pybiolib 1.2.122__py3-none-any.whl → 1.2.141.dev1__py3-none-any.whl

biolib/__init__.py

@@ -49,8 +49,8 @@ def get_data_record(uri: str) -> _DataRecord:
     return _DataRecord.get_by_uri(uri)
 
 
-def fetch_jobs(count: int = 25) -> List[_Job]:
-    return _Job.fetch_jobs(count)
+def fetch_jobs(count: int = 25, status: Optional[str] = None) -> List[_Job]:
+    return _Job.fetch_jobs(count, status)
 
 
 def fetch_data_records(uri: Optional[str] = None, count: Optional[int] = None) -> List[_DataRecord]:

biolib/_internal/push_application.py

@@ -76,7 +76,8 @@ def push_application(
     app_uri: str,
     app_path: str,
     app_version_to_copy_images_from: Optional[str],
-    is_dev_version: Optional[bool],
+    set_as_active: bool,
+    set_as_published: bool,
 ):
     app_uri_parts = app_uri.split(':')
     if len(app_uri_parts) > 2:
@@ -276,12 +277,11 @@ def push_application(
     app_version_uuid = new_app_version_json['public_id']
     api.client.post(
         path=f'/app-versions/{app_version_uuid}/complete-push/',
-        data={'set_as_active': not is_dev_version},
+        data={'set_as_active': set_as_active, 'set_as_published': set_as_published},
     )
 
     sematic_version = f"{new_app_version_json['major']}.{new_app_version_json['minor']}.{new_app_version_json['patch']}"
-    logger.info(
-        f"Successfully pushed new {'development ' if is_dev_version else ''}version {sematic_version} of {app_uri}."
-    )
+    version_name = 'development ' if not set_as_published else ''
+    logger.info(f'Successfully pushed new {version_name}version {sematic_version} of {app_uri}.')
 
     return {'app_uri': app_uri, 'sematic_version': sematic_version}

biolib/cli/push.py

@@ -12,12 +12,25 @@ from biolib.biolib_logging import logger, logger_no_user_data
 @click.option('--path', default='.', required=False)
 @click.option('--copy-images-from-version', required=False)
 @click.option('--dev', is_flag=True, default=False, required=False)
-def push(uri, path: str, copy_images_from_version: Optional[str], dev: bool) -> None:
+@click.option('--pre-release', is_flag=True, default=False, required=False)
+def push(uri, path: str, copy_images_from_version: Optional[str], dev: bool, pre_release: bool) -> None:
     logger.configure(default_log_level=logging.INFO)
     logger_no_user_data.configure(default_log_level=logging.INFO)
+    set_as_active = True
+    set_as_published = True
+    if dev and pre_release:
+        print('Error: you cannot set both --dev and --pre-release, please select one.')
+        exit(1)
+    elif dev:
+        set_as_active = False
+        set_as_published = False
+    elif pre_release:
+        set_as_active = False
+        set_as_published = True
     push_application(
         app_path=path,
         app_uri=uri,
         app_version_to_copy_images_from=copy_images_from_version,
-        is_dev_version=dev,
+        set_as_active=set_as_active,
+        set_as_published=set_as_published,
     )

biolib/jobs/job.py

@@ -22,7 +22,7 @@ from biolib.compute_node.utils import SystemExceptionCodeMap, SystemExceptionCod
 from biolib.jobs.job_result import JobResult
 from biolib.jobs.types import CloudJobDict, CloudJobStartedDict, JobDict
 from biolib.tables import BioLibTable
-from biolib.typing_utils import Dict, List, Optional, cast
+from biolib.typing_utils import Dict, List, Optional, Union, cast
 from biolib.utils import IS_RUNNING_IN_NOTEBOOK
 from biolib.utils.app_uri import parse_app_uri
 
@@ -232,8 +232,8 @@ class Job:
         self._result = JobResult(job_uuid=self._uuid, job_auth_token=self._auth_token, module_output=module_output)
 
     @staticmethod
-    def fetch_jobs(count: int) -> List['Job']:
-        job_dicts = Job._get_job_dicts(count)
+    def fetch_jobs(count: int, status: Optional[str] = None) -> List['Job']:
+        job_dicts = Job._get_job_dicts(count, status)
         return [Job(job_dict) for job_dict in job_dicts]
 
