docker compose for deployment

.dockerignore

@@ -0,0 +1,162 @@
+.idea
+/instance
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  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/

Dockerfile

@@ -0,0 +1,17 @@
+FROM fnndsc/python-poetry
+
+WORKDIR /app/
+
+# plz install everything globally in docker
+RUN apt-get update && apt-get install -y build-essential
+RUN poetry config virtualenvs.create false
+
+# install our dependencies first
+COPY pyproject.toml poetry.lock /app/
+
+RUN poetry install --no-dev
+
+# now copy over everything
+COPY . /app/
+
+ENTRYPOINT ["gunicorn", "-b", "0.0.0.0:5000", "app:app"]

app.py

@@ -13,14 +13,19 @@ app = Flask(__name__)
 app.config["SQLALCHEMY_DATABASE_URI"] = "sqlite:///project.db"
 app.secret_key = '98d31240f9fbe14c8083586db49c19c3a8d3f726'
 
+db.init_app(app)
+with app.app_context():
+    db.create_all()
 
 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)
@@ -245,14 +250,11 @@ def search_api():
     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})
@@ -265,7 +267,4 @@ def search():
 
 
 if __name__ == "__main__":
-    db.init_app(app)
-    with app.app_context():
-        db.create_all()
     app.run(debug=True)

docker-compose.yml

@@ -0,0 +1,8 @@
+version: '3.9'
+services:
+  web:
+    ports:
+      - "5002:5000"
+    build: .
+    volumes:
+      - ./instance:/app/instance/

poetry.lock

@@ -124,6 +124,20 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
 docs = ["sphinx", "docutils (<0.18)"]
 test = ["objgraph", "psutil", "faulthandler"]
 
+[[package]]
+name = "gunicorn"
+version = "20.1.0"
+description = "WSGI HTTP Server for UNIX"
+category = "main"
+optional = false
+python-versions = ">=3.5"
+
+[package.extras]
+eventlet = ["eventlet (>=0.24.1)"]
+gevent = ["gevent (>=1.4.0)"]
+setproctitle = ["setproctitle"]
+tornado = ["tornado (>=0.2)"]
+
 [[package]]
 name = "idna"
 version = "3.4"
@@ -414,7 +428,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-co
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.9"
-content-hash = "2bf62dac3f38c6f5d62cd5a4dfdef4916bfaa6a1db6be9c68cc842bbdf719795"
+content-hash = "f2618675cce387206217c9e139800f6c6e7d5bd103a45e88712ff59902812042"
 
 [metadata.files]
 autopep8 = []
@@ -430,6 +444,7 @@ flask = []
 flask-sqlalchemy = []
 flask-wtf = []
 greenlet = []
+gunicorn = []
 idna = []
 importlib-metadata = []
 infinity = []

pyproject.toml

@@ -12,6 +12,7 @@ py-bcrypt = "^0.4"
 wtforms = "^3.0.1"
 wtforms-alchemy = "^0.18.0"
 flask-wtf = "^1.0.1"
+gunicorn = "^20.1.0"
 
 [tool.poetry.dev-dependencies]
 autopep8 = "^2.0.1"