173 lines
6.3 KiB
Python
173 lines
6.3 KiB
Python
import logging.config
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import os
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import traceback
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import click
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import sentry_sdk
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import connexion
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from connexion import ProblemException
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from flask import Response
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from flask_cors import CORS
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from flask_marshmallow import Marshmallow
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from flask_mail import Mail
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from flask_migrate import Migrate
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from flask_sqlalchemy import SQLAlchemy
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from sentry_sdk.integrations.flask import FlaskIntegration
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from apscheduler.schedulers.background import BackgroundScheduler
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from werkzeug.middleware.proxy_fix import ProxyFix
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connexion_app = connexion.FlaskApp(__name__)
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app = connexion_app.app
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app.wsgi_app = ProxyFix(app.wsgi_app, x_proto=1) # respect the X-Forwarded-Proto if behind a proxy.
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app.config.from_object('config.default')
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if "TESTING" in os.environ and os.environ["TESTING"] == "true":
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app.config.from_pyfile('../config/testing.py')
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import logging
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logging.basicConfig(level=logging.INFO)
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else:
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app.config.root_path = app.instance_path
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app.config.from_pyfile('config.py', silent=True)
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from config.logging import logging_config
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logging.config.dictConfig(logging_config)
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db = SQLAlchemy(app)
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""":type: sqlalchemy.orm.SQLAlchemy"""
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session = db.session
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""":type: sqlalchemy.orm.Session"""
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scheduler = BackgroundScheduler()
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# Mail settings
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mail = Mail(app)
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migrate = Migrate(app, db)
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ma = Marshmallow(app)
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from crc import models
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from crc import api
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from crc.api import admin
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from crc.services.workflow_service import WorkflowService
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connexion_app.add_api('api.yml', base_path='/v1.0')
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# needed function to avoid circular import
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def process_waiting_tasks():
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with app.app_context():
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WorkflowService.do_waiting()
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@app.before_first_request
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def init_scheduler():
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if app.config['PROCESS_WAITING_TASKS']:
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scheduler.add_job(process_waiting_tasks, 'interval', minutes=1)
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scheduler.add_job(WorkflowService().process_erroring_workflows, 'interval', minutes=1440)
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scheduler.start()
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# Convert list of allowed origins to list of regexes
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origins_re = [r"^https?:\/\/%s(.*)" % o.replace('.', '\.') for o in app.config['CORS_ALLOW_ORIGINS']]
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cors = CORS(connexion_app.app, origins=origins_re)
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# Sentry error handling
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if app.config['SENTRY_ENVIRONMENT']:
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sentry_sdk.init(
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environment=app.config['SENTRY_ENVIRONMENT'],
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dsn="https://25342ca4e2d443c6a5c49707d68e9f40@o401361.ingest.sentry.io/5260915",
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integrations=[FlaskIntegration()]
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)
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# Connexion Error handling
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def render_errors(exception):
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from crc.api.common import ApiError, ApiErrorSchema
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error = ApiError(code=exception.title, message=exception.detail, status_code=exception.status)
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return Response(ApiErrorSchema().dumps(error), status=500, mimetype="text/json")
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connexion_app.add_error_handler(ProblemException, render_errors)
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print('=== USING THESE CONFIG SETTINGS: ===')
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print('APPLICATION_ROOT = ', app.config['APPLICATION_ROOT'])
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print('CORS_ALLOW_ORIGINS = ', app.config['CORS_ALLOW_ORIGINS'])
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print('DB_HOST = ', app.config['DB_HOST'])
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print('LDAP_URL = ', app.config['LDAP_URL'])
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print('PB_BASE_URL = ', app.config['PB_BASE_URL'])
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print('PB_ENABLED = ', app.config['PB_ENABLED'])
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print('PRODUCTION = ', app.config['PRODUCTION'])
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print('TESTING = ', app.config['TESTING'])
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print('TEST_UID = ', app.config['TEST_UID'])
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print('ADMIN_UIDS = ', app.config['ADMIN_UIDS'])
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@app.cli.command()
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def clear_db():
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"""Load example data into the database."""
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from example_data import ExampleDataLoader
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ExampleDataLoader.clean_db()
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@app.cli.command()
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@click.argument("study_id")
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@click.argument("category", required=False)
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@click.argument("spec_id", required=False)
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def validate_all(study_id, category=None, spec_id=None):
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"""Step through all the local workflows and validate them, returning any errors. This make take forever.
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Please provide a real study id to use for validation, an optional category can be specified to only validate
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that category, and you can further specify a specific spec, if needed."""
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from crc.services.workflow_service import WorkflowService
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from crc.services.workflow_processor import WorkflowProcessor
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from crc.services.workflow_spec_service import WorkflowSpecService
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from crc.api.common import ApiError
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from crc.models.study import StudyModel
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from crc.models.user import UserModel
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from flask import g
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logging.root.removeHandler(logging.root.handlers[0])
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study = session.query(StudyModel).filter(StudyModel.id == study_id).first()
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g.user = session.query(UserModel).filter(UserModel.uid == study.user_uid).first()
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g.token = "anything_is_fine_just_need_something."
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specs = WorkflowSpecService().get_specs()
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statuses = WorkflowProcessor.run_master_spec(WorkflowSpecService().master_spec, study)
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for spec in specs:
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if spec_id and spec_id != spec.id:
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continue
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if category and (not spec.category or spec.category.display_name != category):
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continue
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print("-----------------------------------------")
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print(f"{spec.category.display_name} / {spec.id}")
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print("-----------------------------------------")
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if spec.id in statuses and statuses[spec.id]['status'] == 'disabled':
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print(f"Skipping {spec.id} in category {spec.category.display_name}, it is disabled for this study.")
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continue
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try:
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WorkflowService.test_spec(spec.id, validate_study_id=study_id)
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print('Success!')
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except ApiError as e:
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if e.code == 'disabled_workflow':
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print(f"Skipping {spec.id} in category {spec.category.display_name}, it is disabled for this study.")
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else:
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print(f"API Error {e.code}, validate workflow {spec.id} in Category {spec.category.display_name}. {e.message}")
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for t in e.task_trace:
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print(f"---> {t}")
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continue
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except WorkflowTaskExecException as e:
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print(f"Workflow Error, {e}, in Task {e.task.name} validate workflow {spec.id} in Category {spec.category.display_name}")
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for t in e.task_trace:
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print(f"---> {t}")
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continue
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except Exception as e:
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print(f"Unexpected Error ({e.__class__.__name__}), {e} validate workflow {spec.id} in Category {spec.category.display_name}")
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# printing stack trace
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traceback.print_exc()
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print(e)
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return |