resolve merge conflicts with develop branch

.github/workflows/test.yml

@@ -9,12 +9,21 @@ on:
  - v*
  workflow_dispatch:
 
+env:
+ AERIE_USERNAME: "${{secrets.AERIE_USERNAME}}"
+ AERIE_PASSWORD: "${{secrets.AERIE_PASSWORD}}"
+ HASURA_GRAPHQL_ADMIN_SECRET: "${{secrets.HASURA_GRAPHQL_ADMIN_SECRET}}"
+ HASURA_GRAPHQL_JWT_SECRET: "${{secrets.HASURA_GRAPHQL_JWT_SECRET}}"
+ POSTGRES_USER: "${{secrets.POSTGRES_USER}}"
+ POSTGRES_PASSWORD: "${{secrets.POSTGRES_PASSWORD}}"
+
 jobs:
  unit-test:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-20.04
+ environment: integration-test-workflow
  strategy:
  matrix:
- python-version: [ "3.9", "3.10", "3.11" ]
+ python-version: [ "3.6.15", "3.7", "3.8", "3.9", "3.10", "3.11" ]
  steps:
  - uses: actions/checkout@v3
  - name: Set up Python ${{ matrix.python-version }}
@@ -30,3 +39,45 @@ jobs:
  run: |
  cd tests
  pytest unit_tests
+ integration-test:
+ timeout-minutes: 10
+ runs-on: ubuntu-20.04
+ environment: integration-test-workflow
+ strategy:
+ matrix:
+ python-version: [ "3.6.15", "3.7", "3.8", "3.9", "3.10", "3.11" ]
+ steps:
+ - uses: actions/checkout@v3
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install pytest
+ pip install .
+ - name: Set up aerie instance
+ run: |
+ docker compose -f docker-compose-test.yml up -d
+ docker images
+ docker ps -a
+ - name: Sleep for 60 Seconds
+ run: sleep 60s
+ shell: bash
+ - name: Run integration tests
+ run: |
+ cd tests
+ pytest integration_tests
+ - name: Print service logs
+ if: always()
+ run: docker compose -f docker-compose-test.yml logs -t
+ - name: Stop services
+ if: always()
+ run: |
+ docker ps -a
+ docker compose -f docker-compose-test.yml down
+ docker ps -a
+ - name: Prune volumes
+ if: always()
+ run: docker volume prune --force

