pybiolib 1.1.1794__tar.gz → 1.1.1810__tar.gz

{pybiolib-1.1.1794 → pybiolib-1.1.1810}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1794
+Version: 1.1.1810
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

pybiolib-1.1.1810/biolib/_internal/utils/__init__.py

@@ -0,0 +1,14 @@
+import time
+import uuid
+
+
+def open_browser_window_from_notebook(url_to_open: str) -> None:
+    try:
+        from IPython.display import (display, Javascript, update_display)  # type:ignore # pylint: disable=import-error, import-outside-toplevel
+    except ImportError as error:
+        raise Exception('Unexpected environment. This function can only be called from a notebook.') from error
+
+    display_id = str(uuid.uuid4())
+    display(Javascript(f'window.open("{url_to_open}");'), display_id=display_id)
+    time.sleep(1)
+    update_display(Javascript(''), display_id=display_id)

{pybiolib-1.1.1794 → pybiolib-1.1.1810}/biolib/cli/auth.py

@@ -8,10 +8,18 @@ from biolib import biolib_errors, api
 
 
 @click.command(help='Login your to BioLib account with web browser')
-def login() -> None:
+@click.option(
+    '-w',
+    is_flag=True,
+    default=False,
+    required=False,
+    type=bool,
+    help='Automatically open the login page in the default web browser',
+)
+def login(w: bool) -> None:  # pylint: disable=invalid-name
     logger.configure(default_log_level=logging.INFO)
     logger_no_user_data.configure(default_log_level=logging.INFO)
-    sign_in()
+    sign_in(open_in_default_browser=w)
 
 
 @click.command(help='Logout of your BioLib account')

{pybiolib-1.1.1794 → pybiolib-1.1.1810}/biolib/cli/download_container.py

@@ -4,7 +4,7 @@ from biolib.biolib_download_container import download_container_from_uri
 from biolib.biolib_logging import logger, logger_no_user_data
 
 
-@click.command(help='Push an application to BioLib', name='download-container')
+@click.command(help='Pull an application from BioLib', name='download-container', hidden=True)
 @click.argument('uri')
 def download_container(uri: str) -> None:
     logger.configure(default_log_level=logging.INFO)

{pybiolib-1.1.1794 → pybiolib-1.1.1810}/biolib/jobs/job.py

@@ -8,6 +8,8 @@ from urllib.parse import urlparse
 
 from biolib import api, utils
 from biolib._internal.http_client import HttpClient
+from biolib._internal.utils import open_browser_window_from_notebook
+from biolib.biolib_api_client import BiolibApiClient
 from biolib.biolib_api_client.biolib_job_api import BiolibJobApi
 from biolib.biolib_binary_format import LazyLoadedFile, ModuleOutputV2, ModuleInput, ModuleInputDict
 from biolib.biolib_binary_format.stdout_and_stderr import StdoutAndStderr
@@ -23,12 +25,14 @@ from biolib.utils import IS_RUNNING_IN_NOTEBOOK
 
 class Job:
     # Columns to print in table when showing Job
-    table_columns_to_row_map = OrderedDict({
-        'ID': {'key': 'uuid', 'params': {'width': 36}},
-        'Application': {'key': 'app_uri', 'params': {}},
-        'Status': {'key': 'state', 'params': {}},
-        'Started At': {'key': 'started_at', 'params': {}},
-    })
+    table_columns_to_row_map = OrderedDict(
+        {
+            'ID': {'key': 'uuid', 'params': {'width': 36}},
+            'Application': {'key': 'app_uri', 'params': {}},
+            'Status': {'key': 'state', 'params': {}},
+            'Started At': {'key': 'started_at', 'params': {}},
+        }
+    )
 
     def __init__(self, job_dict: JobDict):
         self._uuid: str = job_dict['uuid']
@@ -172,6 +176,17 @@ class Job:
             time.sleep(2)
         logger.info(f'Job {self.id} has finished.')
 
+    def open_browser(self) -> None:
+        api_client = BiolibApiClient.get()
+        results_url_to_open = f'{api_client.base_url}/results/{self.id}/?token={self._auth_token}'
+        if IS_RUNNING_IN_NOTEBOOK:
+            print(f'Opening results page at: {results_url_to_open}')
+            print('If your browser does not open automatically, click on the link above.')
+            open_browser_window_from_notebook(results_url_to_open)
+        else:
+            print('Please copy and paste the following link into your browser:')
+            print(results_url_to_open)
+
     def _get_cloud_job(self) -> CloudJobDict:
         self._refetch_job_dict(force_refetch=True)
         if self._job_dict['cloud_job'] is None:
@@ -190,20 +205,11 @@ class Job:
     @staticmethod
     def show_jobs(count: int = 25) -> None:
         job_dicts = Job._get_job_dicts(count)
-        BioLibTable(
-            columns_to_row_map=Job.table_columns_to_row_map,
-            rows=job_dicts,
-            title='Jobs'
-        ).print_table()
+        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']
+        job_dicts: List['JobDict'] = api.client.get(path='/jobs/', params={'page_size': str(count)}).json()['results']
         return job_dicts
 
