pybiolib 1.2.1056__py3-none-any.whl → 1.2.1074__py3-none-any.whl

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -11,10 +11,10 @@ import zipfile
 from copy import copy
 from datetime import datetime
 
-import docker  # type: ignore
-import docker.types  # type: ignore
-from docker.errors import APIError, ImageNotFound  # type: ignore
-from docker.models.containers import Container  # type: ignore
+import docker
+import docker.types
+from docker.errors import APIError, ImageNotFound
+from docker.models.containers import Container
 
 from biolib import utils
 from biolib._internal.runtime import RuntimeJobDataDict
@@ -40,7 +40,7 @@ class DockerExecutor:
         self._options: LocalExecutorOptions = options
         self._is_cleaning_up = False
 
-        self._absolute_image_uri = f"{utils.BIOLIB_SITE_HOSTNAME}/{self._options['module']['image_uri']}"
+        self._absolute_image_uri = f'{utils.BIOLIB_SITE_HOSTNAME}/{self._options["module"]["image_uri"]}'
         self._send_system_exception = options['send_system_exception']
         self._send_stdout_and_stderr = options['send_stdout_and_stderr']
         self._random_docker_id = compute_node_utils.random_string(15)
@@ -308,7 +308,8 @@ class DockerExecutor:
             job_uuid = self._options['job']['public_id']
             logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container...')
             module = self._options['module']
-            logger.debug(f"Initializing docker container with command: {module['command']}")
+            logger.debug(f'Initializing docker container with command: {module["command"]}')
+            docker_client = BiolibDockerClient.get_docker_client()
 
             docker_volume_mounts = [lfs.docker_mount for lfs in self._options['large_file_systems'].values()]
 
@@ -391,6 +392,9 @@ class DockerExecutor:
                 'mounts': docker_volume_mounts,
                 'network': internal_network.name,
                 'working_dir': module['working_directory'],
+                'networking_config': {
+                    internal_network.name: docker_client.api.create_endpoint_config(aliases=['main'])
+                },
             }
 
             if self._options['job'].get('arguments_override_command'):
@@ -429,7 +433,6 @@ class DockerExecutor:
             if docker_runtime is not None:
                 create_container_args['runtime'] = docker_runtime
 
-            docker_client = BiolibDockerClient.get_docker_client()
             logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container. Creating container...')
             self._docker_container = docker_client.containers.create(**create_container_args)
             logger_no_user_data.debug(f'Job "{job_uuid}" finished initializing Docker container.')

biolib/compute_node/job_worker/executors/docker_types.py

@@ -1,6 +1,6 @@
 import enum
 
-from biolib.typing_utils import TypedDict, Any
+from biolib.typing_utils import Any, TypedDict
 
 
 class Proxy(TypedDict):

biolib/compute_node/job_worker/executors/types.py

@@ -1,11 +1,11 @@
-from docker.models.networks import Network  # type: ignore
+from docker.models.networks import Network
 
+from biolib.biolib_api_client.app_types import Module
+from biolib.biolib_api_client.job_types import CloudJob, CreatedJobDict
 from biolib.compute_node.job_worker.large_file_system import LargeFileSystem
-from biolib.compute_node.webserver.webserver_types import ComputeNodeInfo
-from biolib.typing_utils import TypedDict, Callable, Optional, List, Dict
 from biolib.compute_node.remote_host_proxy import RemoteHostProxy
-from biolib.biolib_api_client.app_types import Module
-from biolib.biolib_api_client.job_types import CreatedJobDict, CloudJob
+from biolib.compute_node.webserver.webserver_types import ComputeNodeInfo
+from biolib.typing_utils import Callable, Dict, List, Optional, TypedDict
 
 
 class StatusUpdate(TypedDict):
@@ -43,6 +43,7 @@ class LocalExecutorOptions(TypedDict):
     send_system_exception: SendSystemExceptionType
     send_stdout_and_stderr: SendStdoutAndStderrType
 
