diff --git a/.gitignore b/.gitignore
index c3b06df8c7fd07fed9c5c001b4563673fa614471..b5df72d80a4c50f372b4c94c7060bddfde55feed 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,7 +8,6 @@ datastore_server/source/core-plugins
openbis/source/core-plugins
*/bin/*
**/.DS_Store
-*__pycache__/
*$py.class
**/.pydevproject
**/.shredder
diff --git a/pybis/src/python/.gitignore b/pybis/src/python/.gitignore
index ac37d09509d50a26e266d8690a4fc0a3a67cd0d9..750c2aaaf7232dbd6614ad0a948fe1667767d521 100644
--- a/pybis/src/python/.gitignore
+++ b/pybis/src/python/.gitignore
@@ -5,3 +5,5 @@
dist
deleteDatasetsAlreadyDeletedFromApplicationServerTaskLastSeen
notebooks
+*__pycache__/
+*.mypy_cache/
diff --git a/pybis/src/python/pybis/dataset.py b/pybis/src/python/pybis/dataset.py
index b9dbcbab64d007d6ca52d15bff843ffce9c630ad..9325773d69b25c039208f43410df66f43cf003d6 100644
--- a/pybis/src/python/pybis/dataset.py
+++ b/pybis/src/python/pybis/dataset.py
@@ -1,6 +1,9 @@
import os
+from functools import partialmethod
+from pathlib import Path
from threading import Thread
from queue import Queue
+from typing import Set, Optional, List
from tabulate import tabulate
from .openbis_object import OpenBisObject
from .definitions import openbis_definitions, get_type_for_entity, get_fetchoption_for_entity
@@ -121,7 +124,7 @@ class DataSet(
'add_attachment()', 'get_attachments()', 'download_attachments()',
"get_files()", 'file_list',
'download()',
- 'archive()', 'unarchive()'
+ 'archive()', 'unarchive()', 'sftp_source_dir', 'sftp_source_absolute_path', 'symlink_to()','is_symlink()','is_physical()'
] + super().__dir__()
def __setattr__(self, name, value):
@@ -163,9 +166,72 @@ class DataSet(
except Exception:
return None
@property
- def sftp_path(self):
+ def sftp_source_dir(self):
return os.path.join(self.experiment.identifier[1:], self.permId)
+
+ @property
+ def sftp_source_absolute_path(self):
+ # join mountpoint and source_dir
+ # if source_dir is absolute one has to remove "/" to be able to join it with mountpoint
+ # so far did not find way to achieve this in case they are pathlib.Path
+ if not self.openbis.is_mounted():
+ raise ValueError("Not mounted.")
+
+ source_dir = self.sftp_source_dir
+ if source_dir[0] == "/":
+ source_dir = source_dir[1:]
+ return os.path.join(self.openbis.mountpoint, source_dir)
+
+
+ def symlink_to(self, target_dir: str, replace_if_symlink_exists: bool = True):
+ # replace_if_symlink_exists will replace the the target_dir in case it is an existing symlink
+
+ target_dir_path = Path(target_dir)
+ if target_dir_path.is_symlink() and replace_if_symlink_exists:
+ target_dir_path.unlink()
+
+ target_dir_path.symlink_to(self.sftp_source_absolute_path, target_is_directory=True)
+
+
+ @staticmethod
+ def _file_set(target_dir: str) -> Set[str]:
+ target_dir_path = Path(target_dir)
+ return set(
+ str(el.relative_to(target_dir_path))
+ for el in target_dir_path.glob("**/*")
+ if el.is_file()
+ )
+
+
+ def _is_symlink_or_physical(
+ self, target_dir: str, what: str, expected_file_list: Optional[List[str]] = None,
+ ):
+ target_dir_path = Path(target_dir)
+
+ target_file_set = self._file_set(target_dir)
+
+ if expected_file_list is None:
+ source_file_set = set(self.file_list)
+ else:
+ source_file_set = set(expected_file_list)
+
+ res = source_file_set.issubset(target_file_set)
+ if not res:
+ return res
+ elif what == "symlink":
+ return target_dir_path.exists() and target_dir_path.is_symlink()
+ elif what == "physical":
+ return target_dir_path.exists() and not target_dir_path.is_symlink()
+ else:
+ raise ValueError("Unexpected error")
+
+
+ is_symlink = partialmethod(
+ _is_symlink_or_physical, what="symlink", expected_file_list=None
+ )
+ is_physical = partialmethod(_is_symlink_or_physical, what="physical")
+
def archive(self, remove_from_data_store=True):
fetchopts = {
"removeFromDataStore": remove_from_data_store,
diff --git a/pybis/src/python/pybis/utils.py b/pybis/src/python/pybis/utils.py
index 8c723056940c3111fe3dd53ba3aa5bd2b0bf42e4..24363d7ae95d3f9855a3c1674936f79f16740992 100644
--- a/pybis/src/python/pybis/utils.py
+++ b/pybis/src/python/pybis/utils.py
@@ -253,50 +253,4 @@ def extract_userId(user):
elif isinstance(user, dict):
return user['userId']
else:
- return str(user)
-
-
-def check_symlink(target_dir: str) -> Path:
- # there are several options: basically resolvable symlink, non-resolvable symlink, does not exist at all or exists but it is not a symlink
-
- target_dir_path = Path(target_dir)
-
- if target_dir_path.is_symlink() and target_dir_path.exists():
- return target_dir_path.resolve()
- elif target_dir_path.is_symlink() and not target_dir_path.exists():
- raise FileNotFoundError(
- f"target_dir={target_dir} is non-resolvable symlink. No such file or directory: {target_dir_path.resolve()}"
- )
- elif not target_dir_path.is_symlink() and not target_dir_path.exists():
- raise FileNotFoundError(f"target_dir={target_dir} does not exist")
- else:
- raise ValueError(f"target_dir={target_dir} exists but it is not a symlink")
-
-
-def create_symlink(
- target_dir: str, source_dir: str, mountpoint: str, replace_if_symlink: bool = True
-):
- # Path(mountpoint,ds.experiment.identifier[1:],ds.permId)
- # replace_if_symlink will replace the the target_dir in case it is an existing symlink
-
- mountpoint_path = Path(mountpoint)
-
- # check mountpoint
- if not mountpoint_path.is_mount():
- if not mountpoint_path.exists():
- raise FileNotFoundError(f"mountpoint={mountpoint} does not exist")
- else:
- raise ValueError(f"mountpoint={mountpoint} exists but it is not a mount")
-
- # join mountpoint and source_dir
- # if source_dir is absolute we have to remove "/" to be able to join it with mountpoint
- # I did not find any way to achieve this in case they are pathlib.Path
- if source_dir[0] == "/":
- source_dir = source_dir[1:]
- source_dir_path = Path(mountpoint, source_dir)
-
- target_dir_path = Path(target_dir)
- if target_dir_path.is_symlink() and replace_if_symlink:
- target_dir_path.unlink()
-
- target_dir_path.symlink_to(source_dir_path, target_is_directory=True)
\ No newline at end of file
+ return str(user)
\ No newline at end of file
diff --git a/pybis/src/python/setup.py b/pybis/src/python/setup.py
index 2f9445da8d0d84d767e29137e4d175398dfd5001..ab75d770192f318243be04f70c57408fc1263940 100644
--- a/pybis/src/python/setup.py
+++ b/pybis/src/python/setup.py
@@ -28,7 +28,7 @@ setup(
'texttable',
'tabulate',
],
- python_requires=">=3.3",
+ python_requires=">=3.6",
classifiers=[
"Programming Language :: Python :: 3",
"License :: OSI Approved :: Apache Software License",