
-version = "2.5.9"
+version = "2.5.9.1"
 description = "Typing stubs for Flask-SQLAlchemy"
 category = "dev"
 optional = false
@@ -319,7 +364,7 @@ types-SQLAlchemy = "*"
 
 [[package]]
 name = "types-sqlalchemy"
-version = "1.4.53.19"
+version = "1.4.53.28"
 description = "Typing stubs for SQLAlchemy"
 category = "dev"
 optional = false
@@ -415,104 +460,285 @@ timezone = ["python-dateutil"]
 
 [[package]]
 name = "zipp"
-version = "3.11.0"
+version = "3.12.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "jaraco.tidelift (>=1.4)"]
+docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "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"]
 
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.9"
-content-hash = "f2618675cce387206217c9e139800f6c6e7d5bd103a45e88712ff59902812042"
+content-hash = "8595ab65ac1a098228335d1c012a7f266cea9014f71af835581a10debdf36230"
 
 [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"},
+alembic = [
+    {file = "alembic-1.9.2-py3-none-any.whl", hash = "sha256:e8a6ff9f3b1887e1fed68bfb8fb9a000d8f61c21bdcc85b67bb9f87fcbc4fce3"},
+    {file = "alembic-1.9.2.tar.gz", hash = "sha256:6880dec4f28dd7bd999d2ed13fbe7c9d4337700a44d11a524c0ce0c59aaf0dbd"},
+]
+autopep8 = [
+    {file = "autopep8-2.0.1-py2.py3-none-any.whl", hash = "sha256:be5bc98c33515b67475420b7b1feafc8d32c1a69862498eda4983b45bffd2687"},
+    {file = "autopep8-2.0.1.tar.gz", hash = "sha256:d27a8929d8dcd21c0f4b3859d2d07c6c25273727b98afc984c039df0f0d86566"},
+]
+click = []
+colorama = [
+    {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
+    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
-colorama = []
 decorator = []
-dnspython = []
-email-validator = []
-flask = []
-flask-sqlalchemy = []
-flask-wtf = []
-greenlet = []
-gunicorn = []
-idna = []
-importlib-metadata = []
-infinity = []
-intervals = []
-itsdangerous = []
-jinja2 = [
-    {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
-    {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
+dnspython = [
+    {file = "dnspython-2.3.0-py3-none-any.whl", hash = "sha256:89141536394f909066cabd112e3e1a37e4e654db00a25308b0f130bc3152eb46"},
+    {file = "dnspython-2.3.0.tar.gz", hash = "sha256:224e32b03eb46be70e12ef6d64e0be123a64e621ab4c0822ff6d450d52a540b9"},
+]
+email-validator = [
+    {file = "email_validator-1.3.1-py2.py3-none-any.whl", hash = "sha256:49a72f5fa6ed26be1c964f0567d931d10bf3fdeeacdf97bc26ef1cd2a44e0bda"},
+    {file = "email_validator-1.3.1.tar.gz", hash = "sha256:d178c5c6fa6c6824e9b04f199cf23e79ac15756786573c190d2ad13089411ad2"},
+]
+flask = [
+    {file = "Flask-2.2.2-py3-none-any.whl", hash = "sha256:b9c46cc36662a7949f34b52d8ec7bb59c0d74ba08ba6cb9ce9adc1d8676d9526"},
+    {file = "Flask-2.2.2.tar.gz", hash = "sha256:642c450d19c4ad482f96729bd2a8f6d32554aa1e231f4f6b4e7e5264b16cca2b"},
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-wtforms-alchemy = []
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pyproject.toml

@@ -7,12 +7,14 @@ authors = ["junikimm717 <68165832+junikimm717@users.noreply.github.com>"]
 [tool.poetry.dependencies]
 python = "^3.9"
 flask-sqlalchemy = "^3.0.2"
+sqlalchemy = "^1.4.18"
 Flask = "^2.2.2"
 py-bcrypt = "^0.4"
 wtforms = "^3.0.1"
 wtforms-alchemy = "^0.18.0"
 flask-wtf = "^1.0.1"
 gunicorn = "^20.1.0"
+Flask-Migrate = "^4.0.4"
 
 [tool.poetry.dev-dependencies]
 autopep8 = "^2.0.1"

templates/admin.html

@@ -61,6 +61,7 @@ fields = {
     "adduct_calc_mz": <string>,
     "msms_detected": <string if yes, do not include this field otherwise>
     "msms_purity": <float>
+    "date": "YYYY-MM-DD"
 }
 session.post(baseurl + "/chemical/create", fields)
         </code></pre>