pybiolib 1.2.1247__py3-none-any.whl → 1.2.1295__py3-none-any.whl

biolib/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: I001
 # Imports to hide
 import os
 from urllib.parse import urlparse as _urlparse
@@ -15,6 +16,7 @@ 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
@@ -22,7 +24,6 @@ import biolib.cli
 import biolib.sdk
 import biolib.utils
 
-
 # ------------------------------------ Function definitions for public Python API ------------------------------------
 
 
@@ -83,43 +84,65 @@ def search(
 
 
 def get_job(job_id: str, job_token: Optional[str] = None) -> _Result:
-    r"""Get a job by its ID.
+    r"""Get a job by its ID or full URL.
 
     Args:
-        job_id (str): The UUID of the job to retrieve
+        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')
-        >>> # Access shared job
+        >>> # 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')
     """
-    return _Result.create_from_uuid(uuid=job_id, auth_token=job_token)
+    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.
+    r"""Get a result by its ID or full URL.
 
     Args:
-        result_id (str): The UUID of the result to retrieve
+        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 result that aren't owned by the current user.
+            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')
-        >>> # Access shared result
+        >>> # 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')
     """
-    return _Result.create_from_uuid(uuid=result_id, auth_token=result_token)
+    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:

biolib/_internal/utils/job_url.py

@@ -0,0 +1,33 @@
+import re
+from urllib.parse import urlparse
+
+import biolib.utils
+from biolib.typing_utils import Optional, Tuple
+
+
+def parse_result_id_or_url(result_id_or_url: str, default_token: Optional[str] = None) -> Tuple[str, Optional[str]]:
+    result_id_or_url = result_id_or_url.strip()
+
+    if '/' not in result_id_or_url:
+        return (result_id_or_url, default_token)
+
+    if not result_id_or_url.startswith('http://') and not result_id_or_url.startswith('https://'):
+        result_id_or_url = 'https://' + result_id_or_url
+
+    parsed_url = urlparse(result_id_or_url)
+
+    if biolib.utils.BIOLIB_BASE_URL:
+        expected_base = urlparse(biolib.utils.BIOLIB_BASE_URL)
+        if parsed_url.scheme != expected_base.scheme or parsed_url.netloc != expected_base.netloc:
+            raise ValueError(f'URL must start with {biolib.utils.BIOLIB_BASE_URL}, got: {result_id_or_url}')
+
+    pattern = r'/results?/(?P<uuid>[a-f0-9-]+)/?(?:\?token=(?P<token>[^&]+))?'
+    match = re.search(pattern, result_id_or_url, re.IGNORECASE)
+
+    if not match:
+        raise ValueError(f'URL must be in format <base_url>/results/<UUID>/?token=<token>, got: {result_id_or_url}')
+
+    uuid = match.group('uuid')
+    token = match.group('token') or default_token
+
+    return (uuid, token)

biolib/jobs/job.py

@@ -398,6 +398,7 @@ class Result:
             >>> # Recompute with different arguments
             >>> new_result = result.recompute(arguments=["--new-arg", "value"])
         """
+        self._refetch_job_dict()
         app_response = BiolibAppApi.get_by_uri(uri=app_uri or self._job_dict['app_uri'])
 
         job_storage_input = RemoteJobStorageEndpoint(
@@ -425,6 +426,7 @@ class Result:
             app_uri=app_response['app_uri'],
             app_version_uuid=app_response['app_version']['public_id'],
             module_input_serialized=module_input_serialized,
+            override_command=self._job_dict['arguments_override_command'],
             machine=machine if machine else original_requested_machine,
         )
         if blocking:

biolib/jobs/types.py

@@ -26,6 +26,7 @@ class Result(TypedDict):
 
 class JobDict(TypedDict):
     app_uri: str
+    arguments_override_command: bool
     auth_token: str
     created_at: str
     ended_at: Optional[str]

{pybiolib-1.2.1247.dist-info → pybiolib-1.2.1295.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pybiolib
-Version: 1.2.1247
+Version: 1.2.1295
 Summary: BioLib Python Client
 License: MIT
 License-File: LICENSE

