feat(repo): merge staging from https://gitlab.com/cri-iatlas/iatlas-a…

…pi.git

apps/iatlas/api-gitlab/.coveragerc

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+[run]
+branch = True
+parallel = True
+omit =
+    tests/*
+    config.py
+command_line = -m pytest -n auto
+
+[report]
+precision = 2
+sort = Cover
+
+[html]
+directory = coverage
+extra_css = coverage_assets/coverage.css
+title = iAtlas API Test Coverage

apps/iatlas/api-gitlab/.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/vscode-remote/devcontainer.json or this file's README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.123.0/containers/docker-existing-docker-compose
+// If you want to run as a non-root user in the container, see .devcontainer/docker-compose.yml.
+{
+	"name": "Existing Docker Compose (Extend)",
+	// Update the 'dockerComposeFile' list if you have more compose files or use different names.
+	// The .devcontainer/docker-compose.yml file contains any overrides you need/want to make.
+	"dockerComposeFile": [
+		"../docker-compose.yml",
+		"docker-compose.yml"
+	],
+	// The 'service' property is the name of the service for the container that VS Code should
+	// use. Update this value and .devcontainer/docker-compose.yml to the real service name.
+	"service": "api",
+	// The optional 'workspaceFolder' property is the path VS Code should open by default when
+	// connected. This is typically a file mount in .devcontainer/docker-compose.yml
+	"workspaceFolder": "/workspace",
+	"workspaceMount": "source=remote-workspace,target=/workspace,type=volume",
+	// Set *default* container specific settings.json values on container create.
+	"settings": {
+		"terminal.integrated.shell.linux": null
+	},
+	// Add the IDs of extensions you want installed when the container is created.
+	"extensions": []
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+	// Uncomment the next line if you want start specific services in your Docker Compose config.
+	// "runServices": [],
+	// Uncomment the next line if you want to keep your containers running after VS Code shuts down.
+	// "shutdownAction": "none",
+	// Uncomment the next line to run commands after the container is created - for example installing curl.
+	// "postCreateCommand": "apt-get update && apt-get install -y curl",
+	// Uncomment to connect as a non-root user. See https://aka.ms/vscode-remote/containers/non-root.
+	// "remoteUser": "vscode"
+}

apps/iatlas/api-gitlab/.devcontainer/docker-compose.yml

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+#-------------------------------------------------------------------------------------------------------------
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
+#-------------------------------------------------------------------------------------------------------------
+
+version: '3.8'
+services:
+  # Update this to the name of the service you want to work with in your docker-compose.yml file
+  api:
+    # If you want add a non-root user to your Dockerfile, you can use the "remoteUser"
+    # property in devcontainer.json to cause VS Code its sub-processes (terminals, tasks, 
+    # debugging) to execute as the user. Uncomment the next line if you want the entire 
+    # container to run as this user instead. Note that, on Linux, you may need to 
+    # ensure the UID and GID of the container user you create matches your local user. 
+    # See https://aka.ms/vscode-remote/containers/non-root for details.
+    #
+    # user: vscode
+
+    # Uncomment if you want to override the service's Dockerfile to one in the .devcontainer 
+    # folder. Note that the path of the Dockerfile and context is relative to the *primary* 
+    # docker-compose.yml file (the first in the devcontainer.json "dockerComposeFile"
+    # array). The sample below assumes your primary file is in the root of your project.
+    #
+    # build:
+    #   context: .
+    #   dockerfile: .devcontainer/Dockerfile
+
+    volumes:
+      # Update this to wherever you want VS Code to mount the folder of your project
+      - .:/workspace:cached
+
+      # Uncomment the next line to use Docker from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker-compose for details.
+      # - /var/run/docker.sock:/var/run/docker.sock 
+
+    # Uncomment the next four lines if you will use a ptrace-based debugger like C++, Go, and Rust.
+    # cap_add:
+    #   - SYS_PTRACE
+    # security_opt:
+    #   - seccomp:unconfined
+
+    # Overrides default command so things don't shut down after the process ends.
+    command: /bin/sh -c "while sleep 1000; do :; done"
+

apps/iatlas/api-gitlab/.dockerignore

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+**/*.md
+Dockerfile
+.gitignore
+.git/

apps/iatlas/api-gitlab/.env-SAMPLE

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+FLASK_APP=iatlasapi.py
+FLASK_ENV=development
+FLASK_RUN_PORT=5000
+POSTGRES_DB=iatlas_dev
+POSTGRES_HOST=host.docker.internal
+POSTGRES_PORT=5432
+POSTGRES_PASSWORD=docker
+POSTGRES_USER=postgres
+PYTHON_IMAGE_VERSION=3.8.19-alpine3.20
+SNAKEVIZ_PORT=8020

apps/iatlas/api-gitlab/.env-none

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+# Please do not add anything to this file. it is intended to be empty.

apps/iatlas/api-gitlab/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+bin/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+include/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# cProfile
+.profiles/*
+
+# API and request logs
+.logs/*
+
+# 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/
+coverage/
+
+# Translations
+*.mo
+*.pot
+
+# 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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Environments
+.env
+.env-*
+!.env-SAMPLE
+!.env-none
+.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/
+
+# VScode settings
+.vscode/*
+!.vscode/co-authored-by.code-snippets
+!.vscode/extensions.json
+!.vscode/cspell.json
+!.vscode/settings.json
+*.code-workspace
+!iatlas-api.code-workspace
+
+# OS
+.DS_Store