pybiolib 1.1.1753__tar.gz → 1.1.1769__tar.gz

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1753
+Version: 1.1.1769
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

pybiolib-1.1.1769/biolib/_internal/runtime/__init__.py

@@ -0,0 +1 @@
+from .job_data import RuntimeJobData

pybiolib-1.1.1769/biolib/_internal/runtime/job_data.py

@@ -0,0 +1,29 @@
+import json
+from biolib.typing_utils import TypedDict, Optional, cast
+
+
+class RuntimeJobDataDict(TypedDict):
+    version: str
+    job_requested_machine: str
+    job_uuid: str
+    job_auth_token: str
+
+
+class RuntimeJobData:
+    _job_data: Optional[RuntimeJobDataDict] = None
+
+    @staticmethod
+    def get() -> Optional[RuntimeJobDataDict]:
+        if not RuntimeJobData._job_data:
+            try:
+                with open('/biolib/secrets/biolib_system_secret', mode='r') as file:
+                    job_data: RuntimeJobDataDict = json.load(file)
+            except BaseException:
+                return None
+
+            if not job_data['version'].startswith('1.'):
+                raise Exception(f"Unexpected system secret version {job_data['version']} expected 1.x.x")
+
+            RuntimeJobData._job_data = job_data
+
+        return cast(RuntimeJobDataDict, RuntimeJobData._job_data)

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/biolib/biolib_api_client/api_client.py

@@ -6,6 +6,7 @@ import os
 from datetime import datetime, timezone
 from json.decoder import JSONDecodeError
 
+from biolib._internal.runtime import RuntimeJobData
 from biolib._internal.http_client import HttpClient
 from biolib.typing_utils import Optional
 from biolib.biolib_errors import BioLibError
@@ -188,8 +189,9 @@ class BiolibApiClient:
 
     @staticmethod
     def assert_is_signed_in(authenticated_action_description: str) -> None:
+        runtime_job_data = RuntimeJobData.get()
         api_client = BiolibApiClient.get()
-        if not api_client.is_signed_in:
+        if not api_client.is_signed_in and not runtime_job_data:
             raise BioLibError(
                 f'You must be signed in to {authenticated_action_description}. '
                 f'Please set the environment variable "BIOLIB_TOKEN"'

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/biolib/biolib_api_client/biolib_app_api.py

@@ -35,7 +35,7 @@ def encode_multipart(data, files):
     line_array.append('')
 
     data_encoded = b'\r\n'.join([line.encode() if isinstance(line, str) else line for line in line_array])
-    return 'multipart/form-data; boundary={}'.format(boundary), data_encoded
+    return f'multipart/form-data; boundary={boundary}', data_encoded
 
 
 def _get_git_branch_name() -> str:

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/biolib/compute_node/cloud_utils/cloud_utils.py

@@ -81,8 +81,8 @@ class CloudUtils:
                         'error': error,
                     },
                 )
-            except BaseException as error:
-                logger_no_user_data.error(f'Failed to deregister got error: {error}')
+            except BaseException as error_object:
+                logger_no_user_data.error(f'Failed to deregister got error: {error_object}')
         else:
             logger_no_user_data.error("Not deregistering as environment is not cloud")
 

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/biolib/compute_node/job_worker/executors/docker_executor.py

@@ -18,6 +18,8 @@ from docker.errors import ImageNotFound, APIError  # type: ignore
 from docker.models.containers import Container  # type: ignore
 
 from biolib import utils
+
+from biolib._internal.runtime.job_data import RuntimeJobDataDict
 from biolib.biolib_binary_format import ModuleInput, ModuleOutputV2
 from biolib.biolib_docker_client import BiolibDockerClient
 from biolib.biolib_errors import DockerContainerNotFoundDuringExecutionException, BioLibError
@@ -267,12 +269,12 @@ class DockerExecutor:
             internal_network = self._options['internal_network']
             extra_hosts: Dict[str, str] = {}
 