     @staticmethod
@@ -235,9 +241,7 @@ class Job:
     def show(self) -> None:
         self._refetch_job_dict()
         BioLibTable(
-            columns_to_row_map=Job.table_columns_to_row_map,
-            rows=[self._job_dict],
-            title=f'Job: {self._uuid}'
+            columns_to_row_map=Job.table_columns_to_row_map, rows=[self._job_dict], title=f'Job: {self._uuid}'
         ).print_table()
 
     def stream_logs(self) -> None:
@@ -305,9 +309,7 @@ class Job:
 
     def _print_full_logs(self, node_url: str) -> None:
         try:
-            response_json = HttpClient.request(
-                url=f'{node_url}/v1/job/{self._uuid}/status/?logs=full'
-            ).json()
+            response_json = HttpClient.request(url=f'{node_url}/v1/job/{self._uuid}/status/?logs=full').json()
         except Exception as error:
             logger.error(f'Could not get full streamed logs due to: {error}')
             raise BioLibError('Could not get full streamed logs') from error
@@ -336,9 +338,7 @@ class Job:
     def _get_job_status_from_compute_node(self, compute_node_url):
         for _ in range(15):
             try:
-                return HttpClient.request(
-                    url=f'{compute_node_url}/v1/job/{self._uuid}/status/'
-                ).json()
+                return HttpClient.request(url=f'{compute_node_url}/v1/job/{self._uuid}/status/').json()
             except Exception:  # pylint: disable=broad-except
                 cloud_job = self._get_cloud_job()
                 logger.debug("Failed to get status from compute node, retrying...")
@@ -346,8 +346,7 @@ class Job:
                     logger.debug("Job no longer exists on compute node, checking for error...")
                     if cloud_job['error_code'] != SystemExceptionCodes.COMPLETED_SUCCESSFULLY.value:
                         error_message = SystemExceptionCodeMap.get(
-                            cloud_job['error_code'],
-                            f'Unknown error code {cloud_job["error_code"]}'
+                            cloud_job['error_code'], f'Unknown error code {cloud_job["error_code"]}'
                         )
                         raise BioLibError(f'Cloud: {error_message}') from None
                     else:

{pybiolib-1.1.1794 → pybiolib-1.1.1810}/biolib/user/sign_in.py

@@ -1,19 +1,11 @@
 import time
-import uuid
+import webbrowser
 
 from biolib.biolib_api_client import BiolibApiClient
 from biolib.biolib_api_client.auth import BiolibAuthChallengeApi
 from biolib.biolib_logging import logger_no_user_data
 from biolib.utils import IS_RUNNING_IN_NOTEBOOK
-
-
-def _open_browser_window(url_to_open: str) -> None:
-    from IPython.display import display, Javascript, update_display  # type:ignore # pylint: disable=import-error, import-outside-toplevel
-
-    display_id = str(uuid.uuid4())
-    display(Javascript(f'window.open("{url_to_open}");'), display_id=display_id)
-    time.sleep(1)
-    update_display(Javascript(''), display_id=display_id)
+from biolib._internal.utils import open_browser_window_from_notebook
 
 
 def sign_out() -> None:
@@ -21,7 +13,7 @@ def sign_out() -> None:
     api_client.sign_out()
 
 
-def sign_in() -> None:
+def sign_in(open_in_default_browser: bool = False) -> None:
     api_client = BiolibApiClient.get()
     if api_client.is_signed_in:
         logger_no_user_data.info('Already signed in')
@@ -37,7 +29,11 @@ def sign_in() -> None:
     if IS_RUNNING_IN_NOTEBOOK:
         print(f'Opening authorization page at: {frontend_sign_in_url}')
         print('If your browser does not open automatically, click on the link above.')
-        _open_browser_window(frontend_sign_in_url)
+        open_browser_window_from_notebook(frontend_sign_in_url)
+    elif open_in_default_browser:
+        print(f'Opening authorization page at: {frontend_sign_in_url}')
+        print('If your browser does not open automatically, click on the link above.')
+        webbrowser.open(frontend_sign_in_url)
     else:
         print('Please copy and paste the following link into your browser:')
         print(frontend_sign_in_url)

{pybiolib-1.1.1794 → pybiolib-1.1.1810}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.1794"
+version = "1.1.1810"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"