pybiolib 1.2.223__tar.gz → 1.2.243__tar.gz

{pybiolib-1.2.223 → pybiolib-1.2.243}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.2.223
+Version: 1.2.243
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.2.223 → pybiolib-1.2.243}/biolib/_runtime/runtime.py

@@ -48,6 +48,17 @@ class Runtime:
         except BaseException as error:
             raise BioLibRuntimeError(f'Unable to get system secret: {secret_name}') from error
 
+    @staticmethod
+    def get_temporary_client_secret(secret_name: str) -> bytes:
+        assert re.match(
+            '^[a-zA-Z0-9_-]*$', secret_name
+        ), 'Secret name can only contain alphanumeric characters and dashes or underscores '
+        try:
+            with open(f'/biolib/temporary-client-secrets/{secret_name}', 'rb') as file:
+                return file.read()
+        except BaseException as error:
+            raise BioLibRuntimeError(f'Unable to get secret: {secret_name}') from error
+
     @staticmethod
     def set_main_result_prefix(result_prefix: str) -> None:
         job_data = Runtime._get_job_data()

{pybiolib-1.2.223 → pybiolib-1.2.243}/biolib/biolib_api_client/biolib_app_api.py

@@ -3,6 +3,7 @@ import os
 import random
 import re
 import subprocess
+import urllib.parse
 
 import biolib.api
 from biolib import biolib_errors
@@ -10,6 +11,7 @@ from biolib._internal.http_client import HttpError
 from biolib.biolib_api_client import AppGetResponse
 from biolib.biolib_logging import logger
 from biolib.typing_utils import Optional
+from biolib.utils import load_base_url_from_env
 
 
 def encode_multipart(data, files):
@@ -61,15 +63,29 @@ def _get_git_repository_url() -> str:
     except BaseException:
         return ''
 
+def _get_app_uri_from_str(input_str: str) -> str:
+    parsed_base_url = urllib.parse.urlparse(load_base_url_from_env())
+    parsed_uri = urllib.parse.urlparse(input_str)
+    if parsed_uri.netloc != '' and parsed_base_url.netloc != parsed_uri.netloc:
+        raise biolib_errors.ValidationError(
+            f'Invalid URI. The hostname "{parsed_base_url.netloc}" is not recognized.'
+        )
+    elif parsed_uri.netloc != '' and parsed_uri.path[1] != '@':
+        uri = f'@{parsed_uri.netloc}{parsed_uri.path}'
+    elif parsed_uri.netloc == '' and parsed_uri.path.startswith (parsed_base_url.netloc):
+        uri = f'@{parsed_uri.path}'
+    else:
+        uri = parsed_uri.path
+    uri = uri.strip('/')
+    # Replace frontend version path with app_uri compatible version (if supplied)
+    uri = re.sub(r'/version/(?P<version>(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*))(/)?$', r':\g<version>', uri)
+    return uri
+
 
 class BiolibAppApi:
     @staticmethod
     def get_by_uri(uri: str) -> AppGetResponse:
-        # Replace protocol with @ (if supplied)
-        uri = re.sub(r'^http(s)?://', '@', uri)
-        # Replace frontend version path with app_uri compatible version (if supplied)
-        uri = re.sub(r'/version/(?P<version>(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*))(/)?$', r':\g<version>', uri)
-
+        uri = _get_app_uri_from_str(uri)
         try:
             response = biolib.api.client.get(path='/app/', params={'uri': uri})
             app_response: AppGetResponse = response.json()

{pybiolib-1.2.223 → pybiolib-1.2.243}/biolib/biolib_api_client/job_types.py

@@ -2,7 +2,7 @@ from enum import Enum
 
 from biolib.biolib_api_client.app_types import AppVersionOnJob, RemoteHost
 from biolib.compute_node.webserver.webserver_types import ComputeNodeInfo
-from biolib.typing_utils import List, Optional, TypedDict
+from biolib.typing_utils import Dict, List, Optional, TypedDict
 
 
 class JobState(Enum):
@@ -31,6 +31,7 @@ class _Job(TypedDict):
 # type optional keys with total=False
 class CreatedJobDict(_Job, total=False):
     custom_compute_node_url: str
+    temporary_client_secrets: Dict[str, str]
 
 
 class CloudJob(TypedDict):

{pybiolib-1.2.223 → pybiolib-1.2.243}/biolib/biolib_errors.py

@@ -7,6 +7,9 @@ class BioLibError(Exception):
         super().__init__(message)
         self.message = message
 
