fix: Fix dependencies and the login #673

Workflow file for this run

	name: EpiGraphHub

	on:
	push:
	branches: [ main ]
	pull_request:
	branches: [ main ]

	env:
	_AIRFLOW_DB_UPGRADE: true
	_AIRFLOW_WWW_USER_CREATE: true
	_AIRFLOW_WWW_USER_EMAIL: [email protected]
	_AIRFLOW_WWW_USER_FIRST_NAME: Super
	_AIRFLOW_WWW_USER_LAST_NAME: Admin
	_AIRFLOW_WWW_USER_PASSWORD: airflow
	_AIRFLOW_WWW_USER_USERNAME: airflow
	AIRFLOW_FILES_PATH_DIR_HOST: /home/runner/work/EpiGraphHub/EpiGraphHub/containers/airflow
	AIRFLOW_HOME: /opt/airflow
	AIRFLOW_PORT: 8099
	AIRFLOW__API__AUTH_BACKENDS: airflow.api.auth.backend.basic_auth
	AIRFLOW__CORE__DAGS_ARE_PAUSED_AT_CREATION: true
	AIRFLOW__CORE__FERNET_KEY: rhZaG4rip4DrA4Z93rI9uqWVK2/8Tk+zSixmEe3ZZo8=
	AIRFLOW__DATABASE__SQL_ALCHEMY_CONN: postgresql+psycopg2://dev_airflow_user:airflow_password@postgres:25432/dev_airflow
	AIRFLOW__WEBSERVER__SECRET_KEY: 79197e3bef40d1d2a6cf07cb1f4c9f54e82a3bcfc6b92ed06d081856eee2
	AWS_ACCESS_KEY_ID: minio-user
	AWS_SECRET_ACCESS_KEY: minio-password
	AWS_DEFAULT_REGION: us-east-1
	ENV: dev
	FLOWER_PORT: 28888
	FLOWER_PASSWORD: flowerpass
	MINIO_ROOT_USER: minio-user
	MINIO_ROOT_PASSWORD: minio-password
	MINIO_PORT_1: 9000
	MINIO_PORT_2: 9090
	POSTGRES_HOST_UID: 1001
	POSTGRES_HOST_GID: 121
	POSTGRES_HOST: postgres
	POSTGRES_PORT: 25432
	POSTGRES_USER: postgres
	POSTGRES_PASSWORD: postgres
	POSTGRES_DB: postgres
	POSTGRES_EPIGRAPH_HOST: postgres
	POSTGRES_EPIGRAPH_PORT: 25432
	POSTGRES_EPIGRAPH_USER: dev_epigraph
	POSTGRES_EPIGRAPH_PASSWORD: dev_epigraph
	POSTGRES_EPIGRAPH_DB: dev_epigraphhub
	POSTGRES_EPIGRAPH_DB_PRIVATE: dev_privatehub
	POSTGRES_EPIGRAPH_DB_SANDBOX: dev_sandbox
	REDIS_HOST: redis
	REDIS_PORT: 6379
	REDIS_PASSWORD: redispass
	SUPERSET_PORT: 8088
	SUPERSET_DB_PATH_DIR_HOST: /tmp/superset
	SUPERSET_DB_PATH_HOST: /tmp/superset/superset.db
	SUPERSET_HOME: /opt/data/superset
	SUPERSET_MAIL_DEFAULT_SENDER:
	SUPERSET_MAIL_PASSWORD:
	SUPERSET_MAIL_PORT: 587
	SUPERSET_MAIL_SERVER:
	SUPERSET_MAIL_USERNAME:
	SUPERSET_MAIL_USE_TLS: true
	SUPERSET_SECRET_KEY: superset-on-ci
	POSTGRES_DATA_DIR_HOST: /home/runner/work/psql_data
	POSTGRES_CONFIG_FILE_HOST: /home/runner/work/EpiGraphHub/EpiGraphHub/containers/postgresql/sql/dev/postgresql.conf
	SUPERSET_DB_USER: postgres
	SUPERSET_DB_PASSWORD: postgres
	SUPERSET_DB_DATABASE: postgres

	jobs:
	check-branch:
	runs-on: ubuntu-latest

	timeout-minutes: 2
	concurrency:
	group: ci-check-branch-${{ github.ref }}
	cancel-in-progress: true

	steps:
	- uses: actions/checkout@v4
	if: ${{ github.event_name == 'pull_request' }}
	with:
	fetch-depth: 0