+
 class MetadataToSaveOutput(TypedDict):
     arguments: List[str]
     startup_error_string: Optional[str]

biolib/compute_node/job_worker/job_worker.py

@@ -80,7 +80,6 @@ class JobWorker:
 
             self._remote_host_proxies: List[RemoteHostProxy] = []
             self._internal_network: Optional[Network] = None
-            self._public_network: Optional[Network] = None
             self._executors: List[DockerExecutor] = []
             self.is_cleaning_up: bool = False
 
@@ -217,8 +216,6 @@ class JobWorker:
         logger_no_user_data.debug('Cleaning up networks...')
         self._cleanup_network(self._internal_network)
         self._internal_network = None
-        self._cleanup_network(self._public_network)
-        self._public_network = None
         logger_no_user_data.debug('Cleaned up networks...')
 
     @staticmethod
@@ -291,20 +288,6 @@ class JobWorker:
             ) from exception
 
         if len(remote_hosts) > 0:
-            logger_no_user_data.debug(f'Job "{job_id}" creating networks for remote host proxies...')
-            try:
-                self._public_network = docker_client.networks.create(
-                    name=f'biolib-proxy-network-{job_id}',
-                    internal=False,
-                    driver='bridge',
-                )
-            except Exception as exception:
-                raise ComputeProcessException(
-                    exception,
-                    SystemExceptionCodes.FAILED_TO_CREATE_DOCKER_NETWORKS.value,
-                    self.send_system_exception,
-                    may_contain_user_data=False
-                ) from exception
             logger_no_user_data.debug(f'Job "{job_id}" starting proxies for remote hosts: {remote_hosts}')
             try:
                 hostname_to_ports: Dict[str, List[int]] = {}
@@ -323,11 +306,10 @@ class JobWorker:
 
                 for hostname, ports in hostname_to_ports.items():
                     remote_host_proxy = RemoteHostProxy(
-                        RemoteHost(hostname=hostname),
-                        self._public_network,
-                        self._internal_network,
-                        job_id,
-                        ports,
+                        remote_host=RemoteHost(hostname=hostname),
+                        internal_network=self._internal_network,
+                        job_id=job_id,
+                        ports=ports,
                     )
                     remote_host_proxy.start()
                     self._remote_host_proxies.append(remote_host_proxy)

biolib/compute_node/job_worker/large_file_system.py

@@ -56,17 +56,13 @@ class LargeFileSystem:
         self._path_on_disk_for_write: Optional[str] = None
         self._send_status_update: Callable[[StatusUpdate], None] = send_status_update
 
-    @property
-    def _is_initialized(self) -> bool:
-        return self._path_on_disk is not None
-
     @property
     def uuid(self) -> str:
         return self._lfs_mapping['uuid']
 
     @property
     def docker_mount(self) -> docker.types.Mount:
-        if not self._is_initialized:
+        if not self._path_on_disk:
             raise LargeFileSystemError('LargeFileSystem not initialized')
 
         return docker.types.Mount(
@@ -77,7 +73,7 @@ class LargeFileSystem:
         )
 
     def initialize(self) -> None:
-        if self._is_initialized:
+        if self._path_on_disk:
             logger_no_user_data.debug(f'LFS {self.uuid} is already initialized')
             return
 

biolib/compute_node/remote_host_proxy.py

@@ -1,14 +1,14 @@
 import base64
 import io
-import subprocess
 import tarfile
 import time
 from urllib.parse import urlparse
 
-from docker.errors import ImageNotFound  # type: ignore
-from docker.models.containers import Container  # type: ignore
-from docker.models.images import Image  # type: ignore
-from docker.models.networks import Network  # type: ignore
+from docker.errors import ImageNotFound
+from docker.models.containers import Container
+from docker.models.images import Image
+from docker.models.networks import Network
+from docker.types import EndpointConfig
 
 from biolib import utils
 from biolib.biolib_api_client import BiolibApiClient, RemoteHost
@@ -16,7 +16,8 @@ from biolib.biolib_docker_client import BiolibDockerClient
 from biolib.biolib_errors import BioLibError
 from biolib.biolib_logging import logger_no_user_data
 from biolib.compute_node.cloud_utils import CloudUtils
-from biolib.typing_utils import List, Optional
+from biolib.compute_node.utils import BIOLIB_PROXY_NETWORK_NAME
+from biolib.typing_utils import Dict, List, Optional, cast
 