-            biolib_system_secret = {
-                'version': '1.0.0',
-                'job_requested_machine': self._options['job']['requested_machine'],
-                'job_uuid': self._options['job']['public_id'],
-                'job_auth_token': self._options['job']['auth_token'],
-            }
+            biolib_system_secret = RuntimeJobDataDict(
+                version='1.0.0',
+                job_requested_machine=self._options['job']['requested_machine'],
+                job_uuid=self._options['job']['public_id'],
+                job_auth_token=self._options['job']['auth_token'],
+            )
             secrets: Dict[str, str] = dict(
                 **module.get('secrets', {}),
                 biolib_system_secret=json.dumps(biolib_system_secret, indent=4),

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/biolib/compute_node/job_worker/job_worker.py

@@ -97,7 +97,11 @@ class JobWorker:
         if socket_port:
             self._connect_to_parent()
 
-    def _handle_exit_gracefully(self, signum: int, frame: FrameType) -> None:  # pylint: disable=unused-argument
+    def _handle_exit_gracefully(
+            self,
+            signum: int,
+            frame: Optional[FrameType],  # pylint: disable=unused-argument
+    ) -> None:
         job_id = self._root_job_wrapper["job"]["public_id"] if self._root_job_wrapper else None
         logger_no_user_data.debug(
             f'_JobWorker ({job_id}) got exit signal {signal.Signals(signum).name}'  # pylint: disable=no-member

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/biolib/compute_node/remote_host_proxy.py

@@ -281,9 +281,8 @@ http {{
             proxy_ssl_server_name    on;
         }}
 
-        location ~* "^/api/lfs/.*$" {{
-            # Note: Using $1 here as URI part from regex must be used for proxy_pass
-            proxy_pass               {base_url}/api/lfs/$1;
+        location /api/lfs/ {{
+            proxy_pass               {base_url}/api/lfs/;
             proxy_set_header         authorization {'$bearer_token_on_post' if self._can_push_data_record_for_user else '""'};
             proxy_set_header         cookie "";
             proxy_ssl_server_name    on;

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/biolib/jobs/job.py

@@ -310,7 +310,7 @@ class Job:
             ).json()
         except Exception as error:
             logger.error(f'Could not get full streamed logs due to: {error}')
-            raise BioLibError from error
+            raise BioLibError('Could not get full streamed logs') from error
 
         for status_update in response_json.get('previous_status_updates', []):
             logger.info(f'Cloud: {status_update["log_message"]}')

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/biolib/lfs/utils.py

@@ -6,15 +6,18 @@ from collections import namedtuple
 from pathlib import Path
 from struct import Struct
 
-from biolib import utils
+from biolib import utils, api
+from biolib._internal.runtime import RuntimeJobData as _RuntimeJobData
 from biolib._internal.http_client import HttpClient
 from biolib.app import BioLibApp
 from biolib.biolib_api_client.biolib_account_api import BiolibAccountApi
 from biolib.biolib_api_client.biolib_large_file_system_api import BiolibLargeFileSystemApi
 from biolib.biolib_api_client import BiolibApiClient
+from biolib.biolib_api_client.lfs_types import LargeFileSystem
 from biolib.biolib_logging import logger
 from biolib.biolib_errors import BioLibError
 from biolib.typing_utils import List, Tuple, Iterator, Optional
+from biolib.utils.app_uri import parse_app_uri
 from biolib.utils.zip.remote_zip import RemoteZip  # type:ignore
 
 
@@ -98,11 +101,26 @@ def get_iterable_zip_stream(files: List[str], chunk_size: int) -> Iterator[bytes
         yield chunk
 
