pybiolib 1.2.1121__tar.gz → 1.2.1133__tar.gz

{pybiolib-1.2.1121 → pybiolib-1.2.1133}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.1121
+Version: 1.2.1133
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.1121 → pybiolib-1.2.1133}/biolib/compute_node/webserver/compute_node_results_proxy.py

@@ -1,32 +1,67 @@
 import io
+import os
 import tarfile
+import threading
 import time
 
 from docker.models.containers import Container
 
 from biolib.biolib_docker_client import BiolibDockerClient
 from biolib.biolib_errors import BioLibError
-from biolib.biolib_logging import logger_no_user_data
+from biolib.biolib_logging import logger, logger_no_user_data
 from biolib.compute_node.utils import BIOLIB_PROXY_NETWORK_NAME
-from biolib.typing_utils import Optional
 from biolib.compute_node.webserver.proxy_utils import get_biolib_nginx_proxy_image
+from biolib.typing_utils import Optional
+
+
+class LogStreamingThread(threading.Thread):
+    def __init__(self, container, container_name: str):
+        super().__init__(daemon=True)
+        self._container = container
+        self._container_name = container_name
+        self._stop_event = threading.Event()
+
+    def run(self) -> None:
+        try:
+            logger_no_user_data.debug(f'Starting log streaming for container "{self._container_name}"')
+            log_stream = self._container.logs(follow=True, stream=True)
+            for log_line in log_stream:
+                if self._stop_event.is_set():
+                    break
+                if log_line:
+                    logger.debug(f'ComputeNodeResultsProxy | {log_line.decode("utf-8", errors="replace").rstrip()}')
+        except Exception as error:
+            logger_no_user_data.debug(f'Log streaming for container "{self._container_name}" ended: {error}')
+
+    def stop(self) -> None:
+        self._stop_event.set()
+
 
 class ComputeNodeResultsProxy:
     _instance: Optional['ComputeNodeResultsProxy'] = None
 
     def __init__(self, tls_pem_certificate_path: str, tls_pem_key_path: str):
-        assert tls_pem_certificate_path, "tls_pem_certificate_path is required"
-        assert tls_pem_key_path, "tls_pem_key_path is required"
+        assert tls_pem_certificate_path, 'tls_pem_certificate_path is required'
+        assert tls_pem_key_path, 'tls_pem_key_path is required'
         self._name = 'biolib-compute-node-results-proxy'
         self._container: Optional[Container] = None
         self._docker = BiolibDockerClient().get_docker_client()
         self._tls_pem_certificate_path = tls_pem_certificate_path
         self._tls_pem_key_path = tls_pem_key_path
+        self._log_streaming_thread: Optional[LogStreamingThread] = None
 
     @staticmethod
     def start_proxy(tls_pem_certificate_path: str, tls_pem_key_path: str) -> None:
+        abs_cert_path = os.path.abspath(tls_pem_certificate_path)
+        abs_key_path = os.path.abspath(tls_pem_key_path)
+        assert os.path.exists(abs_cert_path), f'TLS certificate file does not exist: {abs_cert_path}'
+        assert os.path.exists(abs_key_path), f'TLS key file does not exist: {abs_key_path}'
+
         if ComputeNodeResultsProxy._instance is None:
-            ComputeNodeResultsProxy._instance = ComputeNodeResultsProxy(tls_pem_certificate_path, tls_pem_key_path)
+            logger_no_user_data.debug(
+                f'Creating ComputeNodeResultsProxy instance with cert: {abs_cert_path}, key: {abs_key_path}'
+            )
+            ComputeNodeResultsProxy._instance = ComputeNodeResultsProxy(abs_cert_path, abs_key_path)
             ComputeNodeResultsProxy._instance._start()  # pylint: disable=protected-access
 
     @staticmethod
@@ -67,6 +102,7 @@ class ComputeNodeResultsProxy:
         self._write_nginx_config_to_container()
         self._container.start()
 
+        logger_no_user_data.debug(f'Waiting for container "{self._name}" to be ready...')
         proxy_is_ready = False
         for retry_count in range(1, 5):
             time.sleep(0.5 * retry_count)
@@ -76,15 +112,27 @@ class ComputeNodeResultsProxy:
                 break
 
         if not proxy_is_ready:
+            logger_no_user_data.error('ComputeNodeResultsProxy did not start properly.')
             self._terminate()
             raise Exception('ComputeNodeResultsProxy did not start properly')
 
         self._container.reload()
+        logger.debug(f'ComputeNodeResultsProxy container "{self._name}" started with ID: {self._container.id}')
+
+        self._log_streaming_thread = LogStreamingThread(self._container, self._name)
+        self._log_streaming_thread.start()
+        logger_no_user_data.debug(f'Started log streaming for container "{self._name}"')
 
     def _terminate(self):
-        if self._container:
-            self._container.remove(force=True)
+        logger_no_user_data.debug(f'Terminating ComputeNodeResultsProxy container "{self._name}"')
+        if self._log_streaming_thread:
+            self._log_streaming_thread.stop()
+            self._log_streaming_thread = None
 
+        logger.debug(f'Docker container removal temporarily disabled for debugging purposes (container "{self._name}")')
+        # TODO: Figure if we need to remove the container or keep it for debugging purposes
+        # if self._container:
+        #     self._container.remove(force=True)
 
     def _write_nginx_config_to_container(self) -> None:
         if not self._container:
@@ -137,4 +185,5 @@ http {
 
         tarfile_bytes = tarfile_in_memory.getvalue()
         tarfile_in_memory.close()
+        logger_no_user_data.debug('Writing NGINX configuration to ComputeNodeResultsProxy container')
         docker.api.put_archive(self._container.id, '/etc/nginx', tarfile_bytes)

{pybiolib-1.2.1121 → pybiolib-1.2.1133}/biolib/compute_node/webserver/webserver.py

@@ -154,7 +154,7 @@ def start_webserver(
 
         if utils.IS_RUNNING_IN_CLOUD:
             try:
-                logger_no_user_data.debug('Stopping ComputeNodeResultsProxy')
+                logger_no_user_data.debug('Stopping ComputeNodeResultsProxy...')
                 ComputeNodeResultsProxy.stop_proxy()
             except BaseException:
                 logger_no_user_data.exception('Failed to stop ComputeNodeResultsProxy')
@@ -192,7 +192,7 @@ def start_webserver(
 
             if biolib_proxy_network:
                 try:
-                    logger_no_user_data.debug('Starting ComputeNodeResultsProxy')
+                    logger_no_user_data.debug('Starting ComputeNodeResultsProxy...')
                     ComputeNodeResultsProxy.start_proxy(tls_pem_certificate_path, tls_pem_key_path)
                 except BaseException:
                     logger_no_user_data.exception('Failed to start ComputeNodeResultsProxy')

{pybiolib-1.2.1121 → pybiolib-1.2.1133}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.1121"
+version = "1.2.1133"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"