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Resolves acg-team#3 adding gene expr correlation with str length in c…
…rc support + docker-compose + alembic migrations (optional)
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// For format details, see https://aka.ms/devcontainer.json. For config options, see the | ||
// README at: https:/devcontainers/templates/tree/main/src/docker-existing-dockerfile | ||
{ | ||
"name": "Existing Dockerfile", | ||
"build": { | ||
// Sets the run context to one level up instead of the .devcontainer folder. | ||
"context": "..", | ||
// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename. | ||
"dockerfile": "../Dockerfile" | ||
}, | ||
"features": { | ||
"ghcr.io/devcontainers/features/python:1": {} | ||
} | ||
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// Features to add to the dev container. More info: https://containers.dev/features. | ||
// "features": {}, | ||
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// Use 'forwardPorts' to make a list of ports inside the container available locally. | ||
// "forwardPorts": [], | ||
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// Uncomment the next line to run commands after the container is created. | ||
// "postCreateCommand": "cat /etc/os-release", | ||
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// Configure tool-specific properties. | ||
// "customizations": {}, | ||
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// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root. | ||
// "remoteUser": "devcontainer" | ||
} |
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**/__pycache__ | ||
**/.venv | ||
**/.classpath | ||
**/.dockerignore | ||
**/.env | ||
**/.git | ||
**/.gitignore | ||
**/.project | ||
**/.settings | ||
**/.toolstarget | ||
**/.vs | ||
**/.vscode | ||
**/*.*proj.user | ||
**/*.dbmdl | ||
**/*.jfm | ||
**/bin | ||
**/charts | ||
**/docker-compose* | ||
**/compose* | ||
**/Dockerfile* | ||
**/node_modules | ||
**/npm-debug.log | ||
**/obj | ||
**/secrets.dev.yaml | ||
**/values.dev.yaml | ||
**/db/ | ||
LICENSE | ||
README.md |
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# Rename this file to .env and docker compose wil automatically use envornment variables fro it | ||
DATABASE_URL=postgresql://webstr:webstr@webstr_db:5432/webstr | ||
# DATABASE_URL=sqlite:///db/debug.sqlite | ||
PYTHONPATH="./" | ||
WEBSTR_DATABASE_DATA=True | ||
WEBSTR_DEVELOPMENT=False | ||
WEBSTR_SOURCE_MOUNT_PATH=/temp/src #/usr/src/strs |
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strAPI/local_queries.ipynb | ||
data/repeats | ||
db/docker_data/ | ||
.venv/ | ||
db/debug.db | ||
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*/migrations/versions0/* |
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{ | ||
"configurations": [ | ||
{ | ||
"name": "Python: main", | ||
"type": "python", | ||
"request": "launch", | ||
"program": "strAPI/main.py", | ||
"cwd": "${workspaceFolder}", | ||
"console": "integratedTerminal", | ||
"justMyCode": true, | ||
"env": { | ||
// "PYTHONPATH": "${workspaceFolder}/strAPI/" | ||
} | ||
}, | ||
{ | ||
"name": "Docker: Python - Fastapi", | ||
"type": "docker", | ||
"request": "launch", | ||
"preLaunchTask": "docker-run: debug", | ||
"python": { | ||
"pathMappings": [ | ||
{ | ||
"localRoot": "${workspaceFolder}", | ||
"remoteRoot": "/usr/src/strs" | ||
} | ||
], | ||
"projectType": "fastapi" | ||
}, | ||
}, | ||
{ | ||
"name": "Python: Remote Attach 5000", | ||
"type": "python", | ||
"request": "attach", | ||
"connect": { | ||
"host": "0.0.0.0", | ||
"port": 5000 | ||
}, | ||
"pathMappings": [ | ||
{ | ||
"localRoot": "${workspaceFolder}", | ||
"remoteRoot": "/usr/src/app" | ||
} | ||
] | ||
} | ||
] | ||
} |
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{ | ||
"version": "2.0.0", | ||
"tasks": [ | ||
{ | ||
"type": "docker-build", | ||
"label": "docker-build", | ||
"platform": "python", | ||
"dockerBuild": { | ||
"tag": "webstrapi:latest", | ||
"dockerfile": "${workspaceFolder}/Dockerfile", | ||
"context": "${workspaceFolder}", | ||
"pull": true, | ||
} | ||
}, | ||
{ | ||
"type": "docker-run", | ||
"label": "docker-run: debug", | ||
"dependsOn": [ | ||
"docker-build" | ||
], | ||
"dockerRun": { | ||
"env": { | ||
"DATABASE_URL": "sqlite:///db/debug.db", | ||
"WEBSTR_DATABAS_UPGRADE": "True" | ||
}, | ||
"mounts": [ | ||
"source=${workspaceFolder},target=/app,type=bind,consistency=cached" | ||
], | ||
}, | ||
"python": { | ||
"args": [ | ||
"strAPI.main:app", | ||
"--host", | ||
"0.0.0.0", | ||
"--port", | ||
"5000", | ||
"--reload" | ||
], | ||
"module": "uvicorn", | ||
} | ||
} | ||
] | ||
} |
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FROM python:3.8-slim-buster | ||
FROM python:3.8-slim-buster as base | ||
LABEL maintainer="merenlin -- follow me on medium https://medium.com/@merenlin" | ||
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RUN apt-get update && apt-get install -y python3-dev build-essential | ||
ENV PYTHONDONTWRITEBYTECODE=1 | ||
ENV PYTHONUNBUFFERED=1 | ||
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RUN mkdir -p /usr/src/strs | ||
WORKDIR /usr/src/strs | ||
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COPY requirements.txt . | ||
RUN pip3 install -r requirements.txt | ||
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RUN apt-get update && \ | ||
apt-get install -y gcc python3-dev build-essential && \ | ||
python -m pip install -r requirements.txt --no-cache-dir && \ | ||
apt-get remove -y gcc python3-dev build-essential && \ | ||
apt-get clean && rm -rf /var/lib/apt/lists/* | ||
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ENV DATABASE_URL=sqlite:///db/debug.db | ||
