pybiolib 0.2.951__py3-none-any.whl → 1.2.1890__py3-none-any.whl

biolib/__init__.py

@@ -1,39 +1,385 @@
+# ruff: noqa: I001
+# Imports to hide
 import os
+from urllib.parse import urlparse as _urlparse
 
-from biolib import typing_utils
+from biolib import typing_utils as _typing_utils
 from biolib.app import BioLibApp as _BioLibApp
-from biolib.biolib_logging import logger as _logger
-from biolib.biolib_api_client import BiolibApiClient as _BioLibApiClient
 
+# TODO: Fix ignore of type
+from biolib.app.search_apps import search_apps  # type: ignore
+from biolib.biolib_errors import BioLibError
+from biolib.biolib_logging import logger as _logger, logger_no_user_data as _logger_no_user_data
+from biolib.experiments.experiment import Experiment
+from biolib.biolib_api_client import BiolibApiClient as _BioLibApiClient, App
+from biolib.jobs.job import Result as _Result
+from biolib import user as _user
+from biolib.typing_utils import List, Optional, cast as _cast
+from biolib._data_record.data_record import DataRecord as _DataRecord
+from biolib._internal.utils.job_url import parse_result_id_or_url as _parse_result_id_or_url
+
+import biolib.api
 import biolib.app
 import biolib.cli
+import biolib.sdk
 import biolib.utils
 
-
 # ------------------------------------ Function definitions for public Python API ------------------------------------
 
+
 def call_cli() -> None:
-    biolib.cli.main()
+    biolib.cli.cli()
+
+
+def load(uri: str, suppress_version_warning: bool = False) -> _BioLibApp:
+    r"""Load a BioLib application by its URI or website URL.
+
+    Args:
+        uri (str): The URI or website URL of the application to load. Can be either:
+            - App URI (e.g., 'biolib/myapp:1.0.0')
+            - Website URL (e.g., 'https://biolib.com/biolib/myapp/')
+        suppress_version_warning (bool): If True, don't print a warning when no version is specified.
+            Defaults to False.
+
+    Returns:
+        BioLibApp: The loaded application object
+
+    Example::
+
+        >>> # Load by URI
+        >>> app = biolib.load('biolib/myapp:1.0.0')
+        >>> # Load by website URL
+        >>> app = biolib.load('https://biolib.com/biolib/myapp/')
+        >>> result = app.cli('--help')
+    """
+    return _BioLibApp(uri, suppress_version_warning=suppress_version_warning)
+
+
+def search(
+    search_query: Optional[str] = None,
+    team: Optional[str] = None,
+    count: int = 100,
+) -> List[str]:
+    r"""Search for BioLib applications.
+
+    Args:
+        search_query (str, optional): Search query string
+        team (str, optional): Filter by team name
+        count (int): Maximum number of results to return. Defaults to 100.
+
+    Returns:
+        List[str]: List of application URIs matching the search criteria
+
+    Example::
+
+        >>> # Search all apps
+        >>> apps = biolib.search()
+        >>> # Search by query
+        >>> alignment_apps = biolib.search('alignment')
+        >>> # Search team's apps
+        >>> team_apps = biolib.search(team='myteam')
+    """
+    apps: List[str] = search_apps(search_query, team, count)
+    return apps
+
+
+def get_job(job_id: str, job_token: Optional[str] = None) -> _Result:
+    r"""Get a job by its ID or full URL.
+
+    Args:
+        job_id (str): The UUID of the job to retrieve, or a full URL to the job.
+            Can be either:
+            - Job UUID (e.g., 'abc123')
+            - Full URL (e.g., 'https://biolib.com/result/abc123/?token=xyz789')
+            - Full URL with token parameter (e.g., 'biolib.com/result/abc123/token=xyz789')
+        job_token (str, optional): Authentication token for accessing the job.
+            Only needed for jobs that aren't owned by the current user.
+            If the URL contains a token, this parameter is ignored.
+
+    Returns:
+        Job: The job object
+
+    Example::
+
+        >>> # Get by UUID
+        >>> job = biolib.get_job('abc123')
+        >>> # Get with explicit token
+        >>> job = biolib.get_job('abc123', job_token='xyz789')
+        >>> # Get by full URL with token
+        >>> job = biolib.get_job('https://biolib.com/result/abc123/?token=xyz789')
+        >>> # Get by URL with inline token format
+        >>> job = biolib.get_job('biolib.com/result/abc123/token=xyz789')
+    """
+    uuid, token = _parse_result_id_or_url(job_id, job_token)
+    return _Result.create_from_uuid(uuid=uuid, auth_token=token)
+
+
+def get_result(result_id: str, result_token: Optional[str] = None) -> _Result:
+    r"""Get a result by its ID or full URL.
+
+    Args:
+        result_id (str): The UUID of the result to retrieve, or a full URL to the result.
+            Can be either:
+            - Result UUID (e.g., 'abc123')
+            - Full URL (e.g., 'https://biolib.com/result/abc123/?token=xyz789')
+            - Full URL with token parameter (e.g., 'biolib.com/result/abc123/token=xyz789')
+        result_token (str, optional): Authentication token for accessing the result.
+            Only needed for results that aren't owned by the current user.
+            If the URL contains a token, this parameter is ignored.
+
+    Returns:
+        Result: The result object
+
+    Example::
+
+        >>> # Get by UUID
+        >>> result = biolib.get_result('abc123')
+        >>> # Get with explicit token
+        >>> result = biolib.get_result('abc123', result_token='xyz789')
+        >>> # Get by full URL with token
+        >>> result = biolib.get_result('https://biolib.com/result/abc123/?token=xyz789')
+        >>> # Get by URL with inline token format
+        >>> result = biolib.get_result('biolib.com/result/abc123/token=xyz789')
+    """
+    uuid, token = _parse_result_id_or_url(result_id, result_token)
+    return _Result.create_from_uuid(uuid=uuid, auth_token=token)
+
+
+def get_data_record(uri: str) -> _DataRecord:
+    r"""Get a data record by its URI.
+
+    Args:
+        uri (str): The URI of the data record to retrieve
+
+    Returns:
+        DataRecord: The data record object
+
+    Example::
+
+        >>> record = biolib.get_data_record('biolib/data/sequences:1.0.0')
+    """
+    return _DataRecord.get_by_uri(uri)
+
+
+def fetch_jobs(count: int = 25, status: Optional[str] = None) -> List[_Result]:
+    r"""Fetch a list of jobs from the server.
+
+    Args:
+        count (int): Maximum number of jobs to fetch. Defaults to 25.
+        status (str, optional): Filter jobs by status. One of:
+            'in_progress', 'completed', 'failed', 'cancelled'
+
+    Returns:
+        List[Job]: List of job objects matching the criteria
+
+    Example::
+
+        >>> # Get last 10 completed jobs
+        >>> jobs = biolib.fetch_jobs(10, status='completed')
+        >>> # Get last 100 jobs of any status
+        >>> all_jobs = biolib.fetch_jobs(100)
+    """
+    return _Result.fetch_jobs(count, status)
+
+
+def fetch_data_records(uri: Optional[str] = None, count: Optional[int] = None) -> List[_DataRecord]:
+    r"""Fetch a list of data records from the server.
+
+    Args:
+        uri (str, optional): Filter records by URI prefix
+        count (int, optional): Maximum number of records to fetch
+
+    Returns:
+        List[DataRecord]: List of data record objects matching the criteria
+
+    Example::
+
+        >>> # Get all records
+        >>> records = biolib.fetch_data_records()
+        >>> # Get records with URI prefix
+        >>> seq_records = biolib.fetch_data_records('biolib/data/sequences')
+    """
+    return _DataRecord.fetch(uri, count)
+
 
