pybiolib 1.2.230__py3-none-any.whl → 1.2.249__py3-none-any.whl

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')"
 """)
 

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()

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()

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):
 

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.dist-info → pybiolib-1.2.249.dist-info}/METADATA

@@ -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.dist-info → pybiolib-1.2.249.dist-info}/RECORD

@@ -31,14 +31,14 @@ biolib/_runtime/runtime.py,sha256=bZQ0m39R9jOBVAtlyvzDnOobKueOAQUCwMUZjDQnO7E,44
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
 biolib/api/client.py,sha256=FRpdH5aI187b_I_4HUNi680v4iOP65z5f2RcUo8D8MA,3559
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
-biolib/app/app.py,sha256=2bbwSZOYfWk-_Cw2n0yvMo0maYp1lZ0Z0YlhS1iK-jY,8727
+biolib/app/app.py,sha256=mJafDLtnoX66egHF94NrUhmhzjpFzvRj2STh0RVGJCY,8862
 biolib/app/search_apps.py,sha256=K4a41f5XIWth2BWI7OffASgIsD0ko8elCax8YL2igaY,1470
 biolib/biolib_api_client/__init__.py,sha256=E5EMa19wJoblwSdQPYrxc_BtIeRsAuO0L_jQweWw-Yk,182
 biolib/biolib_api_client/api_client.py,sha256=ciNx4ybpyKG5LEf4KQdGEz13r0jTxImyQat4_HDecD0,7373
 biolib/biolib_api_client/app_types.py,sha256=1sXz9XnLRKNALMglNdTbew7AL6OkcUan0MPdj4xQLis,2456
 biolib/biolib_api_client/auth.py,sha256=kjm0ZHnH3I8so3su2sZbBxNHYp-ZUdrZ5lwQ0K36RSw,949
-biolib/biolib_api_client/biolib_app_api.py,sha256=i5KPZNpopU7cqcjVfICml-31ca-1-CU_rdZgKiZt0Vs,4343
-biolib/biolib_api_client/biolib_job_api.py,sha256=7bKfav3-12ewXkEUoLdCmbWdebW8148kxfGJW9SsXZI,7125
+biolib/biolib_api_client/biolib_app_api.py,sha256=RUXrTxk7XKzm4wxv7NBXttuFjT60DI9vNOvkS-cjKNc,5065
+biolib/biolib_api_client/biolib_job_api.py,sha256=49SBozudLYlOByuQMABiHZkwK5Jt5_orjv8Vw0rJpks,7306
 biolib/biolib_api_client/common_types.py,sha256=RH-1KNHqUF-EkTpfPOSTt5Mq1GPdfju_cqXDesscO1I,123
 biolib/biolib_api_client/job_types.py,sha256=yBdBwjharbQJuXCi2xKMi0t_r6XxnbWnkchHekTpCJY,1351
 biolib/biolib_api_client/lfs_types.py,sha256=joZWP6-sa5_Ug_6xIp5fHAgEo_bqLE3rbleQocZtDcg,339
@@ -57,7 +57,7 @@ biolib/biolib_binary_format/system_status_update.py,sha256=aOELuQ0k-GtpaZTUxYd0G
 biolib/biolib_binary_format/utils.py,sha256=jq31QEShs7TSrSKZBr8jif-bJAwVzQrqVxmymL6crpU,5453
 biolib/biolib_docker_client/__init__.py,sha256=aBfA6mtWSI5dBEfNNMD6bIZzCPloW4ghKm0wqQiljdo,1481
 biolib/biolib_download_container.py,sha256=8TmBV8iv3bCvkNlHa1SSsc4zl0wX_eaxhfnW5rvFIh8,1779
-biolib/biolib_errors.py,sha256=5m4lK2l39DafpoXBImEBD4EPH3ayXBX0JgtPzmGClow,689
+biolib/biolib_errors.py,sha256=xtdo3ybqnc0jhd959kVmBczFdBczrFMr8cZyd4hjKLk,842
 biolib/biolib_logging.py,sha256=J3E5H_LL5k6ZUim2C8gqN7E6lCBZMTpO4tnMpOPwG9U,2854
 biolib/cli/__init__.py,sha256=0v3c_J-U0k46c5ZWeQjLG_kTaKDJm81LBxQpDO2B_aI,1286
 biolib/cli/auth.py,sha256=rpWGmXs6Fz6CGrO9K8ibPRszOdXG78Vig_boKaVCD9A,2082
@@ -103,7 +103,7 @@ biolib/compute_node/webserver/worker_thread.py,sha256=GRRBUqXdMKvbjyLQhYlqGIbFKe
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=m7FB7hot8CMOVrNyWGPB6FTkWQJwI0ytpIvtPxfoPME,7684
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=et1slGdzczp112iJlHVp_7eTyhGoGSKxP31jgAwQuiM,20163
+biolib/jobs/job.py,sha256=W0r9_AbHha1lC99U_kUuzDmavFQe7WLxs83Wp3g_3ZU,20330
 biolib/jobs/job_result.py,sha256=rALHiKYNaC9lHi_JJqBob1RubzNLwG9Z386kwRJjd2M,5885
 biolib/jobs/types.py,sha256=ezvaoTANsWazK6PmfpYcqezdfjP7MNBEBfqIZGoZhz8,997
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
@@ -120,8 +120,8 @@ 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
-pybiolib-1.2.230.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.230.dist-info/METADATA,sha256=pHStJR-mwTW8Plixvbbd1rtb8Msj8BmiCBOi6-ORvnY,1558
-pybiolib-1.2.230.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
-pybiolib-1.2.230.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.230.dist-info/RECORD,,
+pybiolib-1.2.249.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.249.dist-info/METADATA,sha256=x0mgDfo1eBuhQpvLCecpSy035un2h-vPtrwrgVQzyEM,1558
+pybiolib-1.2.249.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
+pybiolib-1.2.249.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.249.dist-info/RECORD,,