docker-compose-test.yml

@@ -0,0 +1,169 @@
+# Pulled from https://github.com/NASA-AMMOS/aerie-ui/blob/fa404631caee079275a8e86d529bb428f6243871/docker-compose-test.yml
+version: '3.7'
+services:
+ aerie_gateway:
+ container_name: aerie_gateway
+ depends_on: ['postgres']
+ environment:
+ AUTH_TYPE: none
+ GQL_API_URL: http://localhost:8080/v1/graphql
+ HASURA_GRAPHQL_JWT_SECRET: '${HASURA_GRAPHQL_JWT_SECRET}'
+ LOG_FILE: console
+ LOG_LEVEL: debug
+ NODE_TLS_REJECT_UNAUTHORIZED: '0'
+ PORT: 9000
+ POSTGRES_AERIE_MERLIN_DB: aerie_merlin
+ POSTGRES_AERIE_SCHEDULER_DB: aerie_scheduler
+ POSTGRES_HOST: postgres
+ POSTGRES_PASSWORD: '${AERIE_PASSWORD}'
+ POSTGRES_PORT: 5432
+ POSTGRES_USER: '${AERIE_USERNAME}'
+ image: 'ghcr.io/nasa-ammos/aerie-gateway:v1.6.2'
+ ports: ['9000:9000']
+ restart: always
+ volumes:
+ - aerie_file_store:/app/files
+ aerie_merlin:
+ container_name: aerie_merlin
+ depends_on: ['postgres']
+ environment:
+ MERLIN_DB: 'aerie_merlin'
+ MERLIN_DB_PASSWORD: '${AERIE_PASSWORD}'
+ MERLIN_DB_PORT: 5432
+ MERLIN_DB_SERVER: postgres
+ MERLIN_DB_USER: '${AERIE_USERNAME}'
+ MERLIN_LOCAL_STORE: /usr/src/app/merlin_file_store
+ MERLIN_PORT: 27183
+ MERLIN_USE_NEW_CONSTRAINT_PIPELINE: 'true'
+ JAVA_OPTS: >
+ -Dorg.slf4j.simpleLogger.defaultLogLevel=DEBUG
+ -Dorg.slf4j.simpleLogger.log.com.zaxxer.hikari=INFO
+ -Dorg.slf4j.simpleLogger.logFile=System.err
+ UNTRUE_PLAN_START: '2000-01-01T11:58:55.816Z'
+ image: 'ghcr.io/nasa-ammos/aerie-merlin:v1.6.2'
+ ports: ['27183:27183']
+ restart: always
+ volumes:
+ - aerie_file_store:/usr/src/app/merlin_file_store
+ aerie_merlin_worker:
+ container_name: aerie_merlin_worker
+ depends_on: ['postgres']
+ environment:
+ MERLIN_WORKER_DB: 'aerie_merlin'
+ MERLIN_WORKER_DB_PASSWORD: '${AERIE_PASSWORD}'
+ MERLIN_WORKER_DB_PORT: 5432
+ MERLIN_WORKER_DB_SERVER: postgres
+ MERLIN_WORKER_DB_USER: '${AERIE_USERNAME}'
+ MERLIN_WORKER_LOCAL_STORE: /usr/src/app/merlin_file_store
+ JAVA_OPTS: >
+ -Dorg.slf4j.simpleLogger.defaultLogLevel=DEBUG
+ -Dorg.slf4j.simpleLogger.log.com.zaxxer.hikari=INFO
+ -Dorg.slf4j.simpleLogger.logFile=System.err
+ UNTRUE_PLAN_START: '2000-01-01T11:58:55.816Z'
+ image: 'ghcr.io/nasa-ammos/aerie-merlin-worker:v1.6.2'
+ ports: ['27187:8080']
+ restart: always
+ volumes:
+ - aerie_file_store:/usr/src/app/merlin_file_store:ro
+ aerie_scheduler:
+ container_name: aerie_scheduler
+ depends_on: ['aerie_merlin', 'postgres']
+ environment:
+ HASURA_GRAPHQL_ADMIN_SECRET: '${HASURA_GRAPHQL_ADMIN_SECRET}'
+ MERLIN_GRAPHQL_URL: http://hasura:8080/v1/graphql
+ SCHEDULER_DB: 'aerie_scheduler'
+ SCHEDULER_DB_PASSWORD: '${AERIE_PASSWORD}'
+ SCHEDULER_DB_PORT: 5432
+ SCHEDULER_DB_SERVER: postgres
+ SCHEDULER_DB_USER: '${AERIE_USERNAME}'
+ SCHEDULER_PORT: 27185
+ JAVA_OPTS: >
+ -Dorg.slf4j.simpleLogger.defaultLogLevel=DEBUG
+ -Dorg.slf4j.simpleLogger.log.com.zaxxer.hikari=INFO
+ -Dorg.slf4j.simpleLogger.logFile=System.err
+ image: 'ghcr.io/nasa-ammos/aerie-scheduler:v1.6.2'
+ ports: ['27185:27185']
+ restart: always
+ volumes:
+ - aerie_file_store:/usr/src/app/merlin_file_store
+ aerie_scheduler_worker:
+ container_name: aerie_scheduler_worker
+ depends_on: ['postgres']
+ environment:
+ HASURA_GRAPHQL_ADMIN_SECRET: '${HASURA_GRAPHQL_ADMIN_SECRET}'
+ MERLIN_GRAPHQL_URL: http://hasura:8080/v1/graphql
+ MERLIN_LOCAL_STORE: /usr/src/app/merlin_file_store
+ SCHEDULER_OUTPUT_MODE: UpdateInputPlanWithNewActivities
+ SCHEDULER_RULES_JAR: /usr/src/app/merlin_file_store/scheduler_rules.jar
+ SCHEDULER_WORKER_DB: 'aerie_scheduler'
+ SCHEDULER_WORKER_DB_PASSWORD: '${AERIE_PASSWORD}'
+ SCHEDULER_WORKER_DB_PORT: 5432
+ SCHEDULER_WORKER_DB_SERVER: postgres
+ SCHEDULER_WORKER_DB_USER: '${AERIE_USERNAME}'
+ JAVA_OPTS: >
+ -Dorg.slf4j.simpleLogger.log.com.zaxxer.hikari=INFO
+ -Dorg.slf4j.simpleLogger.logFile=System.err
+ image: 'ghcr.io/nasa-ammos/aerie-scheduler-worker:v1.6.2'
+ ports: ['27189:8080']
+ restart: always
+ volumes:
+ - aerie_file_store:/usr/src/app/merlin_file_store:ro
+ aerie_sequencing:
+ container_name: aerie_sequencing
+ depends_on: ['postgres']
+ environment:
+ HASURA_GRAPHQL_ADMIN_SECRET: '${HASURA_GRAPHQL_ADMIN_SECRET}'
+ LOG_FILE: console
+ LOG_LEVEL: debug
+ MERLIN_GRAPHQL_URL: http://hasura:8080/v1/graphql
+ SEQUENCING_DB: aerie_sequencing
+ SEQUENCING_DB_PASSWORD: '${AERIE_PASSWORD}'
+ SEQUENCING_DB_PORT: 5432
+ SEQUENCING_DB_SERVER: postgres
+ SEQUENCING_DB_USER: '${AERIE_USERNAME}'
+ SEQUENCING_LOCAL_STORE: /usr/src/app/sequencing_file_store
+ SEQUENCING_SERVER_PORT: 27184
+ image: 'ghcr.io/nasa-ammos/aerie-sequencing:v1.6.2'
+ ports: ['27184:27184']
+ restart: always
+ volumes:
+ - aerie_file_store:/usr/src/app/sequencing_file_store
+ hasura:
+ container_name: aerie_hasura
+ depends_on: ['postgres']
+ environment:
+ AERIE_MERLIN_DATABASE_URL: 'postgres://${AERIE_USERNAME}:${AERIE_PASSWORD}@postgres:5432/aerie_merlin'
+ AERIE_MERLIN_URL: 'http://aerie_merlin:27183'
+ AERIE_SCHEDULER_DATABASE_URL: 'postgres://${AERIE_USERNAME}:${AERIE_PASSWORD}@postgres:5432/aerie_scheduler'
+ AERIE_SCHEDULER_URL: 'http://aerie_scheduler:27185'
+ AERIE_SEQUENCING_DATABASE_URL: 'postgres://${AERIE_USERNAME}:${AERIE_PASSWORD}@postgres:5432/aerie_sequencing'
+ AERIE_SEQUENCING_URL: 'http://aerie_sequencing:27184'
+ AERIE_UI_DATABASE_URL: 'postgres://${AERIE_USERNAME}:${AERIE_PASSWORD}@postgres:5432/aerie_ui'
+ HASURA_GRAPHQL_ADMIN_SECRET: '${HASURA_GRAPHQL_ADMIN_SECRET}'
+ HASURA_GRAPHQL_DEV_MODE: 'true'
+ HASURA_GRAPHQL_ENABLE_CONSOLE: 'true'
+ HASURA_GRAPHQL_ENABLED_LOG_TYPES: startup, http-log, webhook-log, websocket-log, query-log
+ HASURA_GRAPHQL_JWT_SECRET: '${HASURA_GRAPHQL_JWT_SECRET}'
+ HASURA_GRAPHQL_LOG_LEVEL: info
+ HASURA_GRAPHQL_METADATA_DATABASE_URL: 'postgres://${AERIE_USERNAME}:${AERIE_PASSWORD}@postgres:5432/aerie_hasura'
+ HASURA_GRAPHQL_METADATA_DIR: /hasura-metadata
+ image: 'ghcr.io/nasa-ammos/aerie-hasura:v1.6.2'
+ ports: ['8080:8080']
+ restart: always
+ postgres:
+ container_name: aerie_postgres
+ environment:
+ AERIE_PASSWORD: '${AERIE_PASSWORD}'
+ AERIE_USERNAME: '${AERIE_USERNAME}'
+ POSTGRES_DB: postgres
+ POSTGRES_PASSWORD: '${POSTGRES_PASSWORD}'
+ POSTGRES_USER: '${POSTGRES_USER}'
+ image: 'ghcr.io/nasa-ammos/aerie-postgres:v1.6.2'
+ ports: ['5432:5432']
+ restart: always
+ volumes:
+ - postgres_data:/var/lib/postgresql/data
+
+volumes:
+ aerie_file_store:
+ postgres_data:

