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session part properties in one.alf.path.PureALFPath (issue #208)
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‎CHANGELOG.md‎

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## [Latest](https://github.com/int-brain-lab/ONE/commits/main) [3.2.0]
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This version adds session part properties to the ALFPath class and turns off save on delete by default.
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### Added
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- session part properties in one.alf.path.PureALFPath (lab, subject, date, sequence)
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- with_\* methods in one.alf.path.PureALFPath for replacing session parts
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### Modified
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- by default, cache tables are not saved when One.\_\_del\_\_ is called

‎one/alf/path.py‎

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@@ -859,6 +859,26 @@ def alf_parts(self):
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"""tuple of str: the full ALF path parts, with empty strings for missing parts."""
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return tuple(p or '' for p in self.parse_alf_path(as_dict=False))
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@property
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def lab(self):
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"""str: The lab part of the ALF path, or an empty str if not present."""
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return self.session_parts[0]
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@property
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def subject(self):
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"""str: The subject part of the ALF path, or an empty str if not present."""
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return self.session_parts[1]
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@property
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def date(self):
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"""str: The date part of the ALF path, or an empty str if not present."""
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return self.session_parts[2]
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@property
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def sequence(self):
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"""str: The number part of the ALF path, or an empty str if not present."""
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return self.session_parts[3]
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@property
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def namespace(self):
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"""str: The namespace part of the ALF name, or and empty str if not present."""
@@ -884,6 +904,134 @@ def extra(self):
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"""str: The extra part of the ALF name, or and empty str if not present."""
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return self.dataset_name_parts[4]
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def with_lab(self, lab, strict=False):
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"""Return a new path with the ALF lab changed.
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Parameters
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----------
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lab : str
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An ALF lab name part to use.
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strict : bool, optional
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If True, the lab part must be present in the path, otherwise the lab/Subjects/ part
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is added if not present.
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Returns
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-------
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PureALFPath
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The same file path but with the lab part replaced with the input.
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Raises
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------
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ValueError
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The lab name is invalid.
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ALFInvalid
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The path is not a valid ALF session path, or the lab part is not present in the path
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when strict is True.
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"""
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if not (lab and spec.regex('^{lab}$').match(lab)):
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raise ValueError(f'Invalid lab name: {lab}')
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if not self.subject or (strict and not self.lab): # FIXME check logic
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raise ALFInvalid(str(self))
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pattern = spec.regex(SESSION_SPEC)
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repl = fr'{lab}/Subjects/\g<subject>/\g<date>/\g<number>'
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return self.__class__(pattern.sub(repl, self.as_posix(), count=1))
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def with_subject(self, subject):
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"""Return a new path with the ALF subject changed.
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Parameters
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----------
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subject : str
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An ALF subject name part to use.
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Returns
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-------
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PureALFPath
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The same file path but with the subject part replaced with the input.
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Raises
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------
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ValueError
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The subject name is invalid.
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ALFInvalid
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The path is not a valid ALF session path.
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"""
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if not (subject and spec.regex('^{subject}$').match(subject)):
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raise ValueError(f'Invalid subject name: {subject}')
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if not self.subject:
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raise ALFInvalid(str(self))
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pattern = spec.regex('{subject}/{date}/{number}')
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repl = fr'{subject}/\g<date>/\g<number>'
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return self.__class__(pattern.sub(repl, self.as_posix()), count=1)
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def with_date(self, date):
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"""Return a new path with the ALF date changed.
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Parameters
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----------
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date : str, datetime.datetime, datetime.date
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An ALF date part to use, in YYYY-MM-DD format.
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Returns
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-------
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PureALFPath
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The same file path but with the date part replaced with the input.
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Raises
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------
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ValueError
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The date is not in YYYY-MM-DD format.
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ALFInvalid
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The path is not a valid ALF session path.
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"""
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if date and not isinstance(date, str):
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date = str(date)[:10]
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if not (date and spec.regex('^{date}$').match(date)):
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raise ValueError(f'Invalid date: {date}')
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if not self.date:
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raise ALFInvalid(str(self))
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pattern = spec.regex('{subject}/{date}/{number}')
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repl = fr'\g<subject>/{date}/\g<number>'
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return self.__class__(pattern.sub(repl, self.as_posix()), count=1)
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def with_sequence(self, number):
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"""Return a new path with the ALF number changed.
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Parameters
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----------
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number : str, int
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An ALF number part to use, as a string or integer.
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Returns
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-------
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PureALFPath
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The same file path but with the number part replaced with the input.
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Raises
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------
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ValueError
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The number is not a valid ALF number.
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ALFInvalid
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The path is not a valid ALF session path.
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"""
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if isinstance(number, str):
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number = int(number.strip())
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if number is None or not spec.regex('^{number}$').match(str(number)):
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raise ValueError(f'Invalid number: {number}')
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if not self.sequence:
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raise ALFInvalid(str(self))
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pattern = spec.regex('{subject}/{date}/{number}')
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repl = fr'\g<subject>/\g<date>/{number:03d}'
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return self.__class__(pattern.sub(repl, self.as_posix()), count=1)
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def with_object(self, obj):
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"""Return a new path with the ALF object changed.
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‎one/tests/alf/test_alf_path.py‎