{pybiolib-1.2.1247.dist-info → pybiolib-1.2.1295.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biolib/__init__.py,sha256=o0cpNzP7OwPYfdw5Cq-XgsMYooQdQynZTUO3W-LFuKo,10657
+biolib/__init__.py,sha256=-pz1Ipyj1KmB709yYpl2Y-iKOWXpLxcFzL48G8rr9cU,12146
 biolib/_data_record/data_record.py,sha256=BM2WEBnn13reSiAqhBtcV8FLewFWSTcMmFV0bD74bM0,12489
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/add_copilot_prompts.py,sha256=wcIdrceFcfKSoEjvM4uNzhKZ0I1-MCFkfNO4duqtGHA,1861
@@ -60,6 +60,7 @@ biolib/_internal/types/result.py,sha256=MesSTBXCkaw8HydXgHf1OKGVLzsxhZ1KV5z4w-VI
 biolib/_internal/types/typing.py,sha256=qrsk8hHcGEbDpU1QQFzHAKnhQxkMe7uJ6pxHeAnfv1Y,414
 biolib/_internal/types/user.py,sha256=5_hYG0jrdGxynCCWXGaHZCAlVcRKBqMIEA2EBGrnpiE,439
 biolib/_internal/utils/__init__.py,sha256=xp1I-lVnu5owV1CW53jiPEZLKmqqHiPUDfauYDfJ7iQ,1540
+biolib/_internal/utils/job_url.py,sha256=YpwqCP56BD15M8p2tuSY_Z3O9vWAkG2rJbQu2Z5zqq0,1265
 biolib/_internal/utils/multinode.py,sha256=N7kR49xD1PdkMVlxxzRiSYHfgi9MG-kLCwemcY1rojg,8323
 biolib/_runtime/runtime.py,sha256=9q6Wuo8SBcJIezyScAgq2MDfpT0Pg8lcfbBFmeCWiUE,5974
 biolib/_session/session.py,sha256=US1Y1jfFIAm86-Lq3C7nCXpZXUJXXBVBkND9djMNYxI,1649
@@ -141,9 +142,9 @@ biolib/compute_node/webserver/worker_thread.py,sha256=7uD9yQPhePYvP2HCJ27EeZ_h6p
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=4g1xMYmfp5yzSOdwjf3pUUULF9QjqBJb4uQ25FHrFrk,13688
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=7giHZfDt1lux8Nl2BZKwtVNaLr-vCcwFYZ28Cs_tZN0,28957
+biolib/jobs/job.py,sha256=aC3MfyNOC3z1HEK60OASjaS23Bwq0z6Wkjty56JFj7o,29065
 biolib/jobs/job_result.py,sha256=_xqQu9z9BqPQrU6tjqKPuKlQDt5W0Zw5xiQvzEBkDyE,5266
-biolib/jobs/types.py,sha256=ezvaoTANsWazK6PmfpYcqezdfjP7MNBEBfqIZGoZhz8,997
+biolib/jobs/types.py,sha256=rFs6bQWsNI-nb1Hu9QzOW2zFZ8bOVt7ax4UpGVASxVA,1034
 biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
 biolib/sdk/__init__.py,sha256=Z1S5BgpvM87S2o1libtqkYN1CfYUhn_d4ChEJjwdFKM,2356
@@ -157,8 +158,8 @@ 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-1.2.1247.dist-info/METADATA,sha256=f94G6AXhnvGJnMSaFtVGT-NGsache1UooDU6--u6W88,1644
-pybiolib-1.2.1247.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-pybiolib-1.2.1247.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.1247.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.1247.dist-info/RECORD,,
+pybiolib-1.2.1295.dist-info/METADATA,sha256=URIKfpKORBz-C5Wvjq34LuMh7unEverSx9TMzQzMFhE,1644
+pybiolib-1.2.1295.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+pybiolib-1.2.1295.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.1295.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1295.dist-info/RECORD,,