 
 # Prepare for remote hosts with specified port
@@ -28,14 +29,12 @@ class RemoteHostProxy:
     def __init__(
         self,
         remote_host: RemoteHost,
-        public_network: Network,
         internal_network: Optional[Network],
         job_id: str,
         ports: List[int],
     ):
         self.is_app_caller_proxy = remote_host['hostname'] == 'AppCallerProxy'
         self._remote_host: RemoteHostExtended = RemoteHostExtended(hostname=remote_host['hostname'], ports=ports)
-        self._public_network: Network = public_network
         self._internal_network: Optional[Network] = internal_network
 
         if not job_id:
@@ -44,7 +43,6 @@ class RemoteHostProxy:
         self._name = f'biolib-remote-host-proxy-{job_id}-{self.hostname}'
         self._job_uuid = job_id
         self._container: Optional[Container] = None
-        self._enclave_traffic_forwarder_processes: List[subprocess.Popen] = []
         self._docker = BiolibDockerClient().get_docker_client()
 
     @property
@@ -70,6 +68,16 @@ class RemoteHostProxy:
 
         docker = BiolibDockerClient.get_docker_client()
 
+        networking_config: Optional[Dict[str, EndpointConfig]] = (
+            None
+            if not self.is_app_caller_proxy
+            else {
+                BIOLIB_PROXY_NETWORK_NAME: docker.api.create_endpoint_config(
+                    aliases=[f'biolib-app-caller-proxy-{self._job_uuid}']
+                )
+            }
+        )
+
         for index in range(3):
             logger_no_user_data.debug(f'Attempt {index} at creating RemoteHostProxy container "{self._name}"...')
             try:
@@ -77,16 +85,17 @@ class RemoteHostProxy:
                     detach=True,
                     image=self._get_biolib_remote_host_proxy_image(),
                     name=self._name,
-                    network=self._public_network.name,
+                    network=BIOLIB_PROXY_NETWORK_NAME,
+                    networking_config=networking_config,
                 )
                 break
-            except Exception as error:  # pylint: disable=broad-except
+            except Exception as error:
                 logger_no_user_data.exception(f'Failed to create container "{self._name}" hit error: {error}')
 
             logger_no_user_data.debug('Sleeping before re-trying container creation...')
             time.sleep(3)
 
-        if not self._container:
+        if not self._container or not self._container.id:
             raise BioLibError(f'Exceeded re-try limit for creating container {self._name}')
 
         self._write_nginx_config_to_container(
@@ -121,14 +130,11 @@ class RemoteHostProxy:
         if self._container:
             self._container.remove(force=True)
 
-        for process in self._enclave_traffic_forwarder_processes:
-            process.terminate()
-
     def _get_biolib_remote_host_proxy_image(self) -> Image:
         if utils.IS_RUNNING_IN_CLOUD:
             try:
                 logger_no_user_data.debug('Getting local Docker image for remote host proxy')
-                return self._docker.images.get('biolib-remote-host-proxy:latest')
+                return cast(Image, self._docker.images.get('biolib-remote-host-proxy:latest'))
             except ImageNotFound:
                 logger_no_user_data.debug(
                     'Local Docker image for remote host proxy not available. Falling back to public image...'
@@ -137,10 +143,10 @@ class RemoteHostProxy:
         public_image_uri = 'public.ecr.aws/h5y4b3l1/biolib-remote-host-proxy:latest'
         try:
             logger_no_user_data.debug('Getting public Docker image for remote host proxy')
-            return self._docker.images.get(public_image_uri)
+            return cast(Image, self._docker.images.get(public_image_uri))
         except ImageNotFound:
             logger_no_user_data.debug('Pulling public Docker image for remote host proxy')
-            return self._docker.images.pull(public_image_uri)
+            return cast(Image, self._docker.images.pull(public_image_uri))
 