	- name: Check if the PR's branch is updated
	if: ${{ github.event_name == 'pull_request' }}
	uses: osl-incubator/[email protected]
	with:
	remote_branch: origin/main
	pr_sha: ${{ github.event.pull_request.head.sha }}

	main:
	runs-on: ubuntu-latest
	timeout-minutes: 55
	defaults:
	run:
	shell: bash -l {0}
	concurrency:
	group: ci-${{ github.ref }}
	cancel-in-progress: true

	steps:
	- uses: actions/checkout@v4

	- name: Create environment variables file
	run: \|
	export HOST_UID=$(id -u)
	export HOST_GID=$(id -g)
	export POSTGRES_HOST_UID=$(id -u)
	export POSTGRES_HOST_GID=$(id -g)
	envsubst < .env.tpl > .env
	mkdir /home/runner/work/psql_data

	- uses: conda-incubator/setup-miniconda@v3
	with:
	miniconda-version: "latest"
	environment-file: conda/base.yaml
	channels: conda-forge,r,nodefaults
	activate-environment: epigraphhub
	auto-update-conda: true
	conda-solver: libmamba

	- name: setup
	run: makim host.prepare

	- name: configure epigraphhub credentials
	run: \|
	epigraphhub-config --name ci-epigraphhub \
	--db-uri "${POSTGRES_EPIGRAPH_USER}:${POSTGRES_EPIGRAPH_PASSWORD}@${POSTGRES_HOST}:${POSTGRES_PORT}/${POSTGRES_EPIGRAPH_DB}"

	- name: configure aws s3 credentials to minio
	run: makim aws.create-s3-credential

	- name: build docker containers
	run: sugar build

	- name: start services
	run: \|
	sugar ext restart --services superset,airflow,postgres --options -d

	- name: wait for the services are properly working
	run: \|
	sugar ps
	makim containers.wait-all

	- name: run epigraphhub tests
	run: \|
	wget https://edgedl.me.gvt1.com/edgedl/chrome/chrome-for-testing/116.0.5845.96/linux64/chromedriver-linux64.zip -O /tmp/chromedriver-linux64.zip
	unzip /tmp/chromedriver-linux64.zip -d /tmp
	sudo rm /usr/bin/chromedriver
	sudo mv /tmp/chromedriver-linux64/chromedriver /usr/bin
	python -m unittest /home/runner/work/EpiGraphHub/EpiGraphHub/tests/*

	# TODO: Fix containers/postgres/sql/dev/02-epigraphhub.sql script
	# - name: Trigger all DAGs
	# run: \|
	# make containers-exec ARGS="-T" SERVICE=airflow CMD='airflow dags test owid 2022-10-25'
	# make containers-exec ARGS="-T" SERVICE=airflow CMD='airflow dags test foph 2022-10-25'
	# make containers-exec ARGS="-T" SERVICE=airflow CMD='airflow dags test colombia 2022-10-25'
	# make containers-exec ARGS="-T" SERVICE=airflow CMD='airflow dags test web_status_test 2022-10-25'

	- name: Test MinIO access
	run: aws --endpoint-url http://localhost:9000/ s3 ls

	- name: Generate logs
	if: ${{ failure() }}
	run: \|
	sugar logs --options --tail 1000 > /tmp/containers-services.log

	- name: Archive log artifacts
	uses: actions/upload-artifact@v3
	if: ${{ failure() }}
	with:
	name: containers-services
	path: /tmp/containers-services.log

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fix: Fix dependencies and the login #673

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fix: Fix dependencies and the login #673

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