pybiolib 1.2.230__tar.gz → 1.2.249__tar.gz

{pybiolib-1.2.230 → pybiolib-1.2.249}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.2.230
+Version: 1.2.249
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.2.230 → pybiolib-1.2.249}/biolib/app/app.py

@@ -16,7 +16,7 @@ from biolib.biolib_logging import logger
 from biolib.compute_node.job_worker.job_worker import JobWorker
 from biolib.experiments.experiment import Experiment
 from biolib.jobs import Job
-from biolib.typing_utils import Optional
+from biolib.typing_utils import Optional, Dict
 from biolib.utils.app_uri import parse_app_uri
 
 
@@ -58,6 +58,7 @@ class BioLibApp:
         notify: bool = False,
         machine_count: Optional[int] = None,
         experiment: Optional[str] = None,
+        temporary_client_secrets: Optional[Dict[str, str]] = None,
     ) -> Job:
         if experiment_id and experiment:
             raise ValueError('Only one of experiment_id and experiment can be specified')
@@ -91,6 +92,7 @@ class BioLibApp:
             result_prefix=result_prefix,
             timeout=timeout,
             requested_machine_count=machine_count,
+            temporary_client_secrets=temporary_client_secrets,
         )
         if blocking:
             # TODO: Deprecate utils.STREAM_STDOUT and always stream logs by simply calling job.stream_logs()
@@ -115,7 +117,7 @@ class BioLibApp:
         else:
             raise BioLibError("""
 Calling an app directly with app() is currently being reworked.
-To use the previous functionality, please call app.cli() instead. 
+To use the previous functionality, please call app.cli() instead.
 Example: "app.cli('--help')"
 """)
 

{pybiolib-1.2.230 → pybiolib-1.2.249}/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-1.2.230 → pybiolib-1.2.249}/biolib/biolib_api_client/biolib_job_api.py

@@ -47,6 +47,7 @@ class BiolibJobApi:
             timeout: Optional[int] = None,
             notify: bool = False,
             requested_machine_count: Optional[int] = None,
+            temporary_client_secrets: Optional[Dict[str, str]] = None,
     ):
         data = {
             'app_version_id': app_version_id,
@@ -83,6 +84,9 @@ class BiolibJobApi:
         if timeout:
             data['requested_timeout_seconds'] = timeout
 
+        if temporary_client_secrets:
+            data['temporary_client_secrets'] = temporary_client_secrets
+
         response = biolib.api.client.post(path='/jobs/', data=data)
 
         return response.json()

{pybiolib-1.2.230 → pybiolib-1.2.249}/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-1.2.230 → pybiolib-1.2.249}/biolib/jobs/job.py

@@ -437,8 +437,9 @@ class Job:
         timeout: Optional[int] = None,
         notify: bool = False,
         requested_machine_count: Optional[int] = None,
+        temporary_client_secrets: Optional[Dict[str, str]] = None,
     ) -> 'Job':
-        if len(module_input_serialized) < 500_000:
+        if len(module_input_serialized) < 500_000 and temporary_client_secrets is None:
             _job_dict = BiolibJobApi.create_job_with_data(
                 app_resource_name_prefix=parse_app_uri(app_uri)['resource_name_prefix'],
                 app_version_uuid=app_version_uuid,
@@ -462,6 +463,7 @@ class Job:
             override_command=override_command,
             timeout=timeout,
             requested_machine_count=requested_machine_count,
+            temporary_client_secrets=temporary_client_secrets,
         )
         JobStorage.upload_module_input(job=job_dict, module_input_serialized=module_input_serialized)
         cloud_job = BiolibJobApi.create_cloud_job(job_id=job_dict['public_id'], result_name_prefix=result_prefix)

{pybiolib-1.2.230 → pybiolib-1.2.249}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.230"
+version = "1.2.249"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"