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"""Unit tests for the one.alf.path module."""
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import unittest
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import tempfile
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from datetime import datetime
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from types import GeneratorType
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from uuid import uuid4
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from pathlib import Path, PurePath, PureWindowsPath, PurePosixPath
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self.assertRaises(ValueError, self.alfpath.with_extension, '')
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self.assertRaises(ALFInvalid, self.alfpath.with_stem('foo').with_extension, 'ext')
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def test_with_lab(self):
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"""Test for PureALFPath.with_lab method."""
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# Test with lab
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expected = ALFPath(*self.alfpath.parts[:-8], 'newlab', *self.alfpath.parts[-7:])
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self.assertEqual(expected, self.alfpath.with_lab('newlab'))
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# Test without lab
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alfpath = ALFPath(*self.alfpath.parts[:-8], *self.alfpath.parts[-6:])
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self.assertEqual(expected, alfpath.with_lab('newlab'))
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# Test strict
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self.assertEqual(expected, self.alfpath.with_lab('newlab', strict=True))
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self.assertRaises(ALFInvalid, alfpath.with_lab, 'newlab', strict=True)
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# Test validation
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self.assertRaises(ValueError, self.alfpath.with_lab, '')
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self.assertRaises(ValueError, self.alfpath.with_lab, None)
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self.assertRaises(ValueError, self.alfpath.with_lab, '#s!@#')
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self.assertRaises(ALFInvalid, self.alfpath.relative_to_session().with_lab, 'lab')
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def test_with_subject(self):
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"""Test for PureALFPath.with_subject method."""
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# Test with subject
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expected = ALFPath(*self.alfpath.parts[:-6], 'foo', *self.alfpath.parts[-5:])
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self.assertEqual(expected, self.alfpath.with_subject('foo'))
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# Test without lab (should not depend on Subjects folder)
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alfpath = ALFPath(*self.alfpath.parts[:-8], *self.alfpath.parts[-6:])
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expected = ALFPath(*alfpath.parts[:-6], 'foo', *alfpath.parts[-5:])
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self.assertEqual(expected, alfpath.with_subject('foo'))
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# Test validation
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self.assertRaises(ValueError, self.alfpath.with_subject, '')
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self.assertRaises(ValueError, self.alfpath.with_subject, None)
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self.assertRaises(ValueError, self.alfpath.with_subject, '#s!@#')
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self.assertRaises(ALFInvalid, self.alfpath.relative_to_session().with_subject, 'subject')
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def test_with_date(self):
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"""Test for PureALFPath.with_date method."""
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# Test with date
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expected = ALFPath(*self.alfpath.parts[:-5], '2020-01-02', *self.alfpath.parts[-4:])
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self.assertEqual(expected, self.alfpath.with_date('2020-01-02'))
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# Test with datetime object
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date = datetime.fromisoformat('2020-01-02T00:00:00')
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self.assertEqual(expected, self.alfpath.with_date(date))
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# Test validation
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self.assertRaises(ValueError, self.alfpath.with_date, '')
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self.assertRaises(ValueError, self.alfpath.with_date, None)
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self.assertRaises(ValueError, self.alfpath.with_date, '6/1/2020')
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self.assertRaises(ALFInvalid, self.alfpath.relative_to_session().with_date, '2020-01-02')
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def test_with_sequence(self):
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"""Test for PureALFPath.with_sequence method."""
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# Test with number
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expected = ALFPath(*self.alfpath.parts[:-4], '002', *self.alfpath.parts[-3:])
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self.assertEqual(expected, self.alfpath.with_sequence(2))
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self.assertEqual(expected, self.alfpath.with_sequence('002'))
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# Test with zero
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self.assertEqual('000', self.alfpath.with_sequence(0).parts[-4])
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# Test validation
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self.assertRaises(ValueError, self.alfpath.with_sequence, '')
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self.assertRaises(ValueError, self.alfpath.with_sequence, None)
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self.assertRaises(ValueError, self.alfpath.with_sequence, 'foo')
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self.assertRaises(ValueError, self.alfpath.with_sequence, 1e4)
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self.assertRaises(ALFInvalid, self.alfpath.relative_to_session().with_sequence, 2)
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def test_parts_properties(self):
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"""Test the PureALFPath ALF dataset part properties."""
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# Namespace
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alfpath = self.alfpath.with_name('_ns_obj.attr_times_bpod.foo.bar.ext')
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expected = ('ns', 'obj', 'attr_times', 'bpod', 'foo.bar', 'ext')
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self.assertEqual(expected, alfpath.dataset_name_parts)
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# Lab
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self.assertEqual('labname', self.alfpath.lab)
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self.assertEqual('', self.alfpath.relative_to_session().lab)
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# Subject
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self.assertEqual('subject', self.alfpath.subject)
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self.assertEqual('', self.alfpath.relative_to_session().subject)
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# Date
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self.assertEqual('1900-01-01', self.alfpath.date)
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self.assertEqual('', self.alfpath.relative_to_session().date)
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# Number
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self.assertEqual('001', self.alfpath.sequence)
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self.assertEqual('', self.alfpath.relative_to_session().sequence)
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# session_parts
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self.assertEqual(('labname', 'subject', '1900-01-01', '001'), self.alfpath.session_parts)
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alfpath = ALFPath(*self.alfpath.parts[5:])

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