diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..a3669ea --- /dev/null +++ b/.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/ diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..a59a067 --- /dev/null +++ b/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"] \ No newline at end of file diff --git a/app.py b/app.py index dd80c11..5fc0bcb 100755 --- a/app.py +++ b/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) diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 0000000..2ae241d --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,8 @@ +version: '3.9' +services: + web: + ports: + - "5002:5000" + build: . + volumes: + - ./instance:/app/instance/ \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index 4a2ca3c..828fe53 100644 --- a/poetry.lock +++ b/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 = [] diff --git a/pyproject.toml b/pyproject.toml index bab76ea..94969e6 100644 --- a/pyproject.toml +++ b/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"