Add augur api start and augur collection start commands

augur/application/cli/_cli_util.py

@@ -0,0 +1,69 @@
+import resource
+import os
+import subprocess
+import psutil
+import signal
+from urllib.parse import urlparse
+
+from augur.tasks.init.redis_connection import redis_connection 
+
+def clear_redis_caches(logger):
+    """Clears the redis databases that celery and redis use."""
+
+    logger.info("Flushing all redis databases this instance was using")
+    celery_purge_command = "celery -A augur.tasks.init.celery_app.celery_app purge -f"
+    subprocess.call(celery_purge_command.split(" "))
+    redis_connection.flushdb()
+
+
+def clear_rabbitmq_messages(connection_string, queues, logger):
+    #virtual_host_string = connection_string.split("/")[-1]
+
+    logger.info("Clearing all messages from celery queue in rabbitmq")
+    from augur.tasks.init.celery_app import celery_app
+    celery_app.control.purge()
+
+    clear_message_queues(connection_string, queues)
+
+
+def clear_message_queues(connection_string, queues):
+    queues = ['celery','secondary','scheduling','facade']
+
+    virtual_host_string = connection_string.split("/")[-1]
+
+    #Parse username and password with urllib
+    parsed = urlparse(connection_string)
+
+    for q in queues:
+        curl_cmd = f"curl -i -u {parsed.username}:{parsed.password} -XDELETE http://localhost:15672/api/queues/{virtual_host_string}/{q}"
+        subprocess.call(curl_cmd.split(" "),stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+
+def _broadcast_signal_to_processes(processes, logger, broadcast_signal=signal.SIGTERM):
+
+    for process in processes:
+        if process.pid != os.getpid():
+            logger.info(f"Stopping process {process.pid}")
+            try:
+                process.send_signal(broadcast_signal)
+            except psutil.NoSuchProcess:
+                pass
+
+
+def raise_open_file_limit(num_files):
+    """
+    sets number of open files soft limit 
+    """
+    current_soft, current_hard = resource.getrlimit(resource.RLIMIT_NOFILE)
+
+    # if soft is already greater than the requested amount then don't change it
+    if current_soft > num_files:
+        return
+
+    # if the requested amount is greater than the hard limit then set the hard limit to the num_files value
+    if current_hard <= num_files:
+        current_hard = num_files
+
+    resource.setrlimit(resource.RLIMIT_NOFILE, (num_files, current_hard))
+
+    return

augur/application/cli/api.py

@@ -0,0 +1,157 @@
+#SPDX-License-Identifier: MIT
+"""
+Augur library commands for controlling the backend components
+"""
+import os
+import time
+import subprocess
+import click
+import logging
+import psutil
+import signal
+import uuid
+import traceback
+
+from augur.application.db.session import DatabaseSession
+from augur.application.logs import AugurLogger
+from augur.application.config import AugurConfig
+from augur.application.cli import test_connection, test_db_connection 
+from augur.application.cli._cli_util import _broadcast_signal_to_processes, raise_open_file_limit, clear_redis_caches, clear_rabbitmq_messages
+
+logger = AugurLogger("augur", reset_logfiles=True).get_logger()
+
+@click.group('api', short_help='Commands for controlling the backend API server')
+def cli():
+    pass
+
+@cli.command("start")
+@click.option("--development", is_flag=True, default=False, help="Enable development mode")
+@click.option('--port')
+@test_connection
+@test_db_connection
+def start(development, port):
+    """Start Augur's backend server."""
+
+    try:
+        if os.environ.get('AUGUR_DOCKER_DEPLOY') != "1":
+            raise_open_file_limit(100000)
+    except Exception as e: 
+        logger.error(
+                    ''.join(traceback.format_exception(None, e, e.__traceback__)))
+
+        logger.error("Failed to raise open file limit!")
+        raise e
+
+    if development:
+        os.environ["AUGUR_DEV"] = "1"
+        logger.info("Starting in development mode")
+
+    try:
+        gunicorn_location = os.getcwd() + "/augur/api/gunicorn_conf.py"
+    except FileNotFoundError:
+        logger.error("\n\nPlease run augur commands in the root directory\n\n")
+
+    with DatabaseSession(logger) as db_session:
+        config = AugurConfig(logger, db_session)
+        host = config.get_value("Server", "host")
+
+        if not port:
+            port = config.get_value("Server", "port")
+
+    gunicorn_command = f"gunicorn -c {gunicorn_location} -b {host}:{port} augur.api.server:app --log-file gunicorn.log"
+    server = subprocess.Popen(gunicorn_command.split(" "))
+
+    time.sleep(3)
+    logger.info('Gunicorn webserver started...')
+    logger.info(f'Augur is running at: {"http" if development else "https"}://{host}:{port}')
+
+    frontend_worker = f"celery -A augur.tasks.init.celery_app.celery_app worker -l info --concurrency=1 -n frontend:{uuid.uuid4().hex}@%h -Q frontend"
+    frontend_worker_process = subprocess.Popen(frontend_worker.split(" "))
+
+    try:
+        server.wait()
+    except KeyboardInterrupt:
+
+        if server:
+            logger.info("Shutting down server")
+            server.terminate()
+
+        logger.info("Shutting down frontend celery worker process")
+        if frontend_worker_process:
+            frontend_worker_process.terminate()
+
+@cli.command('stop')
+def stop():
+    """
+    Sends SIGTERM to all Augur api processes
+    """
+    logger = logging.getLogger("augur.cli")
+
+    augur_stop(signal.SIGTERM, logger)
+
+@cli.command('kill')
+def kill():
+    """
+    Sends SIGKILL to all Augur api processes
+    """
+    logger = logging.getLogger("augur.cli")
+    augur_stop(signal.SIGKILL, logger)
+
+@cli.command('processes')
+def processes():
+    """
+    Outputs the name/PID of all Augur api process"""
+    augur_processes = get_augur_api_processes()
+    for process in augur_processes:
+        logger.info(f"Found process {process.pid}")
+
+def augur_stop(signal, logger):
+    """
+    Stops augur with the given signal, 
+    and cleans up the api
+    """
+
+    augur_processes = get_augur_api_processes()
+
+    _broadcast_signal_to_processes(augur_processes, logger=logger, broadcast_signal=signal)
+
+    cleanup_after_api_halt(logger)
+
+
+def cleanup_after_api_halt(logger):
+
+    connection_string = ""
+    queues = ['frontend','celery']
+    with DatabaseSession(logger) as session:
+        config = AugurConfig(logger, session)
+        connection_string = config.get_section("RabbitMQ")['connection_string']
+
+    clear_rabbitmq_messages(connection_string, queues, logger)
+    clear_redis_caches(logger)
+
+def get_augur_api_processes():
+    augur_api_processes = []
+    for process in psutil.process_iter(['cmdline', 'name', 'environ']):
+        if process.info['cmdline'] is not None and process.info['environ'] is not None:
+            try:
+                if is_api_process(process):
+                    augur_api_processes.append(process)
+            except (KeyError, FileNotFoundError):
+                pass
+    return augur_api_processes
+
+def is_api_process(process):
+
+    command = ''.join(process.info['cmdline'][:]).lower()
+    if os.getenv('VIRTUAL_ENV') in process.info['environ']['VIRTUAL_ENV'] and 'python' in command:
+
+        if process.pid != os.getpid():
+
+            if ("augur.api.server:app" in command or 
+                "augurbackendapi" in command or 
+               ("augur.tasks.init.celery_app.celery_app" in command and "frontend" in command)):
+                return True
+
+    return False
+
+