     def _write_nginx_config_to_container(self, upstream_server_name: str, upstream_server_ports: List[int]) -> None:
         if not self._container:

biolib/compute_node/utils.py

@@ -4,6 +4,8 @@ from enum import Enum
 
 from biolib.biolib_logging import logger
 
+BIOLIB_PROXY_NETWORK_NAME = 'biolib-proxy-network'
+
 
 def get_package_type(package):
     package_type = int.from_bytes(package[1:2], 'big')

biolib/compute_node/webserver/webserver.py

@@ -1,19 +1,23 @@
 # pylint: disable=unsubscriptable-object
 
 import json
+import logging
 import os
-import time
 import tempfile
-import logging
-from flask import Flask, request, Response, jsonify
+import time
+
+from docker.models.networks import Network  # type: ignore
+from flask import Flask, Response, jsonify, request
 
 from biolib import utils
 from biolib.biolib_api_client import BiolibApiClient
 from biolib.biolib_binary_format import SavedJob
-from biolib.compute_node.webserver import webserver_utils
+from biolib.biolib_docker_client import BiolibDockerClient
+from biolib.biolib_logging import TRACE, logger, logger_no_user_data
 from biolib.compute_node.cloud_utils.cloud_utils import CloudUtils
+from biolib.compute_node.utils import BIOLIB_PROXY_NETWORK_NAME
+from biolib.compute_node.webserver import webserver_utils
 from biolib.compute_node.webserver.gunicorn_flask_application import GunicornFlaskApplication
-from biolib.biolib_logging import logger, TRACE
 from biolib.compute_node.webserver.webserver_utils import get_job_compute_state_or_404
 from biolib.typing_utils import Optional
 
@@ -102,15 +106,14 @@ def status(job_id):
     response_data['is_completed'] = compute_state['is_completed']
 
     if current_status['stdout_and_stderr_packages_b64']:
-        compute_state['streamed_logs_packages_b64'] = compute_state['streamed_logs_packages_b64'] + \
-                                                      current_status['stdout_and_stderr_packages_b64']
+        compute_state['streamed_logs_packages_b64'] = (
+            compute_state['streamed_logs_packages_b64'] + current_status['stdout_and_stderr_packages_b64']
+        )
 
         compute_state['status']['stdout_and_stderr_packages_b64'] = []
 
     if current_status['status_updates']:
-        compute_state['previous_status_updates'].extend(
-            current_status['status_updates']
-        )
+        compute_state['previous_status_updates'].extend(current_status['status_updates'])
         compute_state['status']['status_updates'] = []
 
     if return_full_logs:
@@ -132,21 +135,31 @@ def send_package_to_compute_process(job_id, package_bytes):
 
 
 def start_webserver(
-        host: str,
-        port: int,
-        tls_pem_certificate_path: Optional[str] = None,
-        tls_pem_key_path: Optional[str] = None,
+    host: str,
+    port: int,
+    tls_pem_certificate_path: Optional[str] = None,
+    tls_pem_key_path: Optional[str] = None,
 ) -> None:
     def worker_exit(server, worker):  # pylint: disable=unused-argument
-        active_compute_states = list(
-            webserver_utils.JOB_ID_TO_COMPUTE_STATE_DICT.values()) + webserver_utils.UNASSIGNED_COMPUTE_PROCESSES
+        active_compute_states = (
+            list(webserver_utils.JOB_ID_TO_COMPUTE_STATE_DICT.values()) + webserver_utils.UNASSIGNED_COMPUTE_PROCESSES
+        )
         logger.debug(f'Sending terminate signal to {len(active_compute_states)} compute processes')
         if active_compute_states:
             for compute_state in active_compute_states:
                 if compute_state['worker_thread']:
                     compute_state['worker_thread'].terminate()
             time.sleep(2)
-        return
+
+        if utils.IS_RUNNING_IN_CLOUD:
+            try:
+                logger_no_user_data.debug(f'Removing Docker network {BIOLIB_PROXY_NETWORK_NAME}')
+                docker_client = BiolibDockerClient.get_docker_client()
+                biolib_proxy_network: Network = docker_client.networks.get(BIOLIB_PROXY_NETWORK_NAME)
+                biolib_proxy_network.remove()
+                logger_no_user_data.debug(f'Successfully removed Docker network {BIOLIB_PROXY_NETWORK_NAME}')
+            except BaseException:
+                logger_no_user_data.exception(f'Failed to clean up network {BIOLIB_PROXY_NETWORK_NAME}')
 
