pybiolib 1.2.1361__py3-none-any.whl → 1.2.1379__py3-none-any.whl

biolib/app/app.py

@@ -7,6 +7,8 @@ import string
 from pathlib import Path
 
 from biolib import utils
+from biolib._internal.file_utils import path_to_renamed_path
+from biolib._runtime.runtime import Runtime
 from biolib.api.client import ApiClient
 from biolib.biolib_api_client import JobState
 from biolib.biolib_api_client.app_types import App, AppVersion
@@ -20,8 +22,6 @@ from biolib.experiments.experiment import Experiment
 from biolib.jobs.job import Result
 from biolib.typing_utils import Dict, Optional
 from biolib.utils.app_uri import parse_app_uri
-from biolib._runtime.runtime import Runtime
-from biolib._internal.file_utils import path_to_renamed_path
 
 
 class BioLibApp:
@@ -95,7 +95,7 @@ class BioLibApp:
             experiment_to_use = experiment if experiment is not None else self._experiment
             experiment_instance: Optional[Experiment]
             if experiment_to_use:
-                experiment_instance = Experiment(experiment_to_use)
+                experiment_instance = Experiment(experiment_to_use, _api_client=self._api_client)
             else:
                 experiment_instance = Experiment.get_experiment_in_context()
             experiment_id = experiment_instance.uuid if experiment_instance else None

biolib/experiments/experiment.py

@@ -6,6 +6,7 @@ from biolib import api
 from biolib._internal.types.experiment import DeprecatedExperimentDict, ExperimentDict
 from biolib._internal.types.resource import ResourceDetailedDict
 from biolib._internal.utils import open_browser_window_from_notebook
+from biolib.api.client import ApiClient
 from biolib.biolib_api_client import BiolibApiClient
 from biolib.biolib_errors import BioLibError
 from biolib.jobs.job import Job
@@ -28,7 +29,13 @@ class Experiment:
         }
     )
 
-    def __init__(self, uri: str, _resource_dict: Optional[ResourceDetailedDict] = None):
+    def __init__(
+        self,
+        uri: str,
+        _resource_dict: Optional[ResourceDetailedDict] = None,
+        _api_client: Optional[ApiClient] = None,
+    ):
+        self._api_client = _api_client or api.client
         self._resource_dict: ResourceDetailedDict = _resource_dict or self._get_or_create_resource_dict(uri)
 
     def __enter__(self):
@@ -113,7 +120,7 @@ class Experiment:
             job_id = job
         elif job is None and job_id is None:
             raise BioLibError('A job ID or job object must be provided to add job')
-        api.client.post(
+        self._api_client.post(
             path=f'/experiments/{self.uuid}/jobs/',
             data={'job_uuid': job_id},
         )
@@ -126,7 +133,7 @@ class Experiment:
         else:
             raise BioLibError('A job ID or job object must be provided to remove job')
 
-        api.client.delete(path=f'/experiments/{self.uuid}/jobs/{job_id}/')
+        self._api_client.delete(path=f'/experiments/{self.uuid}/jobs/{job_id}/')
 
     def mount_files(self, mount_path: str) -> None:
         try:
@@ -175,7 +182,7 @@ class Experiment:
 
     # Prints a table listing info about the jobs in this experiment
     def show_jobs(self) -> None:
-        response: JobsPaginatedResponse = api.client.get(
+        response: JobsPaginatedResponse = self._api_client.get(
             path=f'/experiments/{self.uuid}/jobs/',
             params=dict(page_size=10),
         ).json()
@@ -197,11 +204,13 @@ class Experiment:
         if status:
             params['status'] = status
 
-        response: JobsPaginatedResponse = api.client.get(url, params=params).json()
+        response: JobsPaginatedResponse = self._api_client.get(url, params=params).json()
         jobs: List[Job] = [Job(job_dict) for job_dict in response['results']]
 
         for page_number in range(2, response['page_count'] + 1):
-            page_response: JobsPaginatedResponse = api.client.get(url, params=dict(**params, page=page_number)).json()
+            page_response: JobsPaginatedResponse = self._api_client.get(
+                url, params=dict(**params, page=page_number)
+            ).json()
             jobs.extend([Job(job_dict) for job_dict in page_response['results']])
 
         return jobs
@@ -300,21 +309,19 @@ class Experiment:
             )
 
     def rename(self, destination: str) -> None:
-        api.client.patch(f'/resources/{self.uuid}/', data={'uri': destination})
+        self._api_client.patch(f'/resources/{self.uuid}/', data={'uri': destination})
         self._refetch()
 