pyproject.toml

@@ -18,14 +18,14 @@ packages = [
 Changelog = "https://github.com/NASA-AMMOS/aerie-cli/releases"
 
 [tool.poetry.dependencies]
-python = "^3.9"
+python = "^3.6.8"
 click = "^8.0.1"
 typer = "^0.4.0"
 arrow = "^1.2.2"
 requests = "^2.27.1"
 rich = "^12.6.0"
-dataclasses-json = "^0.5.6"
-pandas = "^1.5.1"
+attrs = "^22.2.0"
+pandas = "^1.1.5"
 appdirs = "^1.4.4"
 
 [tool.poetry.dev-dependencies]

src/aerie_cli/__main__.py

@@ -15,6 +15,7 @@
 from .persistent import NoActiveSessionError
 from aerie_cli.commands.command_context import CommandContext
 from aerie_cli.__version__ import __version__
+from aerie_cli.utils.configurations import find_configuration
 
 app = typer.Typer()
 app.add_typer(plans.app, name="plans")
@@ -31,6 +32,12 @@ def print_version(print_version: bool):
  typer.echo(__version__)
  raise typer.Exit()
 
+def set_alternate_configuration(configuration_identifier: str):
+ if configuration_identifier == None:
+ return
+ found_configuration = find_configuration(configuration_identifier)
+
+ CommandContext.alternate_configuration = found_configuration
 
 @app.callback()
 def app_callback(
@@ -45,6 +52,15 @@ def app_callback(
  default="",
  help="Hasura admin secret that will be put in the header of graphql requests.",
  ),
+ configuration=typer.Option(
+ None,
+ "--configuration",
+ "-c",
+ callback=set_alternate_configuration,
+ help="Set a configuration to use rather than the persistent configuration.\n\
+ Accepts either a configuration name or the path to a configuration json.\n\
+ Configuration names are prioritized over paths.",
+ ),
 ):
  setup_global_command_context(hasura_admin_secret)
 

src/aerie_cli/__version__.py

@@ -1,7 +1,7 @@
 import sys
 
-if sys.version_info < (3, 10):
- # compatibility for python <3.10
+if sys.version_info < (3, 8):
+ # compatibility for python <3.8
  import importlib_metadata
 else:
  from importlib import metadata as importlib_metadata