From ef05f6a888660bb4c28517db64f1cee89255d7f6 Mon Sep 17 00:00:00 2001
From: k1o0 <k1o0@3tk.co>
Date: Tue, 8 Feb 2022 18:44:44 +0200
Subject: [PATCH] Update FAQ; version var; check min api version; lazy auth
(#36)
---
CHANGELOG.md | 11 ++++++++++-
docs/FAQ.md | 31 +++++++++++++++++++++++++++++++
one/__init__.py | 1 +
one/api.py | 10 +++++++++-
one/params.py | 10 ++++++++--
one/tests/test_one.py | 7 +++++++
one/tests/test_params.py | 11 ++++++++++-
one/webclient.py | 7 ++++---
requirements.txt | 1 +
setup.py | 13 ++++++++++++-
10 files changed, 93 insertions(+), 9 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 31c91c4..6fbf090 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,13 +1,22 @@
# Changelog
## [Latest](https://github.com/int-brain-lab/ONE/commits/main) [1.8.0]
+### Added
+
+- added `from_df` method to one.alf.io.AlfBunch
+- added `__version__` variable
+- added check for remote cache minimum API version
+- user prompted to verify settings correct in setup
+
### Modified
- datasets cache table expected to have index of (eid, id). NB: This changes the order of datasets returned by some functions
- multithreading moved from One._download_datasets to one.webclient.http_download_file_list
- cache_dir kwarg renamed to target_dir in one.webclient.http_download_file
- 'table' attribute now split into columns and merged
-- added `from_df` method to one.alf.io.AlfBunch
+- when no username or password provided to constructor, AlyxClient init doesn't call authenticate
+- 'stay_logged_in' kwarg removed from AlyxClient constructor; must manually call `authenticate` or remember to call `logout`
+- user prompted whether to make url default in setup even if default already set
## [1.7.1]
diff --git a/docs/FAQ.md b/docs/FAQ.md
index 2b1ad4c..2686077 100644
--- a/docs/FAQ.md
+++ b/docs/FAQ.md
@@ -56,3 +56,34 @@ called. To avoid this, run the following command instead:
from one.api import OneAlyx
new_one = OneAlyx.setup(base_url='https://alyx.example.com')
```
+
+## How do I change my download (a.k.a. cache) directory?
+For one-time changes, simply re-run the setup routine:
+```python
+from one.api import ONE
+new_one = ONE().setup() # Re-run setup for default database
+```
+When prompted ('Enter the location of the download cache') enter the absolute path of the new download location.
+
+## How do check who I'm logged in as?
+```python
+from one.api import ONE
+one = ONE()
+if not one.offline:
+ print(one.alyx.user)
+ print(one.alyx.base_url)
+```
+
+## How do I log out, or temporarily log in as someone else?
+To log out:
+```python
+from one.api import ONE
+one = ONE()
+
+one.alyx.logout()
+```
+
+To log in as someone else temporarily:
+```python
+one.alyx.authenticate(username='other_user', cache_token=False, force=True)
+```
diff --git a/one/__init__.py b/one/__init__.py
index 21b29ce..b493917 100644
--- a/one/__init__.py
+++ b/one/__init__.py
@@ -1 +1,2 @@
"""The Open Neurophysiology Environment (ONE) API"""
+__version__ = '1.8.0'
diff --git a/one/api.py b/one/api.py
index 41550fa..2bd900f 100644
--- a/one/api.py
+++ b/one/api.py
@@ -2,7 +2,6 @@
Things left to complete:
- - TODO Add sig to ONE Light uuids.
- TODO Save changes to cache.
- TODO Fix update cache in AlyxONE - save parquet table.
- TODO save parquet in update_filesystem.
@@ -10,6 +9,7 @@ Things left to complete:
import collections.abc
import warnings
import logging
+import packaging.version
from datetime import datetime, timedelta
from functools import lru_cache, partial
from inspect import unwrap
@@ -1235,6 +1235,14 @@ class OneAlyx(One):
try:
# Determine whether a newer cache is available
cache_info = self.alyx.get('cache/info', expires=True)
+
+ # Check version compatibility
+ min_version = packaging.version.parse(cache_info.get('min_api_version', '0.0.0'))
+ if packaging.version.parse(one.__version__) < min_version:
+ warnings.warn(f'Newer cache tables require ONE version {min_version} or greater')
+ return
+
+ # Check whether remote cache more recent
remote_created = datetime.fromisoformat(cache_info['date_created'])
local_created = cache_meta.get('created_time', None)
if local_created and (remote_created - local_created) < timedelta(minutes=1):
diff --git a/one/params.py b/one/params.py
index 1cb00c0..4661b27 100644
--- a/one/params.py
+++ b/one/params.py
@@ -161,9 +161,15 @@ def setup(client=None, silent=False, make_default=None):
break
cache_dir = input(prompt) or cache_dir # Prompt for another directory
- if make_default is None and 'DEFAULT' not in cache_map.as_dict():
+ if make_default is None:
answer = input('Would you like to set this URL as the default one? [Y/n]')
- make_default = True if not answer or answer[0].lower() == 'y' else False
+ make_default = (answer or 'y')[0].lower() == 'y'
+
+ # Verify setup pars
+ answer = input('Are the above settings correct? [Y/n]')
+ if answer and answer.lower()[0] == 'n':
+ print('SETUP ABANDONED. Please re-run.')