     @staticmethod
@@ -242,9 +242,27 @@ class Job:
         BioLibTable(columns_to_row_map=Job.table_columns_to_row_map, rows=job_dicts, title='Jobs').print_table()
 
     @staticmethod
-    def _get_job_dicts(count: int) -> List['JobDict']:
-        job_dicts: List['JobDict'] = api.client.get(path='/jobs/', params={'page_size': str(count)}).json()['results']
-        return job_dicts
+    def _get_job_dicts(count: int, status: Optional[str] = None) -> List['JobDict']:
+        job_states = ['in_progress', 'completed', 'failed', 'cancelled']
+        if status is not None and status not in job_states:
+            raise Exception('Invalid status filter')
+
+        page_size = min(count, 1_000)
+        params: Dict[str, Union[str, int]] = dict(page_size=page_size)
+        if status:
+            params['state'] = status
+
+        api_path = '/jobs/'
+        response = api.client.get(api_path, params=params).json()
+        jobs = [job_dict for job_dict in response['results']]
+
+        for page_number in range(2, response['page_count'] + 1):
+            page_response = api.client.get(path=api_path, params=dict(**params, page=page_number)).json()
+            jobs.extend([job_dict for job_dict in page_response['results']])
+            if len(jobs) >= count:
+                break
+
+        return jobs
 
     @staticmethod
     def _get_job_dict(uuid: str, auth_token: Optional[str] = None) -> JobDict:

biolib/sdk/__init__.py

@@ -16,7 +16,8 @@ def push_app_version(uri: str, path: str) -> _BioLibApp:
         app_uri=uri,
         app_path=path,
         app_version_to_copy_images_from=None,
-        is_dev_version=True,
+        set_as_active=False,
+        set_as_published=False,
     )
     uri = f'{push_data["app_uri"]}:{push_data["sematic_version"]}'
     return _BioLibApp(uri)

{pybiolib-1.2.122.dist-info → pybiolib-1.2.141.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.2.122
+Version: 1.2.141.dev1
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.2.122.dist-info → pybiolib-1.2.141.dev1.dist-info}/RECORD