 
-def create_large_file_system(lfs_uri: str):
+def create_large_file_system(lfs_uri: str) -> None:
     BiolibApiClient.assert_is_signed_in(authenticated_action_description='create a Large File System')
-    lfs_account, lfs_name = _get_lfs_info_from_uri(lfs_uri)
-    lfs_resource = BiolibLargeFileSystemApi.create(account_uuid=lfs_account['public_id'], name=lfs_name)
-    logger.info(f"Successfully created new Large File System '{lfs_resource['uri']}'")
+
+    runtime_job_data = _RuntimeJobData.get()
+    if runtime_job_data:
+        uri_parsed = parse_app_uri(lfs_uri)
+        response = api.client.post(
+            path='/lfs/',
+            data={
+                'account_handle': uri_parsed['account_handle_normalized'],
+                'name': uri_parsed['app_name_normalized'],
+            },
+        )
+        lfs: LargeFileSystem = response.json()
+    else:
+        # TODO: Also use account_handle directly in POST request when backends are updated
+        lfs_account, lfs_name = _get_lfs_info_from_uri(lfs_uri)
+        lfs = BiolibLargeFileSystemApi.create(account_uuid=lfs_account['public_id'], name=lfs_name)
+
+    logger.info(f"Successfully created new Large File System '{lfs['uri']}'")
 
 
 def push_large_file_system(lfs_uri: str, input_dir: str, chunk_size_in_mb: Optional[int] = None) -> None:

pybiolib-1.1.1769/biolib/runtime/results.py

@@ -0,0 +1,14 @@
+from biolib import api
+from biolib._internal.runtime import RuntimeJobData as _RuntimeJobData
+
+
+def set_main_result_prefix(result_prefix: str) -> None:
+    runtime_job_data = _RuntimeJobData.get()
+    if not runtime_job_data:
+        raise Exception('Unable to load BioLib runtime job data') from None
+
+    api.client.patch(
+        data={'result_name_prefix': result_prefix},
+        headers={'Job-Auth-Token': runtime_job_data['job_auth_token']},
+        path=f"/jobs/{runtime_job_data['job_uuid']}/main_result/",
+    )

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/biolib/utils/__init__.py

@@ -4,9 +4,9 @@ import os
 import socket
 import sys
 
-from typing import Optional
 from importlib_metadata import version, PackageNotFoundError
 
+from biolib.typing_utils import Optional
 from biolib.utils.seq_util import SeqUtil, SeqUtilRecord
 from biolib._internal.http_client import HttpClient
 from biolib.biolib_logging import logger_no_user_data, logger

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/biolib/utils/cache_state.py

@@ -10,7 +10,7 @@ from biolib.biolib_errors import BioLibError
 from biolib.biolib_logging import logger_no_user_data
 from biolib.typing_utils import Optional, Generic, TypeVar
 
-StateType = TypeVar('StateType')
+StateType = TypeVar('StateType')  # pylint: disable=invalid-name
 
 
 class CacheStateError(BioLibError):

{pybiolib-1.1.1753 → pybiolib-1.1.1769}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.1753"
+version = "1.1.1769"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"
@@ -42,14 +42,15 @@ gunicorn = { version = ">=20.1.0", optional = true }
 compute-node = ["flask", "gunicorn"]
 
 [tool.poetry.dev-dependencies]
-mypy = "==0.910"
-pylint = "==2.7.4"
-pytest = "==6.2.4"
+mypy = "==0.971"
+pylint = "==2.13.9"
+pytest = "==7.0.1"
 pytest-timeout = "^2.1.0"
 types-click = "==7.1.8"
 types-Flask = "==1.1.1"
 types-PyYAML = "==5.4.3"
 types-termcolor = "==0.1.1"
+setuptools = "==59.6.0"
 
 [build-system]
 requires = ["poetry>=0.12"]

pybiolib-1.1.1753/biolib/runtime/results.py

@@ -1,20 +0,0 @@
-import json
-
-from biolib import api
-
-
-def set_main_result_prefix(result_prefix: str) -> None:
-    try:
-        with open('/biolib/secrets/biolib_system_secret', mode='r') as system_secrets_file:
-            system_secrets = json.loads(system_secrets_file.read())
-    except Exception:  # pylint: disable=broad-except
-        raise Exception('Unable to load the BioLib runtime system secret') from None
-
-    if not system_secrets['version'].startswith('1.'):
-        raise Exception(f"Unexpected system secret version {system_secrets['version']} expected 1.x.x")
-
-    api.client.patch(
-        data={'result_name_prefix': result_prefix},
-        headers={'Job-Auth-Token': system_secrets['job_auth_token']},
-        path=f"/jobs/{system_secrets['job_uuid']}/main_result/",
-    )