pybiolib 1.1.1979__py3-none-any.whl → 1.1.1986__py3-none-any.whl

biolib/_internal/fuse_mount/experiment_fuse_mount.py

@@ -3,12 +3,11 @@ import os
 import stat
 from datetime import datetime, timezone
 from time import time
-from typing import Iterable
 
 from biolib._internal.libs.fusepy import FUSE, FuseOSError, Operations
 from biolib.biolib_errors import BioLibError
 from biolib.jobs import Job
-from biolib.typing_utils import Dict, Optional, Tuple, TypedDict
+from biolib.typing_utils import Dict, List, Optional, Tuple, TypedDict
 
 
 class _AttributeDict(TypedDict):
@@ -27,94 +26,96 @@ class ExperimentFuseMount(Operations):
         self._experiment = experiment
         self._job_names_map: Optional[Dict[str, Job]] = None
         self._jobs_last_fetched_at: float = 0.0
-        self._root_path: str = '/'
         self._mounted_at_epoch_seconds: int = int(time())
 
     @staticmethod
-    def mount(experiment, path: str) -> None:
+    def mount_experiment(experiment, mount_path: str) -> None:
         FUSE(
             operations=ExperimentFuseMount(experiment),
-            mountpoint=path,
+            mountpoint=mount_path,
             nothreads=True,
             foreground=True,
             allow_other=False,
         )
 
     def getattr(self, path: str, fh=None) -> _AttributeDict:
-        full_path = self._full_path(path)
-        if full_path == '/':
-            # return folder dir
-            return self._get_folder_attr(timestamp_epoch_seconds=self._mounted_at_epoch_seconds)
-
-        job_name, job_path = self._parse_path(path)
-        job = self._get_job_names_map().get(job_name)
-        if not job:
-            # job not found
-            raise FuseOSError(errno.ENOENT)
+        if path == '/':
+            return self._get_directory_attributes(timestamp_epoch_seconds=self._mounted_at_epoch_seconds)
 
+        job, path_in_job = self._parse_path(path)
         job_finished_at_epoch_seconds: int = int(
             datetime.fromisoformat(job.to_dict()['finished_at'].rstrip('Z')).replace(tzinfo=timezone.utc).timestamp()
         )
-        if not job_path or job_path == '/':
-            # job root path
-            return self._get_folder_attr(timestamp_epoch_seconds=job_finished_at_epoch_seconds)
+
+        if path_in_job == '/':
+            return self._get_directory_attributes(timestamp_epoch_seconds=job_finished_at_epoch_seconds)
 
         try:
-            file = job.get_output_file(job_path)
+            file = job.get_output_file(path_in_job)
+            return self._get_file_attributes(
+                timestamp_epoch_seconds=job_finished_at_epoch_seconds,
+                size_in_bytes=file.length,
+            )
         except BioLibError:
             # file not found
-            raise FuseOSError(errno.ENOENT) from None
+            pass
 
-        return _AttributeDict(
-            st_atime=job_finished_at_epoch_seconds,
-            st_ctime=job_finished_at_epoch_seconds,
-            st_gid=os.getgid(),
-            st_mode=stat.S_IFREG | 0o444,  # Regular file with read permissions for owner, group, and others.
-            st_mtime=job_finished_at_epoch_seconds,
-            st_nlink=1,
-            st_size=file.length,
-            st_uid=os.getuid(),
-        )
+        file_paths_in_job = [file.path for file in job.list_output_files()]
+
+        for file_path_in_job in file_paths_in_job:
+            if file_path_in_job.startswith(path_in_job):
+                return self._get_directory_attributes(timestamp_epoch_seconds=job_finished_at_epoch_seconds)
+
+        raise FuseOSError(errno.ENOENT) from None  # No such file or directory
 
-    def readdir(self, path: str, fh: int) -> Iterable[str]:
+    def readdir(self, path: str, fh: int) -> List[str]:
         directory_entries = ['.', '..']
+
         if path == '/':
-            for name in self._get_job_names_map(refresh_jobs=True):
-                directory_entries.append(name)
+            directory_entries.extend(self._get_job_names_map(refresh_jobs=True).keys())
         else:
-            job_name, job_path = self._parse_path(path)
-            job = self._get_job_names_map()[job_name]
-            in_target_directory = set(
-                [k.path.split('/')[1] for k in job.list_output_files() if k.path.startswith(job_path)]
+            job, path_in_job = self._parse_path(path)
+            dir_path_in_job = '/' if path_in_job == '/' else path_in_job + '/'
+            depth = dir_path_in_job.count('/')
+            directory_entries.extend(
+                set(
+                    [
+                        file.path.split('/')[depth]
+                        for file in job.list_output_files()
+                        if file.path.startswith(dir_path_in_job)
+                    ]
+                )
             )
 
-            for key in in_target_directory:
-                directory_entries.append(key)
-
-        yield from directory_entries
+        return directory_entries
 
     def open(self, path: str, flags: int) -> int:
-        job_name, job_path = self._parse_path(path)
-        job = self._get_job_names_map()[job_name]
+        job, path_in_job = self._parse_path(path)
         try:
-            job.get_output_file(job_path)
-            return 0  # return dummy file handle
+            job.get_output_file(path_in_job)
         except BioLibError:
             # file not found
             raise FuseOSError(errno.ENOENT) from None
 
+        return 0  # return dummy file handle
+
     def read(self, path: str, size: int, offset: int, fh: int) -> bytes:
-        job_name, job_path = self._parse_path(path)
-        job = self._get_job_names_map()[job_name]
+        job, path_in_job = self._parse_path(path)
         try:
-            file = job.get_output_file(job_path)
+            file = job.get_output_file(path_in_job)
         except BioLibError:
-            # file not found
-            raise FuseOSError(errno.ENOENT) from None
+            raise FuseOSError(errno.ENOENT) from None  # No such file or directory
 
         return file.get_data(start=offset, length=size)
 