     def post_fork(server, worker):  # pylint: disable=unused-argument
         logger.info('Started compute node')
@@ -157,8 +170,27 @@ def start_webserver(
             utils.IS_DEV = config['is_dev']
             BiolibApiClient.initialize(config['base_url'])
 
-            CloudUtils.initialize()
-            webserver_utils.start_auto_shutdown_timer()
+            biolib_proxy_network: Optional[Network] = None
+            try:
+                logger_no_user_data.debug(f'Creating Docker network {BIOLIB_PROXY_NETWORK_NAME}')
+                docker_client = BiolibDockerClient.get_docker_client()
+                biolib_proxy_network = docker_client.networks.create(
+                    name=BIOLIB_PROXY_NETWORK_NAME,
+                    internal=False,
+                    driver='bridge',
+                )
+                logger_no_user_data.debug(f'Successfully created Docker network {BIOLIB_PROXY_NETWORK_NAME}')
+            except BaseException:
+                logger_no_user_data.exception(f'Failed to create Docker network {BIOLIB_PROXY_NETWORK_NAME}')
+
+            if biolib_proxy_network:
+                CloudUtils.initialize()
+                webserver_utils.start_auto_shutdown_timer()
+            else:
+                logger_no_user_data.error(
+                    f'Docker network {BIOLIB_PROXY_NETWORK_NAME} was not created, shutting down...'
+                )
+                CloudUtils.deregister_and_shutdown()
 
     if logger.level == TRACE:
         gunicorn_log_level_name = 'DEBUG'

{pybiolib-1.2.1056.dist-info → pybiolib-1.2.1074.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.1056
+Version: 1.2.1074
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.1056.dist-info → pybiolib-1.2.1074.dist-info}/RECORD