@@ -1,6 +1,6 @@
 LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
 PYPI_README.md,sha256=_IH7pxFiqy2bIAmaVeA-iVTyUwWRjMIlfgtUbYTtmls,368
-biolib/__init__.py,sha256=q_YhAYw51Vq16IKtSk8_MJclDAa4CfCmPhvWDYmrSIg,4393
+biolib/__init__.py,sha256=4Rfa0AJKztqkCG5D67kFgSwdOUiBTa5HkAzIOqHNREU,4431
 biolib/_data_record/data_record.py,sha256=zVAhFU1RLI1-ptoQ_l639RNwrMANXV9j75yXHvB7dtA,10950
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/data_record/__init__.py,sha256=fGdME6JGRU_2VxpJbYpGXYndjN-feUkmKY4fuMyq3cg,76
@@ -15,7 +15,7 @@ biolib/_internal/lfs/__init__.py,sha256=gSWo_xg61UniYgD7yNYxeT4I9uaXBCBSi3_nmZjn
 biolib/_internal/lfs/cache.py,sha256=pQS2np21rdJ6I3DpoOutnzPHpLOZgUIS8TMltUJk_k4,2226
 biolib/_internal/libs/__init__.py,sha256=Jdf4tNPqe_oIIf6zYml6TiqhL_02Vyqwge6IELrAFhw,98
 biolib/_internal/libs/fusepy/__init__.py,sha256=AWDzNFS-XV_5yKb0Qx7kggIhPzq1nj_BZS5y2Nso08k,41944
-biolib/_internal/push_application.py,sha256=OtfH4xsyOZE_bjVZAVWe7LSNo4t2OUKY_6dfzWDfNts,11874
+biolib/_internal/push_application.py,sha256=eu9TGTDQUkgY42SAjbURycrrbX8hesBCWBEg0H5CdQQ,11948
 biolib/_internal/runtime.py,sha256=BiHl4klUHr36MCpqKaUso4idHeBZfPAahLYRQrabFqA,486
 biolib/_internal/types/__init__.py,sha256=xLgOQJFh3GRtiqIJq7MaqHReZx4pp34_zcaFQ_JjuJ4,198
 biolib/_internal/types/app.py,sha256=Mz2QGD_jESX-K9JYnLWPo4YA__Q_1FQQTk9pvidCohU,118
@@ -64,7 +64,7 @@ biolib/cli/data_record.py,sha256=t8DfJK2EZ_SNZ9drDA_N5Jqy8DNwf9f5SlFrIaOvtv0,350
 biolib/cli/download_container.py,sha256=HIZVHOPmslGE5M2Dsp9r2cCkAEJx__vcsDz5Wt5LRos,483
 biolib/cli/init.py,sha256=wQOfii_au-d30Hp7DdH-WVw-WVraKvA_zY4za1w7DE8,821
 biolib/cli/lfs.py,sha256=z2qHUwink85mv9yDgifbVKkVwuyknGhMDTfly_gLKJM,4151
-biolib/cli/push.py,sha256=TFi7O9tJ3zFe0VmtVTV3Vh9_xIMHnrc41xxcaBKU46g,813
+biolib/cli/push.py,sha256=RxB4RHpjtL27Fpq7WRGojJ53R9jUuE1Cq9_NmHFzNsM,1306
 biolib/cli/run.py,sha256=BbvXLQ-XibjQ71Y2d4URMH_8dflNVwM0i3TIWhw_u_c,1634
 biolib/cli/runtime.py,sha256=Xv-nrma5xX8NidWcvbUKcUvuN5TCarZa4A8mPVmF-z0,361
 biolib/cli/start.py,sha256=rg8VVY8rboFhf1iQo3zE3WA5oh_R1VWWfYJEO1gMReY,1737
@@ -102,11 +102,11 @@ biolib/compute_node/webserver/worker_thread.py,sha256=GRRBUqXdMKvbjyLQhYlqGIbFKe
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=jIRixmQm3Gq9YdJ3I0-rE1vFukXqq6U4zXehFOJ1yZk,7614
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=OfG8cLd3AjGjiMWRlJRZdVVbLsRWSX-OM5nxJhR6mPQ,19136
+biolib/jobs/job.py,sha256=ej-dxt1hMBQXzTfUZ2SLqIV8dtTbMSMn_q2rjIA7oN4,19903
 biolib/jobs/job_result.py,sha256=rALHiKYNaC9lHi_JJqBob1RubzNLwG9Z386kwRJjd2M,5885
 biolib/jobs/types.py,sha256=qhadtH2KDC2WUOOqPiwke0YgtQY4FtuB71Stekq1k48,970
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
-biolib/sdk/__init__.py,sha256=amVp_jMxi2nqCcTsmL2aKUNGCAH3Yk4EzAnps9d1VH8,1928
+biolib/sdk/__init__.py,sha256=8uyOAKt8-Xo11jAWXCg14NkE1u0FkOBC07L3V7wGsCg,1960
 biolib/tables.py,sha256=acH7VjwAbadLo8P84FSnKEZxCTVsF5rEg9VPuxElNs8,872
 biolib/templates/__init__.py,sha256=Yx62sSyDCDesRQDQgmbDsLpfgEh93fWE8r9u4g2azXk,36
 biolib/templates/example_app.py,sha256=EB3E3RT4SeO_ii5nVQqJpi5KDGNE_huF1ub-e5ZFveE,715
@@ -119,8 +119,8 @@ 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=WJnU9vZdwY8RHXvzATyV80OXzyJ7w9EkG33Tna9Nr6A,5698
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.122.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.122.dist-info/METADATA,sha256=ZqN7f5Rlsd29avkwSDiZmCoUi7OUiMlBqUmIl7OdDq8,1507
-pybiolib-1.2.122.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.2.122.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.122.dist-info/RECORD,,
+pybiolib-1.2.141.dev1.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.141.dev1.dist-info/METADATA,sha256=9NEHC1fbAZuf_mpTlZyUtdPhEGFvBkhcyKwWzxugvfI,1512
+pybiolib-1.2.141.dev1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.2.141.dev1.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.141.dev1.dist-info/RECORD,,