+def get_experiment(uri: Optional[str] = None, name: Optional[str] = None) -> Experiment:
+    r"""Get an experiment by its URI or name.
 
-def load(uri: str) -> _BioLibApp:
-    return _BioLibApp(uri)
+    Args:
+        uri (str, optional): The URI of the experiment
+        name (str, optional): The name of the experiment
+
+    Returns:
+        Experiment: The experiment object
+
+    Raises:
+        ValueError: If neither or both uri and name are provided
+
+    Example::
+
+        >>> # Get by URI
+        >>> exp = biolib.get_experiment(uri='biolib/experiments/analysis')
+        >>> # Get by name
+        >>> exp = biolib.get_experiment(name='sequence-analysis')
+    """
+    if (not uri and not name) or (uri and name):
+        raise ValueError('Must provide either uri or name')
+
+    return Experiment.get_by_uri(uri=_cast(str, uri or name))
+
+
+def show_jobs(count: int = 25) -> None:
+    r"""Display a table of recent jobs.
+
+    Args:
+        count (int): Maximum number of jobs to display. Defaults to 25.
+
+    Example::
+
+        >>> biolib.show_jobs()  # Show last 25 jobs
+        >>> biolib.show_jobs(100)  # Show last 100 jobs
+    """
+    _Result.show_jobs(count=count)
+
+
+def show_experiments(count: int = 25) -> None:
+    r"""Display a table of experiments.
+
+    Args:
+        count (int): Maximum number of experiments to display. Defaults to 25.
+
+    Example::
+
+        >>> biolib.show_experiments()  # Show last 25 experiments
+        >>> biolib.show_experiments(100)  # Show last 100 experiments
+    """
+    Experiment.show_experiments(count=count)
+
+
+def sign_in() -> None:
+    _user.sign_in()
+
+
+def sign_out() -> None:
+    _user.sign_out()
+
+
+def login() -> None:
+    r"""Alias for :func:`sign_in`.
+
+    Example::
+
+        >>> biolib.login()  # Same as biolib.sign_in()
+    """
+    sign_in()
+
+
+def logout() -> None:
+    r"""Alias for :func:`sign_out`.
+
+    Example::
+
+        >>> biolib.logout()  # Same as biolib.sign_out()
+    """
+    sign_out()
 
