pybiolib 1.1.1957__py3-none-any.whl → 1.1.1971__py3-none-any.whl

biolib/biolib_binary_format/utils.py

@@ -148,8 +148,15 @@ class LazyLoadedFile:
     def get_file_handle(self) -> io.BufferedIOBase:
         return io.BytesIO(self.get_data())
 
-    def get_data(self) -> bytes:
-        return self._buffer.get_data(start=self.start, length=self._length)
+    def get_data(self, start=0, length=None) -> bytes:
+        start_offset = start + self.start
+        # make sure length doesn't go outside file boundaries
+        length_to_end_of_file = max(self._length - start, 0)
+        if length is None:
+            length_to_request = length_to_end_of_file
+        else:
+            length_to_request = min(length, length_to_end_of_file)
+        return self._buffer.get_data(start=start_offset, length=length_to_request)
 
     def get_data_iterator(self) -> Iterator[bytes]:
         if self._length == 0:

biolib/experiments/experiment.py

@@ -1,27 +1,26 @@
 import time
 from collections import OrderedDict
 
-from biolib.biolib_errors import BioLibError
-from biolib.jobs.types import JobsPaginatedResponse
-from biolib.typing_utils import List, Optional
-
 from biolib import api
+from biolib.biolib_errors import BioLibError
 from biolib.experiments.types import ExperimentDict
 from biolib.jobs.job import Job
-from biolib.typing_utils import Dict, Union
-
+from biolib.jobs.types import JobsPaginatedResponse
 from biolib.tables import BioLibTable
+from biolib.typing_utils import Dict, List, Optional, Union
 
 
 class Experiment:
     _BIOLIB_EXPERIMENTS: List['Experiment'] = []
 
     # Columns to print in table when showing Job
-    _table_columns_to_row_map = OrderedDict({
-        'Name': {'key': 'name', 'params': {}},
-        'Job Count': {'key': 'job_count', 'params': {}},
-        'Created At': {'key': 'created_at', 'params': {}}
-    })
+    _table_columns_to_row_map = OrderedDict(
+        {
+            'Name': {'key': 'name', 'params': {}},
+            'Job Count': {'key': 'job_count', 'params': {}},
+            'Created At': {'key': 'created_at', 'params': {}},
+        }
+    )
 
     def __init__(self, name: str):
         self._experiment_dict: ExperimentDict = self._create_in_backend_or_get_experiment_dict(name)
@@ -55,16 +54,11 @@ class Experiment:
     # Prints a table listing info about experiments accessible to the user
     @staticmethod
     def show_experiments(count: int = 25) -> None:
-        experiment_dicts = api.client.get(
-            path='/experiments/',
-            params={
-                'page_size': str(count)
-            }
-        ).json()['results']
+        experiment_dicts = api.client.get(path='/experiments/', params={'page_size': str(count)}).json()['results']
         BioLibTable(
             columns_to_row_map=Experiment._table_columns_to_row_map,
             rows=experiment_dicts,
-            title='Experiments'
+            title='Experiments',
         ).print_table()
 
     def wait(self) -> None:
@@ -77,10 +71,20 @@ class Experiment:
         print(f'All jobs of experiment {self.name} have finished')
 
     def add_job(self, job_id: str) -> None:
-        api.client.patch(
-            path=f'/jobs/{job_id}/',
-            data={'experiment_uuid': self.uuid}
-        )
+        api.client.patch(path=f'/jobs/{job_id}/', data={'experiment_uuid': self.uuid})
+
+    def mount_files(self, path: str) -> None:
+        try:
+            # Only attempt to import FUSE dependencies when strictly necessary
+            from biolib._internal.fuse_mount import (  # pylint: disable=import-outside-toplevel
+                ExperimentFuseMount as _ExperimentFuseMount,
+            )
+        except ImportError as error:
+            raise ImportError(
+                'Failed to import FUSE mounting utils. Please ensure FUSE is installed on your system.'
+            ) from error
+
+        _ExperimentFuseMount.mount(experiment=self, path=path)
 
     def export_job_list(self, export_format='dicts'):
         valid_formats = ('dicts', 'dataframe')
@@ -98,7 +102,7 @@ class Experiment:
                 raise ImportError(
                     'Pandas must be installed to use this method. '
                     'Alternatively, use .get_jobs() to get a list of job objects.'
-                 ) from error
+                ) from error
 
             jobs_df = pd.DataFrame.from_dict(job_dict_list)
             jobs_df.started_at = pd.to_datetime(jobs_df.started_at)
@@ -125,7 +129,7 @@ class Experiment:
         BioLibTable(
             columns_to_row_map=Job.table_columns_to_row_map,
             rows=[job._job_dict for job in jobs],  # pylint: disable=protected-access
-            title=f'Jobs in experiment: "{self.name}"'
+            title=f'Jobs in experiment: "{self.name}"',
         ).print_table()
 
     def get_jobs(self, status: Optional[str] = None) -> List[Job]:
@@ -149,12 +153,7 @@ class Experiment:
 
     def _create_in_backend_or_get_experiment_dict(self, name: str) -> ExperimentDict:
         # This endpoint returns experiment dict if already created
-        experiment_dict: ExperimentDict = api.client.post(
-            path='/experiments/',
-            data={
-                'name': name
-            }
-        ).json()
+        experiment_dict: ExperimentDict = api.client.post(path='/experiments/', data={'name': name}).json()
         return experiment_dict
 
     def _refetch_experiment_dict(self) -> None:

{pybiolib-1.1.1957.dist-info → pybiolib-1.1.1971.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1957
+Version: 1.1.1971
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1957.dist-info → pybiolib-1.1.1971.dist-info}/RECORD

@@ -5,7 +5,11 @@ biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,
 biolib/_internal/data_record/__init__.py,sha256=1Bk303i3rFet9veS56fIsrBYtT5X3n9vcsYMA6T6c5o,36
 biolib/_internal/data_record/data_record.py,sha256=ctijrrZ-LfUxtwzS8PEVa1VBuBLVWEhmo2yHcEDkC0A,7178
 biolib/_internal/data_record/remote_storage_endpoint.py,sha256=LPq8Lr5FhKF9_o5K-bUdT7TeLe5XFUD0AAeTkNEVZug,1133
+biolib/_internal/fuse_mount/__init__.py,sha256=B_tM6RM2dBw-vbpoHJC4X3tOAaN1H2RDvqYJOw3xFwg,55
+biolib/_internal/fuse_mount/experiment_fuse_mount.py,sha256=tRkgPncbf9Nl22adcjBTJuFfiYMkayYJSJ--WQrB-Ps,6629
 biolib/_internal/http_client.py,sha256=DdooXei93JKGYGV4aQmzue_oFzvHkozg2UCxgk9dfDM,5081
+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=H1PGNtVJ0vRC0li39gFMpPpjm6QeZ8Ob-7cLkLmxS_Y,10009
 biolib/_internal/runtime.py,sha256=BnFvRWYnxPXCgOtfxupN255Zxx9Gw6oPZyzUIGODw3k,3060
 biolib/_internal/utils/__init__.py,sha256=p5vsIFyu-zYqBgdSMfwW9NC_jk7rXvvCbV4Bzd3As7c,630
@@ -35,7 +39,7 @@ biolib/biolib_binary_format/saved_job.py,sha256=nFHVFRNTNcAFGODLSiBntCtMk55QKwre
 biolib/biolib_binary_format/stdout_and_stderr.py,sha256=WfUUJFFCBrtfXjuWIaRPiWCpuBLxfko68oxoTKhrwx8,1023
 biolib/biolib_binary_format/system_exception.py,sha256=T3iL4_cSHAHim3RSDPS8Xyb1mfteaJBZonSXuRltc28,853
 biolib/biolib_binary_format/system_status_update.py,sha256=aOELuQ0k-GtpaZTUxYd0GFomP_OInmrK585y6fuQuKE,1191
-biolib/biolib_binary_format/utils.py,sha256=-QQExlpZqzOZ89tkZrLoMh5eHbffKyHvvkHqJ-On_U4,4814
+biolib/biolib_binary_format/utils.py,sha256=ra_plrh_Z10u98O2gW9uW2qzscQZCfq91SOznmDTY64,5170
 biolib/biolib_docker_client/__init__.py,sha256=aBfA6mtWSI5dBEfNNMD6bIZzCPloW4ghKm0wqQiljdo,1481
 biolib/biolib_download_container.py,sha256=8TmBV8iv3bCvkNlHa1SSsc4zl0wX_eaxhfnW5rvFIh8,1779
 biolib/biolib_errors.py,sha256=5m4lK2l39DafpoXBImEBD4EPH3ayXBX0JgtPzmGClow,689
@@ -82,7 +86,7 @@ biolib/compute_node/webserver/webserver_types.py,sha256=Vmt1ZDecYhGBVEYWcW1DVxee
 biolib/compute_node/webserver/webserver_utils.py,sha256=XWvwYPbWNR3qS0FYbLLp-MDDfVk0QdaAmg3xPrT0H2s,4234
 biolib/compute_node/webserver/worker_thread.py,sha256=26tG73TADnOcXsAr7Iyf6smrLlCqB4x-vvmpUb8WqnA,11569
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/experiments/experiment.py,sha256=xUd3LkV5ztFIjTx_ehBu8e-flvfuQnYimFtPj1upzb0,5942
+biolib/experiments/experiment.py,sha256=kUQsH9AGAckPKT_nzaRuTh8Mb2pVUpxnuX9IstRTOEo,6351
 biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
 biolib/jobs/job.py,sha256=WFcHYYOkvAhmYRUykWFbjhshiF_dy1-eiPIMCS1CIeo,16157
@@ -105,8 +109,8 @@ 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=jC5WhH63FTD7SLFJbxQGA2hOt9NTwq9zHl_BEec1Z0c,4907
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.1.1957.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1957.dist-info/METADATA,sha256=dzeKnljFiNgqOp-j8BxQxOYZT_VHpj7yUabW8-HwR_k,1508
-pybiolib-1.1.1957.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.1957.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1957.dist-info/RECORD,,
+pybiolib-1.1.1971.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1971.dist-info/METADATA,sha256=Ldnxyz9Y43LOU6soZJP8EulbEQuVLL1zVaz-bGEObK4,1508
+pybiolib-1.1.1971.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.1971.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1971.dist-info/RECORD,,