-    @staticmethod
-    def _get_resource_dict_by_uuid(uuid: str) -> ResourceDetailedDict:
-        resource_dict: ResourceDetailedDict = api.client.get(f'/resources/{uuid}/').json()
+    def _get_resource_dict_by_uuid(self, uuid: str) -> ResourceDetailedDict:
+        resource_dict: ResourceDetailedDict = self._api_client.get(f'/resources/{uuid}/').json()
         if not resource_dict['experiment']:
             raise ValueError('Resource from URI is not an experiment')
 
         return resource_dict
 
-    @staticmethod
-    def _get_or_create_resource_dict(uri: str) -> ResourceDetailedDict:
-        response_dict = api.client.post(path='/experiments/', data={'uri' if '/' in uri else 'name': uri}).json()
-        return Experiment._get_resource_dict_by_uuid(uuid=response_dict['uuid'])
+    def _get_or_create_resource_dict(self, uri: str) -> ResourceDetailedDict:
+        response_dict = self._api_client.post(path='/experiments/', data={'uri' if '/' in uri else 'name': uri}).json()
+        return self._get_resource_dict_by_uuid(uuid=response_dict['uuid'])
 
     def _refetch(self) -> None:
         self._resource_dict = self._get_resource_dict_by_uuid(uuid=self._resource_dict['uuid'])

{pybiolib-1.2.1361.dist-info → pybiolib-1.2.1379.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pybiolib
-Version: 1.2.1361
+Version: 1.2.1379
 Summary: BioLib Python Client
 License: MIT
 License-File: LICENSE

{pybiolib-1.2.1361.dist-info → pybiolib-1.2.1379.dist-info}/RECORD

@@ -70,7 +70,7 @@ biolib/_session/session.py,sha256=Ymi9OQW_u_CfYA3JlBakPwRhNaKlb20P2G8SmtJhnzA,18
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
 biolib/api/client.py,sha256=2GpKE7QrPgyPdgJgrV7XnZByIJf1n26UCy3aoaHBs1M,7881
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
-biolib/app/app.py,sha256=FjiqT7jCH0pSzKpG_v2Z9ysdUaPhhdPmW5gC-IbnAl0,12230
+biolib/app/app.py,sha256=8k7M8G3HO1TPfBTZrE_iODKX28rxxf-7g-OsUa3x-fY,12260
 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=IONzXeFCHl4wuct6fqOC_7NiTv_zFy6ys0hsAtvLzTA,7578
@@ -143,7 +143,7 @@ biolib/compute_node/webserver/webserver_types.py,sha256=2t8EaFKESnves3BA_NBdnS2y
 biolib/compute_node/webserver/webserver_utils.py,sha256=XWvwYPbWNR3qS0FYbLLp-MDDfVk0QdaAmg3xPrT0H2s,4234
 biolib/compute_node/webserver/worker_thread.py,sha256=7uD9yQPhePYvP2HCJ27EeZ_h6psfIWFgqm1RHZxzobs,12483
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/experiments/experiment.py,sha256=4g1xMYmfp5yzSOdwjf3pUUULF9QjqBJb4uQ25FHrFrk,13688
+biolib/experiments/experiment.py,sha256=ePipnJs6TW84jr9iBfYYRpYuEXUVGIxaD8Z8Jf0FYIA,13909
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
 biolib/jobs/job.py,sha256=X7F_jCwAwtPcI1qu-oLamZNzt1IVSIeOPWlax1ztfAM,29674
 biolib/jobs/job_result.py,sha256=_xqQu9z9BqPQrU6tjqKPuKlQDt5W0Zw5xiQvzEBkDyE,5266
@@ -161,8 +161,8 @@ 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=rImaghQGuIqTVWks6b9P2yKuN34uePUYPUFW_Wyoa4A,6737
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.1361.dist-info/METADATA,sha256=Mc0J-5SkgNFy4G4hYW2XaekpJp1qODDRm2TB6LlMaww,1644
-pybiolib-1.2.1361.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-pybiolib-1.2.1361.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.1361.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.1361.dist-info/RECORD,,
+pybiolib-1.2.1379.dist-info/METADATA,sha256=K_Bnjzo9XB9Aq5g63v7A6CEKrEc1YC5jh6u0gYMGqCA,1644
+pybiolib-1.2.1379.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+pybiolib-1.2.1379.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.1379.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1379.dist-info/RECORD,,