 
 def set_api_base_url(api_base_url: str) -> None:
+    r"""Set the base URL for the BioLib API.
+
+    Args:
+        api_base_url (str): The base URL for the BioLib API
+
+    Example::
+
+        >>> biolib.set_api_base_url('https://biolib.com')
+
+    Note:
+        This will also update related configuration like site hostname
+        and environment flags.
+    """
     _BioLibApiClient.initialize(base_url=api_base_url)
+    biolib.utils.BIOLIB_BASE_URL = api_base_url
+    biolib.utils.BIOLIB_SITE_HOSTNAME = _urlparse(api_base_url).hostname
+    biolib.utils.BASE_URL_IS_PUBLIC_BIOLIB = api_base_url.endswith('biolib.com') or (
+        os.environ.get('BIOLIB_ENVIRONMENT_IS_PUBLIC_BIOLIB', '').upper() == 'TRUE'
+    )
+
+
+def set_base_url(base_url: str) -> None:
+    r"""Alias for :func:`set_api_base_url`.
+
+    Args:
+        base_url (str): The base URL for the BioLib API
+
+    Example::
+
+        >>> biolib.set_base_url('https://biolib.com')
+    """
+    return set_api_base_url(base_url)
 
 
 def set_api_token(api_token: str) -> None:
-    _BioLibApiClient.get().login(api_token)
+    r"""Sign in using an API token.
+
+    Args:
+        api_token (str): The API token to authenticate with
+
+    Example::
+
+        >>> biolib.set_api_token('my-api-token')
+        # Signed in using API token
+    """
+    api_client = _BioLibApiClient.get()
+    api_client.sign_in_with_api_token(api_token)
+
+
+def set_log_level(level: _typing_utils.Union[str, int]) -> None:
+    r"""Set the logging level for BioLib.
 
+    Args:
+        level (Union[str, int]): The log level to use. Can be a string
+            ('DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL') or an integer
+            level from the logging module.
 
-def set_log_level(level: typing_utils.Union[str, int]) -> None:
+    Example::
+
+        >>> biolib.set_log_level('DEBUG')  # Enable debug logging
+        >>> biolib.set_log_level('WARNING')  # Only show warnings and errors
+    """
     _logger.setLevel(level)
+    _logger_no_user_data.setLevel(level)
+
+
+def _configure_requests_certificates():
+    if os.getenv('REQUESTS_CA_BUNDLE'):
+        if not os.getenv('SSL_CERT_FILE'):
+            # set SSL_CERT_FILE to urllib use same certs
+            os.environ['SSL_CERT_FILE'] = os.getenv('REQUESTS_CA_BUNDLE')
+        return  # don't change REQUESTS_CA_BUNDLE if manually configured
+
+    certs_to_check = [
+        '/etc/ssl/certs/ca-certificates.crt',
+        '/etc/pki/tls/certs/ca-bundle.crt',
+        '/etc/ssl/ca-bundle.pem',
+        '/etc/pki/tls/cacert.pem',
+        '/etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem',
+        '/etc/ssl/cert.pem',
+    ]
+
+    for cert in certs_to_check:
+        if os.path.exists(cert):
+            os.environ['REQUESTS_CA_BUNDLE'] = cert
+            if not os.getenv('SSL_CERT_FILE'):
+                os.environ['SSL_CERT_FILE'] = cert
+            return
 
 
 # -------------------------------------------------- Configuration ---------------------------------------------------
 __version__ = biolib.utils.BIOLIB_PACKAGE_VERSION
-_logger.configure(default_log_level='INFO')
+_DEFAULT_LOG_LEVEL = 'INFO' if biolib.utils.IS_RUNNING_IN_NOTEBOOK else 'WARNING'
+_logger.configure(default_log_level=_DEFAULT_LOG_LEVEL)
+_logger_no_user_data.configure(default_log_level=_DEFAULT_LOG_LEVEL)
+_configure_requests_certificates()
 
-set_api_base_url(os.getenv('BIOLIB_BASE_URL', default='https://biolib.com'))
+set_api_base_url(biolib.utils.load_base_url_from_env())