+ return par_current
else:
par = par_current
diff --git a/one/tests/test_one.py b/one/tests/test_one.py
index b4e1f31..858ada9 100644
--- a/one/tests/test_one.py
+++ b/one/tests/test_one.py
@@ -936,6 +936,13 @@ class TestOneAlyx(unittest.TestCase):
self.one._load_cache(clobber=True)
self.assertEqual('local', self.one.mode)
self.assertTrue('Failed to connect' in lg.output[-1])
+
+ cache_info = {'min_api_version': '200.0.0'}
+ # Check version verification
+ with mock.patch.object(self.one.alyx, 'get', return_value=cache_info),\
+ self.assertWarns(UserWarning):
+ self.one._load_cache(clobber=True)
+
finally: # Restore properties
self.one.mode = 'auto'
self.one.alyx.silent = True
diff --git a/one/tests/test_params.py b/one/tests/test_params.py
index 0bcf1b0..b6b168a 100644
--- a/one/tests/test_params.py
+++ b/one/tests/test_params.py
@@ -26,13 +26,16 @@ class TestParamSetup(unittest.TestCase):
self.get_file_mock.start()
self.addCleanup(self.get_file_mock.stop)
- def _mock_input(self, prompt):
+ def _mock_input(self, prompt, **kwargs):
"""Stub function for builtins.input"""
if prompt.lower().startswith('warning'):
return 'n'
elif 'url' in prompt.lower():
return self.url
else:
+ for k, v in kwargs.items():
+ if k in prompt:
+ return v
return ''
@mock.patch('one.params.getpass', return_value='mock_pwd')
@@ -51,6 +54,12 @@ class TestParamSetup(unittest.TestCase):
self.assertEqual('https://' + self.url, par.ALYX_URL)
self.assertEqual('mock_pwd', par.HTTP_DATA_SERVER_PWD)
+ # Check verification prompt
+ resp_map = {'ALYX_LOGIN': 'mistake', 'settings correct?': 'N'}
+ with mock.patch('one.params.input', new=partial(self._mock_input, **resp_map)):
+ cache = one.params.setup()
+ self.assertNotEqual(cache.ALYX_LOGIN, 'mistake')
+
# Check that raises ValueError when bad URL provided
self.url = 'ftp://'
with self.assertRaises(ValueError), mock.patch('one.params.input', new=self._mock_input):
diff --git a/one/webclient.py b/one/webclient.py
index 84db033..800761c 100644
--- a/one/webclient.py
+++ b/one/webclient.py
@@ -471,7 +471,7 @@ class AlyxClient():
base_url = None
def __init__(self, base_url=None, username=None, password=None,
- cache_dir=None, silent=False, cache_rest='GET', stay_logged_in=True):
+ cache_dir=None, silent=False, cache_rest='GET'):
"""
Create a client instance that allows to GET and POST to the Alyx server.
For One, constructor attempts to authenticate with credentials in params.py.
@@ -498,10 +498,11 @@ class AlyxClient():
self._par = one.params.get(client=base_url, silent=self.silent)
self.base_url = base_url or self._par.ALYX_URL
self._par = self._par.set('CACHE_DIR', cache_dir or self._par.CACHE_DIR)
- self.authenticate(username, password, cache_token=stay_logged_in)
+ if username or password:
+ self.authenticate(username, password)
self._rest_schemes = None
# the mixed accept application may cause errors sometimes, only necessary for the docs
- self._headers['Accept'] = 'application/json'
+ self._headers = {**(self._headers or {}), 'Accept': 'application/json'}
# REST cache parameters
# The default length of time that cache file is valid for,
# The default expiry is overridden by the `expires` kwarg. If False, the caching is
diff --git a/requirements.txt b/requirements.txt
index d39688d..070babb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,3 +4,4 @@ pandas>=1.2.4
tqdm>=4.32.1
requests>=2.22.0
iblutil
+packaging
diff --git a/setup.py b/setup.py
index 2626b28..3750d92 100644
--- a/setup.py
+++ b/setup.py
@@ -22,9 +22,20 @@ with open('README.md', 'r') as f:
with open('requirements.txt') as f:
require = [x.strip() for x in f.readlines() if not x.startswith('git+')]
+
+def get_version(rel_path):
+ here = Path(__file__).parent.absolute()
+ with open(here.joinpath(rel_path), 'r') as fp:
+ for line in fp.read().splitlines():
+ if line.startswith('__version__'):
+ delim = '"' if '"' in line else "'"
+ return line.split(delim)[1]
+ raise RuntimeError('Unable to find version string.')
+
+
setup(
name='ONE-api',
- version='1.8.0',
+ version=get_version(Path('one', '__init__.py')),
python_requires='>={}.{}'.format(*REQUIRED_PYTHON),
description='Open Neurophysiology Environment',
license="MIT",
--
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