@@ -114,25 +114,25 @@ biolib/compute_node/job_worker/cache_state.py,sha256=MwjSRzcJJ_4jybqvBL4xdgnDYSI
 biolib/compute_node/job_worker/cache_types.py,sha256=ajpLy8i09QeQS9dEqTn3T6NVNMY_YsHQkSD5nvIHccQ,818
 biolib/compute_node/job_worker/docker_image_cache.py,sha256=ansHIkJIq_EMW1nZNlW-RRLVVeKWTbzNICYaOHpKiRE,7460
 biolib/compute_node/job_worker/executors/__init__.py,sha256=bW6t1qi3PZTlHM4quaTLa8EI4ALTCk83cqcVJfJfJfE,145
-biolib/compute_node/job_worker/executors/docker_executor.py,sha256=FFN4dn3mV19u6imT8e4vjpfDIxX9d3bpq9x2JPVOAus,31811
-biolib/compute_node/job_worker/executors/docker_types.py,sha256=VhsU1DKtJjx_BbCkVmiPZPH4ROiL1ygW1Y_s1Kbpa2o,216
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=Rp9QAEwSetqk0GrntiIhch573VO0Z5jeBpOsB_xcrdA,31907
+biolib/compute_node/job_worker/executors/docker_types.py,sha256=Hh8SwQYBLdIMGWgITwD2fzoo_sbW2ESx1G8j9Zq2n30,216
 biolib/compute_node/job_worker/executors/tars/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/compute_node/job_worker/executors/types.py,sha256=wbjWZZ2f9FttjqUCCOeZmn7n3L3Hu-7-2PZJ3BVf_Ps,1626
+biolib/compute_node/job_worker/executors/types.py,sha256=dlp7p8KKkd19nC68o-RuAzRBhpdYFMWKg-__LFjvscs,1611
 biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py,sha256=_cvEiZbOwfkv6fYmfrvdi_FVviIEYr_dSClQcOQaUWM,1198
 biolib/compute_node/job_worker/job_max_runtime_timer_thread.py,sha256=K_xgz7IhiIjpLlXRk8sqaMyLoApcidJkgu29sJX0gb8,1174
 biolib/compute_node/job_worker/job_storage.py,sha256=J6B5wkBo3cqmT1AV-qJnm2Lt9Qmcp3qn-1AabjO9m60,4686
-biolib/compute_node/job_worker/job_worker.py,sha256=MpYRikixXBF6iZI0m5xW7vrJ-cdkpO_AQfElZaKoI_Q,29542
-biolib/compute_node/job_worker/large_file_system.py,sha256=XXqRlVtYhs-Ji9zQGIk5KQPXFO_Q5jJH0nnlw4GkeMY,10461
+biolib/compute_node/job_worker/job_worker.py,sha256=2f5WrIkR-9im3fNEDPnNFz4-YtxcF4Us9yob5HiASbY,28721
+biolib/compute_node/job_worker/large_file_system.py,sha256=Xe_LILVfTD9LXb-0HwLqGsp1fWiI-pU55BqgJ-6t8-0,10357
 biolib/compute_node/job_worker/mappings.py,sha256=Z48Kg4nbcOvsT2-9o3RRikBkqflgO4XeaWxTGz-CNvI,2499
 biolib/compute_node/job_worker/utilization_reporter_thread.py,sha256=7tm5Yk9coqJ9VbEdnO86tSXI0iM0omwIyKENxdxiVXk,8575
 biolib/compute_node/job_worker/utils.py,sha256=wgxcIA8yAhUPdCwyvuuJ0JmreyWmmUoBO33vWtG60xg,1282
-biolib/compute_node/remote_host_proxy.py,sha256=IBkBeljiFEos2KZJbYf_k45xjeKqpUmRronY6MlPwo0,17078
+biolib/compute_node/remote_host_proxy.py,sha256=xyjq0zKSxbJGUA6a0q9JCnzquk7gIztbI1clLGnymQM,17278
 biolib/compute_node/socker_listener_thread.py,sha256=T5_UikA3MB9bD5W_dckYLPTgixh72vKUlgbBvj9dbM0,1601
 biolib/compute_node/socket_sender_thread.py,sha256=YgamPHeUm2GjMFGx8qk-99WlZhEs-kAb3q_2O6qByig,971
-biolib/compute_node/utils.py,sha256=fWtFIcGatek1NaVOT9Vaey6UFp8GKLYGLAVu8jgOwi8,4861
+biolib/compute_node/utils.py,sha256=fvdbetPKMdfHkPqNZRw6eln_i13myu-n8tuceTUcfPU,4913
 biolib/compute_node/webserver/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/compute_node/webserver/gunicorn_flask_application.py,sha256=jPfR_YvNBekLUXWo_vHFV-FIwlb8s8tacKmGHvh93qc,914
-biolib/compute_node/webserver/webserver.py,sha256=o4kOAStsqThUtKlnRE-U5TP0JIYntuySDjU7PH310xg,6620
+biolib/compute_node/webserver/webserver.py,sha256=Ec5ZgOUBb_1pINjHrlENMUpLdAPiBiTyiaP51-FZ4gQ,8362
 biolib/compute_node/webserver/webserver_types.py,sha256=2t8EaFKESnves3BA_NBdnS2yAdo1qwamCFHiSt888nE,380
 biolib/compute_node/webserver/webserver_utils.py,sha256=XWvwYPbWNR3qS0FYbLLp-MDDfVk0QdaAmg3xPrT0H2s,4234
 biolib/compute_node/webserver/worker_thread.py,sha256=7uD9yQPhePYvP2HCJ27EeZ_h6psfIWFgqm1RHZxzobs,12483
@@ -155,8 +155,8 @@ biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=Ozk0blGtPur_D9MwShD02r_mphyQmgZkx-lOHOwnlIM,6730
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
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