+class ValidationError(BioLibError):
+    def __init__(self, message: Optional[str] = None):
+        super().__init__(message=message or 'Invalid input.')
 
 class NotFound(BioLibError):
 

{pybiolib-1.2.223 → pybiolib-1.2.243}/biolib/compute_node/job_worker/executors/docker_executor.py

@@ -69,7 +69,9 @@ class DockerExecutor:
 
         # If BIOLIB_SECRETS_TMPFS_PATH is set create the temporary directory there
         self._tmp_secrets_dir = tempfile.TemporaryDirectory(dir=utils.BIOLIB_SECRETS_TMPFS_PATH or None)
+        self._tmp_client_secrets_dir = tempfile.TemporaryDirectory(dir=utils.BIOLIB_SECRETS_TMPFS_PATH or None)
         os.chmod(self._tmp_secrets_dir.name, 0o755)
+        os.chmod(self._tmp_client_secrets_dir.name, 0o755)
 
     @property
     def _container(self) -> Container:
@@ -263,6 +265,7 @@ class DockerExecutor:
 
         logger_no_user_data.debug(f'Deleted compute container in: {time.time() - container_time}')
         self._tmp_secrets_dir.cleanup()
+        self._tmp_client_secrets_dir.cleanup()
 
     # TODO: type this method
     def _initialize_docker_container(self, module_input):
@@ -285,11 +288,23 @@ class DockerExecutor:
                 app_uri=self._options['job']['app_uri'],
                 is_environment_biolib_cloud=bool(utils.IS_RUNNING_IN_CLOUD),
             )
-            secrets: Dict[str, str] = dict(
-                **module.get('secrets', {}),
-                biolib_system_secret=json.dumps(biolib_system_secret, indent=4),
+            docker_volume_mounts.append(
+                self._create_secrets_mount(
+                    source_dir=self._tmp_secrets_dir.name + '/',
+                    target_dir='/biolib/secrets/',
+                    secrets=dict(
+                        **module.get('secrets', {}),
+                        biolib_system_secret=json.dumps(biolib_system_secret, indent=4),
+                    ),
+                )
+            )
+            docker_volume_mounts.append(
+                self._create_secrets_mount(
+                    source_dir=self._tmp_client_secrets_dir.name + '/',
+                    target_dir='/biolib/temporary-client-secrets/',
+                    secrets=self._options['job'].get('temporary_client_secrets', {}),
+                )
             )
-            docker_volume_mounts.append(self._create_secrets_mount(secrets))
 
             environment_vars = {}
 
@@ -498,8 +513,8 @@ class DockerExecutor:
                 stdout=stdout,
             )
         except Exception as exception:
-            logger.error("Hit Error 23")
-            logger.exception("Error")
+            logger.error('Hit Error 23')
+            logger.exception('Error')
             logger.error(str(exception))
             time.sleep(3)
             raise ComputeProcessException(
@@ -586,19 +601,16 @@ class DockerExecutor:
 
         return files_and_empty_dirs
 
-    def _create_secrets_mount(self, secrets: Dict[str, str]) -> docker.types.Mount:
-        job_uuid = self._options['job']['public_id']
+    def _create_secrets_mount(self, source_dir: str, target_dir: str, secrets: Dict[str, str]) -> docker.types.Mount:
+        assert source_dir.startswith('/') and source_dir.endswith('/'), 'source_dir must start and end with slash'
+        assert target_dir.startswith('/') and target_dir.endswith('/'), 'target_dir must start and end with slash'
 
+        job_uuid = self._options['job']['public_id']
         for key, value in secrets.items():
             if re.match(r'^[a-zA-Z0-9-_]+$', key):
-                with open(f'{self._tmp_secrets_dir.name}/{key}', 'w') as secret_file:
+                with open(f'{source_dir}{key}', 'w') as secret_file:
                     secret_file.write(value)
             else:
                 logger_no_user_data.warning(f'Job {job_uuid} uses secret with a key not matching validation regex')
 
-        return docker.types.Mount(
-            read_only=True,
-            source=f'{self._tmp_secrets_dir.name}/',
-            target='/biolib/secrets/',
-            type='bind',
-        )
+        return docker.types.Mount(read_only=True, source=source_dir, target=target_dir, type='bind')

{pybiolib-1.2.223 → pybiolib-1.2.243}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.223"
+version = "1.2.243"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"