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FROM base as prod | ||
LABEL maintainer="merenlin -- follow me on medium https://medium.com/@merenlin" | ||
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RUN adduser -u 1000 --disabled-password --gecos "" appuser && chown -R appuser /usr/src/strs | ||
USER appuser | ||
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COPY . . | ||
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EXPOSE 5000 | ||
ARG PORT=5000 | ||
EXPOSE $PORT | ||
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CMD uvicorn strAPI.main:app --host=0.0.0.0 --port=${PORT:-5000} | ||
CMD bash entrypoint.sh | ||
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# A generic, single database configuration. | ||
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[alembic] | ||
# path to migration scripts | ||
script_location = database_setup/migrations | ||
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# template used to generate migration file names; The default value is %%(rev)s_%%(slug)s | ||
# Uncomment the line below if you want the files to be prepended with date and time | ||
# see https://alembic.sqlalchemy.org/en/latest/tutorial.html#editing-the-ini-file | ||
# for all available tokens | ||
file_template = %%(year)d_%%(month).2d_%%(day).2d_%%(hour).2d%%(minute).2d-%%(rev)s_%%(slug)s | ||
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# sys.path path, will be prepended to sys.path if present. | ||
# defaults to the current working directory. | ||
prepend_sys_path = . | ||
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# timezone to use when rendering the date within the migration file | ||
# as well as the filename. | ||
# If specified, requires the python-dateutil library that can be | ||
# installed by adding `alembic[tz]` to the pip requirements | ||
# string value is passed to dateutil.tz.gettz() | ||
# leave blank for localtime | ||
# timezone = | ||
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# max length of characters to apply to the | ||
# "slug" field | ||
# truncate_slug_length = 40 | ||
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# set to 'true' to run the environment during | ||
# the 'revision' command, regardless of autogenerate | ||
# revision_environment = false | ||
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# set to 'true' to allow .pyc and .pyo files without | ||
# a source .py file to be detected as revisions in the | ||
# versions/ directory | ||
# sourceless = false | ||
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# version location specification; This defaults | ||
# to migrations/versions. When using multiple version | ||
# directories, initial revisions must be specified with --version-path. | ||
# The path separator used here should be the separator specified by "version_path_separator" below. | ||
# version_locations = %(here)s/bar:%(here)s/bat:migrations/versions | ||
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# version path separator; As mentioned above, this is the character used to split | ||
# version_locations. The default within new alembic.ini files is "os", which uses os.pathsep. | ||
# If this key is omitted entirely, it falls back to the legacy behavior of splitting on spaces and/or commas. | ||
# Valid values for version_path_separator are: | ||
# | ||
# version_path_separator = : | ||
# version_path_separator = ; | ||
# version_path_separator = space | ||
version_path_separator = os # Use os.pathsep. Default configuration used for new projects. | ||
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# set to 'true' to search source files recursively | ||
# in each "version_locations" directory | ||
# new in Alembic version 1.10 | ||
# recursive_version_locations = false | ||
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# the output encoding used when revision files | ||
# are written from script.py.mako | ||
# output_encoding = utf-8 | ||
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sqlalchemy.url = sqlite:///db/debug.sqlite | ||
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[post_write_hooks] | ||
# post_write_hooks defines scripts or Python functions that are run | ||
# on newly generated revision scripts. See the documentation for further | ||
# detail and examples | ||
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# format using "black" - use the console_scripts runner, against the "black" entrypoint | ||
# hooks = black | ||
# black.type = console_scripts | ||
# black.entrypoint = black | ||
# black.options = -l 79 REVISION_SCRIPT_FILENAME | ||
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# Logging configuration | ||
[loggers] | ||
keys = root,sqlalchemy,alembic | ||
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[handlers] | ||
keys = console | ||
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[formatters] | ||
keys = generic | ||
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[logger_root] | ||
level = WARN | ||
handlers = console | ||
qualname = | ||
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[logger_sqlalchemy] | ||
level = WARN | ||
handlers = | ||
qualname = sqlalchemy.engine | ||
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[logger_alembic] | ||
level = INFO | ||
handlers = | ||
qualname = alembic | ||
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[handler_console] | ||
class = StreamHandler | ||
args = (sys.stderr,) | ||
level = NOTSET | ||
formatter = generic | ||
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[formatter_generic] | ||
format = %(levelname)-5.5s [%(name)s] %(message)s | ||
datefmt = %H:%M:%S |
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