pybiolib 1.2.122__tar.gz → 1.2.141.dev1__tar.gz

{pybiolib-1.2.122 → pybiolib-1.2.141.dev1}/PKG-INFO

@@ -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 → pybiolib-1.2.141.dev1}/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]:

{pybiolib-1.2.122 → pybiolib-1.2.141.dev1}/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}

{pybiolib-1.2.122 → pybiolib-1.2.141.dev1}/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,
     )

{pybiolib-1.2.122 → pybiolib-1.2.141.dev1}/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:

{pybiolib-1.2.122 → pybiolib-1.2.141.dev1}/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 → pybiolib-1.2.141.dev1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.122"
+version = "1.2.141.dev1"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"