-    def _get_folder_attr(self, timestamp_epoch_seconds: int) -> _AttributeDict:
+    def release(self, path: str, fh: int) -> int:
+        return 0
+
+    def releasedir(self, path: str, fh: int) -> int:
+        return 0
+
+    @staticmethod
+    def _get_directory_attributes(timestamp_epoch_seconds: int) -> _AttributeDict:
         return _AttributeDict(
             st_atime=timestamp_epoch_seconds,
             st_ctime=timestamp_epoch_seconds,
@@ -126,6 +127,19 @@ class ExperimentFuseMount(Operations):
             st_uid=os.getuid(),
         )
 
+    @staticmethod
+    def _get_file_attributes(timestamp_epoch_seconds: int, size_in_bytes: int) -> _AttributeDict:
+        return _AttributeDict(
+            st_atime=timestamp_epoch_seconds,
+            st_ctime=timestamp_epoch_seconds,
+            st_gid=os.getgid(),
+            st_mode=stat.S_IFREG | 0o444,  # Regular file with read permissions for owner, group, and others.
+            st_mtime=timestamp_epoch_seconds,
+            st_nlink=1,
+            st_size=size_in_bytes,
+            st_uid=os.getuid(),
+        )
+
     def _get_job_names_map(self, refresh_jobs=False) -> Dict[str, Job]:
         current_time = time()
         if not self._job_names_map or (current_time - self._jobs_last_fetched_at > 1 and refresh_jobs):
@@ -134,18 +148,15 @@ class ExperimentFuseMount(Operations):
 
         return self._job_names_map
 
-    def _full_path(self, partial: str) -> str:
-        if partial.startswith('/'):
-            partial = partial[1:]
-
-        return os.path.join(self._root_path, partial)
+    def _parse_path(self, path: str) -> Tuple[Job, str]:
+        path_splitted = path.split('/')
+        job_name = path_splitted[1]
+        path_in_job = '/' + '/'.join(path_splitted[2:])
+        job = self._get_job_names_map().get(job_name)
+        if not job:
+            raise FuseOSError(errno.ENOENT)  # No such file or directory
 
-    def _parse_path(self, path: str) -> Tuple[str, str]:
-        full_path = self._full_path(path)
-        full_path_splitted = full_path.split('/')
-        job_name = full_path_splitted[1]
-        job_path = '/'.join(full_path_splitted[2:])
-        return job_name, job_path
+        return job, path_in_job
 
     # ----------------------------------- File system methods not implemented below -----------------------------------
 
@@ -191,8 +202,5 @@ class ExperimentFuseMount(Operations):
     def flush(self, path, fh):
         raise FuseOSError(errno.EACCES)
 
-    def release(self, path, fh):
-        raise FuseOSError(errno.EACCES)
-
     def fsync(self, path, datasync, fh):
         raise FuseOSError(errno.EACCES)

biolib/experiments/experiment.py

@@ -73,7 +73,7 @@ class Experiment:
     def add_job(self, job_id: str) -> None:
         api.client.patch(path=f'/jobs/{job_id}/', data={'experiment_uuid': self.uuid})
 
-    def mount_files(self, path: str) -> None:
+    def mount_files(self, mount_path: str) -> None:
         try:
             # Only attempt to import FUSE dependencies when strictly necessary
             from biolib._internal.fuse_mount import (  # pylint: disable=import-outside-toplevel
@@ -84,7 +84,7 @@ class Experiment:
                 'Failed to import FUSE mounting utils. Please ensure FUSE is installed on your system.'
             ) from error
 
-        _ExperimentFuseMount.mount(experiment=self, path=path)
+        _ExperimentFuseMount.mount_experiment(experiment=self, mount_path=mount_path)
 
     def export_job_list(self, export_format='dicts'):
         valid_formats = ('dicts', 'dataframe')

{pybiolib-1.1.1979.dist-info → pybiolib-1.1.1986.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1979
+Version: 1.1.1986
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1979.dist-info → pybiolib-1.1.1986.dist-info}/RECORD

@@ -6,7 +6,7 @@ biolib/_internal/data_record/__init__.py,sha256=1Bk303i3rFet9veS56fIsrBYtT5X3n9v
 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/fuse_mount/experiment_fuse_mount.py,sha256=MjGY9vNL-QivDF8w4qKuF3P7auv5cGK9qKKYYyDYQY4,6966
 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
@@ -86,7 +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=kUQsH9AGAckPKT_nzaRuTh8Mb2pVUpxnuX9IstRTOEo,6351
+biolib/experiments/experiment.py,sha256=_ied3A3U6NFa6_ewEYn2TCozqeHvDxDqdRhMtZbFL-M,6380
 biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
 biolib/jobs/job.py,sha256=aWKnf_2pYdr76gh3hxPiVs2iuXlpwZkKPTK81Pz4G2U,19072
@@ -109,8 +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-1.1.1979.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1979.dist-info/METADATA,sha256=gaN82MLET8VrqRkqovA4ARsoe1iBCt5eWuA0YoalPaY,1508
-pybiolib-1.1.1979.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.1979.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1979.dist-info/RECORD,,
+pybiolib-1.1.1986.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1986.dist-info/METADATA,sha256=p82i2WtF6K3qM7lWMT00MKh7Eqp2HuFOrqZEeEU98_0,1508
+pybiolib-1.1.1986.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.1986.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1986.dist-info/RECORD,,